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Bibliography on: Ecological Informatics

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Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About:  RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE

RJR: Recommended Bibliography 20 Jan 2019 at 01:36 Created: 

Ecological Informatics

Wikipedia: Ecological Informatics Ecoinformatics, or ecological informatics, is the science of information (Informatics) in Ecology and Environmental science. It integrates environmental and information sciences to define entities and natural processes with language common to both humans and computers. However, this is a rapidly developing area in ecology and there are alternative perspectives on what constitutes ecoinformatics. A few definitions have been circulating, mostly centered on the creation of tools to access and analyze natural system data. However, the scope and aims of ecoinformatics are certainly broader than the development of metadata standards to be used in documenting datasets. Ecoinformatics aims to facilitate environmental research and management by developing ways to access, integrate databases of environmental information, and develop new algorithms enabling different environmental datasets to be combined to test ecological hypotheses. Ecoinformatics characterize the semantics of natural system knowledge. For this reason, much of today's ecoinformatics research relates to the branch of computer science known as Knowledge representation, and active ecoinformatics projects are developing links to activities such as the Semantic Web. Current initiatives to effectively manage, share, and reuse ecological data are indicative of the increasing importance of fields like Ecoinformatics to develop the foundations for effectively managing ecological information. Examples of these initiatives are the National Science Foundation's Datanet , DataONE and Data Conservancy projects.

Created with PubMed® Query: "ecology OR ecological" and ("data management" or informatics) NOT "assays for monitoring autophagy" NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2019-01-18
CmpDate: 2019-01-18

Sánchez-Giraldo C, JM Daza (2019)

Getting better temporal and spatial ecology data for threatened species: using lightweight GPS devices for small primate monitoring in the northern Andes of Colombia.

Primates; journal of primatology, 60(1):93-102.

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.

RevDate: 2019-01-17

Perkins DM, Perna A, Adrian R, et al (2019)

Energetic equivalence underpins the size structure of tree and phytoplankton communities.

Nature communications, 10(1):255 pii:10.1038/s41467-018-08039-3.

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.

RevDate: 2019-01-14
CmpDate: 2019-01-14

Song Z, Stajich JE, Xie Y, et al (2018)

Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesis.

BMC genomics, 19(1):541.

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.

RevDate: 2019-01-09

Ožana S, Burda M, Hykel M, et al (2019)

Dragonfly Hunter CZ: Mobile application for biological species recognition in citizen science.

PloS one, 14(1):e0210370 pii:PONE-D-18-25631.

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.

RevDate: 2019-01-02
CmpDate: 2019-01-02

Horsthemke B (2018)

A critical view on transgenerational epigenetic inheritance in humans.

Nature communications, 9(1):2973.

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.

RevDate: 2019-01-02
CmpDate: 2019-01-02

Butler S, JP O'Dwyer (2018)

Stability criteria for complex microbial communities.

Nature communications, 9(1):2970.

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.

RevDate: 2018-12-31
CmpDate: 2018-12-31

Dai Z, Coker OO, Nakatsu G, et al (2018)

Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers.

Microbiome, 6(1):70.

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.

RevDate: 2018-12-31
CmpDate: 2018-12-31

Gao X, Wang C, Dai W, et al (2017)

Proteomic analysis reveals large amounts of decomposition enzymes and major metabolic pathways involved in algicidal process of Trametes versicolor F21a.

Scientific reports, 7(1):3907.

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.

RevDate: 2018-12-27
CmpDate: 2018-12-27

Stanford BCM, SM Rogers (2018)

R(NA)-tistic expression: The art of matching unknown mRNA and proteins to environmental response in ecological genomics.

Molecular ecology, 27(4):827-830.

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.

RevDate: 2018-12-20

Strassburg BBN, Beyer HL, Crouzeilles R, et al (2019)

Strategic approaches to restoring ecosystems can triple conservation gains and halve costs.

Nature ecology & evolution, 3(1):62-70.

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.

RevDate: 2018-12-17

Jenkins MF, White EP, AH Hurlbert (2018)

The proportion of core species in a community varies with spatial scale and environmental heterogeneity.

PeerJ, 6:e6019.

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.

RevDate: 2018-11-30

Taylor SD, Meiners JM, Riemer K, et al (2018)

Comparison of large-scale citizen science data and long-term study data for phenology modeling.

Ecology [Epub ahead of print].

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.

RevDate: 2018-12-19
CmpDate: 2018-12-19

Felipe-Lucia MR, Soliveres S, Penone C, et al (2018)

Multiple forest attributes underpin the supply of multiple ecosystem services.

Nature communications, 9(1):4839.

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.

RevDate: 2018-12-16

Portnoy GA, Relyea MR, Decker S, et al (2018)

Understanding Gender Differences in Resilience Among Veterans: Trauma History and Social Ecology.

Journal of traumatic stress, 31(6):845-855.

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.

RevDate: 2018-12-07

Mazel F, Davis KM, Loudon A, et al (2018)

Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life?.

mSystems, 3(5):.

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.

RevDate: 2018-12-17

Trotter RT, Lininger MR, Camplain R, et al (2018)

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.

International journal of environmental research and public health, 15(11):.

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.

RevDate: 2018-11-27
CmpDate: 2018-11-27

Munos MK, Maiga A, Do M, et al (2018)

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 of global health, 8(2):020803.

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.

RevDate: 2018-12-12
CmpDate: 2018-12-12

Bamisile BS, Dash CK, Akutse KS, et al (2018)

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.

Microbiological research, 217:34-50.

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.

RevDate: 2018-12-17
CmpDate: 2018-12-11

Meng X, Wang F, Xie Y, et al (2018)

An Ontology-Driven Approach for Integrating Intelligence to Manage Human and Ecological Health Risks in the Geospatial Sensor Web.

Sensors (Basel, Switzerland), 18(11):.

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.

RevDate: 2018-12-07

Gopalakrishnan S, Sinding MS, Ramos-Madrigal J, et al (2018)

Interspecific Gene Flow Shaped the Evolution of the Genus Canis.

Current biology : CB, 28(21):3441-3449.e5.

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.

RevDate: 2018-11-26
CmpDate: 2018-11-26

Li W, Liu S, Pei Y, et al (2018)

Zoning for eco-geological environment before mining in Yushenfu mining area, northern Shaanxi, China.

Environmental monitoring and assessment, 190(10):619.

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.

RevDate: 2018-12-11
CmpDate: 2018-12-11

Song H, Zhang YX, Yang MJ, et al (2018)

Genome survey on invasive veined rapa whelk (Rapana venosa) and development of microsatellite loci on large scale.

Journal of genetics, 97(4):e79-e86.

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.

RevDate: 2018-11-13

Bjorkman AD, Myers-Smith IH, Elmendorf SC, et al (2018)

Plant functional trait change across a warming tundra biome.

Nature, 562(7725):57-62.

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.

RevDate: 2018-11-14

Rokas A, Wisecaver JH, AL Lind (2018)

The birth, evolution and death of metabolic gene clusters in fungi.

Nature reviews. Microbiology, 16(12):731-744.

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.

RevDate: 2018-09-05

de Jonge PA, Nobrega FL, Brouns SJJ, et al (2018)

Molecular and Evolutionary Determinants of Bacteriophage Host Range.

Trends in microbiology pii:S0966-842X(18)30178-1 [Epub ahead of print].

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.

RevDate: 2018-11-19

An S, Zhu X, Shen M, et al (2018)

Mismatch in elevational shifts between satellite observed vegetation greenness and temperature isolines during 2000-2016 on the Tibetan Plateau.

Global change biology, 24(11):5411-5425.

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.

RevDate: 2018-11-14

Dornelas M, Antão LH, Moyes F, et al (2018)

BioTIME: A database of biodiversity time series for the Anthropocene.

Global ecology and biogeography : a journal of macroecology, 27(7):760-786.

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.

RevDate: 2018-12-11
CmpDate: 2018-12-11

D'Alessandro M, Esposito V, Porporato EMD, et al (2018)

Relationships between plastic litter and chemical pollutants on benthic biodiversity.

Environmental pollution (Barking, Essex : 1987), 242(Pt B):1546-1556.

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.

RevDate: 2018-11-14

Liebhold AM, Yamanaka T, Roques A, et al (2018)

Plant diversity drives global patterns of insect invasions.

Scientific reports, 8(1):12095.

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.

RevDate: 2018-09-10
CmpDate: 2018-09-10

Wang Q, Xiong X, Wang X, et al (2018)

Suckling Piglet Intestinal Enterocyte Nutrient Metabolism Changes.

Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology, 48(5):2103-2113.

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.

RevDate: 2018-11-28

Albrecht J, Classen A, Vollstädt MGR, et al (2018)

Plant and animal functional diversity drive mutualistic network assembly across an elevational gradient.

Nature communications, 9(1):3177.

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.

RevDate: 2018-11-14

Bird SM, R King (2018)

Multiple Systems Estimation (or Capture-Recapture Estimation) to Inform Public Policy.

Annual review of statistics and its application, 5:95-118.

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.

RevDate: 2018-10-29
CmpDate: 2018-10-29

Ridding LE, Redhead JW, Oliver TH, et al (2018)

The importance of landscape characteristics for the delivery of cultural ecosystem services.

Journal of environmental management, 206:1145-1154.

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.

RevDate: 2018-10-29
CmpDate: 2018-10-29

He L, Shen J, Y Zhang (2018)

Ecological vulnerability assessment for ecological conservation and environmental management.

Journal of environmental management, 206:1115-1125.

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.

RevDate: 2018-10-12
CmpDate: 2018-10-12

Djikanović V, Skorić S, Spasić S, et al (2018)

Ecological risk assessment for different macrophytes and fish species in reservoirs using biota-sediment accumulation factors as a useful tool.

Environmental pollution (Barking, Essex : 1987), 241:1167-1174.

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.

RevDate: 2018-12-11
CmpDate: 2018-12-11

Bradburd GS, Coop GM, PL Ralph (2018)

Inferring Continuous and Discrete Population Genetic Structure Across Space.

Genetics, 210(1):33-52.

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.

RevDate: 2018-11-14
CmpDate: 2018-11-02

Chen F, Zhang J, Chen J, et al (2018)

realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta).

Database : the journal of biological databases and curation, 2018:.

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/.

RevDate: 2018-11-14
CmpDate: 2018-10-23

Longbottom J, Shearer FM, Devine M, et al (2018)

Vulnerability to snakebite envenoming: a global mapping of hotspots.

Lancet (London, England), 392(10148):673-684.

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.

RevDate: 2018-12-17
CmpDate: 2018-12-17

Ma ZS, L Li (2018)

Measuring metagenome diversity and similarity with Hill numbers.

Molecular ecology resources, 18(6):1339-1355.

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.

RevDate: 2018-07-07

Lant C, Baggio J, Konar M, et al (2018)

The U.S. food-energy-water system: A blueprint to fill the mesoscale gap for science and decision-making.

Ambio pii:10.1007/s13280-018-1077-0 [Epub ahead of print].

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.

RevDate: 2018-12-13
CmpDate: 2018-12-13

Bramon Mora B, Gravel D, Gilarranz LJ, et al (2018)

Identifying a common backbone of interactions underlying food webs from different ecosystems.

Nature communications, 9(1):2603.

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.

RevDate: 2018-12-17
CmpDate: 2018-12-17

Keck F, Vasselon V, Rimet F, et al (2018)

Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units' ecological profiles.

Molecular ecology resources, 18(6):1299-1309.

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.

RevDate: 2018-11-27
CmpDate: 2018-11-27

Celis JS, Wibberg D, Ramírez-Portilla C, et al (2018)

Binning enables efficient host genome reconstruction in cnidarian holobionts.

GigaScience, 7(7):.

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.

RevDate: 2018-06-15
CmpDate: 2018-06-15

Mirtl M, T Borer E, Djukic I, et al (2018)

Genesis, goals and achievements of Long-Term Ecological Research at the global scale: A critical review of ILTER and future directions.

The Science of the total environment, 626:1439-1462.

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.

RevDate: 2018-06-13
CmpDate: 2018-06-13

Dick J, Orenstein DE, Holzer JM, et al (2018)

What is socio-ecological research delivering? A literature survey across 25 international LTSER platforms.

The Science of the total environment, 622-623:1225-1240.

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.

RevDate: 2018-12-17
CmpDate: 2018-12-17

Dellicour S, JF Flot (2018)

The hitchhiker's guide to single-locus species delimitation.

Molecular ecology resources, 18(6):1234-1246.

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.

RevDate: 2018-08-17

Snell Taylor SJ, Evans BS, White EP, et al (2018)

The prevalence and impact of transient species in ecological communities.

Ecology, 99(8):1825-1835.

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.

RevDate: 2018-11-14
CmpDate: 2018-11-08

Couger MB, Arévalo L, P Campbell (2018)

A High Quality Genome for Mus spicilegus, a Close Relative of House Mice with Unique Social and Ecological Adaptations.

G3 (Bethesda, Md.), 8(7):2145-2152.

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.

RevDate: 2018-07-10
CmpDate: 2018-07-10

Meng L, Huang J, J Dong (2018)

Assessment of rural ecosystem health and type classification in Jiangsu province, China.

The Science of the total environment, 615:1218-1228.

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.

RevDate: 2018-11-14
CmpDate: 2018-09-20

Peters K, Worrich A, Weinhold A, et al (2018)

Current Challenges in Plant Eco-Metabolomics.

International journal of molecular sciences, 19(5):.

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.

RevDate: 2018-12-18

Toni M, Manciocco A, Angiulli E, et al (2019)

Review: Assessing fish welfare in research and aquaculture, with a focus on European directives.

Animal : an international journal of animal bioscience, 13(1):161-170.

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.

RevDate: 2018-11-14
CmpDate: 2018-09-04

Muscente AD, Prabhu A, Zhong H, et al (2018)

Quantifying ecological impacts of mass extinctions with network analysis of fossil communities.

Proceedings of the National Academy of Sciences of the United States of America, 115(20):5217-5222.

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.

RevDate: 2018-11-14
CmpDate: 2018-06-18

Hannigan GD, Duhaime MB, Koutra D, et al (2018)

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome.

PLoS computational biology, 14(4):e1006099.

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.

RevDate: 2018-11-14
CmpDate: 2018-08-15

Chen S, Wang W, Xu W, et al (2018)

Plant diversity enhances productivity and soil carbon storage.

Proceedings of the National Academy of Sciences of the United States of America, 115(16):4027-4032.

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.

RevDate: 2018-11-14

Ching T, Himmelstein DS, Beaulieu-Jones BK, et al (2018)

Opportunities and obstacles for deep learning in biology and medicine.

Journal of the Royal Society, Interface, 15(141):.

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.

RevDate: 2018-11-14
CmpDate: 2018-06-26

Emery M, Willis MMS, Hao Y, et al (2018)

Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization.

PLoS genetics, 14(3):e1007267.

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.

RevDate: 2018-12-17
CmpDate: 2018-12-17

Psonis N, Antoniou A, Karameta E, et al (2018)

Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system.

Molecular phylogenetics and evolution, 125:100-115.

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.

RevDate: 2018-04-16

Anderegg LDL, Berner LT, Badgley G, et al (2018)

Within-species patterns challenge our understanding of the leaf economics spectrum.

Ecology letters, 21(5):734-744.

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.

RevDate: 2018-11-14
CmpDate: 2018-07-05

Jablonski KE, Boone RB, PJ Meiman (2018)

An agent-based model of cattle grazing toxic Geyer's larkspur.

PloS one, 13(3):e0194450.

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.

RevDate: 2018-12-02
CmpDate: 2018-06-08

Heider K, Lopez JMR, J Scheffran (2018)

The potential of volunteered geographic information to investigate peri-urbanization in the conservation zone of Mexico City.

Environmental monitoring and assessment, 190(4):219.

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.

RevDate: 2018-11-14
CmpDate: 2018-09-07

Liu XY, Koba K, Koyama LA, et al (2018)

Nitrate is an important nitrogen source for Arctic tundra plants.

Proceedings of the National Academy of Sciences of the United States of America, 115(13):3398-3403.

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.

RevDate: 2018-11-14
CmpDate: 2018-07-02

Lee EC, Arab A, Goldlust SM, et al (2018)

Deploying digital health data to optimize influenza surveillance at national and local scales.

PLoS computational biology, 14(3):e1006020.

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.

RevDate: 2018-12-11
CmpDate: 2018-12-11

Torina A, Blanda V, Blanda M, et al (2018)

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).

International journal of environmental research and public health, 15(3):.

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.

RevDate: 2018-04-11
CmpDate: 2018-04-11

Hervé MR, Nicolè F, KA Lê Cao (2018)

Multivariate Analysis of Multiple Datasets: a Practical Guide for Chemical Ecology.

Journal of chemical ecology, 44(3):215-234.

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.

RevDate: 2018-11-13
CmpDate: 2018-05-22

Ma Z, Guo D, Xu X, et al (2018)

Evolutionary history resolves global organization of root functional traits.

Nature, 555(7694):94-97.

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.

RevDate: 2018-10-04
CmpDate: 2018-10-03

Kim HS, Lee BY, Han J, et al (2018)

The genome of the freshwater monogonont rotifer Brachionus calyciflorus.

Molecular ecology resources, 18(3):646-655.

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.

RevDate: 2018-11-08
CmpDate: 2018-11-08

Stefanidis K, Panagopoulos Y, M Mimikou (2018)

Response of a multi-stressed Mediterranean river to future climate and socio-economic scenarios.

The Science of the total environment, 627:756-769.

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.

RevDate: 2018-11-13
CmpDate: 2018-08-01

Zachar I, Szilágyi A, Számadó S, et al (2018)

Farming the mitochondrial ancestor as a model of endosymbiotic establishment by natural selection.

Proceedings of the National Academy of Sciences of the United States of America, 115(7):E1504-E1510.

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.

RevDate: 2018-11-13
CmpDate: 2018-07-20

Dietze MC, Fox A, Beck-Johnson LM, et al (2018)

Iterative near-term ecological forecasting: Needs, opportunities, and challenges.

Proceedings of the National Academy of Sciences of the United States of America, 115(7):1424-1432.

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.

RevDate: 2018-08-08
CmpDate: 2018-04-23

Tucker MA, Böhning-Gaese K, Fagan WF, et al (2018)

Moving in the Anthropocene: Global reductions in terrestrial mammalian movements.

Science (New York, N.Y.), 359(6374):466-469.

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.

RevDate: 2018-01-24

Filippova N, T Bulyonkova (2017)

The communities of terrestrial macrofungi in different forest types in vicinities of Khanty-Mansiysk (middle taiga zone of West Siberia).

Biodiversity data journal pii:Biodiversity Data Journal.

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.

RevDate: 2018-11-13
CmpDate: 2018-02-21

Marshall HH, Griffiths DJ, Mwanguhya F, et al (2018)

Data collection and storage in long-term ecological and evolutionary studies: The Mongoose 2000 system.

PloS one, 13(1):e0190740.

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.

RevDate: 2018-11-26
CmpDate: 2018-11-26

Lassalle F, Planel R, Penel S, et al (2017)

Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium.

Genome biology and evolution, 9(12):3413-3431.

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.

RevDate: 2018-12-11
CmpDate: 2018-12-11

Matz MV (2018)

Fantastic Beasts and How To Sequence Them: Ecological Genomics for Obscure Model Organisms.

Trends in genetics : TIG, 34(2):121-132.

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.

RevDate: 2018-11-19
CmpDate: 2018-11-19

Richardson MF, Sequeira F, Selechnik D, et al (2018)

Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader.

GigaScience, 7(1):1-7.

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.

RevDate: 2018-11-13

Walter JM, Coutinho FH, Dutilh BE, et al (2017)

Ecogenomics and Taxonomy of Cyanobacteria Phylum.

Frontiers in microbiology, 8:2132.

Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes. Next, the relative abundances of these genomes were determined throughout diverse global marine and freshwater ecosystems, using metagenomic data sets. The whole-genome-based taxonomy of the ninety-nine genomes allowed us to identify 57 (of which 28 are new genera) and 87 (of which 32 are new species) different cyanobacterial genera and species, respectively. The ecogenomic analysis allowed the distinction of three major ecological groups of Cyanobacteria (named as i. Low Temperature; ii. Low Temperature Copiotroph; and iii. High Temperature Oligotroph) that were coherently linked to the genomic taxonomy. This work establishes a new taxonomic framework for Cyanobacteria in the light of genomic taxonomy and ecogenomic approaches.

RevDate: 2018-07-10
CmpDate: 2018-07-10

Dornburg A, Townsend JP, Z Wang (2017)

Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data.

Advances in genetics, 100:1-47.

Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine. However, the rise of big data has also presented phylogenomicists with a new set of challenges to experimental design, quantitative analyses, and computation. The sequencing of a number of very first genomes presented significant challenges to phylogenetic inference, leading fungal phylogenomicists to begin addressing pitfalls and postulating solutions to the issues that arise from genome-scale analyses relevant to any lineage across the Tree of Life. Here we highlight insights from fungal phylogenomics for topics including systematics and species delimitation, ecological and phenotypic diversification, and biogeography while providing an overview of progress made on the reconstruction of the fungal Tree of Life. Finally, we provide a review of considerations to phylogenomic experimental design for robust tree inference. We hope that this special issue of Advances in Genetics not only excites the continued progress of fungal evolutionary biology but also motivates the interdisciplinary development of new theory and methods designed to maximize the power of genomic scale data in phylogenetic analyses.

RevDate: 2018-11-13
CmpDate: 2017-12-26

Mainali KP, Bewick S, Thielen P, et al (2017)

Statistical analysis of co-occurrence patterns in microbial presence-absence datasets.

PloS one, 12(11):e0187132.

Drawing on a long history in macroecology, correlation analysis of microbiome datasets is becoming a common practice for identifying relationships or shared ecological niches among bacterial taxa. However, many of the statistical issues that plague such analyses in macroscale communities remain unresolved for microbial communities. Here, we discuss problems in the analysis of microbial species correlations based on presence-absence data. We focus on presence-absence data because this information is more readily obtainable from sequencing studies, especially for whole-genome sequencing, where abundance estimation is still in its infancy. First, we show how Pearson's correlation coefficient (r) and Jaccard's index (J)-two of the most common metrics for correlation analysis of presence-absence data-can contradict each other when applied to a typical microbiome dataset. In our dataset, for example, 14% of species-pairs predicted to be significantly correlated by r were not predicted to be significantly correlated using J, while 37.4% of species-pairs predicted to be significantly correlated by J were not predicted to be significantly correlated using r. Mismatch was particularly common among species-pairs with at least one rare species (<10% prevalence), explaining why r and J might differ more strongly in microbiome datasets, where there are large numbers of rare taxa. Indeed 74% of all species-pairs in our study had at least one rare species. Next, we show how Pearson's correlation coefficient can result in artificial inflation of positive taxon relationships and how this is a particular problem for microbiome studies. We then illustrate how Jaccard's index of similarity (J) can yield improvements over Pearson's correlation coefficient. However, the standard null model for Jaccard's index is flawed, and thus introduces its own set of spurious conclusions. We thus identify a better null model based on a hypergeometric distribution, which appropriately corrects for species prevalence. This model is available from recent statistics literature, and can be used for evaluating the significance of any value of an empirically observed Jaccard's index. The resulting simple, yet effective method for handling correlation analysis of microbial presence-absence datasets provides a robust means of testing and finding relationships and/or shared environmental responses among microbial taxa.

RevDate: 2018-11-13
CmpDate: 2017-12-12

Schwager E, Mallick H, Ventz S, et al (2017)

A Bayesian method for detecting pairwise associations in compositional data.

PLoS computational biology, 13(11):e1005852.

Compositional data consist of vectors of proportions normalized to a constant sum from a basis of unobserved counts. The sum constraint makes inference on correlations between unconstrained features challenging due to the information loss from normalization. However, such correlations are of long-standing interest in fields including ecology. We propose a novel Bayesian framework (BAnOCC: Bayesian Analysis of Compositional Covariance) to estimate a sparse precision matrix through a LASSO prior. The resulting posterior, generated by MCMC sampling, allows uncertainty quantification of any function of the precision matrix, including the correlation matrix. We also use a first-order Taylor expansion to approximate the transformation from the unobserved counts to the composition in order to investigate what characteristics of the unobserved counts can make the correlations more or less difficult to infer. On simulated datasets, we show that BAnOCC infers the true network as well as previous methods while offering the advantage of posterior inference. Larger and more realistic simulated datasets further showed that BAnOCC performs well as measured by type I and type II error rates. Finally, we apply BAnOCC to a microbial ecology dataset from the Human Microbiome Project, which in addition to reproducing established ecological results revealed unique, competition-based roles for Proteobacteria in multiple distinct habitats.

RevDate: 2018-11-13

Crouzeilles R, Ferreira MS, Chazdon RL, et al (2017)

Ecological restoration success is higher for natural regeneration than for active restoration in tropical forests.

Science advances, 3(11):e1701345.

Is active restoration the best approach to achieve ecological restoration success (the return to a reference condition, that is, old-growth forest) when compared to natural regeneration in tropical forests? Our meta-analysis of 133 studies demonstrated that natural regeneration surpasses active restoration in achieving tropical forest restoration success for all three biodiversity groups (plants, birds, and invertebrates) and five measures of vegetation structure (cover, density, litter, biomass, and height) tested. Restoration success for biodiversity and vegetation structure was 34 to 56% and 19 to 56% higher in natural regeneration than in active restoration systems, respectively, after controlling for key biotic and abiotic factors (forest cover, precipitation, time elapsed since restoration started, and past disturbance). Biodiversity responses were based primarily on ecological metrics of abundance and species richness (74%), both of which take far less time to achieve restoration success than similarity and composition. This finding challenges the widely held notion that natural forest regeneration has limited conservation value and that active restoration should be the default ecological restoration strategy. The proposition that active restoration achieves greater restoration success than natural regeneration may have arisen because previous comparisons lacked controls for biotic and abiotic factors; we also did not find any difference between active restoration and natural regeneration outcomes for vegetation structure when we did not control for these factors. Future policy priorities should align the identified patterns of biophysical and ecological conditions where each or both restoration approaches are more successful, cost-effective, and compatible with socioeconomic incentives for tropical forest restoration.

RevDate: 2018-12-02
CmpDate: 2018-01-04

Goleiji E, Hosseini SM, Khorasani N, et al (2017)

Forest fire risk assessment-an integrated approach based on multicriteria evaluation.

Environmental monitoring and assessment, 189(12):612.

The present study deals with application of the weighted linear combination method for zoning of forest fire risk in Dohezar and Sehezar region of Mazandaran province in northern Iran. In this study, the effective criteria for fires were identified by the Delphi method, and these included ecological and socioeconomic parameters. In this regard, the first step comprised of digital layers; the required data were provided from databases, related centers, and field data collected in the region. Then, the map of criteria was digitized in a geographic information system, and all criteria and indexes were normalized by fuzzy logic. After that, the geographic information system (GIS 10.3) was integrated with the Weighted Linear Combination and the Analytical Network Process, to produce zonation of the forest fire risk map in the Dohezar and Sehezar region. In order to analyze accuracy of the evaluation, the results obtained from the study were compared to records of former fire incidents in the region. This was done using the Kappa coefficient test and a receiver operating characteristic curve. The model showing estimations for forest fire risk explained that the prepared map had accuracy of 90% determined by the Kappa coefficient test and the value of 0.924 by receiver operating characteristic. These results showed that the prepared map had high accuracy and efficacy.

RevDate: 2018-11-13
CmpDate: 2018-07-31

Soranno PA, Bacon LC, Beauchene M, et al (2017)

LAGOS-NE: a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of US lakes.

GigaScience, 6(12):1-22.

Understanding the factors that affect water quality and the ecological services provided by freshwater ecosystems is an urgent global environmental issue. Predicting how water quality will respond to global changes not only requires water quality data, but also information about the ecological context of individual water bodies across broad spatial extents. Because lake water quality is usually sampled in limited geographic regions, often for limited time periods, assessing the environmental controls of water quality requires compilation of many data sets across broad regions and across time into an integrated database. LAGOS-NE accomplishes this goal for lakes in the northeastern-most 17 US states.LAGOS-NE contains data for 51 101 lakes and reservoirs larger than 4 ha in 17 lake-rich US states. The database includes 3 data modules for: lake location and physical characteristics for all lakes; ecological context (i.e., the land use, geologic, climatic, and hydrologic setting of lakes) for all lakes; and in situ measurements of lake water quality for a subset of the lakes from the past 3 decades for approximately 2600-12 000 lakes depending on the variable. The database contains approximately 150 000 measures of total phosphorus, 200 000 measures of chlorophyll, and 900 000 measures of Secchi depth. The water quality data were compiled from 87 lake water quality data sets from federal, state, tribal, and non-profit agencies, university researchers, and citizen scientists. This database is one of the largest and most comprehensive databases of its type because it includes both in situ measurements and ecological context data. Because ecological context can be used to study a variety of other questions about lakes, streams, and wetlands, this database can also be used as the foundation for other studies of freshwaters at broad spatial and ecological scales.

RevDate: 2018-11-13
CmpDate: 2018-06-18

Corander J, Fraser C, Gutmann MU, et al (2017)

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics.

Nature ecology & evolution, 1(12):1950-1960.

Many bacterial species are composed of multiple lineages distinguished by extensive variation in gene content. These often cocirculate in the same habitat, but the evolutionary and ecological processes that shape these complex populations are poorly understood. Addressing these questions is particularly important for Streptococcus pneumoniae, a nasopharyngeal commensal and respiratory pathogen, because the changes in population structure associated with the recent introduction of partial-coverage vaccines have substantially reduced pneumococcal disease. Here we show that pneumococcal lineages from multiple populations each have a distinct combination of intermediate-frequency genes. Functional analysis suggested that these loci may be subject to negative frequency-dependent selection (NFDS) through interactions with other bacteria, hosts or mobile elements. Correspondingly, these genes had similar frequencies in four populations with dissimilar lineage compositions. These frequencies were maintained following substantial alterations in lineage prevalences once vaccination programmes began. Fitting a multilocus NFDS model of post-vaccine population dynamics to three genomic datasets using Approximate Bayesian Computation generated reproducible estimates of the influence of NFDS on pneumococcal evolution, the strength of which varied between loci. Simulations replicated the stable frequency of lineages unperturbed by vaccination, patterns of serotype switching and clonal replacement. This framework highlights how bacterial ecology affects the impact of clinical interventions.

RevDate: 2018-11-13
CmpDate: 2017-10-23

Wang D, Li L, Wu G, et al (2017)

De novo transcriptome sequencing of Isaria cateniannulata and comparative analysis of gene expression in response to heat and cold stresses.

PloS one, 12(10):e0186040.

Isaria cateniannulata is a very important and virulent entomopathogenic fungus that infects many insect pest species. Although I. cateniannulata is commonly exposed to extreme environmental temperature conditions, little is known about its molecular response mechanism to temperature stress. Here, we sequenced and de novo assembled the transcriptome of I. cateniannulata in response to high and low temperature stresses using Illumina RNA-Seq technology. Our assembly encompassed 17,514 unigenes (mean length = 1,197 bp), in which 11,445 unigenes (65.34%) showed significant similarities to known sequences in NCBI non-redundant protein sequences (Nr) database. Using digital gene expression analysis, 4,483 differentially expressed genes (DEGs) were identified after heat treatment, including 2,905 up-regulated genes and 1,578 down-regulated genes. Under cold stress, 1,927 DEGs were identified, including 1,245 up-regulated genes and 682 down-regulated genes. The expression patterns of 18 randomly selected candidate DEGs resulting from quantitative real-time PCR (qRT-PCR) were consistent with their transcriptome analysis results. Although DEGs were involved in many pathways, we focused on the genes that were involved in endocytosis: In heat stress, the pathway of clathrin-dependent endocytosis (CDE) was active; however at low temperature stresses, the pathway of clathrin-independent endocytosis (CIE) was active. Besides, four categories of DEGs acting as temperature sensors were observed, including cell-wall-major-components-metabolism-related (CWMCMR) genes, heat shock protein (Hsp) genes, intracellular-compatible-solutes-metabolism-related (ICSMR) genes and glutathione S-transferase (GST). These results enhance our understanding of the molecular mechanisms of I. cateniannulata in response to temperature stresses and provide a valuable resource for the future investigations.

RevDate: 2018-11-13
CmpDate: 2018-02-23

Tedesco PA, Beauchard O, Bigorne R, et al (2017)

A global database on freshwater fish species occurrence in drainage basins.

Scientific data, 4:170141.

A growing interest is devoted to global-scale approaches in ecology and evolution that examine patterns and determinants of species diversity and the threats resulting from global change. These analyses obviously require global datasets of species distribution. Freshwater systems house a disproportionately high fraction of the global fish diversity considering the small proportion of the earth's surface that they occupy, and are one of the most threatened habitats on Earth. Here we provide complete species lists for 3119 drainage basins covering more than 80% of the Earth surface using 14953 fish species inhabiting permanently or occasionally freshwater systems. The database results from an extensive survey of native and non-native freshwater fish species distribution based on 1436 published papers, books, grey literature and web-based sources. Alone or in combination with further datasets on species biological and ecological characteristics and their evolutionary history, this database represents a highly valuable source of information for further studies on freshwater macroecology, macroevolution, biogeography and conservation.

RevDate: 2018-11-13
CmpDate: 2018-05-29

Soltész Z, Erdélyi K, Bakonyi T, et al (2017)

West Nile virus host-vector-pathogen interactions in a colonial raptor.

Parasites & vectors, 10(1):449.

BACKGROUND: Avian host species have different roles in the amplification and maintenance of West Nile virus (WNV), therefore identifying key taxa is vital in understanding WNV epidemics. Here, we present a comprehensive case study conducted on red-footed falcons, where host-vector, vector-virus and host-virus interactions were simultaneously studied to evaluate host species contribution to WNV circulation qualitatively.

RESULTS: Mosquitoes were trapped inside red-footed falcon nest-boxes by a method originally developed for the capture of blackflies and midges. We showed that this approach is also efficient for trapping mosquitoes and that the number of trapped vectors is a function of host attraction. Brood size and nestling age had a positive effect on the number of attracted Culex pipiens individuals while the blood-feeding success rate of both dominant Culex species (Culex pipiens and Culex modestus) markedly decreased after the nestlings reached 14 days of age. Using RT-PCR, we showed that WNV was present in these mosquitoes with 4.2% (CI: 0.9-7.5%) prevalence. We did not detect WNV in any of the nestling blood samples. However, a relatively high seroprevalence (25.4% CI: 18.8-33.2%) was detected with an enzyme-linked immunoabsorbent assay (ELISA). Using the ELISA OD ratios as a proxy to antibody titers, we showed that older seropositive nestlings have lower antibody levels than their younger conspecifics and that hatching order negatively influences antibody levels in broods with seropositive nestlings.

CONCLUSIONS: Red-footed falcons in the studied system are exposed to a local sylvatic WNV circulation, and the risk of infection is higher for younger nestlings. However, the lack of individuals with viremia and the high WNV seroprevalence, indicate that either host has a very short viremic period or that a large percentage of nestlings in the population receive maternal antibodies. This latter assumption is supported by the age and hatching order dependence of antibody levels found for seropositive nestlings. Considering the temporal pattern in mosquito feeding success, maternal immunity may be effective in protecting progeny against WNV infection despite the short antibody half-life measured in various other species. We conclude that red-footed falcons seem to have low WNV host competence and are unlikely to be effective virus reservoirs in the studied region.

RevDate: 2018-11-13
CmpDate: 2018-08-20

Martin RW, Waits ER, CT Nietch (2018)

Empirically-based modeling and mapping to consider the co-occurrence of ecological receptors and stressors.

The Science of the total environment, 613-614:1228-1239.

Part of the ecological risk assessment process involves examining the potential for environmental stressors and ecological receptors to co-occur across a landscape. In this study, we introduce a Bayesian joint modeling framework for use in evaluating and mapping the co-occurrence of stressors and receptors using empirical data, open-source statistical software, and Geographic Information Systems tools and data. To illustrate the approach, we apply the framework to bioassessment data on stream fishes and nutrients collected from a watershed in southwestern Ohio. The results highlighted the joint model's ability to parse and exploit statistical dependencies in order to provide empirical insight into the potential environmental and ecotoxicological interactions influencing co-occurrence. We also demonstrate how probabilistic predictions can be generated and mapped to visualize spatial patterns in co-occurrences. For practitioners, we believe that this data-driven approach to modeling and mapping co-occurrence can lead to more quantitatively transparent and robust assessments of ecological risk.

RevDate: 2018-11-13
CmpDate: 2017-10-19

Bauer M, Graf IR, Ngampruetikorn V, et al (2017)

Exploiting ecology in drug pulse sequences in favour of population reduction.

PLoS computational biology, 13(9):e1005747.

A deterministic population dynamics model involving birth and death for a two-species system, comprising a wild-type and more resistant species competing via logistic growth, is subjected to two distinct stress environments designed to mimic those that would typically be induced by temporal variation in the concentration of a drug (antibiotic or chemotherapeutic) as it permeates through the population and is progressively degraded. Different treatment regimes, involving single or periodical doses, are evaluated in terms of the minimal population size (a measure of the extinction probability), and the population composition (a measure of the selection pressure for resistance or tolerance during the treatment). We show that there exist timescales over which the low-stress regime is as effective as the high-stress regime, due to the competition between the two species. For multiple periodic treatments, competition can ensure that the minimal population size is attained during the first pulse when the high-stress regime is short, which implies that a single short pulse can be more effective than a more protracted regime. Our results suggest that when the duration of the high-stress environment is restricted, a treatment with one or multiple shorter pulses can produce better outcomes than a single long treatment. If ecological competition is to be exploited for treatments, it is crucial to determine these timescales, and estimate for the minimal population threshold that suffices for extinction. These parameters can be quantified by experiment.

RevDate: 2018-11-13
CmpDate: 2018-06-04

Cardoso D, Särkinen T, Alexander S, et al (2017)

Amazon plant diversity revealed by a taxonomically verified species list.

Proceedings of the National Academy of Sciences of the United States of America, 114(40):10695-10700.

Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests.

RevDate: 2018-10-10
CmpDate: 2018-10-10

Fisher RA, Koven CD, Anderegg WRL, et al (2018)

Vegetation demographics in Earth System Models: A review of progress and priorities.

Global change biology, 24(1):35-54.

Numerous current efforts seek to improve the representation of ecosystem ecology and vegetation demographic processes within Earth System Models (ESMs). These developments are widely viewed as an important step in developing greater realism in predictions of future ecosystem states and fluxes. Increased realism, however, leads to increased model complexity, with new features raising a suite of ecological questions that require empirical constraints. Here, we review the developments that permit the representation of plant demographics in ESMs, and identify issues raised by these developments that highlight important gaps in ecological understanding. These issues inevitably translate into uncertainty in model projections but also allow models to be applied to new processes and questions concerning the dynamics of real-world ecosystems. We argue that stronger and more innovative connections to data, across the range of scales considered, are required to address these gaps in understanding. The development of first-generation land surface models as a unifying framework for ecophysiological understanding stimulated much research into plant physiological traits and gas exchange. Constraining predictions at ecologically relevant spatial and temporal scales will require a similar investment of effort and intensified inter-disciplinary communication.

RevDate: 2018-12-02
CmpDate: 2018-05-23

Jiang SY, Sun HB, Qin JH, et al (2016)

[Functional production regionalization for Fritillariae Cirrhosae Bulbus based on growth and quality suitability assessment].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 41(17):3194-3201.

The major contributing factors for growth of endangered medicinal plants of Fritillariae Cirrhosae Bulbus were screened on the GIS platform by using the MaxEnt model, and spatial distribution data of the medicine quality suitability were generated by geostatistics interpolation based on reported measured data of ecology and quality suitability assessment. On this basis, a functional production cultivation regionalization with high feasibility and operability were formatted for protection, wild monitoring, and cultivation of this plant by fuzzy superposition of spatial suitability data of ecology and quality, as well as integrated with land use and cover data. Therefore, a novel assessment and regionalization method were presented for ecology, growth and quality suitability of the Chinese traditional medicinal plants. This method is expected to overcome shortage of traditional regionalization methods difficult to distinguish the contribution of ecological factors and quality factors, which provide an innovative theory and methodology for regionalization, and is helpful to practical application of wild resource protection, monitoring, and commercialization cultivation for traditional Chinese medicinal plants.

RevDate: 2018-12-02
CmpDate: 2018-05-23

Liu X, Yang YF, Song HP, et al (2016)

[Cultural regionalization for Coptis chinensis based on 3S technology platform Ⅰ. Study on growth suitability for Coptis chinensis based on ecological factors analysis by Maxent and ArcGIS model].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 41(17):3186-3193.

At the urgent request of Coptis chinensis planting,growth suitability as assessment indicators for C. chinensis cultivation was proposed and analyzed in this paper , based on chemical quality determination and ecological fators analysis by Maxent and ArcGIS model. Its potential distribution areas at differernt suitability grade and regionalization map were formulated based on statistical theory and growth suitability theory. The results showed that the most suitable habitats is some parts of Chongqing and Hubei province, such as Shizhu, Lichuan, Wulong, Wuxi, Enshi. There are seven ecological factor is the main ecological factors affect the growth of Coptidis Rhizoma, including altitude, precipitation in February and September and the rise of precipitation and altitude is conducive to the accumulation of total alkaloid content in C. chinensis. Therefore, The results of the study not only illustrates the most suitable for the surroundings of Coptidis Rhizoma, also helpful to further research and practice of cultivation regionalization, wild resource monitoring and large-scale cultivation of traditional Chinese medicine plants.

RevDate: 2018-12-02
CmpDate: 2018-05-23

Miao Q, Yuan YJ, Luo GM, et al (2016)

[Study on ecological suitability of Gardenia jasminoides based on ArcGIS and Maxent model].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 41(17):3181-3185.

The application of ArcGIS and Maxent modelto analyze the ecological suitability of Gardenia jasminoides.Taking 85 batches of Gardenia as the basis of analysis, the selection of ecological factors for the growth of Gardenia. The results showed that the average precipitation in April, the average precipitation in November and the average precipitation in August were the most important factors affecting the growth of Gardenia. The relative concentration of Gardenia suitable growth region,north to the south of Shaanxi province, south of Henan, central Anhui, south to the north of Hainan province, west to central Sichuan province, east of Zhejiang coastal area, northeast of Taiwan.

RevDate: 2018-12-02
CmpDate: 2018-05-23

Lu YY, Yang YM, Ma XH, et al (2016)

[Ecology suitability study of Chinese materia medica Gentianae Macrophyllae Radix].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 41(17):3176-3180.

This paper is aimed to predict ecology suitability distribution of Gentianae Macrophyllae Radix and search the main ecological factors affecting the suitability distribution. The 313 distribution information about G. macrophylla, 186 distribution information about G. straminea, 343 distribution information about G. dauricaand 131 distribution information about G. crasicaulis were collected though investigation and network sharing platform data . The ecology suitable distribution factors for production Gentianae Macrophyllae Radix was analyzed respectively by the software of ArcGIS and MaxEnt with 55 environmental factors. The result of MaxEnt prediction was very well (AUC was above 0.9). The results of predominant factors analysis showed that precipitation and altitude were all the major factors impacting the ecology suitable of Getiana Macrophylla Radix production. G. macrophylla ecology suitable region was mainly concentrated in south of Gansu, Shanxi, central of Shaanxi and east of Qinghai provinces. G. straminea ecology suitable region was mainly concentrated in southwest of Gansu, east of Qinghai, north and northwest of Sichuan, east of Xizang province. G. daurica ecology suitable region was mainly concentrated in south and southwest of Gansu, east of Qinghai, Shanxi and north of Shaanxi province. G. crasicaulis ecology suitable region was mainly concentrated in Sichuan and north of Yunnan, east of Xizang, south of Gansu and east of Qinghai province. The ecological suitability distribution result of Gentianae Macrophyllae Radix was consistent with each species actual distribution. The study could provide reference for the collection and protection of wild resources, meanwhile, provide the basis for the selection of cultivation area of Gentiana Macrophylla Radix.

RevDate: 2018-12-02
CmpDate: 2018-05-23

Shi ZW, Ma CJ, Kang CZ, et al (2016)

[Ecological suitability regionalization for Gastrodia elata in Zhaotong based on Maxent and ArcGIS].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 41(17):3155-3163.

In this paper, the potential distribution information and ecological suitability regionalization for Gastrodia elata in Zhaotong were studied based on the climate, terrain, soil and vegetation factors analysis by Maxent and ArcGIS. The results showed that the highly potential distribution (suitability index>0.6) mainly located in Zhaotong, Yunnan province(Zhenxiong,Yiliang and Daguan county, with an area of 2 872 km²), and Bijie, Guizhou province (Hezhang,Bijie,Weining county, 1 251 km²). The AUC of ROC curve was above 0.99, indicating that the predictive results with the Maxent model were highly precise. The main ecological factors determining the potential distribution were the altitude, average rainfall in November, average rainfall in October, vegetation types, average rainfall in March, average rainfall in April,soil types,isothermal characteristic and average rainfall in June. The environmental variables in the highly potential areas were determined as altitude around 1 450-2 200 m,annual average temperature around 18.0-20.4 ℃,annual average precipitation around 900 mm,yellow soil or yellow brown soil,and acid sandy loam or slightly acidic sandy loam.The results will provide valuable references for plantation regionalization and the siting for imitation wild planting of G. elata in Zhaotong.

RevDate: 2018-12-02
CmpDate: 2018-05-23

Wang HQ, Wang Q, Ma L, et al (2016)

[Production regionalization study of Lycii Fructus].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 41(17):3127-3131.

The distribution information of Lycii Fructus was collected by interview investigation and field survey, and 46 related environmental factors were collected, some kinds of functional chemical constituents the of Lycii Fructus were analyzed. Integrated climate, topography and other related ecological factors, the habitat suitability study was conducted based on Arc geographic information system(ArcGIS),and maximum entropy model. The AUC of ROC curve was both above 0.95, indicating that the predictive results with the maximum model were highly precise. The results showed that 5 major ecological factors had obvious influence on ecology suitability distributions of Lycii Fructus, including soil pH, soil subclass, vegetation type and in August the average temperature et al. It is suitable for the living habits of the Lycii Fructus, dry, cool weather, more hardy, drought-resistant, alkali soil, which is suitable for distribution in the northern temperate plains. In addition, the ecological suitability regionalization based on the chemical constituents of Lycii Fructus also provides a new suitable distribution area other than the traditional distribution area, which provides a scientific basis for the reasonable introduction of Lycii Fructus.

RevDate: 2018-11-13
CmpDate: 2017-10-10

Joshi J, Couzin ID, Levin SA, et al (2017)

Mobility can promote the evolution of cooperation via emergent self-assortment dynamics.

PLoS computational biology, 13(9):e1005732.

The evolution of costly cooperation, where cooperators pay a personal cost to benefit others, requires that cooperators interact more frequently with other cooperators. This condition, called positive assortment, is known to occur in spatially-structured viscous populations, where individuals typically have low mobility and limited dispersal. However many social organisms across taxa, from cells and bacteria, to birds, fish and ungulates, are mobile, and live in populations with considerable inter-group mixing. In the absence of information regarding others' traits or conditional strategies, such mixing may inhibit assortment and limit the potential for cooperation to evolve. Here we employ spatially-explicit individual-based evolutionary simulations to incorporate costs and benefits of two coevolving costly traits: cooperative and local cohesive tendencies. We demonstrate that, despite possessing no information about others' traits or payoffs, mobility (via self-propulsion or environmental forcing) facilitates assortment of cooperators via a dynamically evolving difference in the cohesive tendencies of cooperators and defectors. We show analytically that this assortment can also be viewed in a multilevel selection framework, where selection for cooperation among emergent groups can overcome selection against cooperators within the groups. As a result of these dynamics, we find an oscillatory pattern of cooperation and defection that maintains cooperation even in the absence of well known mechanisms such as kin interactions, reciprocity, local dispersal or conditional strategies that require information on others' strategies or payoffs. Our results offer insights into differential adhesion based mechanisms for positive assortment and reveal the possibility of cooperative aggregations in dynamic fission-fusion populations.

RevDate: 2018-11-13
CmpDate: 2017-10-16

Müller M, Seifert S, Lübbe T, et al (2017)

De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech.

PloS one, 12(9):e0184167.

Despite the ecological and economic importance of European beech (Fagus sylvatica L.) genomic resources of this species are still limited. This hampers an understanding of the molecular basis of adaptation to stress. Since beech will most likely be threatened by the consequences of climate change, an understanding of adaptive processes to climate change-related drought stress is of major importance. Here, we used RNA-seq to provide the first drought stress-related transcriptome of beech. In a drought stress trial with beech saplings, 50 samples were taken for RNA extraction at five points in time during a soil desiccation experiment. De novo transcriptome assembly and analysis of differential gene expression revealed 44,335 contigs, and 662 differentially expressed genes between the stress and normally watered control group. Gene expression was specific to the different time points, and only five genes were significantly differentially expressed between the stress and control group on all five sampling days. GO term enrichment showed that mostly genes involved in lipid- and homeostasis-related processes were upregulated, whereas genes involved in oxidative stress response were downregulated in the stressed seedlings. This study gives first insights into the genomic drought stress response of European beech, and provides new genetic resources for adaptation research in this species.

RevDate: 2018-11-13
CmpDate: 2018-03-05

Oliveira BF, São-Pedro VA, Santos-Barrera G, et al (2017)

AmphiBIO, a global database for amphibian ecological traits.

Scientific data, 4:170123.

Current ecological and evolutionary research are increasingly moving from species- to trait-based approaches because traits provide a stronger link to organism's function and fitness. Trait databases covering a large number of species are becoming available, but such data remains scarce for certain groups. Amphibians are among the most diverse vertebrate groups on Earth, and constitute an abundant component of major terrestrial and freshwater ecosystems. They are also facing rapid population declines worldwide, which is likely to affect trait composition in local communities, thereby impacting ecosystem processes and services. In this context, we introduce AmphiBIO, a comprehensive database of natural history traits for amphibians worldwide. The database releases information on 17 traits related to ecology, morphology and reproduction features of amphibians. We compiled data from more than 1,500 literature sources, and for more than 6,500 species of all orders (Anura, Caudata and Gymnophiona), 61 families and 531 genera. This database has the potential to allow unprecedented large-scale analyses in ecology, evolution, and conservation of amphibians.

RevDate: 2018-12-02
CmpDate: 2018-09-18

Tumolo BB, MB Flinn (2017)

Top-down effects of an invasive omnivore: detection in long-term monitoring of large-river reservoir chlorophyll-a.

Oecologia, 185(2):293-303.

Invasive species are capable of altering ecosystems through the consumption of basal resources. However, quantifying the effects of invasive species in large ecosystems is challenging. Measuring changes in basal resources (i.e., phytoplankton) at an ecosystem scale is an important and potentially translatable response vital to the understanding of how introduced species influence ecosystems. In this study, we analyzed patterns of early summer chlorophyll-a in a large-river reservoir in response to invasion of silver carp (Hypophthalmichthys molitrix). We used 25 years of ecological data from a 30-km reach of Kentucky Lake collected before and after silver carp establishment. We found significant decreases in chlorophyll-a within certain reservoir habitats since establishment of silver carp. Additionally, environmental and biological drivers of phytoplankton production showed no significant differences before and after invasion. These results suggest seasonal, and habitat-specific consumptive effects of invasive silver carp on an important basal food web resource. Further, our results convey the utility of long-term quantitative biological and physiochemical data in understanding ecosystem responses to elements of global change (i.e., species invasions). Importantly, the observed changes in the basal food web resource of Kentucky Lake may apply to other ecosystems facing invasion by silver carp (e.g., Laurentian Great Lakes). Our study offers insight into the mechanisms by which silver carp may influence ecosystems and furthers our understanding of invasive omnivores.

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RJR Experience and Expertise

Researcher

Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.

Educator

Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.

Administrator

Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.

Technologist

Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.

Publisher

While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.

Speaker

Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.

Facilitator

Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.

Designer

Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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This is a must read book for anyone with an interest in invasion biology. The full title of the book lays out the author's premise — The New Wild: Why Invasive Species Will Be Nature's Salvation. Not only is species movement not bad for ecosystems, it is the way that ecosystems respond to perturbation — it is the way ecosystems heal. Even if you are one of those who is absolutely convinced that invasive species are actually "a blight, pollution, an epidemic, or a cancer on nature", you should read this book to clarify your own thinking. True scientific understanding never comes from just interacting with those with whom you already agree. R. Robbins

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Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

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Curriculum Vitae for R J Robbins

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