@article {pmid30782660,
year = {2019},
author = {López-Pérez, M and Jayakumar, JM and Haro-Moreno, JM and Zaragoza-Solas, A and Reddi, G and Rodriguez-Valera, F and Shapiro, OH and Alam, M and Almagro-Moreno, S},
title = {Evolutionary Model of Cluster Divergence of the Emergent Marine Pathogen Vibrio vulnificus: From Genotype to Ecotype.},
journal = {mBio},
volume = {10},
number = {1},
pages = {},
doi = {10.1128/mBio.02852-18},
pmid = {30782660},
issn = {2150-7511},
mesh = {Aquaculture ; Aquatic Organisms/microbiology ; Cluster Analysis ; Computational Biology ; *Ecotype ; Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; *Genotype ; Phenotype ; Recombination, Genetic ; Vibrio vulnificus/*classification/*genetics/isolation & purification/physiology ; },
abstract = {Vibrio vulnificus, an opportunistic pathogen, is the causative agent of a life-threatening septicemia and a rising problem for aquaculture worldwide. The genetic factors that differentiate its clinical and environmental strains remain enigmatic. Furthermore, clinical strains have emerged from every clade of V. vulnificus In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species from an evolutionary and ecological point of view. Genome comparisons and bioinformatic analyses of 113 V. vulnificus isolates indicate that the population of V. vulnificus is made up of four different clusters. We found evidence that recombination and gene flow between the two largest clusters (cluster 1 [C1] and C2) have drastically decreased to the point where they are diverging independently. Pangenome and phenotypic analyses showed two markedly different lifestyles for these two clusters, indicating commensal (C2) and bloomer (C1) ecotypes, with differences in carbohydrate utilization, defense systems, and chemotaxis, among other characteristics. Nonetheless, we identified frequent intra- and interspecies exchange of mobile genetic elements (e.g., antibiotic resistance plasmids, novel "chromids," or two different and concurrent type VI secretion systems) that provide high levels of genetic diversity in the population. Surprisingly, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together. We propose an evolutionary model of V. vulnificus that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections and emergence.IMPORTANCEVibrio vulnificus is an emergent marine pathogen and is the cause of a deadly septicemia. However, the genetic factors that differentiate its clinical and environmental strains and its several biotypes remain mostly enigmatic. In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species to elucidate the traits that make these strains emerge as a human pathogen. The acquisition of different ecological determinants could have allowed the development of highly divergent clusters with different lifestyles within the same environment. However, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together, posing a potential risk of recombination and of emergence of novel variants. We propose a new evolutionary model that provides a perspective that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections.},
}

Aquaculture
Aquatic Organisms/microbiology
Cluster Analysis
Computational Biology
*Ecotype
Evolution, Molecular
Gene Flow
Gene Transfer, Horizontal
*Genetic Variation
Genome, Bacterial
*Genotype
Phenotype
Recombination, Genetic
Vibrio vulnificus/*classification/*genetics/isolation & purification/physiology

@article {pmid30897417,
year = {2019},
author = {Szabó, B and Lang, Z and Bakonyi, G and Mariën, J and Roelofs, D and van Gestel, CAM and Seres, A},
title = {Transgenerational and multigenerational stress gene responses to the insecticide etofenprox in Folsomia candida (Collembola).},
journal = {Ecotoxicology and environmental safety},
volume = {175},
number = {},
pages = {181-191},
doi = {10.1016/j.ecoenv.2019.03.052},
pmid = {30897417},
issn = {1090-2414},
abstract = {Insecticide exposure may cause both transgenerational and multigenerational effects on populations, but the molecular mechanisms of these changes remain largely unclear. Many studies have focused on either transgenerational or multigenerational mechanisms but did neglect the comparative aspects. This study assessed whether the pyrethroid insecticide etofenprox (formulation Trebon® 30 EC) shows transgenerational and/or multigenerational effects on the survival and reproduction of Folsomia candida (Collembola). The activation of stress-related genes was studied to detect whether etofenprox modifies the expression of reproduction-associated genes in trans- and multigenerational treatments. A laboratory study was carried out for three generations with five insecticide concentrations in LUFA 2.2 soil. In the transgenerational treatment, only the parent generation (P) was exposed, but the subsequent generations were not. In the multigenerational treatment, all three generations were exposed to the insecticide in the same manner. Multigenerational exposure resulted in reduced reproduction effects over generations, suggesting that F. candida is capable of acclimating to enhanced concentration levels of etofenprox during prolonged exposure over multiple generations. In the transgenerational treatment, the heat shock protein 70 was up-regulated and cytochrome oxidase 6N4v1 expression down-regulated in a dose-dependent manner in the F2 generation. This finding raises the possibility of the epigenetic inheritance of insecticide impacts on parents. Furthermore, CYP6N4v1 expression was oppositely regulated in the trans- and multigenerational treatments. Our results draw attention to the differences in molecular level responses of F. candida to trans- and multigenerational etofenprox exposure.},
}

@article {pmid30325353,
year = {2018},
author = {Du, E},
title = {A database of annual atmospheric acid and nutrient deposition to China's forests.},
journal = {Scientific data},
volume = {5},
number = {},
pages = {180223},
pmid = {30325353},
issn = {2052-4463},
mesh = {Acid Rain ; Air Pollutants/*analysis ; China ; *Databases, Factual ; *Environmental Monitoring ; *Forests ; },
abstract = {Anthropogenic emissions have substantially altered atmospheric acid and nutrient deposition in China. Understanding the status and characteristics of acid and nutrient deposition to China's forests is crucial to assess the consequent impacts, and to better guide forest management options. Based on a comprehensive literature review, here I present an updated database for annual acid and nutrient deposition during the period 1991-2015 in China's forests (CFAND 2.0). The database includes information from 56 forested sites on the water fluxes of bulk precipitation and throughfall, the concentrations of H+ (pH), dissolved inorganic nitrogen (N) (NH4+ and NO3-), sulfur (S), dissolved phosphorus (P), potassium (K+), calcium (Ca2+) and magnesium (Mg2+) in bulk precipitation and throughfall, and the fluxes of dissolved inorganic N, S, dissolved P, K+, Ca2+ and Mg2+ in bulk deposition and throughfall. This database will help to understand the spatial patterns of acid and nutrient deposition, validate modelling results of acid and nutrient deposition and assess the ecological effects of acid and nutrient deposition in China's forests.},
}

Acid Rain
Air Pollutants/*analysis
China
*Databases, Factual
*Environmental Monitoring
*Forests

@article {pmid30884039,
year = {2019},
author = {Piao, S and Liu, Q and Chen, A and Janssens, IA and Fu, Y and Dai, J and Liu, L and Lian, X and Shen, M and Zhu, X},
title = {Plant phenology and global climate change: current progresses and challenges.},
journal = {Global change biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/gcb.14619},
pmid = {30884039},
issn = {1365-2486},
abstract = {Plant phenology, the annually recurring sequence of plant developmental stages, is important for plant functioning and ecosystem services and their biophysical and biogeochemical feedbacks to the climate system. Plant phenology depends on temperature, and the current rapid climate change has revived interest in understanding and modelling the responses of plant phenology to the warming trend and the consequences thereof for ecosystems. Here, we review recent progresses in plant phenology and its interactions with climate change. Focusing on the start (leaf unfolding) and end (leaf coloring) of plant growing seasons, we show that the recent rapid expansion in ground- and remote sensing- based phenology data acquisition has been highly beneficial and has supported major advances in plant phenology research. Studies using multiple data sources and methods generally agree on the trends of advanced leaf unfolding and delayed leaf coloring due to climate change, yet these trends appear to have decelerated or even reversed in recent years. Our understanding of the mechanisms underlying the plant phenology responses to climate warming is still limited. The interactions between multiple drivers complicates the modelling and prediction of plant phenology changes. Furthermore, changes in plant phenology have important implications for ecosystem carbon cycles and ecosystem feedbacks to climate, yet the quantification of such impacts remains challenging. We suggest that future studies should primarily focus on using new observation tools to improve the understanding of tropical plant phenology, on improving process-based phenology modelling, and on the scaling of phenology from species to landscape-level. This article is protected by copyright. All rights reserved.},
}

@article {pmid30883574,
year = {2019},
author = {Giezendanner, J and Bertuzzo, E and Pasetto, D and Guisan, A and Rinaldo, A},
title = {A minimalist model of extinction and range dynamics of virtual mountain species driven by warming temperatures.},
journal = {PloS one},
volume = {14},
number = {3},
pages = {e0213775},
doi = {10.1371/journal.pone.0213775},
pmid = {30883574},
issn = {1932-6203},
abstract = {A longstanding question in ecology concerns the prediction of the fate of mountain species under climate change, where climatic and geomorphic factors but also endogenous species characteristics are jointly expected to control species distributions. A significant step forward would single out reliably landscape effects, given their constraining role and relative ease of theoretical manipulation. Here, we address population dynamics in ecosystems where the substrates for ecological interactions are mountain landscapes subject to climate warming. We use a minimalist model of metapopulation dynamics based on virtual species (i.e. a suitable assemblage of focus species) where dispersal processes interact with the spatial structure of the landscape. Climate warming is subsumed by an upward shift of species habitat altering the metapopulation capacity of the landscape and hence species viability. We find that the landscape structure is a powerful determinant of species survival, owing to the specific role of the predictably evolving connectivity of the various habitats. Range shifts and lags in tracking suitable habitat experienced by virtual species under warming conditions are singled out in different landscapes. The range of parameters is identified for which these virtual species (characterized by comparable viability thus restricting their possible fitnesses and niche widths) prove unable to cope with environmental change. The statistics of the proportion of species bound to survive is identified for each landscape, providing the temporal evolution of species range shifts and the related expected occupation patterns. A baseline dynamic model for predicting species fates in evolving habitats is thus provided.},
}

@article {pmid29652093,
year = {2018},
author = {Wilson, K and Sheldon, BC and Gaillard, JM and Sanders, NJ and Hoggart, SPG and Newton, E},
title = {And the winner of the inaugural Sidnie Manton Award is….},
journal = {The Journal of animal ecology},
volume = {87},
number = {3},
pages = {527-529},
doi = {10.1111/1365-2656.12825},
pmid = {29652093},
issn = {1365-2656},
mesh = {Animals ; *Awards and Prizes ; Ecology/*history ; History, 21st Century ; Image Interpretation, Computer-Assisted/*methods ; Oregon ; Societies, Scientific ; United Kingdom ; },
}

Animals
*Awards and Prizes
Ecology/*history
History, 21st Century
Image Interpretation, Computer-Assisted/*methods
Oregon
Societies, Scientific
United Kingdom

@article {pmid29111567,
year = {2018},
author = {Weinstein, BG},
title = {A computer vision for animal ecology.},
journal = {The Journal of animal ecology},
volume = {87},
number = {3},
pages = {533-545},
doi = {10.1111/1365-2656.12780},
pmid = {29111567},
issn = {1365-2656},
mesh = {Animals ; Ecology/*methods ; Image Interpretation, Computer-Assisted/*methods ; },
abstract = {A central goal of animal ecology is to observe species in the natural world. The cost and challenge of data collection often limit the breadth and scope of ecological study. Ecologists often use image capture to bolster data collection in time and space. However, the ability to process these images remains a bottleneck. Computer vision can greatly increase the efficiency, repeatability and accuracy of image review. Computer vision uses image features, such as colour, shape and texture to infer image content. I provide a brief primer on ecological computer vision to outline its goals, tools and applications to animal ecology. I reviewed 187 existing applications of computer vision and divided articles into ecological description, counting and identity tasks. I discuss recommendations for enhancing the collaboration between ecologists and computer scientists and highlight areas for future growth of automated image analysis.},
}

Animals
Ecology/*methods
Image Interpretation, Computer-Assisted/*methods

@article {pmid30721227,
year = {2019},
author = {Marsland, R and Cui, W and Goldford, J and Sanchez, A and Korolev, K and Mehta, P},
title = {Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities.},
journal = {PLoS computational biology},
volume = {15},
number = {2},
pages = {e1006793},
doi = {10.1371/journal.pcbi.1006793},
pmid = {30721227},
issn = {1553-7358},
support = {R35 GM119461/GM/NIGMS NIH HHS/United States ; },
mesh = {Computational Biology ; Databases, Factual ; *Ecosystem ; Energy Metabolism/*physiology ; Microbial Consortia/*physiology ; Models, Biological ; Stochastic Processes ; Thermodynamics ; },
abstract = {A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences between the microbes and their chemical environment through the consumption and production of metabolites. By analyzing a generalized consumer resource model that explicitly includes cross-feeding, stochastic colonization, and thermodynamics, we show that complex microbial communities generically exhibit a transition as a function of available energy fluxes from a "resource-limited" regime where community structure and stability is shaped by energetic and metabolic considerations to a diverse regime where the dominant force shaping microbial communities is the overlap between species' consumption preferences. These two regimes have distinct species abundance patterns, different functional profiles, and respond differently to environmental perturbations. Our model reproduces large-scale ecological patterns observed across multiple experimental settings such as nestedness and differential beta diversity patterns along energy gradients. We discuss the experimental implications of our results and possible connections with disorder-induced phase transitions in statistical physics.},
}

Computational Biology
Databases, Factual
*Ecosystem
Energy Metabolism/*physiology
Microbial Consortia/*physiology
Models, Biological
Stochastic Processes
Thermodynamics

@article {pmid30106390,
year = {2018},
author = {Duarte, G and Moreira, M and Branco, P and da Costa, L and Ferreira, MT and Segurado, P},
title = {One millennium of historical freshwater fish occurrence data for Portuguese rivers and streams.},
journal = {Scientific data},
volume = {5},
number = {},
pages = {180163},
pmid = {30106390},
issn = {2052-4463},
mesh = {Animals ; Databases, Factual ; Ecology/history ; Ecosystem ; *Fishes ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, Medieval ; Portugal ; Rivers ; },
abstract = {The insights that historical evidence of human presence and man-made documents provide are unique. For example, using historical data may be critical to adequately understand the ecological requirements of species. However, historical information about freshwater species distribution remains largely a knowledge gap. In this Data Descriptor, we present the Portuguese Historical Fish Database (PHish-DB), a compilation of 2214 records (557 at the basin scale, 184 at the sub-basin scale and 1473 at the segment scale) resulting from a survey of 194 historical documents. The database was developed using a three-scale approach that maximises the inclusion of information by allowing different degrees of spatial acuity. PHish database contains records of 25 taxonomical groups and covers a time span of one millennium, from the 11th until the 20th century. This database has already proven useful for two scientific studies, and PHish further use will contribute to correctly assess the full range of conditions tolerated by species, by establishing adequate benchmark conditions, and/or to improve existing knowledge of the species distribution limits.},
}

Animals
Databases, Factual
Ecology/history
Ecosystem
*Fishes
History, 15th Century
History, 16th Century
History, 17th Century
History, 18th Century
History, 19th Century
History, 20th Century
History, Medieval
Portugal
Rivers

@article {pmid30842894,
year = {2019},
author = {Sumsion, GR and Bradshaw, MS and Hill, KT and Pinto, LDG and Piccolo, SR},
title = {Remote sensing tree classification with a multilayer perceptron.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6101},
doi = {10.7717/peerj.6101},
pmid = {30842894},
issn = {2167-8359},
abstract = {To accelerate scientific progress on remote tree classification-as well as biodiversity and ecology sampling-The National Institute of Science and Technology created a community-based competition where scientists were invited to contribute informatics methods for classifying tree species and genus using crown-level images of trees. We classified tree species and genus at the pixel level using hyperspectral and LiDAR observations. We compared three algorithms that have been implemented extensively across a broad range of research applications: support vector machines, random forests, and multilayer perceptron. At the pixel level, the multilayer perceptron algorithm classified species or genus with high accuracy (92.7% and 95.9%, respectively) on the training data and performed better than the other two algorithms (85.8-93.5%). This indicates promise for the use of the multilayer perceptron (MLP) algorithm for tree-species classification based on hyperspectral and LiDAR observations and coincides with a growing body of research in which neural network-based algorithms outperform other types of classification algorithm for machine vision. To aggregate patterns across the images, we used an ensemble approach that averages the pixel-level outputs of the MLP algorithm to classify species at the crown level. The average accuracy of these classifications on the test set was 68.8% for the nine species.},
}

@article {pmid29989590,
year = {2018},
author = {Tavşanoğlu, Ç and Pausas, JG},
title = {A functional trait database for Mediterranean Basin plants.},
journal = {Scientific data},
volume = {5},
number = {},
pages = {180135},
pmid = {29989590},
issn = {2052-4463},
mesh = {*Databases, Factual ; Ecosystem ; Mediterranean Region ; *Plants ; },
abstract = {Functional trait databases are emerging as crucial tools for a wide range of ecological studies across the world. Here, we provide a database of functional traits for vascular plant species of the Mediterranean Basin. The database includes 25,764 individual records of 44 traits from 2,457 plant taxa distributed in 119 taxonomic families. This database (BROT 2.0) is an updated and enlarged version of a previous database (BROT 1.0; 8,263 records, 14 traits, 952 taxa). Trait data were obtained from a comprehensive literature review, plus some field and experimental observations. All records are fully referenced and, in many cases, include geographic coordinates. The database is structured to include different levels of accuracy of trait information for each entry. BROT 2.0 should facilitate testing hypotheses on plant functional ecology within the Mediterranean Basin, and comparing this region with other ecosystems worldwide. The BROT 2.0 database and its trait definitions can be used as a template for creating similar trait databases in other regions of the world.},
}

*Databases, Factual
Ecosystem
Mediterranean Region
*Plants

@article {pmid30832282,
year = {2019},
author = {Wu, Z and Lei, S and He, BJ and Bian, Z and Wang, Y and Lu, Q and Peng, S and Duo, L},
title = {Assessment of Landscape Ecological Health: A CaseStudy of a Mining City in a Semi-Arid Steppe.},
journal = {International journal of environmental research and public health},
volume = {16},
number = {5},
pages = {},
doi = {10.3390/ijerph16050752},
pmid = {30832282},
issn = {1660-4601},
support = {2016YFC0501107//China University of Mining and Technology/ ; U1710120//China University of Mining and Technology/ ; 2014FY110800//China University of Mining and Technology/ ; },
abstract = {The ecological status of the semi-arid steppes in China is fragile. Under the long-term and high-intensity development of mining, the ecological integrity and biodiversity of steppe landscapes have been destroyed, causing soil pollution, grassland degradation, landscape function defect, and so on. Previous studies have mainly focused on ecosystem health assessment in mining areas. Landscape ecological health (LEH) pays more attention to the interactions between different ecosystems. Therefore, the ecological assessment of mining cities is more suitable on a landscape scale. Meanwhile, the existing LEH assessment index systems are not applicable in ecologically fragile areas with sparse population, underdeveloped economy, and in relatively small research areas. The purpose of this study was to construct a LEH assessment index system and evaluate the LEH of a mining city located in a semi-arid steppe. Xilinhot is a typical semi-arid steppe mining city in China. The contradictions between the human, land and ecological environment are serious. A new model Condition, Vigor, Organization, Resilience, and Ecosystem (CVORE) model was constructed that integrated five subsystems (services) from the perspectives of ecology, landscape ecology, mining science, and geography. This study used the CVORE model to systematically evaluate the LEH in Xilinhot city in terms of five LEH levels, including very healthy, healthy, sub-healthy, unhealthy and morbid landscape. Research results show that the areas of the very healthy, healthy, sub-healthy, unhealthy and morbid landscapes are 13.23, 736.35, 184.5, 66.76 and 20.63 km², respectively. The healthy landscapes area accounts for 72.08% and most grasslands are healthy. The sub-healthy landscapes are mainly located around areas with higher disturbances due to human activities. The morbid or unhealthy landscapes are concentrated in the mining areas. The proposed CVORE model can enrich the foundations for the quantitative assessment of Landscape Ecological Health of Mining Cities in Semi-arid Steppe (LEHMCSS). This study provided a new LEH assessment approach (CVORE model), which can support landscape ecological restoration, ecological environmental protection and urban planning of the semi-arid steppe mining cities.},
}

@article {pmid28743947,
year = {2017},
author = {Santos, CD and Hanssen, F and Muñoz, AR and Onrubia, A and Wikelski, M and May, R and Silva, JP},
title = {Match between soaring modes of black kites and the fine-scale distribution of updrafts.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {6421},
pmid = {28743947},
issn = {2045-2322},
mesh = {Animals ; Falconiformes/*physiology ; Flight, Animal/*physiology ; Geographic Information Systems ; Models, Biological ; Spain ; },
abstract = {Understanding how soaring birds use updrafts at small spatial scales is important to identify ecological constraints of movement, and may help to prevent conflicts between wind-energy development and the conservation of wildlife. We combined high-frequency GPS animal tracking and fine-spatial-scale uplift modelling to establish a link between flight behaviour of soaring birds and the distribution of updrafts. We caught 21 black kites (Milvus migrans) and GPS-tracked them while flying over the Tarifa region, on the Spanish side of the Strait of Gibraltar. This region has a diverse topography and land cover, favouring a heterogeneous updraft spatial distribution. Bird tracks were segmented and classified into flight modes from motion parameters. Thermal and orographic uplift velocities were modelled from publically available remote-sensing and meteorological data. We found that birds perform circular soaring in areas of higher predicted thermal uplift and linear soaring in areas of higher predicted orographic uplift velocity. We show that updraft maps produced from publically available data can be used to predict where soaring birds will concentrate their flight paths and how they will behave in flight. We recommend the use of this methodological approach to improve environmental impact assessments of new wind-energy installations.},
}

Animals
Falconiformes/*physiology
Flight, Animal/*physiology
Geographic Information Systems
Models, Biological
Spain

@article {pmid30096816,
year = {2018},
author = {Liu, Y and Liu, Y and Li, J and Lu, W and Wei, X and Sun, C},
title = {Evolution of Landscape Ecological Risk at the Optimal Scale: A Case Study of the Open Coastal Wetlands in Jiangsu, China.},
journal = {International journal of environmental research and public health},
volume = {15},
number = {8},
pages = {},
pmid = {30096816},
issn = {1660-4601},
mesh = {China ; Conservation of Natural Resources/*methods ; Ecology ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geological Phenomena ; Human Activities ; Humans ; Remote Sensing Technology ; Risk ; *Wetlands ; },
abstract = {Detailed analysis of the evolution characteristics of landscape ecological risk is crucial for coastal sustainable management and for understanding the potential environmental impacts of a man-made landform landscapes (MMLL). As a typical open coastal wetland, large-scale human activities (e.g., tidal reclamation, fishery activities, wind farm construction, and port construction) have substantially affected the evolution of the coastal ecological environment. Previous landscape ecological risk assessment studies have documented the effectiveness of assessing the quality of ecological environment processes. However, these studies have either focused on the noncoastal zone, or they have not considered the evolution of the spatial characteristics and ecological risk evolution of the landscape at an optimal scale. Here, we present a landscape ecological risk pattern (LERP) evolution model, based on two successive steps: first, we constructed an optimal scale method with an appropriate extent and grain using multi⁻temporal Landsat TM/OLI images acquired in the years 2000, 2004, 2008, 2013 and 2017, and then we calculated landscape ecological risk indices. Based on this model, the entire process of the spatiotemporal evolution of ecological risk patterns of the open coastal wetlands in Jiangsu, China, was determined. The principal findings are as follows: (1) The main landscape types in the study area are tidal flats and farmland, and the main features of the landscape evolution are a significant increase in aquafarming and a substantial decrease in the tidal flat area, while the landscape heterogeneity increased; (2) In the past 20 years, the areas of low and relatively low ecological risk in the study region were greatly reduced, while the areas of medium, relatively high, and high ecological risk greatly increased; the areas of high-grade ecological risk areas are mainly around Dongtai and Dafeng; (3) The area of ecological risk from low-grade to high-grade occupied 71.75% of the study area during 2000⁻2017. During the previous periods (2000⁻2004 and 2004⁻2008), the areas of low-grade ecological risk were transformed to areas of middle-grade ecological risk area, while during the later periods (2008⁻2013 and 2013⁻2017) there was a substantial increase in the proportion of areas of high-grade ecological risk. Our results complement the official database of coastal landscape planning, and provide important information for assessing the potential effects of MMLL processes on coastal environments.},
}

China
Conservation of Natural Resources/*methods
Ecology
Environmental Monitoring/*methods
Geographic Information Systems
Geological Phenomena
Human Activities
Humans
Remote Sensing Technology
Risk
*Wetlands

@article {pmid28602241,
year = {2017},
author = {Giles, KL and McCornack, BP and Royer, TA and Elliott, NC},
title = {Incorporating biological control into IPM decision making.},
journal = {Current opinion in insect science},
volume = {20},
number = {},
pages = {84-89},
doi = {10.1016/j.cois.2017.03.009},
pmid = {28602241},
issn = {2214-5753},
mesh = {Animals ; Crop Production/methods ; *Decision Support Techniques ; Ecology ; Pest Control/methods ; Pest Control, Biological/*methods ; Plants ; },
abstract = {Of the many ways biological control can be incorporated into Integrated Pest Management (IPM) programs, natural enemy thresholds are arguably most easily adopted by stakeholders. Integration of natural enemy thresholds into IPM programs requires ecological and cost/benefit crop production data, threshold model validation, and an understanding of the socioeconomic factors that influence stakeholder decisions about biological control. These thresholds are more likely to be utilized by stakeholders when integrated into dynamic web-based IPM decision support systems that summarize pest management data and push site-specific biological control management recommendations to decision-makers. We highlight recent literature on topics related to natural enemy thresholds and how findings may allow pest suppression services to be incorporated into advanced IPM programs.},
}

Animals
Crop Production/methods
*Decision Support Techniques
Ecology
Pest Control/methods
Pest Control, Biological/*methods
Plants

@article {pmid30571696,
year = {2018},
author = {Somveille, M and Firth, JA and Aplin, LM and Farine, DR and Sheldon, BC and Thompson, RN},
title = {Movement and conformity interact to establish local behavioural traditions in animal populations.},
journal = {PLoS computational biology},
volume = {14},
number = {12},
pages = {e1006647},
doi = {10.1371/journal.pcbi.1006647},
pmid = {30571696},
issn = {1553-7358},
support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Behavior, Animal ; Computational Biology ; Ecosystem ; England ; Learning ; *Models, Biological ; Models, Psychological ; Passeriformes/physiology ; Population Dynamics ; *Social Behavior ; },
abstract = {The social transmission of information is critical to the emergence of animal culture. Two processes are predicted to play key roles in how socially-transmitted information spreads in animal populations: the movement of individuals across the landscape and conformist social learning. We develop a model that, for the first time, explicitly integrates these processes to investigate their impacts on the spread of behavioural preferences. Our results reveal a strong interplay between movement and conformity in determining whether locally-variable traditions establish across a landscape or whether a single preference dominates the whole population. The model is able to replicate a real-world cultural diffusion experiment in great tits Parus major, but also allows for a range of predictions for the emergence of animal culture under various initial conditions, habitat structure and strength of conformist bias to be made. Integrating social behaviour with ecological variation will be important for understanding the stability and diversity of culture in animals.},
}

Animals
*Behavior, Animal
Computational Biology
Ecosystem
England
Learning
*Models, Biological
Models, Psychological
Passeriformes/physiology
Population Dynamics
*Social Behavior

@article {pmid30055354,
year = {2018},
author = {Linard, B and Crampton-Platt, A and Moriniere, J and Timmermans, MJTN and Andújar, C and Arribas, P and Miller, KE and Lipecki, J and Favreau, E and Hunter, A and Gómez-Rodríguez, C and Barton, C and Nie, R and Gillett, CPDT and Breeschoten, T and Bocak, L and Vogler, AP},
title = {The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera.},
journal = {Molecular phylogenetics and evolution},
volume = {128},
number = {},
pages = {1-11},
doi = {10.1016/j.ympev.2018.07.008},
pmid = {30055354},
issn = {1095-9513},
mesh = {Algorithms ; Animals ; Base Sequence ; Coleoptera/classification/*genetics ; Databases, Genetic ; *Metagenomics ; Mitochondria/*genetics ; *Phylogeny ; },
abstract = {A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16,000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.},
}

Algorithms
Animals
Base Sequence
Coleoptera/classification/*genetics
Databases, Genetic
*Metagenomics
Mitochondria/*genetics
*Phylogeny

@article {pmid29334414,
year = {2018},
author = {Fišer, C and Robinson, CT and Malard, F},
title = {Cryptic species as a window into the paradigm shift of the species concept.},
journal = {Molecular ecology},
volume = {27},
number = {3},
pages = {613-635},
doi = {10.1111/mec.14486},
pmid = {29334414},
issn = {1365-294X},
mesh = {Amphipoda/physiology ; Animals ; Biodiversity ; Databases as Topic ; *Genetic Speciation ; Phylogeny ; Species Specificity ; },
abstract = {The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new "species" paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category-which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a "process" counterpart to the long-studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance-based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large-scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.},
}

Amphipoda/physiology
Animals
Biodiversity
Databases as Topic
*Genetic Speciation
Phylogeny
Species Specificity

@article {pmid30208069,
year = {2018},
author = {Mariac, C and Vigouroux, Y and Duponchelle, F and García-Dávila, C and Nunez, J and Desmarais, E and Renno, JF},
title = {Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms.},
journal = {PloS one},
volume = {13},
number = {9},
pages = {e0202976},
pmid = {30208069},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; Fishes/*classification/genetics ; High-Throughput Nucleotide Sequencing ; Larva/*genetics ; },
abstract = {The ability to determine the composition and relative frequencies of fish species in large ichthyoplankton swarms could have extremely important ecological applications However, this task is currently hampered by methodological limitations. We proposed a new method for Amazonian species based on hybridization capture of the COI gene DNA from a distant species (Danio rerio), absent from our study area (the Amazon basin). The COI sequence of this species is approximately equidistant from all COI of Amazonian species available. By using this sequence as probe we successfully facilitated the simultaneous identification of fish larvae belonging to the order Siluriformes and to the Characiformes represented in our ichthyoplankton samples. Species relative frequencies, estimated by the number of reads, showed almost perfect correlations with true frequencies estimated by a Sanger approach, allowing the development of a quantitative approach. We also proposed a further improvement to a previous protocol, which enables lowering the sequencing effort by 40 times. This new Metabarcoding by Capture using a Single Probe (MCSP) methodology could have important implications for ecology, fisheries management and conservation in fish biodiversity hotspots worldwide. Our approach could easily be extended to other plant and animal taxa.},
}

Animals
Biodiversity
DNA Barcoding, Taxonomic/*methods
Databases, Genetic
Fishes/*classification/genetics
High-Throughput Nucleotide Sequencing
Larva/*genetics

@article {pmid29673182,
year = {2018},
author = {Li, C and Liu, M and Hu, Y and Shi, T and Zong, M and Walter, MT},
title = {Assessing the Impact of Urbanization on Direct Runoff Using Improved Composite CN Method in a Large Urban Area.},
journal = {International journal of environmental research and public health},
volume = {15},
number = {4},
pages = {},
pmid = {29673182},
issn = {1660-4601},
mesh = {China ; Geographic Information Systems ; Hydrology ; *Models, Theoretical ; Remote Sensing Technology ; Urbanization/*trends ; },
abstract = {Urbanization is one of the most widespread anthropogenic activities, which brings a range of physical and biochemical changes to hydrological system and processes. Increasing direct runoff caused by land use change has become a major challenge for urban ecological security. Reliable prediction of the quantity and rate of surface runoff is an inherently difficult and time-consuming task for large ungauged urban areas. In this study, we combined Geographic Information System and remote sensing technology with an improved Soil Conservation Service curve number model to evaluate the effects of land use change on direct runoff volume of the four-ring area in Shenyang, China, and analyzed trends of direct runoff at different scales. Through analyzing trends of direct runoff from 1984 to 2015 at different scales, we explored how urbanization and other potential factors affect direct runoff changes. Total direct runoff volume increased over time, and trends varied from the inner urban area to suburban area. Zones 1 and 2 had a tendency toward decreasing direct runoff volume and risks, while Zones 3 and 4 showed gradual increases at both regional and pixel scales. The most important influence on direct runoff change was urban surface change caused by urbanization. This study presents a framework for identifying hotspots of runoff increase, which can provide important guidance to urban managers in future green infrastructure planning, in the hopes of improving the security of urban water ecological patterns.},
}

China
Geographic Information Systems
Hydrology
*Models, Theoretical
Remote Sensing Technology
Urbanization/*trends

@article {pmid30216600,
year = {2018},
author = {Lennox, GD and Gardner, TA and Thomson, JR and Ferreira, J and Berenguer, E and Lees, AC and Mac Nally, R and Aragão, LEOC and Ferraz, SFB and Louzada, J and Moura, NG and Oliveira, VHF and Pardini, R and Solar, RRC and Vaz-de Mello, FZ and Vieira, ICG and Barlow, J},
title = {Second rate or a second chance? Assessing biomass and biodiversity recovery in regenerating Amazonian forests.},
journal = {Global change biology},
volume = {24},
number = {12},
pages = {5680-5694},
doi = {10.1111/gcb.14443},
pmid = {30216600},
issn = {1365-2486},
mesh = {Animals ; *Biodiversity ; *Biomass ; Birds/physiology ; Carbon Cycle ; Coleoptera/physiology ; Conservation of Natural Resources ; Datasets as Topic ; Ecosystem ; *Forests ; Trees ; Tropical Climate ; },
abstract = {Secondary forests (SFs) regenerating on previously deforested land account for large, expanding areas of tropical forest cover. Given that tropical forests rank among Earth's most important reservoirs of carbon and biodiversity, SFs play an increasingly pivotal role in the carbon cycle and as potential habitat for forest biota. Nevertheless, their capacity to regain the biotic attributes of undisturbed primary forests (UPFs) remains poorly understood. Here, we provide a comprehensive assessment of SF recovery, using extensive tropical biodiversity, biomass, and environmental datasets. These data, collected in 59 naturally regenerating SFs and 30 co-located UPFs in the eastern Amazon, cover >1,600 large- and small-stemmed plant, bird, and dung beetles species and a suite of forest structure, landscape context, and topoedaphic predictors. After up to 40 years of regeneration, the SFs we surveyed showed a high degree of biodiversity resilience, recovering, on average among taxa, 88% and 85% mean UPF species richness and composition, respectively. Across the first 20 years of succession, the period for which we have accurate SF age data, biomass recovered at 1.2% per year, equivalent to a carbon uptake rate of 2.25 Mg/ha per year, while, on average, species richness and composition recovered at 2.6% and 2.3% per year, respectively. For all taxonomic groups, biomass was strongly associated with SF species distributions. However, other variables describing habitat complexity-canopy cover and understory stem density-were equally important occurrence predictors for most taxa. Species responses to biomass revealed a successional transition at approximately 75 Mg/ha, marking the influx of high-conservation-value forest species. Overall, our results show that naturally regenerating SFs can accumulate substantial amounts of carbon and support many forest species. However, given that the surveyed SFs failed to return to a typical UPF state, SFs are not substitutes for UPFs.},
}

Animals
*Biodiversity
*Biomass
Birds/physiology
Carbon Cycle
Coleoptera/physiology
Conservation of Natural Resources
Datasets as Topic
Ecosystem
*Forests
Trees
Tropical Climate

@article {pmid30713051,
year = {2019},
author = {Reiczigel, J and Marozzi, M and Fábián, I and Rózsa, L},
title = {Biostatistics for Parasitologists - A Primer to Quantitative Parasitology.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2019.01.003},
pmid = {30713051},
issn = {1471-5007},
abstract = {The aggregated distributions of host-parasite systems require several different infection parameters to characterize them. We advise readers how to choose infection indices with clear and distinct biological interpretations, and recommend statistical tests to compare them across samples. A user-friendly and free software is available online to overcome technical difficulties.},
}

@article {pmid29936291,
year = {2018},
author = {Venter, PC and Nitsche, F and Scherwass, A and Arndt, H},
title = {Discrepancies Between Molecular and Morphological Databases of Soil Ciliates Studied for Temperate Grasslands of Central Europe.},
journal = {Protist},
volume = {169},
number = {4},
pages = {521-538},
doi = {10.1016/j.protis.2018.04.001},
pmid = {29936291},
issn = {1618-0941},
mesh = {Ciliophora/*classification ; *Databases, Factual/standards ; Databases, Genetic ; Europe ; *Grassland ; High-Throughput Nucleotide Sequencing ; Molecular Typing ; *Soil Microbiology ; },
abstract = {By measuring the change in soil protist communities, the effect of human land use on grasslands can be monitored to promote sustainable ecosystem functioning. Protists form the active link in the rhizosphere between the plant roots and higher trophic organisms; however, only few morphological species and their ecological values have yet been described in this context. To investigate the communicability between morphological and molecular databases used in the molecular barcoding of protists and in the biomonitoring of grassland soil, the present high-throughput sequencing (HTS) study (N=150) covered the area of central Europe (mesoscale) known to be well studied for ciliated protists. HTS delivered 2,404 unique reads identifying taxa in all major ciliophoran classes but exact reference matches were few. The study identified clear discrepancies between databases for well-studied taxa, where molecular databases contained multiple gene variants for single morphospecies of dominant taxa. Gene variants presented own biogeography - the eukaryotic microdiversity along gradients (e.g., land-use intensity, soil water). It is possible that many of the so called novel phylogenetic lineages and hidden diversity pointed out in environmental surveys could be evidence for the severe lack of molecular data for already known and morphologically described species, present in morphological databases.},
}

Ciliophora/*classification
*Databases, Factual/standards
Databases, Genetic
Europe
*Grassland
High-Throughput Nucleotide Sequencing
Molecular Typing
*Soil Microbiology

@article {pmid30695030,
year = {2019},
author = {Yenni, GM and Christensen, EM and Bledsoe, EK and Supp, SR and Diaz, RM and White, EP and Ernest, SKM},
title = {Developing a modern data workflow for regularly updated data.},
journal = {PLoS biology},
volume = {17},
number = {1},
pages = {e3000125},
doi = {10.1371/journal.pbio.3000125},
pmid = {30695030},
issn = {1545-7885},
abstract = {Over the past decade, biology has undergone a data revolution in how researchers collect data and the amount of data being collected. An emerging challenge that has received limited attention in biology is managing, working with, and providing access to data under continual active collection. Regularly updated data present unique challenges in quality assurance and control, data publication, archiving, and reproducibility. We developed a workflow for a long-term ecological study that addresses many of the challenges associated with managing this type of data. We do this by leveraging existing tools to 1) perform quality assurance and control; 2) import, restructure, version, and archive data; 3) rapidly publish new data in ways that ensure appropriate credit to all contributors; and 4) automate most steps in the data pipeline to reduce the time and effort required by researchers. The workflow leverages tools from software development, including version control and continuous integration, to create a modern data management system that automates the pipeline.},
}

@article {pmid29930200,
year = {2018},
author = {Venturelli, OS and Carr, AC and Fisher, G and Hsu, RH and Lau, R and Bowen, BP and Hromada, S and Northen, T and Arkin, AP},
title = {Deciphering microbial interactions in synthetic human gut microbiome communities.},
journal = {Molecular systems biology},
volume = {14},
number = {6},
pages = {e8157},
pmid = {29930200},
issn = {1744-4292},
support = {T32 GM008349/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacterial Physiological Phenomena ; Computational Biology/methods ; Gastrointestinal Microbiome/*physiology ; Humans ; Metabolomics ; *Microbial Interactions ; Models, Biological ; },
abstract = {The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-dimensional consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi-species community dynamics, as opposed to higher-order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history-dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human-associated intestinal species and illuminated design principles of microbial communities.},
}

Bacterial Physiological Phenomena
Computational Biology/methods
Gastrointestinal Microbiome/*physiology
Humans
Metabolomics
*Microbial Interactions
Models, Biological

@article {pmid30413903,
year = {2019},
author = {Sánchez-Giraldo, C and Daza, JM},
title = {Getting better temporal and spatial ecology data for threatened species: using lightweight GPS devices for small primate monitoring in the northern Andes of Colombia.},
journal = {Primates; journal of primatology},
volume = {60},
number = {1},
pages = {93-102},
doi = {10.1007/s10329-018-0696-1},
pmid = {30413903},
issn = {1610-7365},
mesh = {Animals ; Colombia ; Ecology/*methods ; Endangered Species ; Female ; Geographic Information Systems/*instrumentation ; *Homing Behavior ; Male ; Saguinus/*physiology ; },
abstract = {The use of GPS telemetry has been a reliable research tool for the study of primate biology in recent years. Although in the past technological restrictions limited its use mainly to large primates, recent improvements in battery size make it possible to use this technology for small species. We used GPS devices for monitoring two adult white-footed tamarins (Saguinus leucopus) from a free-ranging group, and assessed its applicability for recording spatial and ecological data. GPS devices were operational for 66 and 85 days, recording 221 positions (36.6% acquisition rate; 73% of which were highly accurate) and 3195 activity values for both individuals. Depending on the estimation method, we calculated the home range size for the group to be 19.4 and 22.9 ha, which were within the range for the species in other localities. The animals were active each day for 11 h, with high activity during the early morning. The monkeys showed a constant and alternate use of four sleeping sites with a limited reuse of the same site on consecutive nights. These daily activity and sleeping site use patterns are similar to those reported for other Saguinus species. Based on the kind and quality of the data recorded, we consider GPS telemetry to be an efficient and advantageous method for tracking and obtaining ecological information from S. leucopus. In comparison to other data collection methods, GPS telemetry required fewer personnel and less time commitment to record data without compromising the accuracy of the spatial and activity information we obtained.},
}

Animals
Colombia
Ecology/*methods
Endangered Species
Female
Geographic Information Systems/*instrumentation
*Homing Behavior
Male
Saguinus/*physiology

@article {pmid30651533,
year = {2019},
author = {Perkins, DM and Perna, A and Adrian, R and Cermeño, P and Gaedke, U and Huete-Ortega, M and White, EP and Yvon-Durocher, G},
title = {Energetic equivalence underpins the size structure of tree and phytoplankton communities.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {255},
doi = {10.1038/s41467-018-08039-3},
pmid = {30651533},
issn = {2041-1723},
abstract = {The size structure of autotroph communities - the relative abundance of small vs. large individuals - shapes the functioning of ecosystems. Whether common mechanisms underpin the size structure of unicellular and multicellular autotrophs is, however, unknown. Using a global data compilation, we show that individual body masses in tree and phytoplankton communities follow power-law distributions and that the average exponents of these individual size distributions (ISD) differ. Phytoplankton communities are characterized by an average ISD exponent consistent with three-quarter-power scaling of metabolism with body mass and equivalence in energy use among mass classes. Tree communities deviate from this pattern in a manner consistent with equivalence in energy use among diameter size classes. Our findings suggest that whilst universal metabolic constraints ultimately underlie the emergent size structure of autotroph communities, divergent aspects of body size (volumetric vs. linear dimensions) shape the ecological outcome of metabolic scaling in forest vs. pelagic ecosystems.},
}

@article {pmid30016947,
year = {2018},
author = {Song, Z and Stajich, JE and Xie, Y and Liu, X and He, Y and Chen, J and Hicks, GR and Wang, G},
title = {Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesis.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {541},
pmid = {30016947},
issn = {1471-2164},
support = {IOS-1027542//National Science Foundation/ ; CA-R-PPA-5062-H//National Institute of Food and Agriculture Hatch project/ ; 31670044//National Natural Science Foundation of China/ ; 91751115//National Natural Science Foundation of China/ ; S10 OD016290/OD/NIH HHS/United States ; # 2016YFA0601401//The National Key Research Program of China/ ; 201305022//National Marine Public Welfare Industry Special Scientific Research Project/ ; },
mesh = {Biosynthetic Pathways/genetics ; Docosahexaenoic Acids/*biosynthesis ; Ecological and Environmental Phenomena ; Fatty Acids, Unsaturated/biosynthesis ; Gene Ontology ; *Genome ; Genomics ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Stramenopiles/classification/enzymology/*genetics/metabolism ; },
abstract = {BACKGROUND: Thraustochytrids are unicellular fungal-like marine protists with ubiquitous existence in marine environments. They are well-known for their ability to produce high-valued omega-3 polyunsaturated fatty acids (ω-3-PUFAs) (e.g., docosahexaenoic acid (DHA)) and hydrolytic enzymes. Thraustochytrid biomass has been estimated to surpass that of bacterioplankton in both coastal and oceanic waters indicating they have an important role in microbial food-web. Nevertheless, the molecular pathway and regulatory network for PUFAs production and the molecular mechanisms underlying ecological functions of thraustochytrids remain largely unknown.

RESULTS: The genomes of two thraustochytrids strains (Mn4 and SW8) with ability to produce DHA were sequenced and assembled with a hybrid sequencing approach utilizing Illumina short paired-end reads and Pacific Biosciences long reads to generate a highly accurate genome assembly. Phylogenomic and comparative genomic analyses found that DHA-producing thraustochytrid strains were highly similar and possessed similar gene content. Analysis of the conventional fatty acid synthesis (FAS) and the polyketide synthase (PKS) systems for PUFAs production only detected incomplete and fragmentary pathways in the genome of these two strains. Surprisingly, secreted carbohydrate active enzymes (CAZymes) were found to be significantly depleted in the genomes of these 2 strains as compared to other sequenced relatives. Furthermore, these two strains possess an expanded gene repertoire for signal transduction and self-propelled movement, which could be important for their adaptations to dynamic marine environments.

CONCLUSIONS: Our results demonstrate the possibility of a third PUFAs synthesis pathway besides previously described FAS and PKS pathways encoded in the genome of these two thraustochytrid strains. Moreover, lack of a complete set of hydrolytic enzymatic machinery for degrading plant-derived organic materials suggests that these two DHA-producing strains play an important role as a nutritional source rather than a nutrient-producer in marine microbial-food web. Results of this study suggest the existence of two types of saprobic thraustochytrids in the world's ocean. The first group, which does not produce cellulosic enzymes and live as 'left-over' scavenger of bacterioplankton, serves as a dietary source for the plankton of higher trophic levels and the other possesses capacity to live on detrital organic matters in the marine ecosystems.},
}

Biosynthetic Pathways/genetics
Docosahexaenoic Acids/*biosynthesis
Ecological and Environmental Phenomena
Fatty Acids, Unsaturated/biosynthesis
Gene Ontology
*Genome
Genomics
Molecular Sequence Annotation
Multigene Family
Phylogeny
Stramenopiles/classification/enzymology/*genetics/metabolism

@article {pmid30625219,
year = {2019},
author = {Ožana, S and Burda, M and Hykel, M and Malina, M and Prášek, M and Bárta, D and Dolný, A},
title = {Dragonfly Hunter CZ: Mobile application for biological species recognition in citizen science.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0210370},
doi = {10.1371/journal.pone.0210370},
pmid = {30625219},
issn = {1932-6203},
abstract = {Citizen science and data collected from various volunteers have an interesting potential in aiding the understanding of many biological and ecological processes. We describe a mobile application that allows the public to map and report occurrences of the odonata species (dragonflies and damselflies) found in the Czech Republic. The application also helps in species classification based on observation details such as date, GPS coordinates, and the altitude, biotope, suborder, and colour. Dragonfly Hunter CZ is a free Android application built on the open-source framework NativeScript using the JavaScript programming language which is now fully available on Google Play. The server side is powered by Apache Server with PHP and MariaDB SQL database. A mobile application is a fast and accurate way to obtain data pertaining to the odonata species, which can be used after expert verification for ecological studies and conservation basis like Red Lists and policy instruments. We expect it to be effective in encouraging Citizen Science and in promoting the proactive reporting of odonates. It can also be extended to the reporting and monitoring of other plant and animal species.},
}

@article {pmid30061690,
year = {2018},
author = {Horsthemke, B},
title = {A critical view on transgenerational epigenetic inheritance in humans.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {2973},
pmid = {30061690},
issn = {2041-1723},
mesh = {Animals ; Biological Evolution ; Culture ; *DNA Methylation ; Databases, Genetic ; Drosophila ; Ecology ; *Epigenesis, Genetic ; Gene-Environment Interaction ; Germ Cells ; Humans ; *Inheritance Patterns ; Models, Genetic ; Mutation ; Nematoda ; Phenotype ; Plants/genetics ; Proteome ; Proteomics ; },
abstract = {Transgenerational epigenetic inheritance refers to the transmission of epigenetic information through the germline. While it has been observed in plants, nematodes and fruit flies, its occurrence in mammals-and humans in particular-is the matter of controversial debate, mostly because the study of transgenerational epigenetic inheritance is confounded by genetic, ecological and cultural inheritance. In this comment, I discuss the phenomenon of transgenerational epigenetic inheritance and the difficulty of providing conclusive proof for it in experimental and observational studies.},
}

Animals
Biological Evolution
Culture
*DNA Methylation
Databases, Genetic
Drosophila
Ecology
*Epigenesis, Genetic
Gene-Environment Interaction
Germ Cells
Humans
*Inheritance Patterns
Models, Genetic
Mutation
Nematoda
Phenotype
Plants/genetics
Proteome
Proteomics

@article {pmid30061657,
year = {2018},
author = {Butler, S and O'Dwyer, JP},
title = {Stability criteria for complex microbial communities.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {2970},
pmid = {30061657},
issn = {2041-1723},
mesh = {Algorithms ; Computational Biology ; *Ecology ; *Microbiota ; Models, Biological ; Software ; *Symbiosis ; },
abstract = {Competition and mutualism are inevitable processes in microbial ecology, and a central question is which and how many taxa will persist in the face of these interactions. Ecological theory has demonstrated that when direct, pairwise interactions among a group of species are too numerous, or too strong, then the coexistence of these species will be unstable to any slight perturbation. Here, we refine and to some extent overturn that understanding, by considering explicitly the resources that microbes consume and produce. In contrast to more complex organisms, microbial cells consume primarily abiotic resources, and mutualistic interactions are often mediated through the mechanism of crossfeeding. We show that if microbes consume, but do not produce resources, then any positive equilibrium will always be stable to small perturbations. We go on to show that in the presence of crossfeeding, stability is no longer guaranteed. However, positive equilibria remain stable whenever mutualistic interactions are either sufficiently weak, or when all pairs of taxa reciprocate each other's assistance.},
}

Algorithms
Computational Biology
*Ecology
*Microbiota
Models, Biological
Software
*Symbiosis

@article {pmid29642940,
year = {2018},
author = {Dai, Z and Coker, OO and Nakatsu, G and Wu, WKK and Zhao, L and Chen, Z and Chan, FKL and Kristiansen, K and Sung, JJY and Wong, SH and Yu, J},
title = {Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {70},
pmid = {29642940},
issn = {2049-2618},
support = {766613, 14106145, 14111216//RGC-GRF/International ; 2016YFC1303200//135 Program Project China/International ; 2013CB531401//973 Program China/International ; 2014BAI09B05//National Key Technology R&D Program/International ; },
mesh = {Aged ; Bacteria/*classification/*genetics ; Cell Transformation, Neoplastic ; Colorectal Neoplasms/diagnosis/*etiology ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome ; Gene Ontology ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; Middle Aged ; },
abstract = {BACKGROUND: Alterations of gut microbiota are associated with colorectal cancer (CRC) in different populations and several bacterial species were found to contribute to the tumorigenesis. The potential use of gut microbes as markers for early diagnosis has also been reported. However, cohort specific noises may distort the structure of microbial dysbiosis in CRC and lead to inconsistent results among studies. In this regard, our study targeted at exploring changes in gut microbiota that are universal across populations at species level.

RESULTS: Based on the combined analysis of 526 metagenomic samples from Chinese, Austrian, American, and German and French cohorts, seven CRC-enriched bacteria (Bacteroides fragilis, Fusobacterium nucleatum, Porphyromonas asaccharolytica, Parvimonas micra, Prevotella intermedia, Alistipes finegoldii, and Thermanaerovibrio acidaminovorans) have been identified across populations. The seven enriched bacterial markers classified cases from controls with an area under the receiver-operating characteristics curve (AUC) of 0.80 across the different populations. Abundance correlation analysis demonstrated that CRC-enriched and CRC-depleted bacteria respectively formed their own mutualistic networks, in which the latter was disjointed in CRC. The CRC-enriched bacteria have been found to be correlated with lipopolysaccharide and energy biosynthetic pathways.

CONCLUSIONS: Our study identified potential diagnostic bacterial markers that are robust across populations, indicating their potential universal use for non-invasive CRC diagnosis. We also elucidated the ecological networks and functional capacities of CRC-associated microbiota.},
}

Aged
Bacteria/*classification/*genetics
Cell Transformation, Neoplastic
Colorectal Neoplasms/diagnosis/*etiology
Computational Biology/methods
Female
*Gastrointestinal Microbiome
Gene Ontology
Humans
Male
*Metagenome
*Metagenomics/methods
Middle Aged

@article {pmid28634367,
year = {2017},
author = {Gao, X and Wang, C and Dai, W and Ren, S and Tao, F and He, X and Han, G and Wang, W},
title = {Proteomic analysis reveals large amounts of decomposition enzymes and major metabolic pathways involved in algicidal process of Trametes versicolor F21a.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {3907},
pmid = {28634367},
issn = {2045-2322},
mesh = {*Antibiosis ; Biomass ; Chlorophyll/metabolism ; Chromatography, Liquid ; Computational Biology/methods ; Cyanobacteria ; Fungal Proteins/*metabolism ; Metabolic Networks and Pathways ; *Proteome ; *Proteomics/methods ; Tandem Mass Spectrometry ; Trametes/*metabolism ; },
abstract = {A recent algicidal mode indicates that fungal mycelia can wrap and eliminate almost all co-cultivated algal cells within a short time span. However, the underlying molecular mechanism is rarely understood. We applied proteomic analysis to investigate the algicidal process of Trametes versicolor F21a and identified 3,754 fungal proteins. Of these, 30 fungal enzymes with endo- or exoglycosidase activities such as β-1,3-glucanase, α-galactosidase, α-glucosidase, alginate lyase and chondroitin lyase were significantly up-regulated. These proteins belong to Glycoside Hydrolases, Auxiliary Activities, Carbohydrate Esterases and Polysaccharide Lyases, suggesting that these enzymes may degrade lipopolysaccharides, peptidoglycans and alginic acid of algal cells. Additionally, peptidase, exonuclease, manganese peroxidase and cytochrome c peroxidase, which decompose proteins and DNA or convert other small molecules of algal cells, could be other major decomposition enzymes. Gene Ontology and KEGG pathway enrichment analysis demonstrated that pyruvate metabolism and tricarboxylic acid cycle pathways play a critical role in response to adverse environment via increasing energy production to synthesize lytic enzymes or uptake molecules. Carbon metabolism, selenocompound metabolism, sulfur assimilation and metabolism, as well as several amino acid biosynthesis pathways could play vital roles in the synthesis of nutrients required by fungal mycelia.},
}

*Antibiosis
Biomass
Chlorophyll/metabolism
Chromatography, Liquid
Computational Biology/methods
Cyanobacteria
Fungal Proteins/*metabolism
Metabolic Networks and Pathways
*Proteome
*Proteomics/methods
Tandem Mass Spectrometry
Trametes/*metabolism

@article {pmid29602265,
year = {2018},
author = {Stanford, BCM and Rogers, SM},
title = {R(NA)-tistic expression: The art of matching unknown mRNA and proteins to environmental response in ecological genomics.},
journal = {Molecular ecology},
volume = {27},
number = {4},
pages = {827-830},
doi = {10.1111/mec.14419},
pmid = {29602265},
issn = {1365-294X},
mesh = {Animals ; *Daphnia ; Ecology ; Gene Ontology ; Genomics ; *RNA, Messenger ; },
abstract = {A challenge of modern ecological genomics is reducing uncertainty surrounding the biological inferences from gene expression. For example, approximately 40% of proteins in eukaryotic model organisms do not contain characterized domains (Gollery et al., 2006). Even proteins of "known function" are typically only characterized in the sense that they have a domain function, but provide no information on their biological role within the cell (e.g., activation, pathways or targets). Yet, as molecular ecologists, a common objective is to elucidate how organisms respond to environmental variation through changes in gene expression, including homoeostatic, acclimatory, and adaptive responses to environmental stressors, a challenge increased by poor protein ecological annotation. Now, in this issue of Molecular Ecology, Orsini et al. (2017) use the quintessential Daphnia system to characterize the differences in stress response in three genotypic backgrounds to common biotic and abiotic stressors found in nature. Using an optimized weighted gene co-expression network analysis, they link genes of unknown function to genes that they co-activate with and enrich for gene ontology. Determining the functional networks of genes that behave in genotype- and treatment-specific responses gives insight into possible pathways and respective ecological roles, helping pave the way for the next generation of transcriptomic studies in molecular ecology.},
}

Animals
*Daphnia
Ecology
Gene Ontology
Genomics
*RNA, Messenger

@article {pmid30568285,
year = {2019},
author = {Strassburg, BBN and Beyer, HL and Crouzeilles, R and Iribarrem, A and Barros, F and de Siqueira, MF and Sánchez-Tapia, A and Balmford, A and Sansevero, JBB and Brancalion, PHS and Broadbent, EN and Chazdon, RL and Filho, AO and Gardner, TA and Gordon, A and Latawiec, A and Loyola, R and Metzger, JP and Mills, M and Possingham, HP and Rodrigues, RR and Scaramuzza, CAM and Scarano, FR and Tambosi, L and Uriarte, M},
title = {Strategic approaches to restoring ecosystems can triple conservation gains and halve costs.},
journal = {Nature ecology & evolution},
volume = {3},
number = {1},
pages = {62-70},
doi = {10.1038/s41559-018-0743-8},
pmid = {30568285},
issn = {2397-334X},
abstract = {International commitments for ecosystem restoration add up to one-quarter of the world's arable land. Fulfilling them would ease global challenges such as climate change and biodiversity decline but could displace food production and impose financial costs on farmers. Here, we present a restoration prioritization approach capable of revealing these synergies and trade-offs, incorporating ecological and economic efficiencies of scale and modelling specific policy options. Using an actual large-scale restoration target of the Atlantic Forest hotspot, we show that our approach can deliver an eightfold increase in cost-effectiveness for biodiversity conservation compared with a baseline of non-systematic restoration. A compromise solution avoids 26% of the biome's current extinction debt of 2,864 plant and animal species (an increase of 257% compared with the baseline). Moreover, this solution sequesters 1 billion tonnes of CO2-equivalent (a 105% increase) while reducing costs by US$28 billion (a 57% decrease). Seizing similar opportunities elsewhere would offer substantial contributions to some of the greatest challenges for humankind.},
}

@article {pmid30533308,
year = {2018},
author = {Jenkins, MF and White, EP and Hurlbert, AH},
title = {The proportion of core species in a community varies with spatial scale and environmental heterogeneity.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e6019},
pmid = {30533308},
issn = {2167-8359},
abstract = {Ecological communities are composed of a combination of core species that maintain local viable populations and transient species that occur infrequently due to dispersal from surrounding regions. Preliminary work indicates that while core and transient species are both commonly observed in community surveys of a wide range of taxonomic groups, their relative prevalence varies substantially from one community to another depending upon the spatial scale at which the community was characterized and its environmental context. We used a geographically extensive dataset of 968 bird community time series to quantitatively describe how the proportion of core species in a community varies with spatial scale and environmental heterogeneity. We found that the proportion of core species in an assemblage increased with spatial scale in a positive decelerating fashion with a concomitant decrease in the proportion of transient species. Variation in the shape of this scaling relationship between sites was related to regional environmental heterogeneity, with lower proportions of core species at a given scale associated with high environmental heterogeneity. Understanding this influence of scale and environmental heterogeneity on the proportion of core species may help resolve discrepancies between studies of biotic interactions, resource availability, and mass effects conducted at different scales, because the importance of these and other ecological processes are expected to differ substantially between core and transient species.},
}

@article {pmid30499218,
year = {2018},
author = {Taylor, SD and Meiners, JM and Riemer, K and Orr, MC and White, EP},
title = {Comparison of large-scale citizen science data and long-term study data for phenology modeling.},
journal = {Ecology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ecy.2568},
pmid = {30499218},
issn = {0012-9658},
abstract = {Large-scale observational data from citizen science efforts are becoming increasingly common in ecology, and researchers often choose between these and data from intensive local-scale studies for their analyses. This choice has trade-offs related to spatial scale, observer variance, and inter-annual variability. Here we explored this issue with phenology by comparing models built using data from the large-scale, citizen science USA National Phenology Network (USANPN) effort with models built using data from more intensive studies at Long Term Ecological Research (LTER) sites. We built statistical and process based phenology models for species common to each dataset. From these models we compared parameter estimates, estimates of phenological events, and out-of-sample errors between models derived from both USA-NPN and LTER data. We found that model parameter estimates for the same species were most similar between the two datasets when using simple models, but parameter estimates varied widely as model complexity increased. Despite this, estimates for the date of phenological events and out-of-sample errors were similar, regardless of the model. Predictions for USA-NPN data had the lowest error using models built from the USA-NPN data, while LTER predictions were best made using LTER-derived models, confirming that models perform best when applied at the same scale they were built. This difference in the cross-scale model comparison is likely due to variation in phenological requirements within species. Models using the USA-NPN dataset can integrate parameters over a large spatial scale while those using an LTER dataset can only estimate parameters for a single location. Accordingly, the choice of dataset depends on the research question. Inferences about species-specific phenological requirements are best made with LTER data, and if USA-NPN or similar data are all that is available, then analyses should be limited to simple models. Large-scale predictive modeling is best done with the larger-scale USA-NPN data, which has high spatial representation and a large regional species pool. LTER datasets, on the other hand, have high site fidelity and thus characterize inter-annual variability extremely well. Future research aimed at forecasting phenology events for particular species over larger scales should develop models which integrate the strengths of both datasets. This article is protected by copyright. All rights reserved.},
}

@article {pmid30446752,
year = {2018},
author = {Felipe-Lucia, MR and Soliveres, S and Penone, C and Manning, P and van der Plas, F and Boch, S and Prati, D and Ammer, C and Schall, P and Gossner, MM and Bauhus, J and Buscot, F and Blaser, S and Blüthgen, N and de Frutos, A and Ehbrecht, M and Frank, K and Goldmann, K and Hänsel, F and Jung, K and Kahl, T and Nauss, T and Oelmann, Y and Pena, R and Polle, A and Renner, S and Schloter, M and Schöning, I and Schrumpf, M and Schulze, ED and Solly, E and Sorkau, E and Stempfhuber, B and Tschapka, M and Weisser, WW and Wubet, T and Fischer, M and Allan, E},
title = {Multiple forest attributes underpin the supply of multiple ecosystem services.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {4839},
pmid = {30446752},
issn = {2041-1723},
mesh = {Conservation of Natural Resources/*methods ; Ecosystem ; Europe ; Forestry/*methods/trends ; *Forests ; Humans ; Trees/*physiology ; },
abstract = {Trade-offs and synergies in the supply of forest ecosystem services are common but the drivers of these relationships are poorly understood. To guide management that seeks to promote multiple services, we investigated the relationships between 12 stand-level forest attributes, including structure, composition, heterogeneity and plant diversity, plus 4 environmental factors, and proxies for 14 ecosystem services in 150 temperate forest plots. Our results show that forest attributes are the best predictors of most ecosystem services and are also good predictors of several synergies and trade-offs between services. Environmental factors also play an important role, mostly in combination with forest attributes. Our study suggests that managing forests to increase structural heterogeneity, maintain large trees, and canopy gaps would promote the supply of multiple ecosystem services. These results highlight the potential for forest management to encourage multifunctional forests and suggest that a coordinated landscape-scale strategy could help to mitigate trade-offs in human-dominated landscapes.},
}

Conservation of Natural Resources/*methods
Ecosystem
Europe
Forestry/*methods/trends
*Forests
Humans
Trees/*physiology

@article {pmid30431668,
year = {2018},
author = {Portnoy, GA and Relyea, MR and Decker, S and Shamaskin-Garroway, A and Driscoll, M and Brandt, CA and Haskell, SG},
title = {Understanding Gender Differences in Resilience Among Veterans: Trauma History and Social Ecology.},
journal = {Journal of traumatic stress},
volume = {31},
number = {6},
pages = {845-855},
doi = {10.1002/jts.22341},
pmid = {30431668},
issn = {1573-6598},
support = {VA IIR 12-118//Health Services Research and Development/ ; },
abstract = {A social-ecological framework for resilience underscores the importance of conceptualizing individuals embedded within their context when evaluating a person's vulnerability and adaptation to stress. Despite a high level of trauma exposure, most veterans exhibit psychological resilience following a traumatic event. Interpersonal trauma is associated with poorer psychological outcomes than noninterpersonal trauma and is experienced more frequently across the lifespan by women as compared to men. In the present study, we examined gender differences in trauma exposure, resilience, and protective factors among veterans. Participants included 665 veterans who completed a baseline survey assessing traumatic events; 544 veterans (81.8%) completed a 1-year follow-up survey assessing resilience, combat exposure, deployment social support, deployment preparedness, and military sexual trauma (MST). Principal component analyses revealed the Traumatic Life Events Questionnaire categorized into four meaningful components: sexual abuse, interpersonal violence, stranger violence, and accidents/unexpected trauma. Women reported greater exposure to sexual abuse, d = 0.76; interpersonal violence, d = 0.31; and MST, Cramer's V = 0.54; men reported greater exposure to stranger violence, accidents/unexpected trauma, and combat exposure, ds = 0.24-0.55. Compared to women, men also reported greater social support during deployment, d = 0.46. Hierarchical linear regression indicated that men's resilience scores were higher than women's, β = .10, p = .032, yet this association was no longer significant once we accounted for trauma type, β = .07, p = .197. Results indicate that trauma type is central to resilience and suggest one must consider the social-ecological context that can promote or inhibit resilient processes.},
}

@article {pmid30417109,
year = {2018},
author = {Mazel, F and Davis, KM and Loudon, A and Kwong, WK and Groussin, M and Parfrey, LW},
title = {Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life?.},
journal = {mSystems},
volume = {3},
number = {5},
pages = {},
pmid = {30417109},
issn = {2379-5077},
abstract = {Host-associated microbiota composition can be conserved over evolutionary time scales. Indeed, closely related species often host similar microbiota; i.e., the composition of their microbiota harbors a phylogenetic signal, a pattern sometimes referred to as "phylosymbiosis." Elucidating the origins of this pattern is important to better understand microbiota ecology and evolution. However, this is hampered by our lack of theoretical expectations and a comprehensive overview of phylosymbiosis prevalence in nature. Here, we use simulations to provide a simple expectation for when we should expect this pattern to occur and then review the literature to document the prevalence and strength of phylosymbiosis across the host tree of life. We demonstrate that phylosymbiosis can readily emerge from a simple ecological filtering process, whereby a given host trait (e.g., gut pH) that varies with host phylogeny (i.e., harbors a phylogenetic signal) filters preadapted microbes. We found marked differences between methods used to detect phylosymbiosis, so we proposed a series of practical recommendations based on using multiple best-performing approaches. Importantly, we found that, while the prevalence of phylosymbiosis is mixed in nature, it appears to be stronger for microbiotas living in internal host compartments (e.g., the gut) than those living in external compartments (e.g., the rhizosphere). We show that phylosymbiosis can theoretically emerge without any intimate, long-term coevolutionary mechanisms and that most phylosymbiosis patterns observed in nature are compatible with a simple ecological process. Deviations from baseline ecological expectations might be used to further explore more complex hypotheses, such as codiversification. IMPORTANCE Phylosymbiosis is a pattern defined as the tendency of closely related species to host microbiota whose compositions resemble each other more than host species drawn at random from the same tree. Understanding the mechanisms behind phylosymbiosis is important because it can shed light on rules governing the assembly of host-associated microbiotas and, potentially, their coevolutionary dynamics with hosts. For example, is phylosymbiosis a result of coevolution, or can it be generated by simple ecological filtering processes? Beyond qualitative theoretical models, quantitative theoretical expectations can provide new insights. For example, deviations from a simple baseline of ecological filtering may be used to test more-complex hypotheses (e.g., coevolution). Here, we use simulations to provide evidence that simple host-related ecological filtering can readily generate phylosymbiosis, and we contrast these predictions with real-world data. We find that while phylosymbiosis is widespread in nature, phylosymbiosis patterns are compatible with a simple ecological model in the majority of taxa. Internal compartments of hosts, such as the animal gut, often display stronger phylosymbiosis than expected from a purely ecological filtering process, suggesting that other mechanisms are also involved.},
}

@article {pmid30413098,
year = {2018},
author = {Trotter, RT and Lininger, MR and Camplain, R and Fofanov, VY and Camplain, C and Baldwin, JA},
title = {A Survey of Health Disparities, Social Determinants of Health, and Converging Morbidities in a County Jail: A Cultural-Ecological Assessment of Health Conditions in Jail Populations.},
journal = {International journal of environmental research and public health},
volume = {15},
number = {11},
pages = {},
pmid = {30413098},
issn = {1660-4601},
support = {N/A//NARBHA Institute/ ; U54MD012388/MD/NIMHD NIH HHS/United States ; },
abstract = {The environmental health status of jail populations in the United States constitutes a significant public health threat for prisoners and the general population. The ecology of jails creates a dynamic condition in relation to general population health due to the concentrated potential exposure to infectious diseases, difficult access to treatment for chronic health conditions, interruption in continuity of care for serious behavioral health conditions, as well as on-going issues for the prevention and treatment of substance abuse disorders. This paper reports on elements of a cross-sectional survey embedded in a parent project, "Health Disparities in Jail Populations." The overall project includes a comprehensive secondary data analysis of the health status of county jail populations, along with primary data collection that includes a cross-sectional health and health care services survey of incarcerated individuals, coupled with collection of biological samples to investigate infectious disease characteristics of a county jail population. This paper reports on the primary results of the survey data collection that indicate that this is a population with complex and interacting co-morbidities, as well as significant health disparities compared to the general population.},
}

@article {pmid30410743,
year = {2018},
author = {Munos, MK and Maiga, A and Do, M and Sika, GL and Carter, ED and Mosso, R and Dosso, A and Leyton, A and Khan, SM},
title = {Linking household survey and health facility data for effective coverage measures: a comparison of ecological and individual linking methods using the Multiple Indicator Cluster Survey in Côte d'Ivoire.},
journal = {Journal of global health},
volume = {8},
number = {2},
pages = {020803},
pmid = {30410743},
issn = {2047-2986},
mesh = {Adolescent ; Adult ; Child, Preschool ; Cote d'Ivoire ; Ecology ; Feasibility Studies ; Female ; *Health Care Surveys ; Health Services Needs and Demand ; Humans ; Infant ; Infant, Newborn ; Information Storage and Retrieval/*methods ; *Medical Record Linkage ; Middle Aged ; Patient Acceptance of Health Care/*statistics & numerical data ; Pregnancy ; Quality of Health Care ; Reproducibility of Results ; Young Adult ; },
abstract = {Background: Population-based measures of intervention coverage are used in low- and middle-income countries for program planning, prioritization, and evaluation. There is increased interest in effective coverage, which integrates information about service quality or health outcomes. Approaches proposed for quality-adjusted effective coverage include linking data on need and service contact from population-based surveys with data on service quality from health facility surveys. However, there is limited evidence about the validity of different linking methods for effective coverage estimation.

Methods: We collaborated with the 2016 Côte d'Ivoire Multiple Indicator Cluster Survey (MICS) to link data from a health provider assessment to care-seeking data collected by the MICS in the Savanes region of Côte d'Ivoire. The provider assessment was conducted in a census of public and non-public health facilities and pharmacies in Savanes in May-June 2016. We also included community health workers managing sick children who served the clusters sampled for the MICS. The provider assessment collected information on structural and process quality for antenatal care, delivery and immediate newborn care, postnatal care, and sick child care. We linked the MICS and provider data using exact-match and ecological linking methods, including aggregate linking and geolinking methods. We compared the results obtained from exact-match and ecological methods.

Results: We linked 731 of 786 care-seeking episodes (93%) from the MICS to a structural quality score for the provider named by the respondent. Effective coverage estimates computed using exact-match methods were 13%-63% lower than the care-seeking estimates from the MICS. Absolute differences between exact match and ecological linking methods were ±7 percentage points for all ecological methods. Incorporating adjustments for provider category and weighting by service-specific utilization into the ecological methods generally resulted in better agreement between ecological and exact match estimates.

Conclusions: Ecological linking may be a feasible and valid approach for estimating quality-adjusted effective coverage when a census of providers is used. Adjusting for provider type and caseload may improve agreement with exact match results. There remain methodological questions to be addressed to develop guidance on using linking methods for estimating quality-adjusted effective coverage, including the effect of facility sampling and time displacement.},
}

Adolescent
Adult
Child, Preschool
Cote d'Ivoire
Ecology
Feasibility Studies
Female
*Health Care Surveys
Health Services Needs and Demand
Humans
Infant
Infant, Newborn
Information Storage and Retrieval/*methods
*Medical Record Linkage
Middle Aged
Patient Acceptance of Health Care/*statistics & numerical data
Pregnancy
Quality of Health Care
Reproducibility of Results
Young Adult

@article {pmid30384907,
year = {2018},
author = {Bamisile, BS and Dash, CK and Akutse, KS and Keppanan, R and Afolabi, OG and Hussain, M and Qasim, M and Wang, L},
title = {Prospects of endophytic fungal entomopathogens as biocontrol and plant growth promoting agents: An insight on how artificial inoculation methods affect endophytic colonization of host plants.},
journal = {Microbiological research},
volume = {217},
number = {},
pages = {34-50},
doi = {10.1016/j.micres.2018.08.016},
pmid = {30384907},
issn = {1618-0623},
mesh = {*Agricultural Inoculants ; Animals ; Beauveria/physiology ; Biological Control Agents/*pharmacology ; Databases, Factual ; Endophytes/growth & development/*physiology ; Host-Pathogen Interactions/physiology ; Insecta/drug effects ; Pest Control, Biological/*methods ; *Plant Development ; Plant Diseases/microbiology/*prevention & control ; Plant Roots/microbiology ; Plant Stems/microbiology ; Plants/*microbiology ; Seedlings/microbiology ; Soil ; Sorghum/microbiology ; },
abstract = {Entomopathogenic fungi (EPF) can be established as endophytes in the host plants to offer a long-term preventive measure for pests and diseases. This practice serves as a better alternative to the common practice of periodic direct application of EPF on plants or the target pests as a short-term defense strategy against pests and diseases. These fungal endophytes, aside from their role in pests and diseases prevention, also act as plant growth promoters. Several fungal endophytes have been associated with improvement in plant height, dry and wet weight and other growth parameters. However, many limiting factors have been identified as mitigating the successful colonization of the host plants by EPF. The inoculation methods used have been identified as one, but sadly, this has received little or less attention. Some previous studies carried out comparison between various artificial inoculation methods; foliar application, seedling dipping, soil drenching, seed inoculation, direct injection and others. In separate studies, some authors had suggested different application methods that are best suitable for certain fungal entomopathogens. For instance, leaf inoculation with conidial suspensions was suggested to be the best inoculation method for Beauveria bassiana in sorghum, stem injection was suggested as the most suitable for coffee, while, root dipping method proved the most successful for B. bassiana colonization of tomato plants for the management of Helicoverpa armigera. Here, we discussed entomopathogenic fungal endophytes as bio-control agents, plant growth promoters and highlighted the effect of various artificial inoculation methods on their endophytic colonization of the host plants.},
}

*Agricultural Inoculants
Animals
Beauveria/physiology
Biological Control Agents/*pharmacology
Databases, Factual
Endophytes/growth & development/*physiology
Host-Pathogen Interactions/physiology
Insecta/drug effects
Pest Control, Biological/*methods
*Plant Development
Plant Diseases/microbiology/*prevention & control
Plant Roots/microbiology
Plant Stems/microbiology
Plants/*microbiology
Seedlings/microbiology
Soil
Sorghum/microbiology

@article {pmid30366399,
year = {2018},
author = {Meng, X and Wang, F and Xie, Y and Song, G and Ma, S and Hu, S and Bai, J and Yang, Y},
title = {An Ontology-Driven Approach for Integrating Intelligence to Manage Human and Ecological Health Risks in the Geospatial Sensor Web.},
journal = {Sensors (Basel, Switzerland)},
volume = {18},
number = {11},
pages = {},
pmid = {30366399},
issn = {1424-8220},
support = {41501441//National Natural Science Foundation of China/ ; 2014HB04//Hubei Provincial Environment Protection Project/ ; GDGTKJ2017001//Guangdong Provincial Land Resource Research Project/ ; 2042017kf0212//Wuhan University Grant/ ; },
mesh = {Ecology ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Humans ; Intelligence ; Software ; },
abstract = {Due to the rapid installation of a massive number of fixed and mobile sensors, monitoring machines are intentionally or unintentionally involved in the production of a large amount of geospatial data. Environmental sensors and related software applications are rapidly altering human lifestyles and even impacting ecological and human health. However, there are rarely specific geospatial sensor web (GSW) applications for certain ecological public health questions. In this paper, we propose an ontology-driven approach for integrating intelligence to manage human and ecological health risks in the GSW. We design a Human and Ecological health Risks Ontology (HERO) based on a semantic sensor network ontology template. We also illustrate a web-based prototype, the Human and Ecological Health Risk Management System (HaEHMS), which helps health experts and decision makers to estimate human and ecological health risks. We demonstrate this intelligent system through a case study of automatic prediction of air quality and related health risk.},
}

Ecology
Environmental Monitoring/*methods
*Geographic Information Systems
Humans
Intelligence
Software

@article {pmid30344120,
year = {2018},
author = {Gopalakrishnan, S and Sinding, MS and Ramos-Madrigal, J and Niemann, J and Samaniego Castruita, JA and Vieira, FG and Carøe, C and Montero, MM and Kuderna, L and Serres, A and González-Basallote, VM and Liu, YH and Wang, GD and Marques-Bonet, T and Mirarab, S and Fernandes, C and Gaubert, P and Koepfli, KP and Budd, J and Rueness, EK and Heide-Jørgensen, MP and Petersen, B and Sicheritz-Ponten, T and Bachmann, L and Wiig, Ø and Hansen, AJ and Gilbert, MTP},
title = {Interspecific Gene Flow Shaped the Evolution of the Genus Canis.},
journal = {Current biology : CB},
volume = {28},
number = {21},
pages = {3441-3449.e5},
pmid = {30344120},
issn = {1879-0445},
support = {U01 MH106874/MH/NIMH NIH HHS/United States ; },
abstract = {The evolutionary history of the wolf-like canids of the genus Canis has been heavily debated, especially regarding the number of distinct species and their relationships at the population and species level [1-6]. We assembled a dataset of 48 resequenced genomes spanning all members of the genus Canis except the black-backed and side-striped jackals, encompassing the global diversity of seven extant canid lineages. This includes eight new genomes, including the first resequenced Ethiopian wolf (Canis simensis), one dhole (Cuon alpinus), two East African hunting dogs (Lycaon pictus), two Eurasian golden jackals (Canis aureus), and two Middle Eastern gray wolves (Canis lupus). The relationships between the Ethiopian wolf, African golden wolf, and golden jackal were resolved. We highlight the role of interspecific hybridization in the evolution of this charismatic group. Specifically, we find gene flow between the ancestors of the dhole and African hunting dog and admixture between the gray wolf, coyote (Canis latrans), golden jackal, and African golden wolf. Additionally, we report gene flow from gray and Ethiopian wolves to the African golden wolf, suggesting that the African golden wolf originated through hybridization between these species. Finally, we hypothesize that coyotes and gray wolves carry genetic material derived from a "ghost" basal canid lineage.},
}

@article {pmid30269263,
year = {2018},
author = {Li, W and Liu, S and Pei, Y and He, J and Wang, Q},
title = {Zoning for eco-geological environment before mining in Yushenfu mining area, northern Shaanxi, China.},
journal = {Environmental monitoring and assessment},
volume = {190},
number = {10},
pages = {619},
pmid = {30269263},
issn = {1573-2959},
support = {2015CB251601//the National Basic Research Program of China (973 Program)/ ; 41430643//the State Key Program of the National Natural Science Foundation of China/ ; },
mesh = {China ; Ecology/*methods ; Ecosystem ; Environment ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geology ; Groundwater ; *Mining ; Remote Sensing Technology/methods ; },
abstract = {Zoning for the eco-geological environment (EGE) aims to protect and improve the regional ecological environment. It is the basis for evaluating the ecological characteristics of a mining area prior to mining activities and has the purpose of implementing water-preserved mining according to zoning type. In this study, four EGE types were proposed following field investigation in the Yushenfu mining area: oasis type with phreatic water and bottomland in desert (OTPWBD), oasis type with surface water and valley river (OTSWVR), loess gully type with surface runoff (LGTSR), and regional deep groundwater enrichment type (RDGET). Nine EGE evaluation indices were selected: rainfall, evaporation capacity, Luohe formation thickness, surface elevation, Sara Wusu aquifer water abundance, surface lithology, topography, slope, and normalized difference vegetation index (NDVI). Remote sensing technology and geographic information systems were first used to generate the evaluation index thematic maps. Then, the weight of each evaluation index was determined based on an analytic hierarchy process (AHP). Third, the index weight was used to form an improved weighted fuzzy C s clustering algorithm, and EGE zones were assigned using the MATLAB computing platform. For comparison, the AHP was also adopted for EGE zoning and a map of zoning differences was obtained. Finally, EGE field surveys of typical mines were carried out, which verified that EGE zoning using fuzzy clustering was accurate and reasonable.},
}

China
Ecology/*methods
Ecosystem
Environment
Environmental Monitoring/*methods
Geographic Information Systems
Geology
Groundwater
*Mining
Remote Sensing Technology/methods

@article {pmid30262689,
year = {2018},
author = {Song, H and Zhang, YX and Yang, MJ and Sun, JC and Zhang, T and Wang, HY},
title = {Genome survey on invasive veined rapa whelk (Rapana venosa) and development of microsatellite loci on large scale.},
journal = {Journal of genetics},
volume = {97},
number = {4},
pages = {e79-e86},
pmid = {30262689},
issn = {0973-7731},
mesh = {Animals ; China ; Computational Biology ; Gastropoda/*genetics ; Genetic Variation ; Genome/*genetics ; *Genomics ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats/*genetics ; Polymorphism, Genetic ; Sequence Analysis, DNA ; },
abstract = {The veined rapa whelk (Rapana venosa) is an economically important gastropod in China, but is considered as an invasive species globally. Only a few studies have examined the R. venosa genome, a genomewide survey is necessary for improving our understanding of the genome structure and size of this organism. Microsatellite markers are powerful tools for characterizing germplasms, genetic diversity and kinship among individuals. The resultant data are applicable to breeding efforts in commercial aquaculture or for understanding invasion mechanisms. Here, we investigated the genome structure of R. venosa on an Illumina Hi-seq platform with ∼92× sequencing depth. We performed a K-mer analysis to estimate genome size, repeat sequences and heterozygosity. Clean reads were de novo assembled for the identification of simple-sequence repeat (SSR) loci that are suitable as markers. The estimated genome size of R. venosa was 2200.07 Mb, with a 1.41% heterozygosity rate and 67.04% repeats. We detected 5,477,450 simple-sequence repeats (SSRs), with 3,400,602 loci present as pure tandem repeats and 2,076,848 as compound motifs. We further selected and characterized 28 polymorphic markers in 78 individuals from Dandong, Laizhou, Weihai and Zhoushan in China. The range of alleles was 2-28 and the observed heterozygosity was 0.2857-0.8676. The data obtained from our genomic survey will aid the design of R. venosa whole-genome sequencing projects and advance the identification of SSR markers. Both these developments are valuable for further studies on ecological, evolutionary and genetic breeding in R. venosa.},
}

Animals
China
Computational Biology
Gastropoda/*genetics
Genetic Variation
Genome/*genetics
*Genomics
High-Throughput Nucleotide Sequencing
Microsatellite Repeats/*genetics
Polymorphism, Genetic
Sequence Analysis, DNA

@article {pmid30258229,
year = {2018},
author = {Bjorkman, AD and Myers-Smith, IH and Elmendorf, SC and Normand, S and Rüger, N and Beck, PSA and Blach-Overgaard, A and Blok, D and Cornelissen, JHC and Forbes, BC and Georges, D and Goetz, SJ and Guay, KC and Henry, GHR and HilleRisLambers, J and Hollister, RD and Karger, DN and Kattge, J and Manning, P and Prevéy, JS and Rixen, C and Schaepman-Strub, G and Thomas, HJD and Vellend, M and Wilmking, M and Wipf, S and Carbognani, M and Hermanutz, L and Lévesque, E and Molau, U and Petraglia, A and Soudzilovskaia, NA and Spasojevic, MJ and Tomaselli, M and Vowles, T and Alatalo, JM and Alexander, HD and Anadon-Rosell, A and Angers-Blondin, S and Beest, MT and Berner, L and Björk, RG and Buchwal, A and Buras, A and Christie, K and Cooper, EJ and Dullinger, S and Elberling, B and Eskelinen, A and Frei, ER and Grau, O and Grogan, P and Hallinger, M and Harper, KA and Heijmans, MMPD and Hudson, J and Hülber, K and Iturrate-Garcia, M and Iversen, CM and Jaroszynska, F and Johnstone, JF and Jørgensen, RH and Kaarlejärvi, E and Klady, R and Kuleza, S and Kulonen, A and Lamarque, LJ and Lantz, T and Little, CJ and Speed, JDM and Michelsen, A and Milbau, A and Nabe-Nielsen, J and Nielsen, SS and Ninot, JM and Oberbauer, SF and Olofsson, J and Onipchenko, VG and Rumpf, SB and Semenchuk, P and Shetti, R and Collier, LS and Street, LE and Suding, KN and Tape, KD and Trant, A and Treier, UA and Tremblay, JP and Tremblay, M and Venn, S and Weijers, S and Zamin, T and Boulanger-Lapointe, N and Gould, WA and Hik, DS and Hofgaard, A and Jónsdóttir, IS and Jorgenson, J and Klein, J and Magnusson, B and Tweedie, C and Wookey, PA and Bahn, M and Blonder, B and van Bodegom, PM and Bond-Lamberty, B and Campetella, G and Cerabolini, BEL and Chapin, FS and Cornwell, WK and Craine, J and Dainese, M and de Vries, FT and Díaz, S and Enquist, BJ and Green, W and Milla, R and Niinemets, Ü and Onoda, Y and Ordoñez, JC and Ozinga, WA and Penuelas, J and Poorter, H and Poschlod, P and Reich, PB and Sandel, B and Schamp, B and Sheremetev, S and Weiher, E},
title = {Plant functional trait change across a warming tundra biome.},
journal = {Nature},
volume = {562},
number = {7725},
pages = {57-62},
doi = {10.1038/s41586-018-0563-7},
pmid = {30258229},
issn = {1476-4687},
abstract = {The tundra is warming more rapidly than any other biome on Earth, and the potential ramifications are far-reaching because of global feedback effects between vegetation and climate. A better understanding of how environmental factors shape plant structure and function is crucial for predicting the consequences of environmental change for ecosystem functioning. Here we explore the biome-wide relationships between temperature, moisture and seven key plant functional traits both across space and over three decades of warming at 117 tundra locations. Spatial temperature-trait relationships were generally strong but soil moisture had a marked influence on the strength and direction of these relationships, highlighting the potentially important influence of changes in water availability on future trait shifts in tundra plant communities. Community height increased with warming across all sites over the past three decades, but other traits lagged far behind predicted rates of change. Our findings highlight the challenge of using space-for-time substitution to predict the functional consequences of future warming and suggest that functions that are tied closely to plant height will experience the most rapid change. They also reveal the strength with which environmental factors shape biotic communities at the coldest extremes of the planet and will help to improve projections of functional changes in tundra ecosystems with climate warming.},
}

@article {pmid30194403,
year = {2018},
author = {Rokas, A and Wisecaver, JH and Lind, AL},
title = {The birth, evolution and death of metabolic gene clusters in fungi.},
journal = {Nature reviews. Microbiology},
volume = {16},
number = {12},
pages = {731-744},
doi = {10.1038/s41579-018-0075-3},
pmid = {30194403},
issn = {1740-1534},
abstract = {Fungi contain a remarkable diversity of both primary and secondary metabolic pathways involved in ecologically specialized or accessory functions. Genes in these pathways are frequently physically linked on fungal chromosomes, forming metabolic gene clusters (MGCs). In this Review, we describe the diversity in the structure and content of fungal MGCs, their population-level and species-level variation, the evolutionary mechanisms that underlie their formation, maintenance and decay, and their ecological and evolutionary impact on fungal populations. We also discuss MGCs from other eukaryotes and the reasons for their preponderance in fungi. Improved knowledge of the evolutionary life cycle of MGCs will advance our understanding of the ecology of specialized metabolism and of the interplay between the lifestyle of an organism and genome architecture.},
}

@article {pmid30181062,
year = {2018},
author = {de Jonge, PA and Nobrega, FL and Brouns, SJJ and Dutilh, BE},
title = {Molecular and Evolutionary Determinants of Bacteriophage Host Range.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2018.08.006},
pmid = {30181062},
issn = {1878-4380},
abstract = {The host range of a bacteriophage is the taxonomic diversity of hosts it can successfully infect. Host range, one of the central traits to understand in phages, is determined by a range of molecular interactions between phage and host throughout the infection cycle. While many well studied model phages seem to exhibit a narrow host range, recent ecological and metagenomics studies indicate that phages may have specificities that range from narrow to broad. There is a growing body of studies on the molecular mechanisms that enable phages to infect multiple hosts. These mechanisms, and their evolution, are of considerable importance to understanding phage ecology and the various clinical, industrial, and biotechnological applications of phage. Here we review knowledge of the molecular mechanisms that determine host range, provide a framework defining broad host range in an evolutionary context, and highlight areas for additional research.},
}

@article {pmid30156039,
year = {2018},
author = {An, S and Zhu, X and Shen, M and Wang, Y and Cao, R and Chen, X and Yang, W and Chen, J and Tang, Y},
title = {Mismatch in elevational shifts between satellite observed vegetation greenness and temperature isolines during 2000-2016 on the Tibetan Plateau.},
journal = {Global change biology},
volume = {24},
number = {11},
pages = {5411-5425},
doi = {10.1111/gcb.14432},
pmid = {30156039},
issn = {1365-2486},
abstract = {Climate warming on the Tibetan Plateau tends to induce an uphill shift of temperature isolines. Observations and process-based models have both shown that climate warming has resulted in an increase in vegetation greenness on the Tibetan Plateau in recent decades. However, it is unclear whether the uphill shift of temperature isolines has caused greenness isolines to shift upward and whether the two shifts match each other. Our analysis of satellite observed vegetation greenness during the growing season (May-Sep) and gridded climate data for 2000-2016 documented a substantial mismatch between the elevational shifts of greenness and temperature isolines. This mismatch is probably associated with a lagging response of greenness to temperature change and with the elevational gradient of greenness. The lagging response of greenness may be associated with water limitation, resources availability, and acclimation. This lag may weaken carbon sequestration by Tibetan ecosystems, given that greenness is closely related to primary carbon uptake and ecosystem respiration increases exponentially with temperature. We also found that differences in terrain slope angle accounted for large spatial variations in the elevational gradient of greenness and thus the velocity of elevational shifts of greenness isolines and the sensitivity of elevational shifts of greenness isolines to temperature, highlighting the role of terrain effects on the elevational shifts of greenness isolines. The mismatches and the terrain effect found in this study suggest that there is potentially large micro-topographical difference in response and acclimation/adaptation of greenness to temperature changes in plants. More widespread in situ measurements and fine-resolution remote sensing observations and fine-gridded climate data are required to attribute the mismatch to specific environmental drivers and ecological processes such as vertical changes in community structure, plant physiology, and distribution of species.},
}

@article {pmid30147447,
year = {2018},
author = {Dornelas, M and Antão, LH and Moyes, F and Bates, AE and Magurran, AE and Adam, D and Akhmetzhanova, AA and Appeltans, W and Arcos, JM and Arnold, H and Ayyappan, N and Badihi, G and Baird, AH and Barbosa, M and Barreto, TE and Bässler, C and Bellgrove, A and Belmaker, J and Benedetti-Cecchi, L and Bett, BJ and Bjorkman, AD and Błażewicz, M and Blowes, SA and Bloch, CP and Bonebrake, TC and Boyd, S and Bradford, M and Brooks, AJ and Brown, JH and Bruelheide, H and Budy, P and Carvalho, F and Castañeda-Moya, E and Chen, CA and Chamblee, JF and Chase, TJ and Siegwart Collier, L and Collinge, SK and Condit, R and Cooper, EJ and Cornelissen, JHC and Cotano, U and Kyle Crow, S and Damasceno, G and Davies, CH and Davis, RA and Day, FP and Degraer, S and Doherty, TS and Dunn, TE and Durigan, G and Duffy, JE and Edelist, D and Edgar, GJ and Elahi, R and Elmendorf, SC and Enemar, A and Ernest, SKM and Escribano, R and Estiarte, M and Evans, BS and Fan, TY and Turini Farah, F and Loureiro Fernandes, L and Farneda, FZ and Fidelis, A and Fitt, R and Fosaa, AM and Daher Correa Franco, GA and Frank, GE and Fraser, WR and García, H and Cazzolla Gatti, R and Givan, O and Gorgone-Barbosa, E and Gould, WA and Gries, C and Grossman, GD and Gutierréz, JR and Hale, S and Harmon, ME and Harte, J and Haskins, G and Henshaw, DL and Hermanutz, L and Hidalgo, P and Higuchi, P and Hoey, A and Van Hoey, G and Hofgaard, A and Holeck, K and Hollister, RD and Holmes, R and Hoogenboom, M and Hsieh, CH and Hubbell, SP and Huettmann, F and Huffard, CL and Hurlbert, AH and Macedo Ivanauskas, N and Janík, D and Jandt, U and Jażdżewska, A and Johannessen, T and Johnstone, J and Jones, J and Jones, FAM and Kang, J and Kartawijaya, T and Keeley, EC and Kelt, DA and Kinnear, R and Klanderud, K and Knutsen, H and Koenig, CC and Kortz, AR and Král, K and Kuhnz, LA and Kuo, CY and Kushner, DJ and Laguionie-Marchais, C and Lancaster, LT and Min Lee, C and Lefcheck, JS and Lévesque, E and Lightfoot, D and Lloret, F and Lloyd, JD and López-Baucells, A and Louzao, M and Madin, JS and Magnússon, B and Malamud, S and Matthews, I and McFarland, KP and McGill, B and McKnight, D and McLarney, WO and Meador, J and Meserve, PL and Metcalfe, DJ and Meyer, CFJ and Michelsen, A and Milchakova, N and Moens, T and Moland, E and Moore, J and Mathias Moreira, C and Müller, J and Murphy, G and Myers-Smith, IH and Myster, RW and Naumov, A and Neat, F and Nelson, JA and Paul Nelson, M and Newton, SF and Norden, N and Oliver, JC and Olsen, EM and Onipchenko, VG and Pabis, K and Pabst, RJ and Paquette, A and Pardede, S and Paterson, DM and Pélissier, R and Peñuelas, J and Pérez-Matus, A and Pizarro, O and Pomati, F and Post, E and Prins, HHT and Priscu, JC and Provoost, P and Prudic, KL and Pulliainen, E and Ramesh, BR and Mendivil Ramos, O and Rassweiler, A and Rebelo, JE and Reed, DC and Reich, PB and Remillard, SM and Richardson, AJ and Richardson, JP and van Rijn, I and Rocha, R and Rivera-Monroy, VH and Rixen, C and Robinson, KP and Ribeiro Rodrigues, R and de Cerqueira Rossa-Feres, D and Rudstam, L and Ruhl, H and Ruz, CS and Sampaio, EM and Rybicki, N and Rypel, A and Sal, S and Salgado, B and Santos, FAM and Savassi-Coutinho, AP and Scanga, S and Schmidt, J and Schooley, R and Setiawan, F and Shao, KT and Shaver, GR and Sherman, S and Sherry, TW and Siciński, J and Sievers, C and da Silva, AC and Rodrigues da Silva, F and Silveira, FL and Slingsby, J and Smart, T and Snell, SJ and Soudzilovskaia, NA and Souza, GBG and Maluf Souza, F and Castro Souza, V and Stallings, CD and Stanforth, R and Stanley, EH and Mauro Sterza, J and Stevens, M and Stuart-Smith, R and Rondon Suarez, Y and Supp, S and Yoshio Tamashiro, J and Tarigan, S and Thiede, GP and Thorn, S and Tolvanen, A and Teresa Zugliani Toniato, M and Totland, Ø and Twilley, RR and Vaitkus, G and Valdivia, N and Vallejo, MI and Valone, TJ and Van Colen, C and Vanaverbeke, J and Venturoli, F and Verheye, HM and Vianna, M and Vieira, RP and Vrška, T and Quang Vu, C and Van Vu, L and Waide, RB and Waldock, C and Watts, D and Webb, S and Wesołowski, T and White, EP and Widdicombe, CE and Wilgers, D and Williams, R and Williams, SB and Williamson, M and Willig, MR and Willis, TJ and Wipf, S and Woods, KD and Woehler, EJ and Zawada, K and Zettler, ML and Hickler, T},
title = {BioTIME: A database of biodiversity time series for the Anthropocene.},
journal = {Global ecology and biogeography : a journal of macroecology},
volume = {27},
number = {7},
pages = {760-786},
pmid = {30147447},
issn = {1466-822X},
support = {//Wellcome Trust/United Kingdom ; 250189//European Research Council/International ; },
abstract = {Motivation: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.

The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.

Spatial location and grain: BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).

Time period and grain: BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.

BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.

Software format: .csv and .SQL.},
}

@article {pmid30145518,
year = {2018},
author = {D'Alessandro, M and Esposito, V and Porporato, EMD and Berto, D and Renzi, M and Giacobbe, S and Scotti, G and Consoli, P and Valastro, G and Andaloro, F and Romeo, T},
title = {Relationships between plastic litter and chemical pollutants on benthic biodiversity.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {242},
number = {Pt B},
pages = {1546-1556},
doi = {10.1016/j.envpol.2018.08.002},
pmid = {30145518},
issn = {1873-6424},
mesh = {Animals ; *Biodiversity ; Ecology ; Environmental Monitoring ; Introduced Species ; Mediterranean Sea ; Mollusca/classification ; Plastics/*analysis ; Polychaeta/classification ; Water Pollutants, Chemical/*analysis ; },
abstract = {Five Descriptors (D) of Marine Strategy Framework Directive (MSFD): marine litter (D10), non-indigenous species (D2) and organic and inorganic pollutants (D8), were estimated in a coastal area of GSA 16 (Augusta harbour, Central Mediterranean Sea) in order to study their effects on the biodiversity (D1) of the benthic community D6) and to improve data for the MSFD. Investigation of plastic debris had led to the identification of 38 fragments divided into four categories, among which microplastics resulted as the most abundant. Six non-indigenous species, belonging to Polychaeta (Kirkegaardia dorsobranchialis, Notomastus aberans, Pista unibranchia, Pseudonereis anomala, Branchiomma bairdi) and Mollusca (Brachidontes pharaonis) were found. Biodiversity and benthic indices suggested a generalised, slightly disturbed ecological status. Anthracene, Zinc and Chrome were the most abundant chemical compounds in analysed sediments. Significant correlations were found between the abundance of trace elements vs biotic indices and between plastic debris vs biodiversity and benthic indices. This study represents the first report about the abundance of plastic debris and its relationship to contaminants and infauna in Augusta harbour. Our results can provide useful information for national and international laws and directives.},
}

Animals
*Biodiversity
Ecology
Environmental Monitoring
Introduced Species
Mediterranean Sea
Mollusca/classification
Plastics/*analysis
Polychaeta/classification
Water Pollutants, Chemical/*analysis

@article {pmid30108295,
year = {2018},
author = {Liebhold, AM and Yamanaka, T and Roques, A and Augustin, S and Chown, SL and Brockerhoff, EG and Pyšek, P},
title = {Plant diversity drives global patterns of insect invasions.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {12095},
pmid = {30108295},
issn = {2045-2322},
abstract = {During the last two centuries, thousands of insect species have been transported (largely inadvertently) and established outside of their native ranges worldwide, some with catastrophic ecological and economic impacts. Global variation in numbers of invading species depends on geographic variation in propagule pressure and heterogeneity of environmental resistance to invasions. Elton's diversity-invasibility hypothesis, proposed over sixty years ago, has been widely explored for plants but little is known on how biodiversity affects insect invasions. Here we use species inventories from 44 land areas, ranging from small oceanic islands to entire continents in various world regions, to show that numbers of established insect species are primarily driven by diversity of plants, with both native and non-native plant species richness being the strongest predictor of insect invasions. We find that at large spatial scales, plant diversity directly explains variation in non-native insect species richness among world regions, while geographic factors such as land area, climate and insularity largely affect insect invasions indirectly via their effects on local plant richness.},
}

@article {pmid30107371,
year = {2018},
author = {Wang, Q and Xiong, X and Wang, X and Tu, Q and Li, J and Ding, X and Li, Y and Huang, P and He, S and Yin, Y and Yang, H},
title = {Suckling Piglet Intestinal Enterocyte Nutrient Metabolism Changes.},
journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology},
volume = {48},
number = {5},
pages = {2103-2113},
doi = {10.1159/000492552},
pmid = {30107371},
issn = {1421-9778},
mesh = {Amino Acids/analysis/metabolism ; Animals ; Animals, Suckling ; Cells, Cultured ; Chromatography, High Pressure Liquid ; Citric Acid Cycle/genetics ; Databases, Factual ; Enterocytes/cytology/*metabolism ; Fatty Acids/analysis/metabolism ; Glucose/analysis/metabolism ; Jejunum/cytology ; Peptides/analysis ; Swine ; Tandem Mass Spectrometry ; },
abstract = {BACKGROUND/AIMS: Intestinal morphology and the types of enterocytes are changed in piglets during the suckling period, but it is unclear whether these changes are associated with metabolic changes in epithelium. The present study was conducted to test the hypothesis that glucose, fatty acids, and amino acid metabolism in differentiated piglet enterocytes changed during suckling.

METHODS: Twenty-four piglets (Duroc × [Landrace × Yorkshire]) from 8 litters (3 piglets/litter) were selected. A single piglet from each litter was randomly selected and euthanized at days 7, 14, and 21. Differentiated enterocytes (DE) were isolated from their mid-jejunum. Isobaric tags for relative and absolute quantification and subsequent liquid chromatography-tandem mass spectrometry were used to identify and measure protein synthesis.

RESULTS: The results showed that various activities, including: cellular processes; metabolic processes; biological regulation; pigmentation; and, localization, in DEs changed during suckling. Metabolic process analyses revealed that protein expression related to glycolysis and citrate cycle was decreased from day 7 to day 14. The number of differentiated enterocytes of 21 d piglets increased compared to 7 d piglets. Most of the proteins involved in fatty acid and amino acids metabolism had decreased DE expression between day 7 and day 14. Some, but not all, detected proteins down-regulated in DEs of 21 day piglets compared to 7 day piglets.

CONCLUSION: These results indicate that glucose, fatty acids, and amino acids metabolism changed during suckling. This may provide useful information for designing feed formulas and regulating piglet intestinal growth and development.},
}

Amino Acids/analysis/metabolism
Animals
Animals, Suckling
Cells, Cultured
Chromatography, High Pressure Liquid
Citric Acid Cycle/genetics
Databases, Factual
Enterocytes/cytology/*metabolism
Fatty Acids/analysis/metabolism
Glucose/analysis/metabolism
Jejunum/cytology
Peptides/analysis
Swine
Tandem Mass Spectrometry

@article {pmid30093613,
year = {2018},
author = {Albrecht, J and Classen, A and Vollstädt, MGR and Mayr, A and Mollel, NP and Schellenberger Costa, D and Dulle, HI and Fischer, M and Hemp, A and Howell, KM and Kleyer, M and Nauss, T and Peters, MK and Tschapka, M and Steffan-Dewenter, I and Böhning-Gaese, K and Schleuning, M},
title = {Plant and animal functional diversity drive mutualistic network assembly across an elevational gradient.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {3177},
pmid = {30093613},
issn = {2041-1723},
support = {For1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; },
abstract = {Species' functional traits set the blueprint for pair-wise interactions in ecological networks. Yet, it is unknown to what extent the functional diversity of plant and animal communities controls network assembly along environmental gradients in real-world ecosystems. Here we address this question with a unique dataset of mutualistic bird-fruit, bird-flower and insect-flower interaction networks and associated functional traits of 200 plant and 282 animal species sampled along broad climate and land-use gradients on Mt. Kilimanjaro. We show that plant functional diversity is mainly limited by precipitation, while animal functional diversity is primarily limited by temperature. Furthermore, shifts in plant and animal functional diversity along the elevational gradient control the niche breadth and partitioning of the respective other trophic level. These findings reveal that climatic constraints on the functional diversity of either plants or animals determine the relative importance of bottom-up and top-down control in plant-animal interaction networks.},
}

@article {pmid30046636,
year = {2018},
author = {Bird, SM and King, R},
title = {Multiple Systems Estimation (or Capture-Recapture Estimation) to Inform Public Policy.},
journal = {Annual review of statistics and its application},
volume = {5},
number = {},
pages = {95-118},
pmid = {30046636},
issn = {2326-8298},
support = {MC_U105260794//Medical Research Council/United Kingdom ; },
abstract = {Estimating population sizes has long been of interest, from the estimation of the human or ecological population size within regions or countries to the hidden number of civilian casualties in a war. Total enumeration of the population, for example, via a census, is often infeasible or simply impractical. However, a series of partial enumerations or observations of the population is often possible. This has led to the ideas of capture-recapture methods, which have been extensively used within ecology to estimate the size of wildlife populations, with an associated measure of uncertainty, and are most effectively applied when there are multiple capture occasions. Capture-recapture ideology can be more widely applied to multiple data-sources, by the linkage of individuals across the multiple lists. This is often referred to as Multiple Systems Estimation (MSE). The MSE approach has been preferred when estimating "capture-shy" or hard-to-reach populations, including those caught up in the criminal justice system; or homeless; or trafficked; or civilian casualties of war. Motivated by a range of public policy applications of MSE, each briefly introduced, we discuss practical problems with potentially substantial methodological implications. They include: "period" definition; "case" definition; when an observed count is not a true count of the population of interest but an upper bound due to mismatched definitions; exact or probabilistic matching of "cases" across different lists; demographic or other information about the "case" which may influence capture-propensities; required permissions to access extant-lists; list-creation by research-teams or interested parties; referrals (if presence on list A results - almost surely - in presence on list B); different mathematical models leading to widely different estimated population sizes; uncertainty in estimation; computational efficiency; external validation; hypothesis-generation; and additional independent external information. Returning to our motivational applications, we focus on whether the uncertainty which qualified their estimates was sufficiently narrow to orient public policy; and, if not, what options were available and/or taken to reduce the uncertainty or to seek external validation. We also consider whether MSE was hypothesis-generating: in the sense of having spawned new lines of inquiry.},
}

@article {pmid30029348,
year = {2018},
author = {Ridding, LE and Redhead, JW and Oliver, TH and Schmucki, R and McGinlay, J and Graves, AR and Morris, J and Bradbury, RB and King, H and Bullock, JM},
title = {The importance of landscape characteristics for the delivery of cultural ecosystem services.},
journal = {Journal of environmental management},
volume = {206},
number = {},
pages = {1145-1154},
doi = {10.1016/j.jenvman.2017.11.066},
pmid = {30029348},
issn = {1095-8630},
mesh = {*Conservation of Natural Resources ; Ecology ; *Ecosystem ; England ; *Geographic Information Systems ; Humans ; },
abstract = {The importance of Cultural Ecosystem Services (CES) to human wellbeing is widely recognised. However, quantifying these non-material benefits is challenging and consequently they are often not assessed. Mapping approaches are increasingly being used to understand the spatial distribution of different CES and how this relates to landscape characteristics. This study uses an online Public Participation Geographic Information System (PPGIS) to elicit information on outdoor locations important to respondents in Wiltshire, a dynamic lowland landscape in southern England. We analysed these locations in a GIS with spatial datasets representing potential influential factors, including protected areas, land use, landform, and accessibility. We assess these characteristics at different spatial and visual scales for different types of cultural engagement. We find that areas that are accessible, near to urban centres, with larger views, and a high diversity of protected habitats, are important for the delivery of CES. Other characteristics including a larger area of woodland and the presence of sites of historic interest in the surrounding landscape were also influential. These findings have implications for land-use planning and the management of ecosystems, by demonstrating the benefits of high quality ecological sites near to towns. The importance of maintaining and restoring landscape features, such as woodlands, to enhance the delivery of CES were also highlighted.},
}

*Conservation of Natural Resources
Ecology
*Ecosystem
England
*Geographic Information Systems
Humans

@article {pmid30029345,
year = {2018},
author = {He, L and Shen, J and Zhang, Y},
title = {Ecological vulnerability assessment for ecological conservation and environmental management.},
journal = {Journal of environmental management},
volume = {206},
number = {},
pages = {1115-1125},
doi = {10.1016/j.jenvman.2017.11.059},
pmid = {30029345},
issn = {1095-8630},
mesh = {China ; *Climate Change ; *Conservation of Natural Resources ; Ecology ; Ecosystem ; *Geographic Information Systems ; Humans ; },
abstract = {Identifying ecological vulnerable regions is a significant aspect in ecological conservation and environmental management. This paper presents a first attempt to provide a prototype framework that can assess ecological vulnerability and evaluate potential impacts of natural, social, economic, environmental pollution, and human health elements on ecological vulnerability with integrating spatial analysis of Geographic Information System (GIS) method and multi-criteria decision analysis (MCDA). A general ecological vulnerability index was constructed to describe the vulnerability status in an ecological hotspot of China. The assessment results of this study confirm the poor ecological vulnerability in China that only 1.32% of the China's population lives in not vulnerable ecosystem. A very high percentage (98.68%) of Chinese with 1.34 billion people lives in vulnerable and highly vulnerable area. This situation is mainly caused by increasing population pressure, exhausted nature resources, extensive economic growth, severe environmental pollution, insufficient environmental protection investment, and accelerating population aging. The spatial comparison indicates that spatial disparity existed in China with the central and northwestern provinces showing higher ecological vulnerability than the northeastern and southern provinces. The results of ecological vulnerability assessment can support effective guidance for mid- or long-term ecologic management. The developed framework can be replicated at different spatial and temporal scales using context-specific datasets to support ecological managers and government with decision-making. With available robust climate change models, future research might incorporate climate change into the ecological vulnerability framework.},
}

China
*Climate Change
*Conservation of Natural Resources
Ecology
Ecosystem
*Geographic Information Systems
Humans

@article {pmid30029326,
year = {2018},
author = {Djikanović, V and Skorić, S and Spasić, S and Naunovic, Z and Lenhardt, M},
title = {Ecological risk assessment for different macrophytes and fish species in reservoirs using biota-sediment accumulation factors as a useful tool.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {241},
number = {},
pages = {1167-1174},
doi = {10.1016/j.envpol.2018.06.054},
pmid = {30029326},
issn = {1873-6424},
mesh = {Animals ; Aquatic Organisms/*chemistry ; Biota ; Canada ; Catfishes ; Cyprinidae ; Ecology ; Environmental Monitoring/*methods ; Gills/chemistry ; Liver/chemistry ; Metals/analysis ; Metals, Heavy/analysis ; Muscles/chemistry ; Netherlands ; Risk Assessment ; Serbia ; Trace Elements/analysis ; Water Pollutants, Chemical/*analysis ; },
abstract = {Metal content was evaluated in the sediment, macrophytes and fish in the Medjuvršje reservoir (Western Serbia). Concentrations of 16 trace elements (Ag; Al; As; B; Ba; Cd; Co; Cr; Cu; Fe; Li; Mn; Ni; Pb; Sr; Zn) were analysed in the sediment, macrophytes and fish of an aquatic ecosystem. Five macrophyte species and three fish tissues (liver, muscle, gills) from five fish species (freshwater bream, common nase, Prussian carp, chub, wels catfish) were sampled and the metal content was analysed with ICP-OES. The sediment concentrations of Cu, Cd, and Zn exceeded the Canadian sediment quality guidelines while concentrations of Cr and Ni were above the Netherlands' target values. Bioaccumulation factors (BSAF) were calculated for analysed macrophytes and fish tissue. The BSAF had higher values for macrophytes for all investigated elements except for Cu and Zn; Cu had a higher value in the liver of the freshwater bream (0.823) and Zn had a higher value in the liver of freshwater bream (0.914) and chub (0.834) as well as in gills of Prussian carp (2.58) and chub (1.26). Potamogeton pectinatus, Ceratophylum demersum and the root of Phragmites communis showed higher accumulation of elements than Trapa natans and Potamogeton fluitans and the body of P. communis. The highest BSAF values for Ba, Mn, Sr and Ni were recorded in the gills. Cd and Cu had the highest BSAF values in the liver. Results confirmed that particular macrophyte and fish species could be a good indicator of reservoir water and sediment pollution.},
}

Animals
Aquatic Organisms/*chemistry
Biota
Canada
Catfishes
Cyprinidae
Ecology
Environmental Monitoring/*methods
Gills/chemistry
Liver/chemistry
Metals/analysis
Metals, Heavy/analysis
Muscles/chemistry
Netherlands
Risk Assessment
Serbia
Trace Elements/analysis
Water Pollutants, Chemical/*analysis

@article {pmid30026187,
year = {2018},
author = {Bradburd, GS and Coop, GM and Ralph, PL},
title = {Inferring Continuous and Discrete Population Genetic Structure Across Space.},
journal = {Genetics},
volume = {210},
number = {1},
pages = {33-52},
pmid = {30026187},
issn = {1943-2631},
support = {R01 GM108779/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Cluster Analysis ; Data Interpretation, Statistical ; Gene Flow/genetics ; Genetic Variation/genetics ; Genetics, Population/*methods/*statistics & numerical data ; Humans ; Models, Genetic ; North America ; Population Groups/genetics ; Populus/genetics ; Ursidae/genetics ; },
abstract = {A classic problem in population genetics is the characterization of discrete population structure in the presence of continuous patterns of genetic differentiation. Especially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations. This reflects a shortcoming of current methods for inferring and visualizing population structure when applied to genetic data deriving from geographically distributed populations. Here, we present a statistical framework for the simultaneous inference of continuous and discrete patterns of population structure. The method estimates ancestry proportions for each sample from a set of two-dimensional population layers, and, within each layer, estimates a rate at which relatedness decays with distance. This thereby explicitly addresses the "clines versus clusters" problem in modeling population genetic variation, and remedies some of the overfitting to which nonspatial models are prone. The method produces useful descriptions of structure in genetic relatedness in situations where separated, geographically distributed populations interact, as after a range expansion or secondary contact. We demonstrate the utility of this approach using simulations and by applying it to empirical datasets of poplars and black bears in North America.},
}

Animals
Cluster Analysis
Data Interpretation, Statistical
Gene Flow/genetics
Genetic Variation/genetics
Genetics, Population/*methods/*statistics & numerical data
Humans
Models, Genetic
North America
Population Groups/genetics
Populus/genetics
Ursidae/genetics

@article {pmid30020436,
year = {2018},
author = {Chen, F and Zhang, J and Chen, J and Li, X and Dong, W and Hu, J and Lin, M and Liu, Y and Li, G and Wang, Z and Zhang, L},
title = {realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta).},
journal = {Database : the journal of biological databases and curation},
volume = {2018},
number = {},
pages = {},
pmid = {30020436},
issn = {1758-0463},
mesh = {Algal Proteins/chemistry/genetics/metabolism ; *Databases, Genetic ; *Genome ; Internet ; Molecular Sequence Annotation ; Rhodophyta/*genetics ; Sequence Alignment ; Transcriptome/*genetics ; },
abstract = {With over 6000 species in seven classes, red algae (Rhodophyta) have diverse economic, ecological, experimental and evolutionary values. However, red algae are usually absent or rare in comparative analyses because genomic information of this phylum is often under-represented in various comprehensive genome databases. To improve the accessibility to the ome data and omics tools for red algae, we provided 10 genomes and 27 transcriptomes representing all seven classes of Rhodophyta. Three genomes and 18 transcriptomes were de novo assembled and annotated in this project. User-friendly BLAST suit, Jbrowse tools and search system were developed for online analyses. Detailed introductions to red algae taxonomy and the sequencing status are also provided. In conclusion, realDB (realDB.algaegenome.org) provides a platform covering the most genome and transcriptome data for red algae and a suite of tools for online analyses, and will attract both red algal biologists and those working on plant ecology, evolution and development.Database URL: http://realdb.algaegenome.org/.},
}

Algal Proteins/chemistry/genetics/metabolism
*Databases, Genetic
*Genome
Internet
Molecular Sequence Annotation
Rhodophyta/*genetics
Sequence Alignment
Transcriptome/*genetics

@article {pmid30017551,
year = {2018},
author = {Longbottom, J and Shearer, FM and Devine, M and Alcoba, G and Chappuis, F and Weiss, DJ and Ray, SE and Ray, N and Warrell, DA and Ruiz de Castañeda, R and Williams, DJ and Hay, SI and Pigott, DM},
title = {Vulnerability to snakebite envenoming: a global mapping of hotspots.},
journal = {Lancet (London, England)},
volume = {392},
number = {10148},
pages = {673-684},
pmid = {30017551},
issn = {1474-547X},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Africa, Northern/epidemiology ; Animals ; Antivenins/therapeutic use ; Geographic Mapping ; Health Resources/economics/statistics & numerical data ; Health Services Accessibility/standards ; Humans ; Indonesia/epidemiology ; Neglected Diseases/drug therapy/epidemiology/prevention & control ; Public Health/education ; Quality of Health Care/standards ; Snake Bites/*drug therapy/*epidemiology/mortality/prevention & control ; Snakes/*classification/injuries ; Vulnerable Populations/*statistics & numerical data ; },
abstract = {BACKGROUND: Snakebite envenoming is a frequently overlooked cause of mortality and morbidity. Data for snake ecology and existing snakebite interventions are scarce, limiting accurate burden estimation initiatives. Low global awareness stunts new interventions, adequate health resources, and available health care. Therefore, we aimed to synthesise currently available data to identify the most vulnerable populations at risk of snakebite, and where additional data to manage this global problem are needed.

METHODS: We assembled a list of snake species using WHO guidelines. Where relevant, we obtained expert opinion range (EOR) maps from WHO or the Clinical Toxinology Resources. We also obtained occurrence data for each snake species from a variety of websites, such as VertNet and iNaturalist, using the spocc R package (version 0.7.0). We removed duplicate occurrence data and categorised snakes into three groups: group A (no available EOR map or species occurrence records), group B (EOR map but <5 species occurrence records), and group C (EOR map and ≥5 species occurrence records). For group C species, we did a multivariate environmental similarity analysis using the 2008 WHO EOR maps and newly available evidence. Using these data and the EOR maps, we produced contemporary range maps for medically important venomous snake species at a 5 × 5 km resolution. We subsequently triangulated these data with three health system metrics (antivenom availability, accessibility to urban centres, and the Healthcare Access and Quality [HAQ] Index) to identify the populations most vulnerable to snakebite morbidity and mortality.

FINDINGS: We provide a map showing the ranges of 278 snake species globally. Although about 6·85 billion people worldwide live within range of areas inhabited by snakes, about 146·70 million live within remote areas lacking quality health-care provisioning. Comparing opposite ends of the HAQ Index, 272·91 million individuals (65·25%) of the population within the lowest decile are at risk of exposure to any snake for which no effective therapy exists compared with 519·46 million individuals (27·79%) within the highest HAQ Index decile, showing a disproportionate coverage in reported antivenom availability. Antivenoms were available for 119 (43%) of 278 snake species evaluated by WHO, while globally 750·19 million (10·95%) of those living within snake ranges live more than 1 h from population centres. In total, we identify about 92·66 million people living within these vulnerable geographies, including many sub-Saharan countries, Indonesia, and other parts of southeast Asia.

INTERPRETATION: Identifying exact populations vulnerable to the most severe outcomes of snakebite envenoming at a subnational level is important for prioritising new data collection and collation, reinforcing envenoming treatment, existing health-care systems, and deploying currently available and future interventions. These maps can guide future research efforts on snakebite envenoming from both ecological and public health perspectives and better target future estimates of the burden of this neglected tropical disease.

FUNDING: Bill & Melinda Gates Foundation.},
}

Africa, Northern/epidemiology
Animals
Antivenins/therapeutic use
Geographic Mapping
Health Resources/economics/statistics & numerical data
Health Services Accessibility/standards
Humans
Indonesia/epidemiology
Neglected Diseases/drug therapy/epidemiology/prevention & control
Public Health/education
Quality of Health Care/standards
Snake Bites/*drug therapy/*epidemiology/mortality/prevention & control
Snakes/*classification/injuries
Vulnerable Populations/*statistics & numerical data

@article {pmid29985552,
year = {2018},
author = {Ma, ZS and Li, L},
title = {Measuring metagenome diversity and similarity with Hill numbers.},
journal = {Molecular ecology resources},
volume = {18},
number = {6},
pages = {1339-1355},
doi = {10.1111/1755-0998.12923},
pmid = {29985552},
issn = {1755-0998},
support = {//Industry Technology Talent Grant/ ; //A China-US International Collaborative Project/ ; 71473243//National Science Foundation of China/ ; },
mesh = {Cluster Analysis ; Computational Biology/*methods ; DNA, Ribosomal/chemistry/genetics ; *Genetic Variation ; *Metagenome ; Metagenomics/*methods ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {The first step of any metagenome sequencing project is to get the inventory of OTU abundances (operational taxonomic units) and/or metagenomic gene abundances. The former is generated with 16S-rRNA-tagged amplicon sequencing technology, and the latter can be generated from either gene-targeted or whole-sample shotgun metagenomics technologies. With 16S-rRNA data sets, measuring community diversity with diversity indexes such as species richness and Shannon's index has been a de facto standard analysis; nevertheless, similarly comprehensive approaches to metagenomic gene abundances are still largely missing, despite that both OTU and gene abundances are DNA reads. Here, we adapt the Hill numbers, which were reintroduced to macrocommunity ecology recently and are now widely regarded as a most appropriate measure system for ecological diversity, for measuring metagenome alpha-, beta- and gamma-diversities, and similarity. Our proposal includes the following: (a) Metagenomic gene (MG) diversity measures the single-gene-level metagenome diversity; (b) Type-I metagenome functional gene cluster (MFGC) diversity measures the diversity of functional gene clusters but ignoring within-cluster gene abundance information; (c) Type-II MFGC diversity considers within-cluster gene abundances information and integrates gene-cluster-level metagenome diversity and functional gene redundancy information; and (d) Four classes of Hill-numbers-based similarity metrics, including local gene overlap, regional gene overlap, gene homogeneity measure and gene turnover complement, were introduced in terms of MG and MFGC, respectively. We demonstrate the proposal with the gut metagenomes from healthy and IBD (inflammatory bowel disease) cohorts. The Hill numbers offer a unified approach to cohesively and comprehensively measuring the ecological and metagenome diversities of microbiomes.},
}

Cluster Analysis
Computational Biology/*methods
DNA, Ribosomal/chemistry/genetics
*Genetic Variation
*Metagenome
Metagenomics/*methods
*Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid29981010,
year = {2018},
author = {Lant, C and Baggio, J and Konar, M and Mejia, A and Ruddell, B and Rushforth, R and Sabo, JL and Troy, TJ},
title = {The U.S. food-energy-water system: A blueprint to fill the mesoscale gap for science and decision-making.},
journal = {Ambio},
volume = {},
number = {},
pages = {},
doi = {10.1007/s13280-018-1077-0},
pmid = {29981010},
issn = {1654-7209},
support = {1639529//National Science Foundation/ ; },
abstract = {Food, energy, and water (FEW) are interdependent and must be examined as a coupled natural-human system. This perspective essay defines FEW systems and outlines key findings about them as a blueprint for future models to satisfy six key objectives. The first three focus on linking the FEW production and consumption to impacts on Earth cycles in a spatially specific manner in order to diagnose problems and identify potential solutions. The second three focus on describing the evolution of FEW systems to identify risks, thus empowering the FEW actors to better achieve the goals of resilience and sustainability. Four key findings about the FEW systems that guide future model development are (1) that they engage ecological, carbon, water, and nutrient cycles most powerfully among all human systems; (2) that they operate primarily at a mesoscale best captured by counties, districts, and cities; (3) that cities are hubs within the FEW system; and (4) that the FEW system forms a complex network.},
}

@article {pmid29973596,
year = {2018},
author = {Bramon Mora, B and Gravel, D and Gilarranz, LJ and Poisot, T and Stouffer, DB},
title = {Identifying a common backbone of interactions underlying food webs from different ecosystems.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {2603},
pmid = {29973596},
issn = {2041-1723},
mesh = {Animals ; Competitive Behavior/*physiology ; Datasets as Topic ; Ecosystem ; *Food Chain ; *Models, Statistical ; Predatory Behavior/*physiology ; Principal Component Analysis ; },
abstract = {Although the structure of empirical food webs can differ between ecosystems, there is growing evidence of multiple ways in which they also exhibit common topological properties. To reconcile these contrasting observations, we postulate the existence of a backbone of interactions underlying all ecological networks-a common substructure within every network comprised of species playing similar ecological roles-and a periphery of species whose idiosyncrasies help explain the differences between networks. To test this conjecture, we introduce a new approach to investigate the structural similarity of 411 food webs from multiple environments and biomes. We first find significant differences in the way species in different ecosystems interact with each other. Despite these differences, we then show that there is compelling evidence of a common backbone of interactions underpinning all food webs. We expect that identifying a backbone of interactions will shed light on the rules driving assembly of different ecological communities.},
}

Animals
Competitive Behavior/*physiology
Datasets as Topic
Ecosystem
*Food Chain
*Models, Statistical
Predatory Behavior/*physiology
Principal Component Analysis

@article {pmid29923321,
year = {2018},
author = {Keck, F and Vasselon, V and Rimet, F and Bouchez, A and Kahlert, M},
title = {Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units' ecological profiles.},
journal = {Molecular ecology resources},
volume = {18},
number = {6},
pages = {1299-1309},
doi = {10.1111/1755-0998.12919},
pmid = {29923321},
issn = {1755-0998},
mesh = {Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Diatoms/classification/genetics ; Environmental Monitoring/*methods ; Metagenomics/*methods ; Microscopy ; Phylogeny ; Rivers/microbiology ; Sensitivity and Specificity ; },
abstract = {DNA metabarcoding has been introduced as a revolutionary way to identify organisms and monitor ecosystems. However, the potential of this approach for biomonitoring remains partially unfulfilled because a significant part of the sampled DNA cannot be affiliated to species due to incomplete reference libraries. Thus, biotic indices, which are based on the estimated abundances of species in a community and their ecological profiles, can be inaccurate. We propose to compute biotic indices using phylogenetic imputation of operational taxonomic units (OTUs') ecological profiles (OTU-PITI approach). First, OTUs sequences are inserted within a reference phylogeny. Second, OTUs' ecological profiles are estimated on the basis of their phylogenetic relationships with reference species whose ecology is known. Based on these ecological profiles, biotic indices can be computed using all available OTUs. Using freshwater diatoms as a case study, we show that short DNA barcodes can be placed accurately within a phylogeny and their ecological preferences estimated with a satisfactory level of precision. In the light of these results, we tested the approach with a data set of 139 environmental samples of benthic river diatoms for which the same biotic index (specific sensitivity index) was calculated using (a) traditional microscopy, (b) OTUs with taxonomic assignment approach, (c) OTUs with phylogenetic estimation of ecological profiles (OTU-PITI) and (d) OTU with taxonomic assignment completed by the phylogenetic approach (OTU-PITI) for unclassified OTUs. Using traditional microscopy as a reference, we found that the combination of the OTUs' taxonomic assignment completed by the phylogenetic method performed satisfactorily and substantially better than the other methods tested.},
}

Computational Biology/*methods
DNA Barcoding, Taxonomic/*methods
Diatoms/classification/genetics
Environmental Monitoring/*methods
Metagenomics/*methods
Microscopy
Phylogeny
Rivers/microbiology
Sensitivity and Specificity

@article {pmid29917104,
year = {2018},
author = {Celis, JS and Wibberg, D and Ramírez-Portilla, C and Rupp, O and Sczyrba, A and Winkler, A and Kalinowski, J and Wilke, T},
title = {Binning enables efficient host genome reconstruction in cnidarian holobionts.},
journal = {GigaScience},
volume = {7},
number = {7},
pages = {},
pmid = {29917104},
issn = {2047-217X},
mesh = {Algorithms ; Animals ; Anthozoa/*physiology ; Cnidaria/*genetics ; Computational Biology ; Coral Reefs ; DNA/analysis ; Ecology ; *Genome ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; Symbiosis ; Transcriptome ; },
abstract = {Background: Many cnidarians, including stony corals, engage in complex symbiotic associations, comprising the eukaryotic host, photosynthetic algae, and highly diverse microbial communities-together referred to as holobiont. This taxonomic complexity makes sequencing and assembling coral host genomes extremely challenging. Therefore, previous cnidarian genomic projects were based on symbiont-free tissue samples. However, this approach may not be applicable to the majority of cnidarian species for ecological reasons. We therefore evaluated the performance of an alternative method based on sequence binning for reconstructing the genome of the stony coral Porites rus from a hologenomic sample and compared it to traditional approaches.

Results: Our results demonstrate that binning performs well for hologenomic data, producing sufficient reads for assembling the draft genome of P. rus. An assembly evaluation based on operational criteria showed results that were comparable to symbiont-free approaches in terms of completeness and usefulness, despite a high degree of fragmentation in our assembly. In addition, we found that binning provides sufficient data for exploratory k-mer estimation of genomic features, such as genome size and heterozygosity.

Conclusions: Binning constitutes a powerful approach for disentangling taxonomically complex coral hologenomes. Considering the recent decline of coral reefs on the one hand and previous limitations to coral genome sequencing on the other hand, binning may facilitate rapid and reliable genome assembly. This study also provides an important milestone in advancing binning from the metagenomic to the hologenomic and from the prokaryotic to the eukaryotic level.},
}

Algorithms
Animals
Anthozoa/*physiology
Cnidaria/*genetics
Computational Biology
Coral Reefs
DNA/analysis
Ecology
*Genome
Genomics/*methods
High-Throughput Nucleotide Sequencing
Metagenomics/*methods
Phylogeny
RNA, Ribosomal, 16S/analysis
Sequence Analysis, DNA
Symbiosis
Transcriptome

@article {pmid29898550,
year = {2018},
author = {Mirtl, M and T Borer, E and Djukic, I and Forsius, M and Haubold, H and Hugo, W and Jourdan, J and Lindenmayer, D and McDowell, WH and Muraoka, H and Orenstein, DE and Pauw, JC and Peterseil, J and Shibata, H and Wohner, C and Yu, X and Haase, P},
title = {Genesis, goals and achievements of Long-Term Ecological Research at the global scale: A critical review of ILTER and future directions.},
journal = {The Science of the total environment},
volume = {626},
number = {},
pages = {1439-1462},
doi = {10.1016/j.scitotenv.2017.12.001},
pmid = {29898550},
issn = {1879-1026},
abstract = {Since its founding in 1993 the International Long-term Ecological Research Network (ILTER) has gone through pronounced development phases. The current network comprises 44 active member LTER networks representing 700 LTER Sites and ~80 LTSER Platforms across all continents, active in the fields of ecosystem, critical zone and socio-ecological research. The critical challenges and most important achievements of the initial phase have now become state-of-the-art in networking for excellent science. At the same time increasing integration, accelerating technology, networking of resources and a strong pull for more socially relevant scientific information have been modifying the mission and goals of ILTER. This article provides a critical review of ILTER's mission, goals, development and impacts. Major characteristics, tools, services, partnerships and selected examples of relative strengths relevant for advancing ILTER are presented. We elaborate on the tradeoffs between the needs of the scientific community and stakeholder expectations. The embedding of ILTER in an increasingly collaborative landscape of global environmental observation and ecological research networks and infrastructures is also reflected by developments of pioneering regional and national LTER networks such as SAEON in South Africa, CERN/CEOBEX in China, TERN in Australia or eLTER RI in Europe. The primary role of ILTER is currently seen as a mechanism to investigate ecosystem structure, function, and services in response to a wide range of environmental forcings using long-term, place-based research. We suggest four main fields of activities and advancements for the next decade through development/delivery of a: (1) Global multi-disciplinary community of researchers and research institutes; (2) Strategic global framework and strong partnerships in ecosystem observation and research; (3) Global Research Infrastructure (GRI); and (4) a scientific knowledge factory for societally relevant information on sustainable use of natural resources.},
}

@article {pmid29890590,
year = {2018},
author = {Dick, J and Orenstein, DE and Holzer, JM and Wohner, C and Achard, AL and Andrews, C and Avriel-Avni, N and Beja, P and Blond, N and Cabello, J and Chen, C and Díaz-Delgado, R and Giannakis, GV and Gingrich, S and Izakovicova, Z and Krauze, K and Lamouroux, N and Leca, S and Melecis, V and Miklós, K and Mimikou, M and Niedrist, G and Piscart, C and Postolache, C and Psomas, A and Santos-Reis, M and Tappeiner, U and Vanderbilt, K and Van Ryckegem, G},
title = {What is socio-ecological research delivering? A literature survey across 25 international LTSER platforms.},
journal = {The Science of the total environment},
volume = {622-623},
number = {},
pages = {1225-1240},
doi = {10.1016/j.scitotenv.2017.11.324},
pmid = {29890590},
issn = {1879-1026},
abstract = {With an overarching goal of addressing global and regional sustainability challenges, Long Term Socio-Ecological Research Platforms (LTSER) aim to conduct place-based research, to collect and synthesize both environmental and socio-economic data, and to involve a broader stakeholder pool to set the research agenda. To date there have been few studies examining the output from LTSER platforms. In this study we enquire if the socio-ecological research from 25 self-selected LTSER platforms of the International Long-Term Ecological Research (ILTER) network has produced research products which fulfil the aims and ambitions of the paradigm shift from ecological to socio-ecological research envisaged at the turn of the century. In total we assessed 4983 publically available publications, of which 1112 were deemed relevant to the socio-ecological objectives of the platform. A series of 22 questions were scored for each publication, assessing relevance of responses in terms of the disciplinary focus of research, consideration of human health and well-being, degree of stakeholder engagement, and other relevant variables. The results reflected the diverse origins of the individual platforms and revealed a wide range in foci, temporal periods and quantity of output from participating platforms, supporting the premise that there is a growing trend in socio-ecological research at long-term monitoring platforms. Our review highlights the challenges of realizing the top-down goal to harmonize international network activities and objectives and the need for bottom-up, self-definition for research platforms. This provides support for increasing the consistency of LTSER research while preserving the diversity of regional experiences.},
}

@article {pmid29847023,
year = {2018},
author = {Dellicour, S and Flot, JF},
title = {The hitchhiker's guide to single-locus species delimitation.},
journal = {Molecular ecology resources},
volume = {18},
number = {6},
pages = {1234-1246},
doi = {10.1111/1755-0998.12908},
pmid = {29847023},
issn = {1755-0998},
mesh = {Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Metagenomics/*methods ; *Phylogeny ; },
abstract = {Molecular approaches to species delimitation are increasingly used to ascertain the number of species in a sample prior to taxonomic, ecological or physiological studies. Although multilocus approaches are gaining fast in popularity, single-gene methods still predominate in the literature. However, available simulation benchmarks of these methods focus exclusively on species-poor samples and/or tree-based approaches: as a result, travellers in the land of single-locus species delimitation lack a comprehensive "hitchhiker's guide" highlighting the sweet spots and dangers on their road. To fill this gap, we compared the performances of distance-based (ABGD, "automatic barcode gap discovery"), allele sharing-based (haplowebs) and tree-based approaches (GMYC, "generalized mixed Yule-coalescent" and PTP, "Poisson tree processes") to detect interspecific boundaries in samples of 6, 60 and 120 simulated species with various speciation rates, effective population sizes, mutation rates and sampling patterns. We found that all approaches performed poorly when population sizes and speciation rates were large, with haplowebs yielding best results followed by ABGD then tree-based approaches. The latter's error type was mostly oversplitting, whereas ABGD chiefly overlumped and haplowebs leaned either way depending on simulation parameters: such widely divergent error patterns suggest that, if all three types of methods agree, then the resulting delimitation is probably correct. Perfect congruence being quite rare, travellers in search of a one-size-fit-all approach to single-locus species delimitation should forget it; however, our hitchhiker's guide raises hope that such species delimitation's Holy Grail may be found in the relatively uncharted nearby land of multilocus species delimitation.},
}

Computational Biology/*methods
DNA Barcoding, Taxonomic/*methods
Metagenomics/*methods
*Phylogeny

@article {pmid29802772,
year = {2018},
author = {Snell Taylor, SJ and Evans, BS and White, EP and Hurlbert, AH},
title = {The prevalence and impact of transient species in ecological communities.},
journal = {Ecology},
volume = {99},
number = {8},
pages = {1825-1835},
doi = {10.1002/ecy.2398},
pmid = {29802772},
issn = {0012-9658},
abstract = {Transient species occur infrequently in a community over time and do not maintain viable local populations. Because transient species interact differently than non-transients with their biotic and abiotic environment, it is important to characterize the prevalence of these species and how they impact our understanding of ecological systems. We quantified the prevalence and impact of transient species in communities using data on over 19,000 community time series spanning an array of ecosystems, taxonomic groups, and spatial scales. We found that transient species are a general feature of communities regardless of taxa or ecosystem. The proportion of these species decreases with increasing spatial scale leading to a need to control for scale in comparative work. Removing transient species from analyses influences the form of a suite of commonly studied ecological patterns including species-abundance distributions, species-energy relationships, species-area relationships, and temporal turnover. Careful consideration should be given to whether transient species are included in analyses depending on the theoretical and practical relevance of these species for the question being studied.},
}

@article {pmid29794166,
year = {2018},
author = {Couger, MB and Arévalo, L and Campbell, P},
title = {A High Quality Genome for Mus spicilegus, a Close Relative of House Mice with Unique Social and Ecological Adaptations.},
journal = {G3 (Bethesda, Md.)},
volume = {8},
number = {7},
pages = {2145-2152},
pmid = {29794166},
issn = {2160-1836},
mesh = {Animals ; Computational Biology/methods ; Ecology ; Gene Expression Profiling ; *Genome ; *Genomics/methods ; Geography ; Hungary ; Mice ; Molecular Sequence Annotation ; Phylogeny ; Species Specificity ; Transcriptome ; },
abstract = {Genomic data for the closest relatives of house mice (Mus musculus species complex) are surprisingly limited. Here, we present the first complete genome for a behaviorally and ecologically unique member of the sister clade to house mice, the mound-building mouse, Mus spicilegus Using read cloud sequencing and de novo assembly we produced a 2.50 Gbp genome with a scaffold N50 of 2.27 Mbp. We constructed >25 000 gene models, of which the majority had high homology to other Mus species. To evaluate the utility of the M. spicilegus genome for behavioral and ecological genomics, we extracted 196 vomeronasal receptor (VR) sequences from our genome and analyzed phylogenetic relationships between M. spicilegus VRs and orthologs from M. musculus and the Algerian mouse, M. spretus While most M. spicilegus VRs clustered with orthologs in M. musculus and M. spretus, 10 VRs with evidence of rapid divergence in M. spicilegus are strong candidate modulators of species-specific chemical communication. A high quality assembly and genome for M. spicilegus will help to resolve discordant ancestry patterns in house mouse genomes, and will provide an essential foundation for genetic dissection of phenotypes that distinguish commensal from non-commensal species, and the social and ecological characteristics that make M. spicilegus unique.},
}

Animals
Computational Biology/methods
Ecology
Gene Expression Profiling
*Genome
*Genomics/methods
Geography
Hungary
Mice
Molecular Sequence Annotation
Phylogeny
Species Specificity
Transcriptome

@article {pmid29751427,
year = {2018},
author = {Meng, L and Huang, J and Dong, J},
title = {Assessment of rural ecosystem health and type classification in Jiangsu province, China.},
journal = {The Science of the total environment},
volume = {615},
number = {},
pages = {1218-1228},
doi = {10.1016/j.scitotenv.2017.09.312},
pmid = {29751427},
issn = {1879-1026},
mesh = {China ; Conservation of Natural Resources ; *Ecosystem ; *Environmental Monitoring ; Geographic Information Systems ; Urbanization ; },
abstract = {Quantitative analysis of rural ecosystem health (REH) is required to comprehend the spatial differentiation of rural landscape and promote rural sustainable development under the pressure of urbanization and industrialization, especially those with dramatic changes in rural ecology of China and other developing countries. In this study, taking Jiangsu province as the case study, appropriate indicators were selected in the perspective of compound ecosystem and the rural ecosystem health index (REHI) was developed including four rural ecological subsystems of resource, environmental, social and economic. The comprehensive indicator assessment models and geographic information system (GIS) spatial methods were used to analyze the REH status and spatial differentiation of 57 counties in Jiangsu province. The REH scores of 57 rural counties were in a higher range of 0.686-0.882 and fluctuating increased from north to south, indicating that the rural ecosystem in Jiangsu province was at a relatively healthy level and counties in southern Jiangsu were healthier than those in central and northern regions. The spatial concentration of REH in Jiangsu was poor and the spatial distribution of four subsystems health levels were significantly different by spatial Gini coefficient analysis. The REH of 57 counties in Jiangsu province were classified into 13 types according to the identification of the health levels and quantity of four subsystems. Moreover, we analyzed the influencing factors of each type and proposed paths to promote the development and management of rural ecosystem.},
}

China
Conservation of Natural Resources
*Ecosystem
*Environmental Monitoring
Geographic Information Systems
Urbanization

@article {pmid29734799,
year = {2018},
author = {Peters, K and Worrich, A and Weinhold, A and Alka, O and Balcke, G and Birkemeyer, C and Bruelheide, H and Calf, OW and Dietz, S and Dührkop, K and Gaquerel, E and Heinig, U and Kücklich, M and Macel, M and Müller, C and Poeschl, Y and Pohnert, G and Ristok, C and Rodríguez, VM and Ruttkies, C and Schuman, M and Schweiger, R and Shahaf, N and Steinbeck, C and Tortosa, M and Treutler, H and Ueberschaar, N and Velasco, P and Weiß, BM and Widdig, A and Neumann, S and Dam, NMV},
title = {Current Challenges in Plant Eco-Metabolomics.},
journal = {International journal of molecular sciences},
volume = {19},
number = {5},
pages = {},
pmid = {29734799},
issn = {1422-0067},
mesh = {*Ecology ; Metabolomics/*trends ; Plants/*genetics/metabolism ; },
abstract = {The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant⁻organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology.},
}

*Ecology
Metabolomics/*trends
Plants/*genetics/metabolism

@article {pmid29717679,
year = {2019},
author = {Toni, M and Manciocco, A and Angiulli, E and Alleva, E and Cioni, C and Malavasi, S},
title = {Review: Assessing fish welfare in research and aquaculture, with a focus on European directives.},
journal = {Animal : an international journal of animal bioscience},
volume = {13},
number = {1},
pages = {161-170},
doi = {10.1017/S1751731118000940},
pmid = {29717679},
issn = {1751-732X},
abstract = {The number of farmed fish in the world has increased considerably. Aquaculture is a growing industry that will in the future provide a large portion of fishery products. Moreover, in recent years, the number of teleost fish used as animal models for scientific research in both biomedical and ecological fields has increased. Therefore, it is increasingly important to implement measures designed to enhance the welfare of these animals. Currently, a number of European rules exist as requirements for the establishment, care and accommodation of fish maintained for human purposes. As far as (teleost) fish are concerned, the fact that the number of extant species is much greater than that of all other vertebrates must be considered. Of further importance is that each species has its own specific physical and chemical requirements. These factors make it difficult to provide generalized recommendations or requirements for all fish species. An adequate knowledge is required of the physiology and ecology of each species bred. This paper integrates and discusses, in a single synthesis, the current issues related to fish welfare, considering that teleosts are target species for both aquaculture and experimental models in biological and biomedical research. We first focus on the practical aspects, which must be considered when assessing fish welfare in both research and aquaculture contexts. Next, we address husbandry and the care of fish housed in research laboratories and aquaculture facilities in relation to their physiological and behavioural requirements, as well as in reference to the suggestions provided by European regulations. Finally, to evaluate precisely which parameters described by Directive 2010/63/EU are reported in scientific papers, we analysed 82 articles published by European researchers in 2014 and 2015. This review found that there is a general lack of information related to the optimal environmental conditions that should be provided for the range of species covered by this directive.},
}

@article {pmid29686079,
year = {2018},
author = {Muscente, AD and Prabhu, A and Zhong, H and Eleish, A and Meyer, MB and Fox, P and Hazen, RM and Knoll, AH},
title = {Quantifying ecological impacts of mass extinctions with network analysis of fossil communities.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {20},
pages = {5217-5222},
pmid = {29686079},
issn = {1091-6490},
mesh = {Animals ; *Biodiversity ; Biological Evolution ; *Databases, Factual ; *Ecosystem ; *Extinction, Biological ; *Fossils ; Geology ; Invertebrates ; *Paleontology ; },
abstract = {Mass extinctions documented by the fossil record provide critical benchmarks for assessing changes through time in biodiversity and ecology. Efforts to compare biotic crises of the past and present, however, encounter difficulty because taxonomic and ecological changes are decoupled, and although various metrics exist for describing taxonomic turnover, no methods have yet been proposed to quantify the ecological impacts of extinction events. To address this issue, we apply a network-based approach to exploring the evolution of marine animal communities over the Phanerozoic Eon. Network analysis of fossil co-occurrence data enables us to identify nonrandom associations of interrelated paleocommunities. These associations, or evolutionary paleocommunities, dominated total diversity during successive intervals of relative community stasis. Community turnover occurred largely during mass extinctions and radiations, when ecological reorganization resulted in the decline of one association and the rise of another. Altogether, we identify five evolutionary paleocommunities at the generic and familial levels in addition to three ordinal associations that correspond to Sepkoski's Cambrian, Paleozoic, and Modern evolutionary faunas. In this context, we quantify magnitudes of ecological change by measuring shifts in the representation of evolutionary paleocommunities over geologic time. Our work shows that the Great Ordovician Biodiversification Event had the largest effect on ecology, followed in descending order by the Permian-Triassic, Cretaceous-Paleogene, Devonian, and Triassic-Jurassic mass extinctions. Despite its taxonomic severity, the Ordovician extinction did not strongly affect co-occurrences of taxa, affirming its limited ecological impact. Network paleoecology offers promising approaches to exploring ecological consequences of extinctions and radiations.},
}

Animals
*Biodiversity
Biological Evolution
*Databases, Factual
*Ecosystem
*Extinction, Biological
*Fossils
Geology
Invertebrates
*Paleontology

@article {pmid29668682,
year = {2018},
author = {Hannigan, GD and Duhaime, MB and Koutra, D and Schloss, PD},
title = {Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome.},
journal = {PLoS computational biology},
volume = {14},
number = {4},
pages = {e1006099},
pmid = {29668682},
issn = {1553-7358},
support = {T32AI007528/NH/NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; P30DK034933/NH/NIH HHS/United States ; U01AI124255/NH/NIH HHS/United States ; U19AI09087/NH/NIH HHS/United States ; },
mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Bacteriophages/*genetics/*physiology ; Computational Biology ; Diet ; Humans ; Metagenomics ; Microbial Consortia/genetics/physiology ; Microbiota/*genetics/*physiology ; Models, Biological ; Phylogeography ; Skin/microbiology/virology ; },
abstract = {Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks.},
}

Bacteria/*genetics
*Bacterial Physiological Phenomena
Bacteriophages/*genetics/*physiology
Computational Biology
Diet
Humans
Metagenomics
Microbial Consortia/genetics/physiology
Microbiota/*genetics/*physiology
Models, Biological
Phylogeography
Skin/microbiology/virology

@article {pmid29666315,
year = {2018},
author = {Chen, S and Wang, W and Xu, W and Wang, Y and Wan, H and Chen, D and Tang, Z and Tang, X and Zhou, G and Xie, Z and Zhou, D and Shangguan, Z and Huang, J and He, JS and Wang, Y and Sheng, J and Tang, L and Li, X and Dong, M and Wu, Y and Wang, Q and Wang, Z and Wu, J and Chapin, FS and Bai, Y},
title = {Plant diversity enhances productivity and soil carbon storage.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {16},
pages = {4027-4032},
pmid = {29666315},
issn = {1091-6490},
mesh = {*Biodiversity ; Biomass ; Carbon/*analysis ; *Carbon Sequestration ; China ; Conservation of Natural Resources ; Datasets as Topic ; *Ecosystem ; Farms ; Forests ; Grassland ; Human Activities ; Humans ; Hydrogen-Ion Concentration ; Nitrogen/analysis ; Plant Dispersal ; Plants/chemistry/classification/*metabolism ; Rain ; Soil/*chemistry ; Temperature ; },
abstract = {Despite evidence from experimental grasslands that plant diversity increases biomass production and soil organic carbon (SOC) storage, it remains unclear whether this is true in natural ecosystems, especially under climatic variations and human disturbances. Based on field observations from 6,098 forest, shrubland, and grassland sites across China and predictions from an integrative model combining multiple theories, we systematically examined the direct effects of climate, soils, and human impacts on SOC storage versus the indirect effects mediated by species richness (SR), aboveground net primary productivity (ANPP), and belowground biomass (BB). We found that favorable climates (high temperature and precipitation) had a consistent negative effect on SOC storage in forests and shrublands, but not in grasslands. Climate favorability, particularly high precipitation, was associated with both higher SR and higher BB, which had consistent positive effects on SOC storage, thus offsetting the direct negative effect of favorable climate on SOC. The indirect effects of climate on SOC storage depended on the relationships of SR with ANPP and BB, which were consistently positive in all biome types. In addition, human disturbance and soil pH had both direct and indirect effects on SOC storage, with the indirect effects mediated by changes in SR, ANPP, and BB. High soil pH had a consistently negative effect on SOC storage. Our findings have important implications for improving global carbon cycling models and ecosystem management: Maintaining high levels of diversity can enhance soil carbon sequestration and help sustain the benefits of plant diversity and productivity.},
}

*Biodiversity
Biomass
Carbon/*analysis
*Carbon Sequestration
China
Conservation of Natural Resources
Datasets as Topic
*Ecosystem
Farms
Forests
Grassland
Human Activities
Humans
Hydrogen-Ion Concentration
Nitrogen/analysis
Plant Dispersal
Plants/chemistry/classification/*metabolism
Rain
Soil/*chemistry
Temperature

@article {pmid29618526,
year = {2018},
author = {Ching, T and Himmelstein, DS and Beaulieu-Jones, BK and Kalinin, AA and Do, BT and Way, GP and Ferrero, E and Agapow, PM and Zietz, M and Hoffman, MM and Xie, W and Rosen, GL and Lengerich, BJ and Israeli, J and Lanchantin, J and Woloszynek, S and Carpenter, AE and Shrikumar, A and Xu, J and Cofer, EM and Lavender, CA and Turaga, SC and Alexandari, AM and Lu, Z and Harris, DJ and DeCaprio, D and Qi, Y and Kundaje, A and Peng, Y and Wiley, LK and Segler, MHS and Boca, SM and Swamidass, SJ and Huang, A and Gitter, A and Greene, CS},
title = {Opportunities and obstacles for deep learning in biology and medicine.},
journal = {Journal of the Royal Society, Interface},
volume = {15},
number = {141},
pages = {},
pmid = {29618526},
issn = {1742-5662},
support = {DP2 GM123485/GM/NIGMS NIH HHS/United States ; P30 ES013508/ES/NIEHS NIH HHS/United States ; R01 GM089753/GM/NIGMS NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; },
abstract = {Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.},
}

@article {pmid29590103,
year = {2018},
author = {Emery, M and Willis, MMS and Hao, Y and Barry, K and Oakgrove, K and Peng, Y and Schmutz, J and Lyons, E and Pires, JC and Edger, PP and Conant, GC},
title = {Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization.},
journal = {PLoS genetics},
volume = {14},
number = {3},
pages = {e1007267},
pmid = {29590103},
issn = {1553-7404},
mesh = {Brassicaceae/*genetics ; Evolution, Molecular ; *Genes, Plant ; *Genomic Imprinting ; *Hybridization, Genetic ; Models, Genetic ; *Polyploidy ; },
abstract = {Polyploidy is increasingly seen as a driver of both evolutionary innovation and ecological success. One source of polyploid organisms' successes may be their origins in the merging and mixing of genomes from two different species (e.g., allopolyploidy). Using POInT (the Polyploid Orthology Inference Tool), we model the resolution of three allopolyploidy events, one from the bakers' yeast (Saccharomyces cerevisiae), one from the thale cress (Arabidopsis thaliana) and one from grasses including Sorghum bicolor. Analyzing a total of 21 genomes, we assign to every gene a probability for having come from each parental subgenome (i.e., derived from the diploid progenitor species), yielding orthologous segments across all genomes. Our model detects statistically robust evidence for the existence of biased fractionation in all three lineages, whereby genes from one of the two subgenomes were more likely to be lost than those from the other subgenome. We further find that a driver of this pattern of biased losses is the co-retention of genes from the same parental genome that share functional interactions. The pattern of biased fractionation after the Arabidopsis and grass allopolyploid events was surprisingly constant in time, with the same parental genome favored throughout the lineages' history. In strong contrast, the yeast allopolyploid event shows evidence of biased fractionation only immediately after the event, with balanced gene losses more recently. The rapid loss of functionally associated genes from a single subgenome is difficult to reconcile with the action of genetic drift and suggests that selection may favor the removal of specific duplicates. Coupled to the evidence for continuing, functionally-associated biased fractionation after the A. thaliana At-α event, we suggest that, after allopolyploidy, there are functional conflicts between interacting genes encoded in different subgenomes that are ultimately resolved through preferential duplicate loss.},
}

Brassicaceae/*genetics
Evolution, Molecular
*Genes, Plant
*Genomic Imprinting
*Hybridization, Genetic
Models, Genetic
*Polyploidy

@article {pmid29574273,
year = {2018},
author = {Psonis, N and Antoniou, A and Karameta, E and Leaché, AD and Kotsakiozi, P and Darriba, D and Kozlov, A and Stamatakis, A and Poursanidis, D and Kukushkin, O and Jablonski, D and Crnobrnja-Isailović, J and Gherghel, I and Lymberakis, P and Poulakakis, N},
title = {Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system.},
journal = {Molecular phylogenetics and evolution},
volume = {125},
number = {},
pages = {100-115},
doi = {10.1016/j.ympev.2018.03.021},
pmid = {29574273},
issn = {1095-9513},
mesh = {Animals ; Balkan Peninsula ; Bayes Theorem ; Biodiversity ; Calibration ; DNA, Mitochondrial/genetics ; Genetic Variation ; Genetics, Population ; Genomics ; Haplotypes/genetics ; Lizards/*classification/genetics ; Microsatellite Repeats/genetics ; *Models, Biological ; Phylogeny ; *Phylogeography ; Species Specificity ; },
abstract = {The Balkan Peninsula constitutes a biodiversity hotspot with high levels of species richness and endemism. The complex geological history of the Balkans in conjunction with the climate evolution are hypothesized as the main drivers generating this biodiversity. We investigated the phylogeography, historical demography, and population structure of closely related wall-lizard species from the Balkan Peninsula and southeastern Europe to better understand diversification processes of species with limited dispersal ability, from Late Miocene to the Holocene. We used several analytical methods integrating genome-wide SNPs (ddRADseq), microsatellites, mitochondrial and nuclear DNA data, as well as species distribution modelling. Phylogenomic analysis resulted in a completely resolved species level phylogeny, population level analyses confirmed the existence of at least two cryptic evolutionary lineages and extensive within species genetic structuring. Divergence time estimations indicated that the Messinian Salinity Crisis played a key role in shaping patterns of species divergence, whereas intraspecific genetic structuring was mainly driven by Pliocene tectonic events and Quaternary climatic oscillations. The present work highlights the effectiveness of utilizing multiple methods and data types coupled with extensive geographic sampling to uncover the evolutionary processes that shaped the species over space and time.},
}

Animals
Balkan Peninsula
Bayes Theorem
Biodiversity
Calibration
DNA, Mitochondrial/genetics
Genetic Variation
Genetics, Population
Genomics
Haplotypes/genetics
Lizards/*classification/genetics
Microsatellite Repeats/genetics
*Models, Biological
Phylogeny
*Phylogeography
Species Specificity

@article {pmid29569818,
year = {2018},
author = {Anderegg, LDL and Berner, LT and Badgley, G and Sethi, ML and Law, BE and HilleRisLambers, J},
title = {Within-species patterns challenge our understanding of the leaf economics spectrum.},
journal = {Ecology letters},
volume = {21},
number = {5},
pages = {734-744},
doi = {10.1111/ele.12945},
pmid = {29569818},
issn = {1461-0248},
abstract = {The utility of plant functional traits for predictive ecology relies on our ability to interpret trait variation across multiple taxonomic and ecological scales. Using extensive data sets of trait variation within species, across species and across communities, we analysed whether and at what scales leaf economics spectrum (LES) traits show predicted trait-trait covariation. We found that most variation in LES traits is often, but not universally, at high taxonomic levels (between families or genera in a family). However, we found that trait covariation shows distinct taxonomic scale dependence, with some trait correlations showing opposite signs within vs. across species. LES traits responded independently to environmental gradients within species, with few shared environmental responses across traits or across scales. We conclude that, at small taxonomic scales, plasticity may obscure or reverse the broad evolutionary linkages between leaf traits, meaning that variation in LES traits cannot always be interpreted as differences in resource use strategy.},
}

@article {pmid29566054,
year = {2018},
author = {Jablonski, KE and Boone, RB and Meiman, PJ},
title = {An agent-based model of cattle grazing toxic Geyer's larkspur.},
journal = {PloS one},
volume = {13},
number = {3},
pages = {e0194450},
pmid = {29566054},
issn = {1932-6203},
mesh = {Agriculture/*methods ; Alkaloids/toxicity ; Animals ; Behavior, Animal ; Biological Variation, Population ; Cattle ; Cattle Diseases/etiology/*prevention & control ; Computational Biology ; Delphinium/chemistry/*toxicity ; *Models, Biological ; Plant Poisoning/etiology/*prevention & control/veterinary ; United States ; },
abstract = {By killing cattle and otherwise complicating management, the many species of larkspur (Delphinium spp.) present a serious, intractable, and complex challenge to livestock grazing management in the western United States. Among the many obstacles to improving our understanding of cattle-larkspur dynamics has been the difficulty of testing different grazing management strategies in the field, as the risk of dead animals is too great. Agent-based models (ABMs) provide an effective method of testing alternate management strategies without risk to livestock. ABMs are especially useful for modeling complex systems such as livestock grazing management, and allow for realistic bottom-up encoding of cattle behavior. Here, we introduce a spatially-explicit, behavior-based ABM of cattle grazing in a pasture with a dangerous amount of Geyer's larkspur (D. geyeri). This model tests the role of herd cohesion and stocking density in larkspur intake, finds that both are key drivers of larkspur-induced toxicosis, and indicates that alteration of these factors within realistic bounds can mitigate risk. Crucially, the model points to herd cohesion, which has received little attention in the discipline, as playing an important role in lethal acute toxicosis. As the first ABM to model grazing behavior at realistic scales, this study also demonstrates the tremendous potential of ABMs to illuminate grazing management dynamics, including fundamental aspects of livestock behavior amidst ecological heterogeneity.},
}

Agriculture/*methods
Alkaloids/toxicity
Animals
Behavior, Animal
Biological Variation, Population
Cattle
Cattle Diseases/etiology/*prevention & control
Computational Biology
Delphinium/chemistry/*toxicity
*Models, Biological
Plant Poisoning/etiology/*prevention & control/veterinary
United States

@article {pmid29541867,
year = {2018},
author = {Heider, K and Lopez, JMR and Scheffran, J},
title = {The potential of volunteered geographic information to investigate peri-urbanization in the conservation zone of Mexico City.},
journal = {Environmental monitoring and assessment},
volume = {190},
number = {4},
pages = {219},
pmid = {29541867},
issn = {1573-2959},
support = {10th call//Center for a Sustainable University/ ; },
mesh = {Cities ; Conservation of Natural Resources/*methods ; Ecology ; Environmental Monitoring/methods ; *Geographic Information Systems ; Mexico ; Rural Population ; Urbanization/*trends ; },
abstract = {Due to the availability of Web 2.0 technologies, volunteered geographic information (VGI) is on the rise. This new type of data is available on many topics and on different scales. Thus, it has become interesting for research. This article deals with the collective potential of VGI and remote sensing to detect peri-urbanization in the conservation zone of Mexico City. On the one hand, remote sensing identifies horizontal urban expansion, and on the other hand, VGI of ecological complaints provides data about informal settlements. This enables the combination of top-down approaches (remote sensing) and bottom-up approaches (ecological complaints). Within the analysis, we identify areas of high urbanization as well as complaint densities and bring them together in a multi-scale analysis using Geographic Information Systems (GIS). Furthermore, we investigate the influence of settlement patterns and main roads on the peri-urbanization process in Mexico City using OpenStreetMap. Peri-urbanization is detected especially in the transition zone between the urban and rural (conservation) area and near main roads as well as settlements.},
}

Cities
Conservation of Natural Resources/*methods
Ecology
Environmental Monitoring/methods
*Geographic Information Systems
Mexico
Rural Population
Urbanization/*trends

@article {pmid29540568,
year = {2018},
author = {Liu, XY and Koba, K and Koyama, LA and Hobbie, SE and Weiss, MS and Inagaki, Y and Shaver, GR and Giblin, AE and Hobara, S and Nadelhoffer, KJ and Sommerkorn, M and Rastetter, EB and Kling, GW and Laundre, JA and Yano, Y and Makabe, A and Yano, M and Liu, CQ},
title = {Nitrate is an important nitrogen source for Arctic tundra plants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {13},
pages = {3398-3403},
pmid = {29540568},
issn = {1091-6490},
mesh = {Denitrification ; Nitrates/*metabolism ; Nitrogen/*analysis ; Plant Leaves/growth & development/*metabolism ; Soil/*chemistry ; *Tundra ; },
abstract = {Plant nitrogen (N) use is a key component of the N cycle in terrestrial ecosystems. The supply of N to plants affects community species composition and ecosystem processes such as photosynthesis and carbon (C) accumulation. However, the availabilities and relative importance of different N forms to plants are not well understood. While nitrate (NO3-) is a major N form used by plants worldwide, it is discounted as a N source for Arctic tundra plants because of extremely low NO3- concentrations in Arctic tundra soils, undetectable soil nitrification, and plant-tissue NO3- that is typically below detection limits. Here we reexamine NO3- use by tundra plants using a sensitive denitrifier method to analyze plant-tissue NO3- Soil-derived NO3- was detected in tundra plant tissues, and tundra plants took up soil NO3- at comparable rates to plants from relatively NO3--rich ecosystems in other biomes. Nitrate assimilation determined by 15N enrichments of leaf NO3- relative to soil NO3- accounted for 4 to 52% (as estimated by a Bayesian isotope-mixing model) of species-specific total leaf N of Alaskan tundra plants. Our finding that in situ soil NO3- availability for tundra plants is high has important implications for Arctic ecosystems, not only in determining species compositions, but also in determining the loss of N from soils via leaching and denitrification. Plant N uptake and soil N losses can strongly influence C uptake and accumulation in tundra soils. Accordingly, this evidence of NO3- availability in tundra soils is crucial for predicting C storage in tundra.},
}

Denitrification
Nitrates/*metabolism
Nitrogen/*analysis
Plant Leaves/growth & development/*metabolism
Soil/*chemistry
*Tundra

@article {pmid29513661,
year = {2018},
author = {Lee, EC and Arab, A and Goldlust, SM and Viboud, C and Grenfell, BT and Bansal, S},
title = {Deploying digital health data to optimize influenza surveillance at national and local scales.},
journal = {PLoS computational biology},
volume = {14},
number = {3},
pages = {e1006020},
pmid = {29513661},
issn = {1553-7358},
support = {P2C HD047879/HD/NICHD NIH HHS/United States ; },
mesh = {Bayes Theorem ; Computer Simulation ; Databases, Factual ; Humans ; Influenza A Virus, H1N1 Subtype/pathogenicity ; Influenza, Human/*epidemiology ; Medical Records ; Models, Theoretical ; Online Systems ; Pandemics ; Population Surveillance/*methods ; Selection Bias ; Sentinel Surveillance ; United States ; },
abstract = {The surveillance of influenza activity is critical to early detection of epidemics and pandemics and the design of disease control strategies. Case reporting through a voluntary network of sentinel physicians is a commonly used method of passive surveillance for monitoring rates of influenza-like illness (ILI) worldwide. Despite its ubiquity, little attention has been given to the processes underlying the observation, collection, and spatial aggregation of sentinel surveillance data, and its subsequent effects on epidemiological understanding. We harnessed the high specificity of diagnosis codes in medical claims from a database that represented 2.5 billion visits from upwards of 120,000 United States healthcare providers each year. Among influenza seasons from 2002-2009 and the 2009 pandemic, we simulated limitations of sentinel surveillance systems such as low coverage and coarse spatial resolution, and performed Bayesian inference to probe the robustness of ecological inference and spatial prediction of disease burden. Our models suggest that a number of socio-environmental factors, in addition to local population interactions, state-specific health policies, as well as sampling effort may be responsible for the spatial patterns in U.S. sentinel ILI surveillance. In addition, we find that biases related to spatial aggregation were accentuated among areas with more heterogeneous disease risk, and sentinel systems designed with fixed reporting locations across seasons provided robust inference and prediction. With the growing availability of health-associated big data worldwide, our results suggest mechanisms for optimizing digital data streams to complement traditional surveillance in developed settings and enhance surveillance opportunities in developing countries.},
}

Bayes Theorem
Computer Simulation
Databases, Factual
Humans
Influenza A Virus, H1N1 Subtype/pathogenicity
Influenza, Human/*epidemiology
Medical Records
Models, Theoretical
Online Systems
Pandemics
Population Surveillance/*methods
Selection Bias
Sentinel Surveillance
United States

@article {pmid29495440,
year = {2018},
author = {Torina, A and Blanda, V and Blanda, M and Auteri, M and La Russa, F and Scimeca, S and D'Agostino, R and Disclafani, R and Villari, S and Currò, V and Caracappa, S},
title = {A Geographical Information System Based Approach for Integrated Strategies of Tick Surveillance and Control in the Peri-Urban Natural Reserve of Monte Pellegrino (Palermo, Southern Italy).},
journal = {International journal of environmental research and public health},
volume = {15},
number = {3},
pages = {},
pmid = {29495440},
issn = {1660-4601},
mesh = {Animals ; Conservation of Natural Resources ; *Geographic Information Systems ; Italy ; Spatio-Temporal Analysis ; Tick Control/*methods ; *Ticks ; Urban Health ; },
abstract = {Ticks (Acari: Ixodidae) are bloodsucking arthropods involved in pathogen transmission in animals and humans. Tick activity depends on various ecological factors such as vegetation, hosts, and temperature. The aim of this study was to analyse the spatial/temporal distribution of ticks in six sites within a peri-urban area of Palermo (Natural Reserve of Monte Pellegrino) and correlate it with field data using Geographical Information System (GIS) data. A total of 3092 ticks were gathered via dragging method from June 2012 to May 2014. The species collected were: Ixodes ventalloi (46.09%), Hyalomma lusitanicum (19.99%), Rhipicephalus sanguineus (17.34%), Rhipicephalus pusillus (16.11%), Haemaphisalis sulcata (0.36%), Dermacentor marginatus (0.10%), and Rhipicephalus turanicus (0.03%). GIS analysis revealed environmental characteristics of each site, and abundance of each tick species was analysed in relation to time (monthly trend) and space (site-specific abundance). A relevant presence of I. ventalloi in site 2 and H. lusitanicum in site 5 was observed, suggesting the possible exposure of animals and humans to tick-borne pathogens. Our study shows the importance of surveillance of ticks in peri-urban areas and the useful implementation of GIS analysis in vector ecology; studies on temporal and spatial distribution of ticks correlated to GIS-based ecological analysis represent an integrated strategy for decision support in public health.},
}

Animals
Conservation of Natural Resources
*Geographic Information Systems
Italy
Spatio-Temporal Analysis
Tick Control/*methods
*Ticks
Urban Health

@article {pmid29479643,
year = {2018},
author = {Hervé, MR and Nicolè, F and Lê Cao, KA},
title = {Multivariate Analysis of Multiple Datasets: a Practical Guide for Chemical Ecology.},
journal = {Journal of chemical ecology},
volume = {44},
number = {3},
pages = {215-234},
doi = {10.1007/s10886-018-0932-6},
pmid = {29479643},
issn = {1573-1561},
mesh = {*Databases, Chemical ; Ecology/*methods ; *Guidelines as Topic ; Models, Statistical ; Multivariate Analysis ; },
abstract = {Chemical ecology has strong links with metabolomics, the large-scale study of all metabolites detectable in a biological sample. Consequently, chemical ecologists are often challenged by the statistical analyses of such large datasets. This holds especially true when the purpose is to integrate multiple datasets to obtain a holistic view and a better understanding of a biological system under study. The present article provides a comprehensive resource to analyze such complex datasets using multivariate methods. It starts from the necessary pre-treatment of data including data transformations and distance calculations, to the application of both gold standard and novel multivariate methods for the integration of different omics data. We illustrate the process of analysis along with detailed results interpretations for six issues representative of the different types of biological questions encountered by chemical ecologists. We provide the necessary knowledge and tools with reproducible R codes and chemical-ecological datasets to practice and teach multivariate methods.},
}

*Databases, Chemical
Ecology/*methods
*Guidelines as Topic
Models, Statistical
Multivariate Analysis

@article {pmid29466331,
year = {2018},
author = {Ma, Z and Guo, D and Xu, X and Lu, M and Bardgett, RD and Eissenstat, DM and McCormack, ML and Hedin, LO},
title = {Evolutionary history resolves global organization of root functional traits.},
journal = {Nature},
volume = {555},
number = {7694},
pages = {94-97},
pmid = {29466331},
issn = {1476-4687},
mesh = {Biodiversity ; *Biological Evolution ; Carbon/metabolism ; Databases, Factual ; Desert Climate ; *Ecosystem ; Mycorrhizae/physiology ; Photosynthesis ; Phylogeny ; Plant Roots/*anatomy & histology/classification/microbiology/*physiology ; Seasons ; Soil/chemistry ; Species Specificity ; Symbiosis ; Tropical Climate ; },
abstract = {Plant roots have greatly diversified in form and function since the emergence of the first land plants, but the global organization of functional traits in roots remains poorly understood. Here we analyse a global dataset of 10 functionally important root traits in metabolically active first-order roots, collected from 369 species distributed across the natural plant communities of 7 biomes. Our results identify a high degree of organization of root traits across species and biomes, and reveal a pattern that differs from expectations based on previous studies of leaf traits. Root diameter exerts the strongest influence on root trait variation across plant species, growth forms and biomes. Our analysis suggests that plants have evolved thinner roots since they first emerged in land ecosystems, which has enabled them to markedly improve their efficiency of soil exploration per unit of carbon invested and to reduce their dependence on symbiotic mycorrhizal fungi. We also found that diversity in root morphological traits is greatest in the tropics, where plant diversity is highest and many ancestral phylogenetic groups are preserved. Diversity in root morphology declines sharply across the sequence of tropical, temperate and desert biomes, presumably owing to changes in resource supply caused by seasonally inhospitable abiotic conditions. Our results suggest that root traits have evolved along a spectrum bounded by two contrasting strategies of root life: an ancestral 'conservative' strategy in which plants with thick roots depend on symbiosis with mycorrhizal fungi for soil resources and a more-derived 'opportunistic' strategy in which thin roots enable plants to more efficiently leverage photosynthetic carbon for soil exploration. These findings imply that innovations of belowground traits have had an important role in preparing plants to colonize new habitats, and in generating biodiversity within and across biomes.},
}

Biodiversity
*Biological Evolution
Carbon/metabolism
Databases, Factual
Desert Climate
*Ecosystem
Mycorrhizae/physiology
Photosynthesis
Phylogeny
Plant Roots/*anatomy & histology/classification/microbiology/*physiology
Seasons
Soil/chemistry
Species Specificity
Symbiosis
Tropical Climate

@article {pmid29451365,
year = {2018},
author = {Kim, HS and Lee, BY and Han, J and Jeong, CB and Hwang, DS and Lee, MC and Kang, HM and Kim, DH and Kim, HJ and Papakostas, S and Declerck, SAJ and Choi, IY and Hagiwara, A and Park, HG and Lee, JS},
title = {The genome of the freshwater monogonont rotifer Brachionus calyciflorus.},
journal = {Molecular ecology resources},
volume = {18},
number = {3},
pages = {646-655},
doi = {10.1111/1755-0998.12768},
pmid = {29451365},
issn = {1755-0998},
mesh = {Animals ; *Databases, Genetic ; *Genome ; Molecular Sequence Annotation ; Rotifera/*genetics ; Sequence Analysis, DNA ; },
abstract = {Monogononta is the most speciose class of rotifers, with more than 2,000 species. The monogonont genus Brachionus is widely distributed at a global scale, and a few of its species are commonly used as ecological and evolutionary models to address questions related to aquatic ecology, cryptic speciation, evolutionary ecology, the evolution of sex and ecotoxicology. With the importance of Brachionus species in many areas of research, it is remarkable that the genome has not been characterized. This study aims to address this lacuna by presenting, for the first time, the whole-genome assembly of the freshwater species Brachionus calyciflorus. The total length of the assembled genome was 129.6 Mb, with 1,041 scaffolds. The N50 value was 786.6 kb, and the GC content was 24%. A total of 16,114 genes were annotated with repeat sequences, accounting for 21% of the assembled genome. This assembled genome may form a basis for future studies addressing key questions on the evolution of monogonont rotifers. It will also provide the necessary molecular resources to mechanistically investigate ecophysiological and ecotoxicological responses.},
}

Animals
*Databases, Genetic
*Genome
Molecular Sequence Annotation
Rotifera/*genetics
Sequence Analysis, DNA

@article {pmid29426200,
year = {2018},
author = {Stefanidis, K and Panagopoulos, Y and Mimikou, M},
title = {Response of a multi-stressed Mediterranean river to future climate and socio-economic scenarios.},
journal = {The Science of the total environment},
volume = {627},
number = {},
pages = {756-769},
doi = {10.1016/j.scitotenv.2018.01.282},
pmid = {29426200},
issn = {1879-1026},
mesh = {*Climate Change ; Ecosystem ; *Environmental Monitoring ; Europe ; Greece ; Mediterranean Region ; *Models, Theoretical ; Rivers/*chemistry ; Socioeconomic Factors ; Water Pollution/*statistics & numerical data ; },
abstract = {Streams and rivers are among the most threatened ecosystems in Europe due to the combined effects of multiple pressures related to anthropogenic activities. Particularly in the Mediterranean region, changes in hydromorphology along with increased nutrient loadings are known to affect the ecological functions and ecosystem services of streams and rivers with the anticipated climate change being likely to further impair their functionality and structure. In this study, we investigated the combined effects of agricultural driven stressors on the ecology and delivered services of the Pinios river basin in Greece under three future world scenarios developed within the EU funded MARS project. Scenarios are based on combinations of Representative Concentration Pathways and Shared Socioeconomic Pathways and refer to early century (2030) and mid-century (2060) representing future climate worlds with particular socioeconomic characteristics. To assess the responses of ecological and ecosystem service indicators to the scenarios we first simulated hydrology and water quality in Pinios with a process-based model. Simulated abiotic stressor parameters (predictors) were linked to two biotic indicators, the macroinvertebrate indicators ASPT and EPT, with empirical modelling based on boosted regression trees and general linear models. Our results showed that the techno world scenario driven by fast economic growth and intensive exploitation of energy resources had the largest impact on both the abiotic status (nutrient loads and concentrations in water) and the biotic indicators. In contrast, the predicted changes under the other two future worlds, consensus and fragmented, were more diverse and were mostly dictated by the projected climate. This work showed that the future scenarios, especially the mid-century ones, had significant impact on both abiotic status and biotic responses underpinning the need for implementing catchment management practices able to mitigate the ecological threat on waters in the long-term.},
}

*Climate Change
Ecosystem
*Environmental Monitoring
Europe
Greece
Mediterranean Region
*Models, Theoretical
Rivers/*chemistry
Socioeconomic Factors
Water Pollution/*statistics & numerical data

@article {pmid29382768,
year = {2018},
author = {Zachar, I and Szilágyi, A and Számadó, S and Szathmáry, E},
title = {Farming the mitochondrial ancestor as a model of endosymbiotic establishment by natural selection.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {7},
pages = {E1504-E1510},
pmid = {29382768},
issn = {1091-6490},
support = {294332//European Research Council/International ; },
mesh = {Animals ; Bacteria/pathogenicity ; *Biological Evolution ; Computational Biology ; Erythrocytes/*microbiology ; Eukaryota ; Humans ; Mitochondria/*physiology ; *Models, Biological ; Predatory Behavior ; *Selection, Genetic ; Symbiosis/*physiology ; },
abstract = {The origin of mitochondria was a major evolutionary transition leading to eukaryotes, and is a hotly debated issue. It is unknown whether mitochondria were acquired early or late, and whether it was captured via phagocytosis or syntrophic integration. We present dynamical models to directly simulate the emergence of mitochondria in an ecoevolutionary context. Our results show that regulated farming of prey bacteria and delayed digestion can facilitate the establishment of stable endosymbiosis if prey-rich and prey-poor periods alternate. Stable endosymbiosis emerges without assuming any initial metabolic benefit provided by the engulfed partner, in a wide range of parameters, despite that during good periods farming is costly. Our approach lends support to the appearance of mitochondria before any metabolic coupling has emerged, but after the evolution of primitive phagocytosis by the urkaryote.},
}

Animals
Bacteria/pathogenicity
*Biological Evolution
Computational Biology
Erythrocytes/*microbiology
Eukaryota
Humans
Mitochondria/*physiology
*Models, Biological
Predatory Behavior
*Selection, Genetic
Symbiosis/*physiology

@article {pmid29382745,
year = {2018},
author = {Dietze, MC and Fox, A and Beck-Johnson, LM and Betancourt, JL and Hooten, MB and Jarnevich, CS and Keitt, TH and Kenney, MA and Laney, CM and Larsen, LG and Loescher, HW and Lunch, CK and Pijanowski, BC and Randerson, JT and Read, EK and Tredennick, AT and Vargas, R and Weathers, KC and White, EP},
title = {Iterative near-term ecological forecasting: Needs, opportunities, and challenges.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {7},
pages = {1424-1432},
pmid = {29382745},
issn = {1091-6490},
mesh = {Bayes Theorem ; Climate Change ; Ecology/*education/*methods/trends ; Ecosystem ; Forecasting ; Humans ; Models, Theoretical ; },
abstract = {Two foundational questions about sustainability are "How are ecosystems and the services they provide going to change in the future?" and "How do human decisions affect these trajectories?" Answering these questions requires an ability to forecast ecological processes. Unfortunately, most ecological forecasts focus on centennial-scale climate responses, therefore neither meeting the needs of near-term (daily to decadal) environmental decision-making nor allowing comparison of specific, quantitative predictions to new observational data, one of the strongest tests of scientific theory. Near-term forecasts provide the opportunity to iteratively cycle between performing analyses and updating predictions in light of new evidence. This iterative process of gaining feedback, building experience, and correcting models and methods is critical for improving forecasts. Iterative, near-term forecasting will accelerate ecological research, make it more relevant to society, and inform sustainable decision-making under high uncertainty and adaptive management. Here, we identify the immediate scientific and societal needs, opportunities, and challenges for iterative near-term ecological forecasting. Over the past decade, data volume, variety, and accessibility have greatly increased, but challenges remain in interoperability, latency, and uncertainty quantification. Similarly, ecologists have made considerable advances in applying computational, informatic, and statistical methods, but opportunities exist for improving forecast-specific theory, methods, and cyberinfrastructure. Effective forecasting will also require changes in scientific training, culture, and institutions. The need to start forecasting is now; the time for making ecology more predictive is here, and learning by doing is the fastest route to drive the science forward.},
}

Bayes Theorem
Climate Change
Ecology/*education/*methods/trends
Ecosystem
Forecasting
Humans
Models, Theoretical

@article {pmid29371471,
year = {2018},
author = {Tucker, MA and Böhning-Gaese, K and Fagan, WF and Fryxell, JM and Van Moorter, B and Alberts, SC and Ali, AH and Allen, AM and Attias, N and Avgar, T and Bartlam-Brooks, H and Bayarbaatar, B and Belant, JL and Bertassoni, A and Beyer, D and Bidner, L and van Beest, FM and Blake, S and Blaum, N and Bracis, C and Brown, D and de Bruyn, PJN and Cagnacci, F and Calabrese, JM and Camilo-Alves, C and Chamaillé-Jammes, S and Chiaradia, A and Davidson, SC and Dennis, T and DeStefano, S and Diefenbach, D and Douglas-Hamilton, I and Fennessy, J and Fichtel, C and Fiedler, W and Fischer, C and Fischhoff, I and Fleming, CH and Ford, AT and Fritz, SA and Gehr, B and Goheen, JR and Gurarie, E and Hebblewhite, M and Heurich, M and Hewison, AJM and Hof, C and Hurme, E and Isbell, LA and Janssen, R and Jeltsch, F and Kaczensky, P and Kane, A and Kappeler, PM and Kauffman, M and Kays, R and Kimuyu, D and Koch, F and Kranstauber, B and LaPoint, S and Leimgruber, P and Linnell, JDC and López-López, P and Markham, AC and Mattisson, J and Medici, EP and Mellone, U and Merrill, E and de Miranda Mourão, G and Morato, RG and Morellet, N and Morrison, TA and Díaz-Muñoz, SL and Mysterud, A and Nandintsetseg, D and Nathan, R and Niamir, A and Odden, J and O'Hara, RB and Oliveira-Santos, LGR and Olson, KA and Patterson, BD and Cunha de Paula, R and Pedrotti, L and Reineking, B and Rimmler, M and Rogers, TL and Rolandsen, CM and Rosenberry, CS and Rubenstein, DI and Safi, K and Saïd, S and Sapir, N and Sawyer, H and Schmidt, NM and Selva, N and Sergiel, A and Shiilegdamba, E and Silva, JP and Singh, N and Solberg, EJ and Spiegel, O and Strand, O and Sundaresan, S and Ullmann, W and Voigt, U and Wall, J and Wattles, D and Wikelski, M and Wilmers, CC and Wilson, JW and Wittemyer, G and Zięba, F and Zwijacz-Kozica, T and Mueller, T},
title = {Moving in the Anthropocene: Global reductions in terrestrial mammalian movements.},
journal = {Science (New York, N.Y.)},
volume = {359},
number = {6374},
pages = {466-469},
doi = {10.1126/science.aam9712},
pmid = {29371471},
issn = {1095-9203},
mesh = {*Animal Migration ; Animals ; Geographic Information Systems ; *Human Activities ; Humans ; *Mammals ; },
abstract = {Animal movement is fundamental for ecosystem functioning and species survival, yet the effects of the anthropogenic footprint on animal movements have not been estimated across species. Using a unique GPS-tracking database of 803 individuals across 57 species, we found that movements of mammals in areas with a comparatively high human footprint were on average one-half to one-third the extent of their movements in areas with a low human footprint. We attribute this reduction to behavioral changes of individual animals and to the exclusion of species with long-range movements from areas with higher human impact. Global loss of vagility alters a key ecological trait of animals that affects not only population persistence but also ecosystem processes such as predator-prey interactions, nutrient cycling, and disease transmission.},
}

*Animal Migration
Animals
Geographic Information Systems
*Human Activities
Humans
*Mammals

@article {pmid29362551,
year = {2017},
author = {Filippova, N and Bulyonkova, T},
title = {The communities of terrestrial macrofungi in different forest types in vicinities of Khanty-Mansiysk (middle taiga zone of West Siberia).},
journal = {Biodiversity data journal},
volume = {},
number = {5},
pages = {e20732},
doi = {10.3897/BDJ.5.e20732},
pmid = {29362551},
issn = {1314-2828},
abstract = {Background: The diversity of macrofungi in the vicinities of Khanty-Mansiysk (Yugra, Russia) was surveyed using a method of permanent sampling plots. Ten plots, each consisting of a number of micro-plots, were established in several different communities ranging from old-growth mixed taiga forest to its derivatives in cutting succession and bogged areas. For more complete registration of the mycota, plots were supplemented with random walking routes directly nearby. Survey results were subjected to various quantitative analyses which allowed not only to evaluate the diversity of fungi but also to obtain valuable information on occurrence, abundance and ecology of individual species as well as community structure and its dynamics in the course of ecological succession. The paper reports the results of the first year of observations.

New information: 460 species of terrestrial macrofungi revealed in a poorly explored area in middle taiga of West Siberia. The plot-based study revealed differences between communities of terrestrial macrofungi of old coniferous forests, their after-cutting secondary formations and bogged stages. The survey allowed to reveal records of 3 species listed in the Red Data Book of Russia and 9 species listed in the Red Data Book of Yugra.},
}

@article {pmid29315317,
year = {2018},
author = {Marshall, HH and Griffiths, DJ and Mwanguhya, F and Businge, R and Griffiths, AGF and Kyabulima, S and Mwesige, K and Sanderson, JL and Thompson, FJ and Vitikainen, EIK and Cant, MA},
title = {Data collection and storage in long-term ecological and evolutionary studies: The Mongoose 2000 system.},
journal = {PloS one},
volume = {13},
number = {1},
pages = {e0190740},
pmid = {29315317},
issn = {1932-6203},
mesh = {Animals ; *Biological Evolution ; Computers ; Data Collection ; Databases, Factual ; *Ecosystem ; Environmental Monitoring/*methods ; Female ; Herpestidae ; Humans ; Male ; Pregnancy ; Smartphone ; Uganda ; },
abstract = {Studying ecological and evolutionary processes in the natural world often requires research projects to follow multiple individuals in the wild over many years. These projects have provided significant advances but may also be hampered by needing to accurately and efficiently collect and store multiple streams of the data from multiple individuals concurrently. The increase in the availability and sophistication of portable computers (smartphones and tablets) and the applications that run on them has the potential to address many of these data collection and storage issues. In this paper we describe the challenges faced by one such long-term, individual-based research project: the Banded Mongoose Research Project in Uganda. We describe a system we have developed called Mongoose 2000 that utilises the potential of apps and portable computers to meet these challenges. We discuss the benefits and limitations of employing such a system in a long-term research project. The app and source code for the Mongoose 2000 system are freely available and we detail how it might be used to aid data collection and storage in other long-term individual-based projects.},
}

Animals
*Biological Evolution
Computers
Data Collection
Databases, Factual
*Ecosystem
Environmental Monitoring/*methods
Female
Herpestidae
Humans
Male
Pregnancy
Smartphone
Uganda

@article {pmid29220487,
year = {2017},
author = {Lassalle, F and Planel, R and Penel, S and Chapulliot, D and Barbe, V and Dubost, A and Calteau, A and Vallenet, D and Mornico, D and Bigot, T and Guéguen, L and Vial, L and Muller, D and Daubin, V and Nesme, X},
title = {Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium.},
journal = {Genome biology and evolution},
volume = {9},
number = {12},
pages = {3413-3431},
pmid = {29220487},
issn = {1759-6653},
mesh = {Agrobacterium/*cytology/*genetics ; *Biological Evolution ; Computational Biology ; *Ecology ; *Genetic Variation ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Software ; },
abstract = {Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species. We identified clade-specific blocks of cotransferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of key Agrobacterium clades. This pattern of gene coevolution rejects a neutral model of transfer, in which neighboring genes would be transferred independently of their function and rather suggests purifying selection on collectively coded acquired pathways. The acquisition of these synapomorphic blocks of cofunctioning genes probably drove the ecological diversification of Agrobacterium and defined features of ancestral ecological niches, which consistently hint at a strong selective role of host plant rhizospheres.},
}

Agrobacterium/*cytology/*genetics
*Biological Evolution
Computational Biology
*Ecology
*Genetic Variation
*Genome, Bacterial
High-Throughput Nucleotide Sequencing
Phylogeny
Software

@article {pmid29198378,
year = {2018},
author = {Matz, MV},
title = {Fantastic Beasts and How To Sequence Them: Ecological Genomics for Obscure Model Organisms.},
journal = {Trends in genetics : TIG},
volume = {34},
number = {2},
pages = {121-132},
doi = {10.1016/j.tig.2017.11.002},
pmid = {29198378},
issn = {0168-9525},
mesh = {Adaptation, Biological/genetics ; Animals ; Biological Evolution ; DNA Methylation ; Ecology ; Gene Ontology ; *Genetics, Population ; *Genome ; Genomics/instrumentation/*methods ; High-Throughput Nucleotide Sequencing/economics/*methods/trends ; *Models, Animal ; Molecular Sequence Annotation ; },
abstract = {The application of genomic approaches to 'obscure model organisms' (OMOs), meaning species with no prior genomic resources, enables increasingly sophisticated studies of the genomic basis of evolution, acclimatization, and adaptation in real ecological contexts. I consider here ecological questions that can be addressed using OMOs, and indicate optimal sequencing and data-handling solutions for each case. With this I hope to promote the diversity of OMO-based projects that would capitalize on the peculiarities of the natural history of OMOs and could feasibly be completed within the scope of a single PhD thesis.},
}

Adaptation, Biological/genetics
Animals
Biological Evolution
DNA Methylation
Ecology
Gene Ontology
*Genetics, Population
*Genome
Genomics/instrumentation/*methods
High-Throughput Nucleotide Sequencing/economics/*methods/trends
*Models, Animal
Molecular Sequence Annotation

@article {pmid29186423,
year = {2018},
author = {Richardson, MF and Sequeira, F and Selechnik, D and Carneiro, M and Vallinoto, M and Reid, JG and West, AJ and Crossland, MR and Shine, R and Rollins, LA},
title = {Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader.},
journal = {GigaScience},
volume = {7},
number = {1},
pages = {1-7},
pmid = {29186423},
issn = {2047-217X},
mesh = {Animals ; Aquatic Organisms/*genetics/growth & development ; Benchmarking ; Bufonidae/*genetics/growth & development ; Chromosome Mapping ; Female ; Gene Library ; Gene Ontology ; *Genome ; High-Throughput Nucleotide Sequencing ; *Introduced Species ; Life Cycle Stages/*genetics ; Male ; Molecular Sequence Annotation ; Sequence Analysis, RNA ; *Transcriptome ; },
abstract = {Background: Cane toads (Rhinella marina) are an iconic invasive species introduced to 4 continents and well utilized for studies of rapid evolution in introduced environments. Despite the long introduction history of this species, its profound ecological impacts, and its utility for demonstrating evolutionary principles, genetic information is sparse. Here we produce a de novo transcriptome spanning multiple tissues and life stages to enable investigation of the genetic basis of previously identified rapid phenotypic change over the introduced range.

Findings: Using approximately 1.9 billion reads from developing tadpoles and 6 adult tissue-specific cDNA libraries, as well as a transcriptome assembly pipeline encompassing 100 separate de novo assemblies, we constructed 62 202 transcripts, of which we functionally annotated ∼50%. Our transcriptome assembly exhibits 90% full-length completeness of the Benchmarking Universal Single-Copy Orthologs data set. Robust assembly metrics and comparisons with several available anuran transcriptomes and genomes indicate that our cane toad assembly is one of the most complete anuran genomic resources available.

Conclusions: This comprehensive anuran transcriptome will provide a valuable resource for investigation of genes under selection during invasion in cane toads, but will also greatly expand our general knowledge of anuran genomes, which are underrepresented in the literature. The data set is publically available in NCBI and GigaDB to serve as a resource for other researchers.},
}

Animals
Aquatic Organisms/*genetics/growth & development
Benchmarking
Bufonidae/*genetics/growth & development
Chromosome Mapping
Female
Gene Library
Gene Ontology
*Genome
High-Throughput Nucleotide Sequencing
*Introduced Species
Life Cycle Stages/*genetics
Male
Molecular Sequence Annotation
Sequence Analysis, RNA
*Transcriptome