@article {pmid40322998,
year = {2025},
author = {Borges, RM},
title = {Why does community ecology need chemistry? Because keystone molecules can govern food webs.},
journal = {Journal of biosciences},
volume = {50},
number = {},
pages = {},
pmid = {40322998},
issn = {0973-7138},
mesh = {*Food Chain ; Biodiversity ; Animals ; *Oxygen/metabolism/chemistry ; Ecosystem ; Herbivory ; Plants/chemistry ; Ecology ; Predatory Behavior ; },
abstract = {In an earlier editorial (Borges 2022), I had talked about the keystone concept formulated by Robert Paine. This important concept (Paine 1966) emphasised the idea that biodiversity is maintained by a top-down process in which the removal of a keystone predator would allow the unchecked proliferation of herbivores; during this process a dominant herbivore might outcompete another herbivore species, resulting in the removal of the lesser competitor from the community and a reduction in overall species richness (i.e., the number of species present). The keystone predator concept is well-established in community ecology. Are there keystone molecules whose presence can influence the diversity of communities? At an extreme, of course, one may say that oxygen is a most important molecule whose presence has fuelled the diversification of autotrophs such as diatoms and plants, and hence the flowering of life. A key feature of Paine's keystone concept is that the species must exert an impact that is disproportionate to its abundance (Power et al. 1996). By this definition, oxygen, although vital to all life, would fail to be recognised as a keystone chemical or molecule in species communities. Are there chemical compounds that can govern species diversity within trophic levels of an ecological community, as defined by Paine's keystone concept?},
}

*Food Chain
Biodiversity
Animals
*Oxygen/metabolism/chemistry
Ecosystem
Herbivory
Plants/chemistry
Ecology
Predatory Behavior

@article {pmid40290393,
year = {2025},
author = {Nguyen, BD and Messick, J and Rodger, AW and Jackson, V and Butler, C and Taylor, AT},
title = {Lumping and Splitting of Distribution Models Across a Biogeographic Divide Informs the Conservation of an Imperiled Fluvial Fish.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71315},
pmid = {40290393},
issn = {2045-7758},
abstract = {Freshwater fishes are among the most threatened taxa in the world. A major challenge for the conservation and management of threatened fishes is scarce information regarding life history, habitat requirements, and the drivers of declines. Species distribution models (SDMs) that leverage existing occurrence records and geospatial data have aided in addressing these challenges. We used SDMs to better understand large-scale distributional patterns of Bluntface Shiner (Cyprinella camura; BFS), a minnow facing declines across its range. We modeled the potential distribution of BFS based on natural, abiotic factors and existing occurrence records to identify landscape-scale factors underlying their distribution. We also compared environmental conditions between their disjunct ranges east and west of the Mississippi River and examined model transferability when projecting models into opposing ranges. Our analyses revealed a naturally fragmented distribution both east and west of the Mississippi River, but populations to the east of the Mississippi River occupy streams with broadscale environmental conditions that differ from those to the west. Models projected across the Mississippi River did not reflect the contemporary range of BFS, underscoring differences in occupied niches on either side of the biogeographic divide and emphasizing the need for caution when projecting SDMs to novel ranges. Our results provide a baseline to gauge range loss of BFS, highlight areas of high suitability for conservation, and identify locations where further sampling or research may be warranted.},
}

@article {pmid40283214,
year = {2025},
author = {Çolak, E and Markov, G and Selvi, E and Kankılıç, T and Şeker, PS and Kocheva, MA and Gospodinova, MK and Çolak, R and Dimitrov, H and Yiğit, N},
title = {Assessment of Intraspecific Variability in the Forest Dormouse (Dryomys nitedula) and Woolly Dormouse (Dryomys laniger) from Türkiye and Adjacent Regions Based on Mitochondrial DNA.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/life15040660},
pmid = {40283214},
issn = {2075-1729},
support = {113Z822//Scientific and Technological Research Council of Turkey/ ; },
abstract = {This study aimed to reveal intraspecific variations in two Dryomys species distributed in Türkiye, based on mitochondrial DNA cytochrome b gene sequences, and to discuss the factors driving these variations in the context of phylogeography and genetic species concepts. As a result of Maximum Likelihood, Bayesian Inference, and Network analyses, which included haplogroups or lineages from Italy, Russia, the Caucasus, and Iran identified in previous studies, along with Turkish haplotypes, three major clades (MC1, MC2, and MC3) were identified within Dryomys nitedula. These clades began to diverge evolutionarily in the middle of the Late Miocene (8.82 million years ago) and exhibit significant genetic differences from one another. The Turkish haplotypes were divided into five distinct lineages (N1-N5), each within five subclades (SC1-SC5), which were nested within these MCs. These lineages, their geographical distributions, and the subspecies defined in previous studies that correspond to these lineages are as follows: N1 from the Thrace region (Dryomys nitedula wingei), N2 from the Black Sea region (potentially a new subspecies), N3 from western and central Anatolia (Dryomys nitedula phrygius), N4 from northeastern Anatolia (Dryomys nitedula tichomirowi), and N5 from eastern Anatolia (Dryomys nitedula pictus). The N2 lineage, distributed in areas close to the coastal side of the Eastern Black Sea region and with a range close to both N3 (D. n. phrygius) and N4 (D. n. tichomirowi), exhibited high genetic differentiation from these two lineages and was a candidate to be treated as a new subspecies of Dryomys nitedula in Türkiye. The N5 lineage, which includes haplotypes from the distribution areas of the populations initially classified as Dryomys pictus and later as Dryomys nitedula pictus in previous studies, was found to be more closely related to Dryomys nitedula kurdistanicus from the Zagros Mountains than to D. n. pictus from the central regions of Iran. Combining the results of this study with previous research, it is clear that the D. nitedula lineages in Türkiye, along with haplogroups or subspecies in neighboring regions diverged between the middle Late Miocene and Middle Pleistocene. This divergence is believed to have been driven by climatic cycles and geomorphological processes that shaped the topography of their distribution range. The high genetic diversity observed in the lineages of Anatolia suggests that the region may have served as a glacial refuge for D. nitedula. Similarly to the processes and factors shaping the evolution of D. nitedula, Dryomys laniger was found to have diverged into two lineages, western (L1) and eastern (L2 or Dryomys anatolicus), within its distribution range during the Late Pliocene (2.94 Mya). To make a more accurate taxonomic assessment of D. laniger, a larger number of samples is needed, and the distribution limits should be more clearly defined.},
}

@article {pmid40278972,
year = {2025},
author = {Bolotov, IN and Eliseeva, TA and Bespyatykh, AV and Kuznetsova, EY and Kondakov, AV},
title = {Rediscovered historical lots uncover the identity of Nikolaj A. Livanow's Protoclepsis species and clarify the taxonomy of Palearctic waterfowl-associated leeches (Hirudinea: Glossiphoniidae).},
journal = {Systematic parasitology},
volume = {102},
number = {3},
pages = {32},
pmid = {40278972},
issn = {1573-5192},
support = {FUUW-2025-0022//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Animals ; *Leeches/classification/anatomy & histology ; Species Specificity ; Russia ; },
abstract = {In 1902, Nikolaj Livanow described a new genus, Protoclepsis, together with three new nominal species: P. meyeri, P. garjaewi, and P. tessellatoides. The syntypes of the first species were collected in Kazan (European Russia), while those of the two latter species were obtained from Lake Baikal (Siberia). The genus Protoclepsis Livanow, 1902 was established for a group of waterfowl-associated leeches with four pairs of eyespots and represents a synonym of Theromyzon Philippi, 1867. In contrast, the taxonomic concept of Livanow's nominal species was a matter of over a century-long discussion. Here, we revise the taxonomic position of these taxa based upon morphological examination of the original type series that were rediscovered in the Edward Eversman Zoology Museum and Herbarium, Kazan (Volga Region) Federal University, Russia. The lectotype is designated for each of the three nominal species. We found that Protoclepsis garjaewi morphologically corresponds to Hyperboreomyzon polaris Bolotov et al., 2022, although the first taxon was incorrectly described by Livanow as having four pairs of eyespots. Hence, Hyperboreomyzon garjaewi (Livanow, 1902) comb. nov. is proposed. Protoclepsis meyeri represents a synonym of Theromyzon maculosum (Rathke, 1862), as suggested by Livanow himself, while Protoclepsis tessellatoides is a synonym of Theromyzon mollissimum (Grube, 1871). Protoclepsis mollissima Livanow, 1902 incertae sedis has strongly reduced papillation and pigmentation and is tentatively considered a deep-water ecological race of Theromyzon mollissimum. A key for reliable morphological identification of the waterfowl-associated glossiphoniid leeches of Northern Eurasia is also presented. Our findings highlight the low level of endemism of glossiphoniid leeches in Lake Baikal.},
}

Animals
*Leeches/classification/anatomy & histology
Species Specificity
Russia

@article {pmid40268598,
year = {2025},
author = {Tai, HH and Shannon, LM and Strömvik, MV},
title = {Polyploidy in potatoes: challenges and possibilities for climate resilience.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2025.03.006},
pmid = {40268598},
issn = {0168-9525},
abstract = {Solanum section Petota Dumort. consists of tuber-bearing species (i.e., the cultivated potatoes and their wild relatives) that have both asexual and sexual propagation, variation in ploidy, and reproductive isolation. These species have undergone adaptation to a diversity of climates, altitudes, photoperiods, and geographical range. The section defies characterization with the biological species concept due to interspecies hybridization, allo- and auto-polyploidy, and phenotypic plasticity. Genetic studies, and more recently genome sequencing and pangenome analyses, are fostering a greater understanding of genetic processes that shape genome evolution and speciation in the section, shedding light on the phylogeny and providing insights on utilization of potato crop wild relatives in breeding for climate-resilient potato varieties.},
}

@article {pmid40265160,
year = {2025},
author = {Fässler, D and Heinken, A and Hertel, J},
title = {Characterising functional redundancy in microbiome communities via relative entropy.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {1482-1497},
pmid = {40265160},
issn = {2001-0370},
abstract = {Functional redundancy has been hypothesised to be at the core of the well-evidenced relation between high ecological microbiome diversity and human health. Here, we conceptualise and operationalise functional redundancy on a single-trait level for functionally annotated microbial communities, utilising an information-theoretic approach based on relative entropy that also allows for the quantification of functional interdependency across species. Via constraint-based microbiome community modelling of a public faecal metagenomic dataset, we demonstrate that the strength of the relation between species diversity and functional redundancy is dependent on specific attributes of the function under consideration such as the rarity and the occurring functional interdependencies. Moreover, by integrating faecal metabolome data, we highlight that measures of functional redundancy have correlates in the host's metabolome. We further demonstrate that microbiomes sampled from colorectal cancer patients display higher levels of species-species functional interdependencies than those of healthy controls. By analysing microbiome community models from an inflammatory bowel disease (IBD) study, we show that although species diversity decreased in IBD subjects, functional redundancy increased for certain metabolites, notably hydrogen sulphide. This finding highlights their potential to provide valuable insights beyond species diversity. Here, we formalise the concept of functional redundancy in microbial communities and demonstrate its usefulness in real microbiome data, providing a foundation for a deeper understanding of how microbiome diversity shapes the functional capacities of a microbiome.},
}

@article {pmid40260497,
year = {2025},
author = {Cribb, TH and Barton, DP and Blair, D and Bott, NJ and Bray, RA and Corner, RD and Cutmore, SC and De Silva, MLI and Duong, B and Faltýnková, A and Gonchar, A and Hechinger, RF and Herrmann, KK and Huston, DC and Johnson, PTJ and Kremnev, G and Kuchta, R and Louvard, C and Luus-Powell, WJ and Martin, SB and Miller, TL and Pérez-Ponce de León, G and Smit, NJ and Tkach, VV and Truter, M and Waki, T and Vermaak, A and Wee, NQ and Yong, RQ and Achatz, TJ},
title = {Challenges in the recognition of trematode species: Consideration of hypotheses in an inexact science.},
journal = {Journal of helminthology},
volume = {99},
number = {},
pages = {e54},
doi = {10.1017/S0022149X25000367},
pmid = {40260497},
issn = {1475-2697},
support = {APSF21048//Australia and Pacific Science Foundation/ ; 101054/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Trematoda/classification/genetics/anatomy & histology ; Animals ; Trematode Infections/parasitology ; Phylogeny ; *Classification/methods ; },
abstract = {The description and delineation of trematode species is a major ongoing task. Across the field there has been, and currently still is, great variation in the standard of this work and in the sophistication of the proposal of taxonomic hypotheses. Although most species are relatively unambiguously distinct from their congeners, many are either morphologically very similar, including the major and rapidly growing component of cryptic species, or are highly variable morphologically despite little to no molecular variation for standard DNA markers. Here we review challenges in species delineation in the context provided to us by the historical literature, and the use of morphological, geographical, host, and molecular data. We observe that there are potential challenges associated with all these information sources. As a result, we encourage careful proposal of taxonomic hypotheses with consideration for underlying species concepts and frank acknowledgement of weaknesses or conflict in the data. It seems clear that there is no single source of data that provides a wholly reliable answer to our taxonomic challenges but that nuanced consideration of information from multiple sources (the 'integrated approach') provides the best possibility of developing hypotheses that will stand the test of time.},
}

*Trematoda/classification/genetics/anatomy & histology
Animals
Trematode Infections/parasitology
Phylogeny
*Classification/methods

@article {pmid40249926,
year = {2025},
author = {Galkin, F and Ren, F and Zhavoronkov, A},
title = {LLMs and AI Life Models for Traditional Chinese Medicine-derived Geroprotector Formulation.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2024.1697},
pmid = {40249926},
issn = {2152-5250},
abstract = {Traditional Chinese Medicine (TCM) represents a vast repository of therapeutic knowledge, but its integration with modern drug discovery remains challenging due to fundamental differences in theoretical frameworks. We developed an AI agent-driven framework combining Precious3GPT (P3GPT), a multi-omics transformer model, with the BATMAN-TCM2 database of TCM compound-target interactions to bridge this gap. As a proof-of-concept, we used P3GPT-generated cross-species and cross-tissue signatures to screen TCM compounds, herbs, and formulas to identify novel natural geroprotectors. The cross-species analysis identified 13 conserved aging-associated genes, leading to the identification of 34 TCM compounds with significant target overlap and enabling identification of HUA SHAN WU ZI DAN and other TCM formulations as a promising historical formula. Our work demonstrates the feasibility of using AI to systematically bridge TCM and modern pharmacology, enabling rational design of multi-component formulations targeting age-related processes across multiple tissues and species. This approach provides a framework for modernizing traditional medicine while maintaining its holistic therapeutic principles. To help other teams integrate AI experimentation in their research process, we publicly release all materials and codebase used in this work, including the multi-agent system, cross-species and cross-tissue signatures of aging, as well as TCM databases formatted for AI interactions.},
}

@article {pmid40246462,
year = {2025},
author = {Qi, R and Zhong, Z and Huang, F and Chen, F and Jia, Y and Yang, Y and Yun, Z and Ye, Q},
title = {Construction of an SnS-based heterostructure catalyst for electrochemical CO2 reduction to formate over a wide potential window.},
journal = {Journal of environmental sciences (China)},
volume = {155},
number = {},
pages = {25-36},
doi = {10.1016/j.jes.2024.12.015},
pmid = {40246462},
issn = {1001-0742},
mesh = {*Carbon Dioxide/chemistry ; Catalysis ; *Formates/chemistry ; *Electrochemical Techniques ; Oxidation-Reduction ; *Models, Chemical ; *Tin Compounds/chemistry ; },
abstract = {SnS has emerged as an attractive catalyst for the electrochemical CO2 reduction reaction (CO2RR) to formate, while its long-term operational stability is hindered by the self-reduction of Sn[2+] and sulfur dissolution. Thus, maintaining high current efficiency across a wide negative potential range to achieve high production rates of formate remains a significant challenge. In this study, we present a heterostructure constructed with SnS and CuS for efficient CO2RR to formate. The SnS-CuS (30) exhibits a remarkable formate Faradaic efficiency (FEf) of 93.94 % at -1 V vs. reversible hydrogen electrode (RHE) and demonstrates long-term stability for 7.5 h, maintaining high activity (with an average FEf of 85.6 %) across a wide negative potential range (from -0.8 to -1.2 V (vs. RHE)). The results reveal that the heterogeneous interface between SnS and CuS mitigates the self-reduction issue of SnS by sacrificing Cu[2+], highlighting that the true active species is SnS, which effectively resists structural changes during the electrolysis process under the protection of CuS. The synergistic interaction within the CuS and SnS heterostructure, combined with the tendency for electron self-conduction, enables the catalyst to maintain high formate activity and selectivity across a wide potential range. Furthermore, theoretical results further indicate that the incorporation of CuS enhances CO2 adsorption and lowers the energy barrier for the formation of formate intermediates. This study inspires the concept of applying protective layers to active species, promoting high selectivity in Sn-based electrocatalysts.},
}

*Carbon Dioxide/chemistry
Catalysis
*Formates/chemistry
*Electrochemical Techniques
Oxidation-Reduction
*Models, Chemical
*Tin Compounds/chemistry

@article {pmid40242291,
year = {2025},
author = {Monfort-Lanzas, P and Gostner, JM and Hackl, H},
title = {Modeling omics dose-response at the pathway level with DoseRider.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {1440-1448},
pmid = {40242291},
issn = {2001-0370},
abstract = {The generation of omics data sets has become an important approach in modern pharmacological and toxicological research as it can provide mechanistic and quantitative information on a large scale. Analyses of these data frequently revealed a non-linear dose-response relationship underscoring the importance of the modeling process to infer biological exposure limits. A number of tools have been developed for dose-response modeling and various thresholds have been defined as a quantitative representation of the effect of a substance, such as effective concentrations or benchmark doses (BMD). Here we present DoseRider an easy-to-use web application and a companion R package for linear and non-linear dose-response modeling and assessment of BMD at the level of biological pathways or signatures using generalized mixed effect models. This approach allows to analyze custom or provided multi-omics data such as RNA sequencing or metabolomics data and its annotation of a collection of pathways and gene sets from various species. Moreover, we introduce the concept of the trend change doses (TCDs) as a numerical descriptor of effects derived from complex dose-response curves. The usability of DoseRider was demonstrated by analyses of RNA sequencing data of bisphenol AF (BPAF) treatment of a human breast cancer cell line (MCF-7) at 8 different concentrations using gene sets for chemical and genetic perturbations (MSigDB). The BMD for BPAF and a set of genes upregulated by estrogen in breast cancer was 0.2 µM (95 %-CI 0.1-0.5 µM) and the lowest TCD (TCD1) was 0.003 µM (95 %-CI 0.0006-0.01 µM). The comprehensive presentation of the results underlines the suitability of the system for pharmacogenomics, toxicogenomics, and applications beyond.},
}

@article {pmid40223652,
year = {2025},
author = {Menon, JC and Sreekrishnan, TP and Nair, SB and Pillay, VV and Kanungo, S and Aravind, MS and Bharti, OK and Joseph, JK and Pati, S},
title = {Snakebite envenoming in India: it is time we look beyond the concept of the Big Four species.},
journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene},
volume = {},
number = {},
pages = {},
doi = {10.1093/trstmh/traf042},
pmid = {40223652},
issn = {1878-3503},
abstract = {India faces substantial challenges from snakebite envenoming secondary to the high morbidity, mortality and financial burden, particularly in rural communities. While concentrated on the 'Big Four' venomous species, recent research indicates a necessity to expand the focus to encompass additional medically relevant species. This review emphasizes the geographic heterogeneity in venom among these snakes, which impacts antivenom effectiveness and necessitating region-specific formulations. This analysis highlights the shortcomings of current antivenoms and identifies non-Big Four species involved in snakebite envenoming, advocating for an urgent shift to inclusive antivenom strategies that integrate local venom profiles to enhance treatment effectiveness and thereby reduce snakebite-related morbidity and mortality. Improved training for healthcare providers and enhancements in anti-snake venom quality are essential for meeting the World Health Organization's 2030 Sustainable Development Goal objective of halving snakebite-related fatalities and disabilities. Incorporating snakebite management into national health programs and conducting epidemiological research systematically are crucial to mitigating this preventable health concern.},
}

@article {pmid40220078,
year = {2025},
author = {Lehmbeck, J and Andersen, B and Sáez-Sáez, J and Frisvad, JC and Arnau, J},
title = {Mycotoxin-free Aspergillus oryzae strain lineage for alternative and novel protein production at industrial scale.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {94},
pmid = {40220078},
issn = {1432-0614},
mesh = {*Aspergillus oryzae/metabolism/genetics ; *Mycotoxins/genetics/biosynthesis ; Propionates/metabolism ; *Recombinant Proteins/biosynthesis/genetics ; Nitro Compounds/metabolism ; *Industrial Microbiology/methods ; Aflatoxins/biosynthesis ; Multigene Family ; Gene Deletion ; Animals ; Indoles ; },
abstract = {Advanced industrial strains of Aspergillus oryzae have been used for decades for the production of recombinant proteins including food and feed enzymes at large scale. The A. oryzae strain lineage evaluated in this review derives from the proprietary Novozymes (now Novonesis) strain collection. A. oryzae wild-type strains have the potential to produce three different mycotoxins (aflatoxins (AFL), cyclopiazonic acid (CPA), and 3-nitropropionic acid (3-NPA)). Here, we review the work originally performed at Novozymes to identify a strain (BECh1) that contained a large chromosomal deletion comprising both AFL and CPA gene clusters, significantly improving the safety of the lineage. The description of the deleted region is presented here. As the genetic basis for 3-NPA biosynthesis was recently revealed, we describe here that this A. oryzae lineage contains an additional large deletion that encompasses the 3-NPA biosynthetic genes npaA and npaB, thereby rendering the strains unable to produce any mycotoxin. Further strain development has resulted in strains devoid of penicillin production by inactivation of the penicillin G gene cluster (penG). This strain lineage represents the first example of mycotoxin-free A. oryzae for production of recombinant (alternative) novel food proteins. Recently, bovine beta-lactoglobulin made using a strain of this lineage has received GRAS status and can be commercialized for use in food in the USA. With its history of safe use in food and feed, the lack of toxigenic potential and the ability to differentiate strains with modern technologies, this A. oryzae strain can be considered safe as other organisms with a Quality Presumption of Safety (QPS) status in Europe. QPS is not applicable to filamentous fungi and only granted at the species level to bacteria and a few yeast species. We suggest modernizing the QPS concept to become strain rather than species specific and present arguments to qualify this strain lineage as QPS or QPS-like. KEY POINTS: • The biosynthetic genes for 3-nitropropionic acid have been recently characterized. • An industrial strain lineage for food protein production lacks all known mycotoxin genes. • Proteins produced in this mycotoxin-free lineage should entail lower regulatory requirements.},
}

*Aspergillus oryzae/metabolism/genetics
*Mycotoxins/genetics/biosynthesis
Propionates/metabolism
*Recombinant Proteins/biosynthesis/genetics
Nitro Compounds/metabolism
*Industrial Microbiology/methods
Aflatoxins/biosynthesis
Multigene Family
Gene Deletion
Animals
Indoles

@article {pmid40214099,
year = {2025},
author = {Owen-Smith, N},
title = {Reconciling Species Concepts: An Ecological Perspective.},
journal = {American journal of biological anthropology},
volume = {186},
number = {4},
pages = {e70047},
doi = {10.1002/ajpa.70047},
pmid = {40214099},
issn = {2692-7691},
mesh = {Animals ; *Biological Evolution ; Humans ; Fossils ; *Hominidae/classification ; Ecosystem ; Phylogeny ; },
abstract = {Species concepts remain contentious, both in paleoanthropology and in modern taxonomy. The lineage-based concept emphasizing evolutionary independence is most fundamental, but in practice is generally represented by proxy evidence of morphological or genetic divergence. This has resulted in a troubling proliferation of species names in the hominin fossil record. Pseudo-extinctions where lineages persisted under a new species name need to be distinguished from cases where lineages ended terminally-the implications for ecological adaptability are diametrically opposed. Furthermore, the ecological criterion for species coexistence is widely overlooked. The competitive exclusion principle holds that species sharing closely similar niches cannot continue to coexist in the same place at the same time. Notably, the largely vegetarian Paranthropus lineage remained distinct from the diverging, more versatile Homo lineage until fading from the fossil record during the later Pleistocene. Claims that additional hominin species existed are ecologically suspect unless supported by evidence of adequate niche separation. Modern examples where there has been equivocation in lineage recognition are illustrated for bovids, giraffids, baboons, and elephants. Furthermore, the mechanisms that resulted in the displacement of Neanderthals by modern humans are reappraised from an ecological perspective. Representations of evolutionary divergence as a bushy tree need to be superseded by the emerging paradigm of reticulate lineages diverging and coalescing through time and space.},
}

Animals
*Biological Evolution
Humans
Fossils
*Hominidae/classification
Ecosystem
Phylogeny

@article {pmid40211980,
year = {2025},
author = {Elena Schmitz, J and Rahmann, S},
title = {A comprehensive review and evaluation of species richness estimation.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf158},
pmid = {40211980},
issn = {1477-4054},
mesh = {*Biodiversity ; Computer Simulation ; Animals ; Computational Biology/methods ; Algorithms ; },
abstract = {MOTIVATION: The statistical problem of estimating the total number of distinct species in a population (or distinct elements in a multiset), given only a small sample, occurs in various areas, ranging from the unseen species problem in ecology to estimating the diversity of immune repertoires. Accurately estimating the true richness from very small samples is challenging, in particular for highly diverse populations with many rare species. Depending on the application, different estimation strategies have been proposed that incorporate explicit or implicit assumptions about either the species distribution or about the sampling process. These methods are scattered across the literature, and an extensive overview of their assumptions, methodology, and performance is currently lacking.

RESULTS: We comprehensively review and evaluate a variety of existing methods on real and simulated data with different compositions of rare and abundant species. Our evaluation shows that, depending on species composition, different methods provide the most accurate richness estimates. Simple methods based on the observed number of singletons yield accurate asymptotic lower bounds for several of the tested simulated species compositions, but tend to underestimate the true richness for heterogeneous populations and small samples containing 1% to 5% of the population. When the population size is known, upsampling (extrapolating) estimators such as PreSeq and RichnEst yield accurate estimates of the total species richness in a sample that is up to 10 times larger than the observed sample.

AVAILABILITY: Source code for data simulation and richness estimation is available at https://gitlab.com/rahmannlab/speciesrichness.},
}

*Biodiversity
Computer Simulation
Animals
Computational Biology/methods
Algorithms

@article {pmid40204735,
year = {2025},
author = {D'Alessio, A and Davoli, M and Rondinini, C and Pacifici, M},
title = {2030 conservation targets for European terrestrial mammals using the favourable conservation status concept.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {591},
pmid = {40204735},
issn = {2052-4463},
mesh = {Animals ; *Conservation of Natural Resources ; *Mammals ; Europe ; Biodiversity ; Endangered Species ; Ecosystem ; European Union ; },
abstract = {The European Habitats Directive lists species and habitats of conservation priority for member states of the European Union, and prescribes that they achieve a favourable conservation status. The benchmark for assessing whether species achieve this status is provided by favourable reference values of distribution and population size. These values cannot be used directly as conservation targets, because they are incomplete, incomparable as they are identified through different methods, and not necessarily achievable in a specified time frame. We set conservation targets for the year 2030 for 81 European terrestrial mammals listed in Annexes II and IV of the Habitats Directive, and/or threatened at European level according to the IUCN Red List of Threatened Species, based on the concept of favourable onservation statuts. We used several methods, including models of population growth and range expansion to 2030, and a reference-based approach. These targets can be used to plan conservation actions for priority mammals, such as increasing protected area coverage to 30% of Europe as envisaged in the European Biodiversity Strategy 2030.},
}

Animals
*Conservation of Natural Resources
*Mammals
Europe
Biodiversity
Endangered Species
Ecosystem
European Union

@article {pmid40199741,
year = {2025},
author = {Taff, CC and Wingfield, JC and Vitousek, MN},
title = {Corticosterone reaction norms to temperature in wild birds: implications for understanding endocrine flexibility and climate vulnerability.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf011},
pmid = {40199741},
issn = {1557-7023},
abstract = {The glucocorticoid mediated stress response plays a major role in coping with both gradual and rapid changes in environmental conditions and may be especially important when conditions depart from expectations. Conceptual models of endocrine flexibility suggest that individual flexibility, measured using reaction norms along an environmental gradient, might predict differences in the ability to cope with challenges. For example, differences in the speed or scope of acute endocrine responses might underpin coping ability. However, empirical results have been limited by the inability to accurately measure individual level endocrine reaction norms. Here, we took advantage of a database of corticosterone measures in 1,727 individuals of 99 bird species sampled around the world to extend the concept of endocrine reaction norms to species differences. We first describe a global reaction norm for birds and then demonstrate species-specific differences in reaction norms for baseline corticosterone, maximum corticosterone, and the speed of corticosterone increase to both absolute temperature and to the difference between current and expected temperature. Overall, we found that in addition to changes in absolute corticosterone, the speed of the acute response increased when minimum daily temperature dropped below 0-2°C. In contrast, we found little evidence for increases at higher temperatures. We found a similar pattern when temperature was colder than expected given the location and date regardless of absolute temperature, but this effect was only seen for baseline corticosterone. Our models also consistently indicated that species differed in the shape of their corticosterone reaction norm to absolute temperature and temperature deviations. However, we did not have adequate data to fully characterize species-specific reaction norms. We suggest that the endocrine flexibility and reaction norm framework applied in a comparative context could help predict species sensitivity to changing climate, but that additional field data will be needed to fully test this idea.},
}

@article {pmid40182484,
year = {2025},
author = {Feng, Y and Yan, C and Tu, WQ and Yuan, YM and Wang, JB and Chen, XJ and Liu, CQ and Gao, Y},
title = {Multi-disciplinary evidence illuminates the speciation history of a monophyletic yet dimorphic lily group.},
journal = {Plant diversity},
volume = {47},
number = {2},
pages = {189-200},
doi = {10.1016/j.pld.2024.12.005},
pmid = {40182484},
issn = {2468-2659},
abstract = {Species boundaries are dynamic and constantly challenged by gene flow. Understanding the strategies different lineages adopt to maintain ecological and genetic distinctiveness requires employing an integrative species concept that incorporates data from a variety of sources. In this study, we incorporated genetic, ecological, and environmental evidence to assess the extent of speciation or evolutionary divergence within a monophyletic yet dimorphic group (i.e., clade Leucolirion consisting of six species) within the genus Lilium. This clade consists of two lineages that exhibit unexpectedly distinct perianth appearances: whitish trumpet (funnel form, encompassing four species) and orange recurved (reflex form, including two species), respectively, which are separated by completely different pollination syndromes. Transcriptome-based nuclear and plastome datasets indicate that these two lineages are isolated, with only weak ancient gene flow between them. Within each lineage, several taxa with incomplete isolation have diverged, as indicated by weak genetic structure, strong gene flow, and conflicts between nuclear and chloroplast phylogenies, especially in the trumpet lineage. Although these taxa are not entirely independent, our evidence indicates that they are diverging, with recent gene flow disappearing and multiple isolation strategies emerging, such as differences in flowering time and niche specialization. Taken together, our findings suggest that species divergence and maintenance in Lilium are driven by a combination of adaptive and non-adaptive processes, highlighting the complex interplay of historical climate changes, ecological adaptation, and gene flow in shaping biodiversity within this genus.},
}

@article {pmid40173689,
year = {2025},
author = {Freyhof, J},
title = {Garra cavernicola, a new species from the Hajar Mountains in Oman (Teleostei: Cyprinidae), with a short discussion on monophyly and the description of evolutionarily young species.},
journal = {Zootaxa},
volume = {5601},
number = {2},
pages = {335-345},
doi = {10.11646/zootaxa.5601.2.7},
pmid = {40173689},
issn = {1175-5334},
abstract = {Garra cavernicola, new species, is described from the Hajar Mountains in Oman. It is very closely related to the sympatric, but not syntopic, G. longipinnis, from which it is distinguished by the absence of an external eye, reduced squamation, and a whitish, or pink-coloured body. Garra cavernicola was identified as a "cave form" of G. longipinnis, but is now recognised as a separate species following the 'Evolutionary Species Concept', with an evolutionary trajectory distinct from those of G. longipinnis. As G. cavernicola is nested within the G. longipinnis clade, this species is now considered a paraphyletic ancestral species.},
}

@article {pmid40173543,
year = {2025},
author = {Mansour, A and Karar, YFM and Hassan, HA and Mohamadain, HS and Abdel-Hakeem, SS},
title = {Integrative supporting techniques for the taxonomy of Schistorchis carneus Lühe, 1906 (Digenea: Megaperidae) with perspective for the existence of species complexes.},
journal = {Zootaxa},
volume = {5569},
number = {2},
pages = {299-327},
doi = {10.11646/zootaxa.5569.2.5},
pmid = {40173543},
issn = {1175-5334},
abstract = {The morphology and host-parasite data of Schistorchis carneus Lühe, 1906 indicate low host specificity and geographical range variation, accompanied by a large scale of intraspecific variability and ambiguous molecular phylogeny, confusing in determining biodiversity extent and specificity to a particular host and/or locality. To address the challenging circumstances of records of S. carneus, a detailed morphological description, molecular characterization and species delimitation analyses were conducted using a combination of comparative morphology, molecular phylogeny, multivariate analyses, and host-parasite data. Several morphological features exhibited an extensive intra-variation, as well as a wide morphometric range in many measurements within and across records. Phylogenetic analyses showed that the classification of schistorchiines is highly correlated with the morphology/nature of the oral sucker and highlighted the limitations of ribosomal 28S rDNA and ITS2 rDNA in distinguishing morphologically close/related taxa. Species delimitation analyses reflected the critical importance of host distinction in schistorchiines recognition/differentiation, even those that are indistinct morphologically. The clustering of schistorchiines into certain groups was driven by host differences. Additionally, host variation typically corresponds to a distinct schistorchiine species, even if it is morphologically identical to another. Cluster analysis associated with host-parasite data revealed high morphometric convergence and significant diversity among Egyptian and Sri-Lankan records of S. carneus. It also confirmed the distinction between Indian records from the Bay of Bengal and those from the Gulf of Mannar (previously mentioned as Manaar), each in their own distant group. In conclusion, the records of S. carneus represent a repository for a group of closely related cryptic species. The restricted concept of S. carneus should include only records from the white-spotted puffer, Arothron hispidus (Linnaeus) and the stellate puffer, Arothron stellatus (Anonymous). The Australian specimens from the narrow-lined puffer, Arothron manilensis (Marion de Procé) and the Indian record from the lunartail puffer, Lagocephalus lunaris (Bloch & Schneider) likely represent a free-standing cryptic species with limited distribution, requiring further characterization.},
}

@article {pmid40161328,
year = {2025},
author = {Friebes, G and Fuljer, F and Boertmann, D and Voglmayr, H and Kautmanová, I},
title = {Hygrophorus citrinofuscus: epitypification of a rare waxcap species from Central Europe and its transfer to the genus Neohygrocybe.},
journal = {Fungal systematics and evolution},
volume = {15},
number = {},
pages = {121-132},
doi = {10.3114/fuse.2025.15.05},
pmid = {40161328},
issn = {2589-3831},
abstract = {Hygrophorus citrinofuscus is a striking and rarely reported grassland species originally described by J. Favre from the Swiss Alps. In absence of sequence data for the type specimen, a recent collection from Austria, which is well documented based on morphology and sequence data, is designated as the epitype of H. citrinofuscus to stabilise the species concept. Further collections from Austria and the Czech Republic are given. Morphologically similar species are discussed. Hygrophorus citrinofuscus is morphologically and phylogenetically well delimited and macroscopically characterised by yellow-brown pileus colours, a fibrillose pileus surface, pale lamellae and a yellow stipe, making it readily recognisable in the field. Morphology of the lamellar trama as well as phylogenetic analyses of a combined matrix of ITS, LSU, SSU and RPB2 sequence data clearly place this species in the genus Neohygrocybe, and a transfer is proposed. Citation: Friebes G, Fuljer F, Boertmann D, Voglmayr H, Kautmanová I (2025). Hygrophorus citrinofuscus: epitypification of a rare waxcap species from Central Europe and its transfer to the genus Neohygrocybe. Fungal Systematics and Evolution 15: 121-132. doi: 10.3114/fuse.2025.15.05.},
}

@article {pmid40137218,
year = {2025},
author = {Peng, LY and Wang, YF and Song, H and Urinboev, I and Zhuang, WY and Gafforov, Y and Wang, XC},
title = {Five New Species of Marquandomyces (Clavicipitaceae, Ascomycota) from Asia.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/jof11030180},
pmid = {40137218},
issn = {2309-608X},
support = {2022YFC2303000//National Key Research and Development Program of China/ ; 32270008//National Natural Science Foundation of China/ ; },
abstract = {Marquandomyces is a recently established genus in the Clavicipitaceae and previously comprised only two known species. This study expands the understanding of its generic concept and species diversity through comprehensive fungal diversity surveys conducted from soil samples in China and Uzbekistan. As a result, five new species were identified based on morphological characterization and molecular phylogenetic analyses, and their detailed descriptions and illustrations are provided. This study emphasizes the unique ecological roles and specific habitats of these fungi and contributes to a relatively deep understanding of the genus Marquandomyces as well as its ecological significance.},
}

@article {pmid40083176,
year = {2025},
author = {Gao, H and Chen, M and Jin, N and Ye, L and Zhang, G and Shen, Q and Xu, Z},
title = {A comprehensive analytical method 'Regulatome' revealed a novel pathway for aerenchyma formation under waterlogging in wheat.},
journal = {Physiologia plantarum},
volume = {177},
number = {2},
pages = {e70157},
doi = {10.1111/ppl.70157},
pmid = {40083176},
issn = {1399-3054},
support = {32171929//National Natural Science Foundation of China/ ; 2021C02064-3//Key Research Projects of Zhejiang Province, China/ ; },
mesh = {*Triticum/genetics/physiology/metabolism/growth & development ; *Gene Expression Regulation, Plant ; *Plant Roots/metabolism/genetics/growth & development/physiology ; Water/metabolism ; Stress, Physiological ; Transcriptome/genetics ; Plant Proteins/metabolism/genetics ; Oxylipins/metabolism ; Ethylenes/metabolism ; Cyclopentanes/metabolism ; Signal Transduction ; Seedlings/genetics/physiology/growth & development/metabolism ; },
abstract = {Waterlogging is a major abiotic stress restricting crop yield globally, and aerenchyma formation is one of the most important adaptive strategies in waterlogging-tolerant plants. However, the conservation of this process remains poorly understood, and additional pathways are yet to be identified. Here, physiological, anatomical, transcriptomic, and metabolomic analyses were conducted on wheat seedlings under normal and waterlogging conditions. Waterlogging caused growth inhibition and physiological damage, as well as induced aerenchyma formation in roots. A total of 10,346 differentially expressed genes and 3,419 differential metabolites were identified in roots. In addition to the AP2/ERF (APETALA2/ETHYLENE RESPONSIVE FACTOR) gene family, integrating analyses also revealed the role of LOB/AS2 (LATERAL ORGAN BOUNDARIES/ASYMMETRIC LEAVES2) in aerenchyma formation under waterlogging. It was revealed that the classical pathway of aerenchyma formation mediated by ethylene response, as well as synergy of calcium ion and reactive oxygen species, was deeply conserved in both monocots and eudicots during 160 million years of evolution through gene co-expression networks of cross-species. The newly introduced concept 'Regulatome' supported the classical pathway of aerenchyma formation, with a proposed model of the jasmonic acid signalling pathway involved in waterlogging, suggesting its usefulness in gene identification and function exploration. These findings provide a novel insight into the regulatory mechanisms of aerenchyma formation and breeding approaches for developing wheat cultivars with high waterlogging tolerance.},
}

*Triticum/genetics/physiology/metabolism/growth & development
*Gene Expression Regulation, Plant
*Plant Roots/metabolism/genetics/growth & development/physiology
Water/metabolism
Stress, Physiological
Transcriptome/genetics
Plant Proteins/metabolism/genetics
Oxylipins/metabolism
Ethylenes/metabolism
Cyclopentanes/metabolism
Signal Transduction
Seedlings/genetics/physiology/growth & development/metabolism

@article {pmid40052070,
year = {2025},
author = {Lebreton, E and Ertz, D and Lücking, R and Aptroot, A and Carriconde, F and Ah-Peng, C and Huang, JP and Chen, KH and Stenger, PL and Cáceres, MEDS and van den Boom, P and Sérusiaux, E and Magain, N},
title = {Global phylogeny of the family Gomphillaceae (Ascomycota, Graphidales) sheds light on the origin, diversification and endemism in foliicolous lineages.},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e144194},
pmid = {40052070},
issn = {2210-6340},
abstract = {Foliicolous lichens grow on living leaves of vascular plants. They are mostly found in tropical to subtropical or temperate rainforests. Many phenotype-based species are considered as pantropical or even sub-cosmopolitan, either attributed to old ages, having existed prior to continental breakups or long-distance dispersal. We built a much expanded, global phylogeny of Gomphillaceae, the most diverse group of leaf-dwelling lichenised fungi. Our sampling encompassed six major biodiversity hotspots: MIOI (Madagascar and the Indian Ocean Islands), the Caribbean, New Caledonia, the Colombian Chocó, Mesoamerica and the Atlantic coast of Brazil. It was based on multilocus sequence data (mtSSU rDNA, nuLSU rDNA and RPB1), including 2207 sequences of 1256 specimens. Species delimitation methods combined with a phenotype matrix identified 473 putative species. Amongst these, 104 are confirmed as described, 213 are classified as cryptic or near cryptic (hidden diversity), 100 represent new species to science (identified on the basis of phenotype) and 56 remain unidentified. Amongst the 104 species with a valid name, 40.5% are distributed across 2-5 continents (lichenogeographical regions) by applying the phenotype-based species concept. However, using the integrative approach to delineate species, this estimate is reduced to 9%. We estimate the global species richness of Gomphillaceae at 1,861-2,356 species. The timing of species-level divergences suggests that the current distribution of foliicolous lichens is shaped more by long-distance dispersal and rapid diversification than by vicariance. The origin of the family and major clades appears to be in the Neotropics, with subsequent numerous dispersal events. Our results support the separation of three major lineages, corresponding to the former families Asterothyriaceae, Gomphillaceae s.str. and Solorinellaceae, which should be recognised at the subfamily level.},
}

@article {pmid40044218,
year = {2025},
author = {Porat, J},
title = {Circuit logic: interdependent RNA modifications shape mRNA and noncoding RNA structure and function.},
journal = {RNA (New York, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1261/rna.080421.125},
pmid = {40044218},
issn = {1469-9001},
abstract = {Continued advances in high throughput detection of post-transcriptional RNA modifications have enabled large-scale, mechanistic studies into the importance of RNA modifications in regulating the structure, function, and stability of coding and noncoding RNAs. More recently, this has expanded beyond investigations of independent single modifications, revealing the breadth of modification complexities in single transcripts and the biogenesis pathways involved that lead to coordinately modified RNA species. This has resulted in the concept of modification circuits, where one modification can promote or inhibit the subsequent installation of other modifications, or when modifications are coordinated across different RNA species. These circuits play important roles in the biogenesis of multi-stepped post-transcriptional modifications, modulate ribonucleoprotein complex formation and conformational switches, and mediate codon-biased translation through the coordination of mRNA and tRNA modifications. Here, I review evidence of complex modification circuits in mRNA and noncoding RNA and highlight open questions concerning the molecular mechanisms giving rise to modification circuits and their importance in the context of RNA processing and maturation.},
}

@article {pmid40041962,
year = {2025},
author = {Lin, D and Zang, N and Song, W and Punt, AE and Gong, Y and Li, G and Chen, X},
title = {Dietary specialization among individual squid: using Illex argentinus as a case and meta-analysis for other squid species.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2042},
pages = {20242591},
pmid = {40041962},
issn = {1471-2954},
support = {//National Natural Science Foundation of China/ ; //Shanghai Talent Development Funding/ ; //Shanghai Science and Technology Innovation Program/ ; },
mesh = {Animals ; *Decapodiformes/physiology ; *Diet/veterinary ; Feeding Behavior ; },
abstract = {Squid, which occupy a similar role to teleost fish as open water predators, are opportunistic foragers. However, there is a lack of empirical evidence related to whether individual squid specialize their diets to optimize fitness. We investigated whether individual squid have specialized diets and what factors impact any specialization using the Argentine shortfin squid as a case study species, coupled with a meta-analysis for other squid species. Hutchinson's n-dimensional hypervolume concept was used to estimate individual dietary niches based on stable isotope and fatty acid analyses. Individual squid showed a high degree of dietary specialization, with individual specialization indices typically greater than 0.70, and pairwise niche overlap less than 0.5, with adults having greater specialization in dietary niche. For the Argentine shortfin squid, higher reproductive investment and water temperature increased individual dietary specialization. Individual dietary specialization probably reduces interindividual competition, optimizes food resource use and increases fitness and hence net energy gain for reproduction. The existence of dietary specialization at the individual level provides insight into the life history of squid.},
}

Animals
*Decapodiformes/physiology
*Diet/veterinary
Feeding Behavior

@article {pmid40041707,
year = {2025},
author = {Liu, X and Gong, X and Ma, K and Song, W and Zhou, J and Wang, M and Li, Y and Ji, M and Li, Y and Han, H and Wang, Y and Tu, Q},
title = {Resolving ecological drivers of temporal variations of β-diversity across intertidal microbiomes.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf025},
pmid = {40041707},
issn = {2730-6151},
abstract = {Resolving the ecological drivers mediating the diversity patterns of microbial communities across space and through time is a central issue in microbial ecology. Both regional species pools and local community assembly contribute to the spatial turnover of biodiversity. In this study, we extended the concept of regional species pool to temporal, and investigated the seasonal dynamics of intertidal microbiomes across four microbial domains/kingdoms (bacteria, archaea, fungi, and protists). The results showed that the seasonal variations of microbial β-diversity were primarily governed by community assembly processes rather than temporal species pools. Different microbial domains/kingdoms were structured by different ecological processes, with homogeneous selection as the major process for all of them. Additionally, bacteria and fungi were critically shaped by drift, and protists by drift and homogeneous dispersal. Among various factors, temperature was important in shaping the temporal patterns of microbial β-diversity. The fluctuation in temperature was strongly associated with fungi and protists, resulting in high drift of community composition. This study demonstrated that community assembly processes governed the dynamic seasonal β-variations of intertidal microbiomes, expanding our understanding from spatial ecology.},
}

@article {pmid39993490,
year = {2025},
author = {Coca, LF and Lumbsch, HT and Mercado-Díaz, JA and Widhelm, TJ and Goffinet, B and Kirika, P and Lücking, R},
title = {Diversity, Phylogeny, and historical biogeography of the genus Coccocarpia (lichenized Ascomycota: Peltigerales) in the tropics.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108312},
doi = {10.1016/j.ympev.2025.108312},
pmid = {39993490},
issn = {1095-9513},
abstract = {Coccocarpia Pers. currently comprises 28 mostly broadly distributed tropical species of fungi associated with cyanobacteria. Three of these taxa, C. erythroxyli, C. palmicola, and C. pellita, are presumably pantropical to subcosmopolitan, with broad morphological variation across their range. This study provides the first global phylogeny of the genus, to test current species concepts and infer distribution patterns, based on samples from Colombia, Puerto Rico, Gabon, Kenya, Thailand, Fiji, and Hawaii. We also estimate divergence times within the clade and provide a first reconstruction of its biogeographic history. Based on phylogenetic reconstructions inferred from maximum likelihood and Bayesian approaches of four molecular markers (mtSSU, nuLSU, ITS, RPB2), Coccocarpia was recovered as monophyletic. However, the currently accepted taxa are largely polyphyletic entities and the underlying diversity in this genus is much higher than currently understood. Different methods for species delimitation boundaries came to agree on a scenario involving more than 150 species in the available, albeit still small, dataset. This suggests that with broader sampling, Coccocarpia may indeed represent a hyper-diverse genus, potentially containing over 200 species. The phylogeny is geographically structured: one clade is exclusive to the Paleotropics, one to the Neotropics, and one is pantropical. Coccocarpia likely emerged during the Late Cretaceous (90 ± 10 Mya) in the tropical regions of Australasia-Oceania, initially colonizing Oceania, and Asia and subsequently the Neotropics. The three main clades diverged between the Late Cretaceous and the Paleocene, with significant diversification in the Oligocene, during which the neotropical clade gave rise to morphological novelties, including the epiphylla and stellata clades.},
}

@article {pmid39980408,
year = {2025},
author = {Sen, A and Sharma, S and Rajaraman, G},
title = {Bridging the Oxo Wall: A New Perspective on High-valent Metal-Oxo Species and Their Reactivity in Mn, Fe, and Co Complexes.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e202419953},
doi = {10.1002/anie.202419953},
pmid = {39980408},
issn = {1521-3773},
abstract = {The theory of "oxo-wall" is a well-established concept in the area of bioinorganic chemistry which refers to the instability of the terminal metal-oxo complexes in +4 oxidation state with tetragonal C4v symmetry beyond group 8 elements. Despite extensive research on first-row terminal metal-oxo complexes and the "oxo wall" concept, studies correlating the reactivity of these species across the periodic table remain scarce. In this work, using a combination of DFT and ab initio CASSCF calculations, we have explored the structure, bonding and reactivity of [MIV/V(15-TMC)(O)(CH3CN)]m+ (M= Mn, Fe and Co) species. Our study reveals several surprising outcomes: (i) while existing literature typically indicates the presence of either CoIV=O or CoIII-O• species beyond the wall, we propose a quantum mechanical mixture of these two species, with the dominance of one dictated by ligand design and symmetry considerations; (ii) we observe that the oxyl radical character increases beyond the wall, correlating with larger Ntrans-M-O tilt angles; and (iii) we identify an inverse relationship between the percentage of M-O• radical character and the kinetic barriers for C-H bond activation. These findings challenge traditional perspectives on the roles of oxidation states, spin states and the nature of the metal ion in reactivity.},
}

@article {pmid39967791,
year = {2025},
author = {Ekanayaka, AH and Karunarathna, SC and Tibpromma, S and Dutta, AK and Tennakoon, DS and Karunarathna, A and Chukeatirote, E and Dai, DQ and Stephenson, SL and Maharachchikumbura, SSN and Liu, C and Phillips, AJL},
title = {Species evolution: cryptic species and phenotypic noise with a particular focus on fungal systematics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1497085},
pmid = {39967791},
issn = {2235-2988},
mesh = {*Fungi/classification/genetics ; *Phenotype ; *Biodiversity ; *Biological Evolution ; Genetic Variation ; Phylogeny ; Evolution, Molecular ; },
abstract = {The evolution of a species can be understood in the context of two major concepts-the cryptic species concept and the phenotypic noise concept. The former represents morphologically indistinguishable but genetically distinct evolutionary lineages, while the latter represents the phenotypic variations of an isogenic population. Although the concept of cryptic species currently represents a general topic, its effect on other aspects of biology, such as biodiversity, ecology, evolutionary biology, and taxonomy, is still unclear. In particular, cryptic species cause complications and prevent the development of a clear taxonomy. The phenotypic noise concept or phenotypic plasticity generally refers to the various expressions of phenotypes in different environments. Hence, the cryptic species concept refers to genetic variations, while the phenotypic noises concept is about non-genetic variations. Although both concepts are opposites, they each contribute significantly to the evolutionary process of an organism. Despite the extensive research studies and publications discussing those two concepts in separate accounts, a concise account that combines and compares both concepts are generally lacking. Nevertheless, these are essential to understand the evolutionary process clearly. This review addresses the available literature on this topic, intending to provide a general and overall discussion on both the cryptic species concept and the phenotypic noise concept and their effect on evolution, ecology, biodiversity, and taxonomy with a special focus on fungal systematics. hence, several fungal case studies representing the two concepts are presented, compared, and discussed for a better understanding.},
}

*Fungi/classification/genetics
*Phenotype
*Biodiversity
*Biological Evolution
Genetic Variation
Phylogeny
Evolution, Molecular

@article {pmid39965215,
year = {2025},
author = {da Silva Masarin, I and de Oliveira, J and Visinho Dos Reis, Y and Ravazi, A and Fernandez Madeira, F and Cristina Antoniassi Fernandes Tadini, S and Galvão, C and Tercília Vilela de Azeredo-Oliveira, M and da Rosa, JA and Alevi, KCC},
title = {Analysis of the Evolutionary Relationship between Species of the New Triatoma pseudomaculata Subcomplex (Hemiptera, Triatominae) and Proposal for the Creation of the Triatoma costalimai Subcomplex.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.23-0415},
pmid = {39965215},
issn = {1476-1645},
abstract = {Triatomines are insects of great importance for public health, as they are vectors of protozoan Trypanosoma cruzi, the etiological agent of Chagas disease. The genus Triatoma is the most representative in number of species and one of the most important from an epidemiological point of view. The Triatoma pseudomaculata subcomplex (composed of the species Triatoma arthurneivai, T. pseudomaculata, and T. wygodzinskyi [from the old subcomplex Triatoma maculata] and Triatoma baratai, Triatoma costalimai, Triatoma deaneorum, Triatoma jatai, and Triatoma williami [from the old Triatoma matogrossensis subcomplex]) was recently proposed based on chromosomal data. Thus, considering that the experimental crossings helped with systematic questions about triatomines, we performed crosses between the species of the T. pseudomaculata subcomplex. Thus, we crossed T. pseudomaculata and Triatoma costalimai to assess the possible presence of interspecific genomic and reproductive compatibility. In addition, based on the molecular data available on GenBank, we performed a phylogenetic systematics study to assess the evolutionary relationship of the species of the T. pseudomaculata subcomplex. Experimental crosses did not result in hybrids, demonstrating that there is a prezygotic barrier established between these species. Based on the above, we confirmed the specific status of T. pseudomaculata and T. costalimai based on the biological species concept. Furthermore, the reproductive incompatibility associated with the phylogenetic systematic analyses demonstrate that T. costalimai does not belong to the T. pseudomaculata subcomplex. Thus, we suggest that the sister species T. costalimai and T. jatai should be grouped into a new subcomplex called T. costalimai.},
}

@article {pmid39951408,
year = {2025},
author = {Xu, C and Liu, Y and Han, S and Chen, Z and Ma, Y and Guo, Q and Zhang, P and Yang, W and Yang, C and Zhao, J and Hu, YS},
title = {Rational Design of Aqueous Na Ion Batteries Toward High Energy Density and Long Cycle Life.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.4c18168},
pmid = {39951408},
issn = {1520-5126},
abstract = {Prussian blue analogues (PBAs) are promising cathode candidates for aqueous Na ion batteries (ANIBs) considering their low-carbon and cost-effective features. However, it is still a huge challenge to achieve desirable energy density coupled with long cycle life due to inherent Na defects in PBAs and the unstable solid-electrolyte interphase (SEI) layer. Herein, we design Na2C4O4 additives as sodium supplements to compensate for Na defects in PBAs, while utilizing the CO2 products decomposed from Na2C4O4 to construct a robust SEI layer containing Na2CO3 species. As proof of concept, our building of full ANIBs using iron-based PBAs and NaTi2(PO4)3 anode with an appropriate amount of Na2C4O4 enable a reversible capacity of ∼144 mA h g[-1] at 0.2 C and an excellent cycling stability of 15,000 cycles with 85% retention at 10 C. The proposed concept is further extended to the manganese-based PBA ANIBs to deliver an energy density of 92 W h kg[-1] with improved cycling stability.},
}

@article {pmid39903560,
year = {2025},
author = {Thomas, GWC and Hughes, JJ and Kumon, T and Berv, JS and Nordgren, CE and Lampson, M and Levine, M and Searle, JB and Good, JM},
title = {The genomic landscape, causes, and consequences of extensive phylogenomic discordance in murine rodents.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf017},
pmid = {39903560},
issn = {1759-6653},
abstract = {A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents - a large and ecologically diverse group that gave rise to the laboratory mouse and rat model systems. Combining recently published linked-read genome assemblies for seven murine species with other available rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust time-calibrated species tree. We then used whole genomes to examine finer-scale patterns of discordance across ∼12 million years of divergence. We found that proximate chromosomal regions tended to have more similar phylogenetic histories. There was no clear relationship between local tree similarity and recombination rates in house mice, but we did observe a correlation between recombination rates and average similarity to the species tree. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to appreciably less discordance. Finally, we show that assuming a single species tree can result in substantial deviation from the results with gene trees when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.},
}

@article {pmid39894347,
year = {2025},
author = {Ruperao, P and Rangan, P and Shah, T and Sharma, V and Rathore, A and Mayes, S and Pandey, MK},
title = {Developing pangenomes for large and complex plant genomes and their representation formats.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.01.052},
pmid = {39894347},
issn = {2090-1224},
abstract = {BACKGROUND: The development of pangenomes has revolutionized genomic studies by capturing the complete genetic diversity within a species. Pangenome assembly integrates data from multiple individuals to construct a comprehensive genomic landscape, revealing both core and accessory genomic elements. This approach enables the identification of novel genes, structural variations, and gene presence-absence variations, providing insights into species evolution, adaptation, and trait variation. Representing pangenomes requires innovative visualization formats that effectively convey the complex genomic structures and variations.

AIM: This review delves into contemporary methodologies and recent advancements in constructing pangenomes, particularly in plant genomes. It examines the structure of pangenome representation, including format comparison, conversion, visualization techniques, and their implications for enhancing crop improvement strategies.

Earlier comparative studies have illuminated novel gene sequences, copy number variations, and presence-absence variations across diverse crop species. The concept of a pan-genome, which captures multiple genetic variations from a broad spectrum of genotypes, offers a holistic perspective of a species' genetic makeup. However, constructing a pan-genome for plants with larger genomes poses challenges, including managing vast genome sequence data and comprehending the genetic variations within the germplasm. To address these challenges, researchers have explored cost-effective alternatives to encapsulate species diversity in a single assembly known as a pangenome. This involves reducing the volume of genome sequences while focusing on genetic variations. With the growing prominence of the pan-genome concept in plant genomics, several software tools have emerged to facilitate pangenome construction. This review sheds light on developing and utilizing software tools tailored for constructing pan-genomes in plants. It also discusses representation formats suitable for downstream analyses, offering valuable insights into the genetic landscape and evolutionary dynamics of plant species. In summary, this review underscores the significance of pan-genome construction and representation formats in resolving the genetic architecture of plants, particularly those with complex genomes. It provides a comprehensive overview of recent advancements, aiding in exploring and understanding plant genetic diversity.},
}

@article {pmid39872325,
year = {2024},
author = {Takahashi, Y and Tomooka, N},
title = {Taxonomic history, morphology, evolution, gene pool and stress tolerances of azuki bean and its related wild Vigna genetic resources.},
journal = {Breeding science},
volume = {74},
number = {4},
pages = {295-310},
pmid = {39872325},
issn = {1344-7610},
abstract = {This review compiles information on the morphology, historical taxonomic treatments, species origin, gene pool concept, geographical and ecological habitats, and stress tolerance of the azuki bean (Vigna angularis) and related species. Willdenow (1802) first described the azuki bean in the genus Dolichos, and Ohwi and Ohashi (1969) finally transferred it to the genus Vigna. The genus Vigna is currently divided into five subgenera: Ceratotropis, Haydonia, Lasiospron, Plectrotropis, and Vigna. The subgenus Ceratotropis includes the moth bean in section Aconitifoliae; the mungbean and black gram in section Ceratotropis; and the azuki bean, rice bean, and creole bean in section Angulares. The wild species in section Angulares generally possess larger standard petal with more prominent appendage, keel petal with longer pocket, pistil with longer style beak compared with those of species in sections Aconitifoliae and Ceratotropis, and characterized by glabrous mature pod, smooth seed coat, hypogeal germination seed, and cordate primary leaves with petiole. Section Angulares currently consists of 13 species. The taxa that cross readily with the azuki beans included in the primary genepool are the wild azuki bean V. angularis var. nipponensis, V. nepalensis, V. tenuicaulis, V. hirtella, V. minima, V. nakashimae, and V. riukiuensis. These wild species are expected to be used as breeding material against biotic and abiotic stresses.},
}

@article {pmid39866570,
year = {2025},
author = {Wardani, RK and Ahsan, R and Shin, MK},
title = {Evolutionary patterns of the SSU rRNA (V4 region) secondary structure in genus Euplotes (Ciliophora, Spirotrichea): insights into cryptic species and primitive traits.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18852},
pmid = {39866570},
issn = {2167-8359},
mesh = {*Euplotes/genetics ; *Phylogeny ; *Evolution, Molecular ; *Nucleic Acid Conformation ; RNA, Ribosomal/genetics ; Republic of Korea ; },
abstract = {The genus Euplotes, a group of ciliated protists, has attracted attention as a model organism due to its widespread distribution and ease of cultivation. This study examines the evolutionary patterns of the SSU rRNA secondary structure within this genus, aiming to elucidate its role in supporting evolutionary relationships and uncovering cryptic species. By predicting the secondary structure of SSU rRNA and applying the CBC (Compensatory Base Change) concept analysis, we examined 69 species of the genus Euplotes, with 57 SSU rRNA gene sequences retrieved from GenBank and 12 newly sequenced specimens from South Korea. Our analysis revealed significant variations in the V4 region secondary structure, particularly in helix E23_8, across different clades of Euplotes. Reconstruction of the ancestral state indicated a transition from a simpler (Type I) to a more complex (Type II) secondary structure, with several species showing a reversal to Type I especially species in clade VI, suggesting of reverse evolution. In addition, our study identified cryptic species within Euplotes based on differences in the secondary structure of the V4 region, particularly evident in clade VI, where CBC analysis highlighted differences in E. minuta compared to E. vannus and E. crassus. These results highlight the utility of molecular data in refining species boundaries and evolutionary patterns within the genus Euplotes.},
}

*Euplotes/genetics
*Phylogeny
*Evolution, Molecular
*Nucleic Acid Conformation
RNA, Ribosomal/genetics
Republic of Korea

@article {pmid39864055,
year = {2025},
author = {Hua, X and Moritz, C},
title = {A phylogenetic approach to delimitate species in a probabilistic way.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syaf004},
pmid = {39864055},
issn = {1076-836X},
abstract = {Different species concepts and their associated criteria have been used to delimit species boundaries, such as the absence of gene flow for the biological species concept and the presence of morphological distinction for the morphological species concept. The need for different delimitation criteria largely reflects the fact that species are generated under various speciation mechanisms. A key question is how to make species delimitation consistent in a species group, especially when we want to delimit the species boundaries over many newly discovered evolutionary lineages and add these new lineages into a comparative analysis. Instead of forcing a single definition of 'species', we can acknowledge different delimitation criteria by modelling how fast lineages in a species group evolve to meet these criteria along a phylogenetic tree. This study presents such a new model and a new delimitation approach that calculates the probability of each possible species identity of a lineage. We use simulations to show that our likelihood function gives accurate estimates of parameters in the model and our approach have high power to correctly identify species identities. We apply the approach to lineages in two real species groups that already have genomic and morphological evidence for their species identities. Our approach gives consistent inference of species identities with these existing pieces of evidence. We also demonstrate how to use our model to test a popular hypothesis about speciation process across all lineages in a species group and discuss further extension of the model to study speciation.},
}

@article {pmid39581687,
year = {2024},
author = {Tabor, AE},
title = {Editorial: ticks & tick-borne parasites and diseases.},
journal = {Parasitology},
volume = {151},
number = {9},
pages = {885-890},
doi = {10.1017/S0031182024001549},
pmid = {39581687},
issn = {1469-8161},
mesh = {Animals ; *Tick-Borne Diseases/transmission/epidemiology/parasitology ; *Ticks/parasitology ; Humans ; },
abstract = {Ticks and tick-borne diseases affect humans, livestock, and wildlife in most regions of the globe. Although there are over 900 tick species globally, only approximately 10% of species are second to mosquitoes as major vectors of human and veterinary diseases. The 17 articles of this themed Special Issue highlight the current research trends associated with newly discovered tick species, concepts of tick evolution, new vaccinology approaches, factors affecting disease transmission, and factors affecting tick ecology and tick-borne disease epidemiology. summarizes the articles in this Special Issue in alphabetical author order and is a word cloud generated from the article titles. Of the 17 articles in this Special Issue, two are review articles (vaccinology) while the remaining 15 are original research articles. The topics range from tick control, to epidemiology, ecology, tick-borne disease control, tick-borne disease transmission, vaccine approaches, and the description of novel extant and extinct tick species. is graphical representation of the articles within this Special Issue including tick hosts and the most representative tick species studied. The articles also include authors from most continents globally with first author contributions from Australia, Bangladesh, Brazil, Czech Republic, Germany, India, Mexico, Pakistan, South Africa, Spain, Turkey, United Arab Emirates, USA and Zambia. This issue is thus truly diverse which reflects the diversity of ticks, tick-borne diseases and they hosts they infest globally.},
}

Animals
*Tick-Borne Diseases/transmission/epidemiology/parasitology
*Ticks/parasitology
Humans

@article {pmid39820741,
year = {2025},
author = {Schoenke, VSAM and Wang, J and Van den Brink, PJ and Hendriks, AJ},
title = {Assessing chronic effects of chemical pollution on biodiversity using mean species abundance relationships.},
journal = {Environmental toxicology and chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/etojnl/vgaf015},
pmid = {39820741},
issn = {1552-8618},
abstract = {Since chemical pollution poses a persistent threat to freshwater ecosystems and biodiversity, innovative methodologies are required to address the ecological risks associated with such pollutants. This study predicts the long-term impacts of chemicals based on an equation that describes the time-dependency of the median lethal and effect concentration (L(E)C50) with the Critical Body Residue concept. This way, the methodology can predict Species Sensitivity Distributions (SSDs) for any given time point. The methodology was extended to predict the Mean Species Abundance Relationships (MSAR) as an indicator of biodiversity. To test and validate the methodology, data from a case study with six freshwater arthropods exposed short- and long-term to imidacloprid was used. The potentially affected fraction of species (PAF) and its opposite (1-PAF) was used to validate the MSAR framework itself. The accuracy of the predicted chronic median lethal concentration (LC50) values was species-dependent. However, except for one species, all predicted chronic LC50 values were within the 95% Confidence Intervals (CIs) of the fits based on only acute data. The mean differences between the predicted and calculated MSARs were between 2% and 6%. The predicted MSARs generally underestimated the impact of imidacloprid. However, all predicted MSARs were either similar or lower than the calculated 1-PAF, and their CIs covered the calculated MSARs. Thus, the study found that the presented methodology is useful for predicting the long-term effects of chemical pollutants.},
}

@article {pmid39800689,
year = {2025},
author = {Loria, SF and Frank, SC and Dupérré, N and Smith, HM and Jones, B and Buzatto, BA and Harms, D},
title = {The world's most venomous spider is a species complex: systematics of the Sydney funnel-web spider (Atracidae: Atrax robustus).},
journal = {BMC ecology and evolution},
volume = {25},
number = {1},
pages = {7},
pmid = {39800689},
issn = {2730-7182},
support = {Award# HA 8785/5 and KO 3944/10//Deutsche Forschungsgemeinschaft/ ; Exploration Grant (NGS-62237R-19)//National Geographic Society/ ; Exploration Grant (NGS-62237R-19)//National Geographic Society/ ; Exploration Grant (NGS-62237R-19)//National Geographic Society/ ; Visiting Research Fellowship 2019-2020//Australian Museum/ ; },
mesh = {*Spiders/classification/anatomy & histology ; Animals ; *Spider Venoms/chemistry/genetics ; *Phylogeny ; Australia ; Female ; Animals, Poisonous ; },
abstract = {The Sydney funnel-web spider Atrax robustus O. Pickard-Cambridge, 1877 is an iconic Australian species and considered among the most dangerously venomous spiders for humans. Originally described in 1877 from a single specimen collected in "New Holland", this spider has a complex taxonomic history. The most recent morphological revision of funnel-web spiders (Atracidae) lists this species as both widespread and common in the Sydney Basin bioregion and beyond, roughly 250 km from the Newcastle area south to the Illawarra, and extending inland across the Blue Mountains. Morphological variability and venom diversity in this species appear to be unusually high, raising questions about species concepts and diversity in these spiders. In this study, we use a combination of molecular phylogenetics, divergence time analyses and morphology to establish the Sydney funnel-web spider as a complex of three species. The "real" Sydney funnel-web spider Atrax robustus is relatively widespread in the Sydney metropolitan region. A second species, Atrax montanus (Rainbow, 1914), which is revalidated here, overlaps but mainly occurs further south and west, and a third larger species, Atrax christenseni sp. nov., is found in a small area surrounding Newcastle to the north. The revised taxonomy for funnel-web spiders may have practical implications for antivenom production and biochemical studies on spider venoms. Although no human fatalities have occurred since the development of antivenom in the 1980s, antivenom for Sydney funnel-web spiders might be optimized by considering biological differentiation at the species level.},
}

*Spiders/classification/anatomy & histology
Animals
*Spider Venoms/chemistry/genetics
*Phylogeny
Australia
Female
Animals, Poisonous

@article {pmid39791299,
year = {2025},
author = {Wu, H and Zhang, YX and Yu, L},
title = {Progress on animal speciation studies.},
journal = {Yi chuan = Hereditas},
volume = {47},
number = {1},
pages = {58-70},
doi = {10.16288/j.yczz.24-206},
pmid = {39791299},
issn = {0253-9772},
mesh = {Animals ; *Genetic Speciation ; Reproductive Isolation ; Biological Evolution ; },
abstract = {Speciation research represents our thinking and exploration about how new species are generated and maintained, and it is one of the most important parts of evolutionary biology. Revealing new species formation modes, processes of reproductive isolation establishment and their intrinsic genetic mechanisms, are not only important issues and primary tasks in the field of speciation, but also the key clues for our understandings about the species diversity in nature. Here, by focusing on animal groups, we first introduced different definitions of species concept, and then summarized present research progress and important breakthroughs made in the speciation modes and molecular mechanism of reproductive isolation. We also pointed out some limitations in current studies. Finally, we discuss the potential opportunities and new breakthroughs that can be made in the future studies of animal speciation.},
}

Animals
*Genetic Speciation
Reproductive Isolation
Biological Evolution

@article {pmid39788675,
year = {2025},
author = {Zhao, J and Guo, J and Li, J and Zhao, C and Gao, Z and Song, YY and Li, X},
title = {Wood membrane: A sustainable electrochemical platform for enzyme-free and pretreatment-free monitoring uric acid in bodily fluids.},
journal = {Analytica chimica acta},
volume = {1336},
number = {},
pages = {343522},
doi = {10.1016/j.aca.2024.343522},
pmid = {39788675},
issn = {1873-4324},
mesh = {*Uric Acid/analysis ; *Electrochemical Techniques/instrumentation/methods ; Humans ; *Wood/chemistry ; Saliva/chemistry ; Ferrocyanides/chemistry ; Nanoparticles/chemistry ; Membranes, Artificial ; Limit of Detection ; },
abstract = {The detection of biomarkers is crucial for assessing disease status and progression. Uric acid (UA), a common biomarker in body fluids, plays an important role in the diagnosis and monitoring of conditions such as hyperuricemia, chronic kidney disease, and cardiovascular disease. However, the low concentration of UA in non-invasive body fluids, combined with numerous interfering substances, makes its detection challenging. Therefore, there is a pressing need to develop advanced sensor platforms that exhibit both high sensitivity and excellent specificity for accurate monitoring of UA levels in various body fluids. In this study, an electrochemical sensing system is developed by integrating a cascade interference-removal zone and a target-response zone on a wooden channel membrane (CM) for the pretreatment-free detection of UA in body fluids. In this design, cysteine-doped ZIF-67(Co) nanocrystals, a mimic with multi-enzyme activity, are modified in the interference-removal zone. The target-response zone on the other side of the CM is contacted with a solution containing Fe[3+] and [Fe(CN)6[]3-] ions. Using saliva as a proof-of-concept, the interference species, including ascorbic acid (AA), dopamine (DA), and glutathione (GSH), are oxidized and removed when passing through the interference-removal zone, while UA reaches the target-response zone and triggers the growth of Prussian blue (PB) on site. Utilizing the peroxidase-like activity of PB, UA concentration is directly determined based on changes in transmembrane ion currents. The resulting sensing system exhibits higher sensitivity than commercial UA meters and demonstrates straightforward, continuous, and non-invasive monitoring of UA in saliva after consuming purine-rich foods. The technology provides a simple, reliable and low-cost device for sensing UA in complex biological matrices. Moreover, the CM based sensing device also provides the benefit of being incineratable and biodegradable, reducing medical and electronic waste, making it eco-friendly for daily diagnostics.},
}

*Uric Acid/analysis
*Electrochemical Techniques/instrumentation/methods
Humans
*Wood/chemistry
Saliva/chemistry
Ferrocyanides/chemistry
Nanoparticles/chemistry
Membranes, Artificial
Limit of Detection

@article {pmid39778636,
year = {2025},
author = {Machado, RAR and Muller, A and Hiltmann, A and Bhat, AH and Půža, V and Malan, AP and Castaneda-Alvarez, C and San-Blas, E and Duncan, LW and Shapiro-Ilan, D and Karimi, J and Lalramliana, and Lalramnghaki, HC and Baimey, H},
title = {Genome-wide analyses provide insights into genetic variation, phylo- and co-phylogenetic relationships, and biogeography of the entomopathogenic nematode genus Heterorhabditis.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108284},
doi = {10.1016/j.ympev.2025.108284},
pmid = {39778636},
issn = {1095-9513},
abstract = {Multigene, genus-wide phylogenetic studies have uncovered the limited taxonomic resolution power of commonly used gene markers, particularly of rRNA genes, to discriminate closely related species of the nematode genus Heterorhabditis. In addition, conflicting tree topologies are often obtained using the different gene markers, which limits our understanding of the phylo- and co-phylogenetic relationships and biogeography of the entomopathogenic nematode genus Heterorhabditis. Here we carried out phylogenomic reconstructions using whole nuclear and mitochondrial genomes, and whole ribosomal operon sequences, as well as multiple phylogenetic reconstructions using various single nuclear and mitochondrial genes. Using the inferred phylogenies, we then investigated co-phylogenetic relationships between Heterorhabditis and their Photorhabdus bacterial symbionts and biogeographical patterns. Robust, well-resolved, and highly congruent phylogenetic relationships were reconstructed using both whole nuclear and mitochondrial genomes. Similarly, whole ribosomal operon sequences proved valuable for phylogenomic reconstructions, though they have limited value to discriminate closely related species. In addition, two mitochondrial genes, the cytochrome c oxidase subunit I (cox-1) and the NADH dehydrogenase subunit 4 (nad-4), and two housekeeping genes, the fanconi-associated nuclease 1 (fan-1) and the serine/threonine-protein phosphatase 4 regulatory subunit 1 (ppfr-1), provided the most robust phylogenetic reconstructions compared to other individual genes. According to our findings, whole nuclear and/or mitochondrial genomes are strongly recommended for reconstructing phylogenetic relationships of the genus Heterorhabditis. If whole nuclear and/or mitochondrial genomes are unavailable, a combination of nuclear and mitochondrial genes can be used as an alternative. Under these circumstances, sequences of multiple conspecific isolates in a genus-wide phylogenetic context should be analyzed to avoid artefactual species over-splitting driven by the high intraspecific sequence divergence of mitochondrial genes and to avoid artefactual species lumping driven by the low interspecific sequence divergence of some nuclear genes. On the other hand, we observed that the genera Heterorhabditis and Photorhabdus exhibit diverse biogeographic patterns, ranging from cosmopolitan species to potentially endemic species, and show high phylogenetic congruence, although host switches have also occurred. Our study contributes to a better understanding of the biodiversity and phylo- and co-phylogenetic relationships of an important group of biological control agents and advances our efforts to develop more tools that are compatible with sustainable and eco-friendly agricultural practices.},
}

@article {pmid39770350,
year = {2024},
author = {Yang, H and Cheng, J and Dili, N and Jiang, N and Ma, R},
title = {Seimatosporium chinense, a Novel Pestalotioid Fungus Associated with Yellow Rose Branch Canker Disease.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/pathogens13121090},
pmid = {39770350},
issn = {2076-0817},
support = {2021xjkk05005//Third Xinjiang Scientific Expedition Program/ ; },
mesh = {*Plant Diseases/microbiology ; *Phylogeny ; China ; *Rosa/microbiology ; DNA, Fungal/genetics ; Plant Bark/microbiology ; Spores, Fungal ; },
abstract = {Yellow rose (Rosa xanthina) is a common ornamental shrub species widely cultivated in China. However, canker disease symptoms were discovered during our investigations in Beijing and Xinjiang, China. The fungal isolates were obtained from diseased barks and identified using combined methods of morphology and phylogeny based on a partial region of ITS, LSU, rpb2, tef1, and tub2 sequences. As a result, a new species of Seimatosporium named S. chinense was proposed and described herein. The new species is distinguished from its phylogenetic sister species, S. gracile and S. nonappendiculatum, by conidial characters. The present study improves the species concept in Seimatosporium and provides fundamental data for the yellow rose canker disease control in the future.},
}

*Plant Diseases/microbiology
*Phylogeny
China
*Rosa/microbiology
DNA, Fungal/genetics
Plant Bark/microbiology
Spores, Fungal

@article {pmid39768173,
year = {2024},
author = {Alegretti, JR and Rocha, AMD and Nogueira-de-Souza, NC and Kato, N and Barros, BC and Motta, ELA and Serafini, PC and Takayama, S and Smith, GD},
title = {Controlled Dynamic Microfluidic Culture of Murine, Bovine, and Human Embryos Improves Development: Proof-of-Concept Studies.},
journal = {Cells},
volume = {13},
number = {24},
pages = {},
doi = {10.3390/cells13242080},
pmid = {39768173},
issn = {2073-4409},
support = {HD 049607//National Institutes of Health - National Institutes of Bio-Imaging and Bioengineering/ ; #35203-16148//United States Department of Agriculture (USDA)-CSREES National Research Initiative Competitive Grants Program Grant/ ; MEDC; GR 696//Michigan Economic De-velopment Corporation/ ; DAAD19-03-1-0168//U.S. Army Research Laboratory and the U.S. Army Research Office under contract/grant, and Coulter foundation/ ; },
mesh = {Animals ; Humans ; Cattle ; Mice ; *Embryonic Development ; *Embryo Culture Techniques/methods ; *Microfluidics/methods ; *Blastocyst/cytology/metabolism ; Female ; Proof of Concept Study ; Embryo, Mammalian/cytology ; Apoptosis ; Zygote/cytology/metabolism ; },
abstract = {Classical preimplantation embryo culture is performed in static fluid environments. Whether a dynamic fluid environment, like the fallopian tube, is beneficial for embryo development remains to be determined across mammalian species. Objectives of these proof-of-concept studies were to determine if controllable dynamic microfluidic culture would enhance preimplantation murine, bovine, and human embryo development compared to static culture. This prospective randomized controlled trial tested static versus controlled dynamic culture of preimplantation mouse (n = 397), bovine (n = 242), and human (n = 512) zygotes to blastocyst stages with outcome measures of embryo cleavage, cellular fragmentation, apoptosis, and blastocyst conversion rates. Dynamic culture of mouse and bovine zygotes with microfluidics significantly improved embryo development. Mouse placental imprinted gene expression was significantly different between embryos derived in vivo, by static culture, and by dynamic culture. Using human sibling zygotes, this dynamic microfluidic culture system increased the number of blastomeres per cleavage-stage embryo, reduced cellular fragmentation or apoptosis, improved blastocyst conversion rates, and enhanced blastocyst developmental stages. In conclusion, species-specific longitudinal studies demonstrated that dynamic microfluidic culture significantly improved embryo development, independent of culture media composition, temperature, and gaseous environment. These cellular indicators represent improved embryo development that can translate into higher pregnancy rates in transgenics, domestic livestock and endangered species and treating human infertility.},
}

Animals
Humans
Cattle
Mice
*Embryonic Development
*Embryo Culture Techniques/methods
*Microfluidics/methods
*Blastocyst/cytology/metabolism
Female
Proof of Concept Study
Embryo, Mammalian/cytology
Apoptosis
Zygote/cytology/metabolism

@article {pmid39763284,
year = {2025},
author = {Schneider, AC},
title = {Multiple genotypes of Phelipanche ramosa indicate repeated introduction to the Americas.},
journal = {American journal of botany},
volume = {},
number = {},
pages = {e16456},
doi = {10.1002/ajb2.16456},
pmid = {39763284},
issn = {1537-2197},
abstract = {PREMISE: Phelipanche ramosa is an economically damaging parasitic plant that has been reported in North America since the late 1800s. While this species comprises a variety of genetically distinct host races in its native range, the genetic composition of adventive populations in the New World remains unexplored. On the basis of morphological and ecological variation, some have suggested that the closely related P. nana may also be present.

METHODS: Genome skimming was used to assess the relationships of 30 populations of Phelipanche spanning the geographic and host ranges in North and South America, plus one P. nana reference population from Lebanon.

RESULTS: Phylogenetic analysis indicated four distinct genetic groups, though plastome and nrDNA data supported conflicting signals of relationships among them. First, specimens from Chilean tomato fields were nearly indistinguishable genetically from the reference P. nana. Second, a pair of samples from Virginia showed similar nrDNA as the first group, but divergent plastomes. The remaining 24 samples sorted into two groups, one which parasitizes cultivated plants, especially tomato, and the other on roadside weeds in different parts of the United States.

CONCLUSIONS: The geographic and ecological cohesiveness of four distinct genetic groups supports a hypothesis of multiple introductions to the Americas, presumably from Eurasia, followed by little to no subsequent gene flow among them. However, such groups do not align with existing morphological or ecological species concepts for P. ramosa and P. nana. In practice, threat assessment of Phelipanche populations to agricultural settings should be evaluated regionally given the phylogeographic and ecological heterogeneity.},
}

@article {pmid39733992,
year = {2024},
author = {Li, Y and Fan, W and Lo, TH and Jiang, JX and Fish, SR and Tomilov, A and Chronopoulos, A and Bansal, V and Mozes, G and Vancza, L and Kunimoto, K and Ye, J and Becker, L and Das, S and Park, H and Wei, Y and Ranjbarvaziri, S and Bernstein, D and Ramsey, J and Cortopassi, G and Török, NJ},
title = {P46Shc Inhibits Mitochondrial ACAA2 Thiolase, Exacerbating Mitochondrial Injury and Inflammation in Aging Livers.},
journal = {The American journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajpath.2024.10.022},
pmid = {39733992},
issn = {1525-2191},
abstract = {Mitochondrial maladaptation and dysfunction contribute to the progression of metabolic dysfunction-associated steatohepatitis (MASH). The authors recently implicated the induction of Shc in progressive MASH during aging and the cytoplasmic p52Shc isoform in the activation of redox enzyme NOX2. The mitochondrial Shc isoform p46Shc was shown to repress acetyl-coenzyme A acyltransferase 2 (ACAA2) in vitro. ACAA2 is a key enzyme for lipid β-oxidation; however, the metabolic consequences of in vivo p46Shc induction were unknown. The authors generated p46Shc-inducible mice; these and littermate controls were aged and fed chow or fast-food diet (high-fat and high-fructose). p46Shc induction increased liver injury, inflammation, and lipid peroxidation. p46Shc overexpression did not significantly change liver triglycerides. On electron microscopy studies, mitochondria were swollen with aberrant cristae. p46Shc induction reduced mitochondrial oxygen consumption as measured by Oroboros, as well as suppressed the production of β-hydroxybutyrate, the central metabolite of therapeutic ketosis. Mitochondria exhibited increased production of reactive oxidative species. By contrast, the expression of dominant negative p46Shc reduced ACAA2 thiolase activity, improved β-oxidation, and reduced lipid peroxidation and production of reactive oxidative species. In summary, these studies support the concept that p46Shc induction in aging represses ACAA2, resulting in decreased mitochondrial β-oxidation and increased lipid peroxidation. Maintaining β-oxidation and ketogenesis could prevent liver injury, and targeting Shc-related maladaptive responses could be a successful therapeutic strategy in aging/MASH.},
}

@article {pmid39722237,
year = {2024},
author = {Hdedeh, O and Mercier, C and Poitout, A and Martinière, A and Zelazny, E},
title = {Membrane nanodomains to shape plant cellular functions and signaling.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.20367},
pmid = {39722237},
issn = {1469-8137},
support = {//I-Site Montpellier University/ ; ANR-19-CE20-0008-01//Agence Nationale de Recherches/ ; ANR-23-CE20-0022//Agence Nationale de Recherches/ ; },
abstract = {Plasma membrane (PM) nanodomains have emerged as pivotal elements in the regulation of plant cellular functions and signal transduction. These nanoscale membrane regions, enriched in specific lipids and proteins, behave as regulatory/signaling hubs spatially and temporally coordinating critical cellular functions. In this review, we first examine the mechanisms underlying the formation and maintenance of PM nanodomains in plant cells, highlighting the roles of PM lipid composition, protein oligomerization and interactions with cytoskeletal and cell wall components. Then, we discuss how nanodomains act as organizing centers by mediating protein-protein interactions that orchestrate essential processes such as symbiosis, defense against pathogens, ion transport or hormonal and reactive oxygen species (ROS) signaling. Finally, we introduce the concept of nanoenvironments, where localized physicochemical variations are generated in the very close proximity of PM nanodomains, in response to stimuli. After decoding by a dedicated machinery likely localized in the vicinity of nanodomains, this enrichment of secondary messengers, such as ROS or Ca[2+], would allow specific downstream cellular responses. This review provides insights into the dynamic nature of nanodomains and proposes future research to better understand their contribution to the intricate signaling networks that govern plant development and stress responses.},
}

@article {pmid39719730,
year = {2024},
author = {Bergin, R and Samperton, K and Bronikowski, M and Hoar, E and Rolison, J and Shollenberger, Q and Marks, N and Wellons, M and Scott, S},
title = {Synthesis and characterization of isotopically barcoded nickel, molybdenum, and tungsten taggants for intentional nuclear forensics.},
journal = {Talanta},
volume = {285},
number = {},
pages = {127425},
doi = {10.1016/j.talanta.2024.127425},
pmid = {39719730},
issn = {1873-3573},
abstract = {Intentional nuclear forensics is a concept wherein the deliberate addition of benign and persistent material signatures to nuclear material can be used to reduce the time between the discovery of material outside of regulatory control and determination of its original provenance. One concept within intentional nuclear forensics involves the use of perturbed stable isotopes to generate unique isotope ratio "barcodes" to encode information (e.g., production batch, location, etc.) and track material throughout the nuclear fuel cycle. Synthesis of taggant species of nickel (Ni), molybdenum (Mo), and tungsten (W) was undertaken via a double-spike mechanism, wherein two highly enriched isotopes of interest per elemental taggant were mixed to form an enriched "double-spike" which was subsequently isotopically diluted with bulk material having a natural isotopic composition. Two taggant species perturbing isotopic ratios, alpha (α) and beta (β), for each of Ni, Mo, and W were synthesized. Independent measurements of double spikes and alpha and beta taggant species agreed within uncertainty and are clearly resolvable from natural compositions. High-precision analyses were independently performed by MC-ICP-MS at two U.S. National Laboratories, with consensus values and uncertainties calculated for all samples. Observed isotopic perturbations in the final taggant species measured on the order of hundreds to thousands of permille (‰) with respect to natural for isotope ratios of interest (e.g., [60]Ni/[58]Ni, [100]Mo/[98]Mo, [186] W/[183]W). Discrepancies between modeled and measured isotopic compositions were observed and are largely attributed to imprecise vendor assay values for starting materials. Using measured starting material compositions as inputs for the mixing model improved the level of agreement between predicted and measured α and β taggant isotope ratios. Overall, characterization of all taggant species demonstrates that this "barcode" concept could have viability for use in nuclear forensics. It is expected that for any two-isotope mixing array dozens of isotopic barcodes could be encoded into a material system and subsequently resolved utilizing modern mass spectrometric methods.},
}

@article {pmid39717659,
year = {2024},
author = {Costa, MM and Sandoval-Denis, M and Moreira, GM and Kandemir, H and Kermode, A and Buddie, AG and Ryan, MJ and Becker, Y and Yurkov, A and Maier, W and Groenewald, JZ and Pfenning, LH and Crous, PW},
title = {Known from trees and the tropics: new insights into the Fusarium lateritium species complex.},
journal = {Studies in mycology},
volume = {109},
number = {},
pages = {403-450},
pmid = {39717659},
issn = {0166-0616},
abstract = {The Fusarium lateritium species complex (FLSC) currently comprises 11 phylogenetic species, including accepted names such as F. lateritium, F. sarcochroum, and F. stilboides, which have mostly been reported in association with citrus and coffee. Many varieties were documented by Wollenweber & Reinking (1935), which is indicative of a wider diversity of species within this group. The lack of type material in some cases, especially for the older names, means that definition by molecular phylogeny is very difficult. In the present study, we examined 179 strains related to F. lateritium from different countries and substrates. Historic reference material, including representative strains from the Wollenweber & Reinking (1935) varieties were included in this study, DNA sequences were generated for comparison, and the morphology correlated with original descriptions to enable the correct application of older names. Strains were characterized by multi-gene phylogenetic analyses based on fragments of the β-tubulin (tub2), calmodulin (CaM), RNA polymerase II second largest subunit (rpb2), and translation elongation factor 1-alpha (tef1) genes, evaluation of morphological characters and host-substrate preferences. The biological species concept was tested by crossings in vitro. Strains previously identified as F. lateritium, F. stilboides, or one of their varieties based on morphology, were found to belong to 16 species in the FLSC, but also to species from six other species complexes (SC), including the F. citricola SC, F. heterosporum SC, F. incarnatum-equiseti SC, F. redolens SC, F. sambucinum SC, and the F. tricinctum SC. Eleven new phylogenetic and two biological species are described in the FLSC, and emended descriptions are provided for four previously described species. An epitype is designated for F. lateritium, and F. lateritium var. longum, a former variety within the FLSC, is lecto- and epitypified, and elevated to species level with a replacement name. Taxonomic novelties: New species: F. aurantii M.M. Costa, Sand.-Den. & Crous, F. chlamydocopiosum M.M. Costa, Sand.-Den. & Crous, F. citri-sinensis L. Zhao & J.X. Deng, F. coffeibaccae M.M. Costa, L.H. Pfenning, Sand.-Den. & Crous, F. crocatum M.M. Costa, Sand.-Den. & Crous, F. malawiense M.M. Costa, Sand.-Den. & Crous, F. microcyclum M.M. Costa, Sand.-Den. & Crous, F. oliniae M.M. Costa, Sand.-Den. & Crous; F. rufum M.M. Costa, Sand.-Den. & Crous, F. stramineum M.M. Costa, Sand.-Den. & Crous, F. velutinum M.M. Costa, Sand.-Den. & Crous, F. verruculosum M.M. Costa, Sand.-Den. & Crous; Replacement name: F. hanswilhelmii M.M. Costa, Sand.-Den. & Crous; Epitype (basionym): F. lateritium Nees, F. lateritium var. longum Wollenw.; Lectotype (basionym): F. lateritium var. longum Wollenw. Citation: Costa MM, Sandoval-Denis M, Moreira GM, Kandemir H, Kermode A, Buddie AG, Ryan MJ, Becker Y, Yurkov A, Maier W, Groenewald JZ, Pfenning LH, Crous PW (2024). Known from trees and the tropics: new insights into the Fusarium lateritium species complex. Studies in Mycology 109: 403-450. doi: 10.3114/sim.2024.109.06.},
}

@article {pmid39717652,
year = {2024},
author = {Pereira, DS and Phillips, AJL},
title = {Diaporthe species on palms - integrative taxonomic approach for species boundaries delimitation in the genus Diaporthe, with the description of D. pygmaeae sp. nov.},
journal = {Studies in mycology},
volume = {109},
number = {},
pages = {487-594},
pmid = {39717652},
issn = {0166-0616},
abstract = {The application of traditional morphological and ecological species concepts to closely related, asexual fungal taxa is challenging due to the lack of distinctive morphological characters and frequent cosmopolitan and plurivorous behaviour. As a result, multilocus sequence analysis (MLSA) has become a powerful and widely used tool to recognise and delimit independent evolutionary lineages (IEL) in fungi. However, MLSA can mask discordances in individual gene trees and lead to misinterpretation of speciation events. This phenomenon has been extensively documented in Diaporthe, and species identifications in this genus remains an ongoing challenge. However, the accurate delimitation of Diaporthe species is critical as the genus encompasses several cosmopolitan pathogens that cause serious diseases on many economically important plant hosts. In this regard, following a survey of palm leaf spotting fungi in Lisbon, Portugal, Diaporthe species occurring on Arecaceae hosts were used as a case study to implement an integrative taxonomic approach for a reliable species identification in the genus. Molecular analyses based on the genealogical concordance phylogenetic species recognition (GCPSR) and DNA-based species delimitation methods revealed that speciation events in the genus have been highly overestimated. Most IEL identified by the GCPSR were also recognised by Poisson tree processes (PTP) coalescent-based methods, which indicated that phylogenetic lineages in Diaporthe are likely influenced by incomplete lineage sorting (ILS) and reticulation events. Furthermore, the recognition of genetic recombination signals and the evaluation of genetic variability based on sequence polymorphisms reinforced these hypotheses. New clues towards the intraspecific variation in the common loci used for phylogenetic inference of Diaporthe species are discussed. These results demonstrate that intraspecific variability has often been used as an indicator to introduce new species in Diaporthe, which has led to a proliferation of species names in the genus. Based on these data, 53 species are reduced to synonymy with 18 existing Diaporthe species, and a new species, D. pygmaeae, is introduced. Thirteen new plant host-fungus associations are reported, all of which represent new host family records for Arecaceae. This study has recognised and resolved a total of 14 valid Diaporthe species associated with Arecaceae hosts worldwide, some of which are associated with disease symptoms. This illustrates the need for more systematic research to examine the complex of Diaporthe taxa associated with palms and determine their potential pathogenicity. By implementing a more rational framework for future studies on species delimitation in Diaporthe, this study provides a solid foundation to stabilise the taxonomy of species in the genus. Guidelines for species recognition, definition and identification in Diaporthe are included. Taxonomic novelties: New species: Diaporthe pygmaeae D.S. Pereira & A.J.L. Phillips. New synonyms: Diaporthe afzeliae Monkai & Lumyong, Diaporthe alangii C.M. Tian & Q. Yang, Diaporthe araliae-chinensis S.Y. Wang et al., Diaporthe australiana R.G. Shivas et al., Diaporthe australpacifica Y.P. Tan & R.G. Shivas, Diaporthe bombacis Monkai & Lumyong, Diaporthe caryae C.M. Tian & Q. Yang, Diaporthe chimonanthi (C.Q. Chang et al.) Y.H. Gao & L. Cai, Diaporthe conferta H. Dong et al., Diaporthe diospyrina Y.K. Bai & X.L. Fan, Diaporthe durionigena L.D. Thao et al., Diaporthe etinsideae Y.P. Tan & R.G. Shivas, Diaporthe eucalyptorum Crous & R.G. Shivas, Diaporthe fujianensis Jayaward. et al., Diaporthe fusiformis Jayaward. et al., Diaporthe globoostiolata Monkai & Lumyong, Diaporthe hainanensis Qin Yang, Diaporthe hongkongensis R.R. Gomes et al., Diaporthe hubeiensis Dissan. et al., Diaporthe infecunda R.R. Gomes et al., Diaporthe italiana Chethana et al., Diaporthe juglandigena S.Y. Wang et al., Diaporthe lagerstroemiae (C.Q. Chang et al.) Y.H. Gao & L. Cai, Diaporthe lithocarpi (Y.H. Gao et al.) Y.H. Gao & L. Cai, Diaporthe lutescens S.T. Huang et al., Diaporthe machili S.T. Huang et al., Diaporthe megabiguttulata M. Luo et al., Diaporthe middletonii R.G. Shivas et al., Diaporthe morindae M. Luo et al., Diaporthe nannuoshanensis S.T. Huang et al., Diaporthe nigra Brahman. & K.D. Hyde, Diaporthe orixae Q.T. Lu & Zhen Zhang, Diaporthe passifloricola Crous & M.J. Wingf., Diaporthe pimpinellae Abeywickrama et al., Diaporthe pseudoinconspicua T.G.L Oliveira et al., Diaporthe pungensis S.T. Huang et al., Diaporthe rhodomyrti C.M. Tian & Qin Yang, Diaporthe rosae M.C. Samar. & K.D. Hyde, Diaporthe rumicicola Manawas et al., Diaporthe salicicola R.G. Shivas et al., Diaporthe samaneae Monkai & Lumyong, Diaporthe subcylindrospora S.K. Huang et al., Diaporthe tectonae Doilom et al., Diaporthe tectonigena Doilom et al., Diaporthe theobromatis H. Dong et al., Diaporthe thunbergiicola Udayanga & K.D. Hyde, Diaporthe tuyouyouiae Y.P. Tan et al., Diaporthe unshiuensis F. Huang et al., Diaporthe vochysiae S.A. Noriler et al., Diaporthe xishuangbannaensis Hongsanan & K.D. Hyde, Diaporthe xylocarpi M.S. Calabon & E.B.G. Jones, Diaporthe zaobaisu Y.S. Guo & G.P. Wang, Diaporthe zhaoqingensis M. Luo et al. Citation: Pereira DS, Phillips AJL (2024). Diaporthe species on palms - integrative taxonomic approach for species boundaries delimitation in the genus Diaporthe, with the description of D. pygmaeae sp. nov. Studies in Mycology 109: 487-594. doi: 10.3114/sim.2024.109.08.},
}

@article {pmid39715720,
year = {2024},
author = {Guerrero, F and Kuang, SY},
title = {Advancing the Teaching of Equilibrium Potential: Five Small Yet Transformative Additions.},
journal = {Advances in physiology education},
volume = {},
number = {},
pages = {},
doi = {10.1152/advan.00208.2024},
pmid = {39715720},
issn = {1522-1229},
abstract = {The equilibrium potential of an ion species is a crucial concept for medical students, as it is a prerequisite to fully understanding the pathophysiology of K[+] imbalances (hyperkalemia and hypokalemia) in clinical practice. However, it remains a challenging concept because current medical physiology textbooks are too simplistic and overlook several essential points. In this article, we present a total of five small but impactful additions to advance the introduction of the equilibrium potential that will eliminate confusion and facilitate mastery-level comprehension.},
}

@article {pmid39701062,
year = {2024},
author = {Anderson, CB},
title = {Unraveling the neural basis of behavioral isolation through the lens of audition in anurans.},
journal = {Brain, behavior and evolution},
volume = {},
number = {},
pages = {1-27},
doi = {10.1159/000542575},
pmid = {39701062},
issn = {1421-9743},
abstract = {Background The origin and maintenance of species is a unifying theme in evolutionary biology. Mate choice and selection on sexual signals have emerged as powerful drivers of reproductive isolation-the key pillar of the Biological Species Concept. The mechanistic underpinnings of isolating behaviors lie in the circuit- and cellular-level properties of the brain and yet remain relatively understudied. Summary Here, I argue that temporal auditory selectivity in anuran amphibians offers a window into the proximate mechanisms of reproductive isolation. First, I discuss anuran behaviors as a longstanding neuroethological model with which to examine behavioral reproductive isolation and its neural correlates. Next, I review how modern neurobiological techniques are revealing the proximate mechanisms of the evolution of divergent mate preferences in anurans, highlighting cellular-level neural shifts in temporal coding. Finally, I discuss future research directions to reveal the neural mechanisms through which behavioral isolation is generated and maintained in anuran model systems. Key messages Anurans offer a powerful model for addressing questions about how neural barriers to gene flow arise across biological scales, and how changes in the brain contribute to speciation. Modern evolutionary neurobiology will benefit from applying new tools to this longstanding neuroethological model clade.},
}

@article {pmid39698222,
year = {2024},
author = {Ho, HC and Kawai, T},
title = {Verification of two barracudina species Lestrolepisjaponica (Tanaka, 1908) and L.philippina (Fowler, 1934) (Aulopiformes, Paralepididae).},
journal = {ZooKeys},
volume = {1220},
number = {},
pages = {79-92},
pmid = {39698222},
issn = {1313-2989},
abstract = {Examination of the type series of Lestidiumjaponica Tanaka reveals that the generally accepted concept of this species does not accord with the type series. A historical review of the literature showed that the characterization of L.japonica changed over time, and what has been recognized as "L.japonica" for more than 70 years actually represents a distinct and different species. Among the junior synonyms of "L.japonica", Paralepisphilippinus Fowler, 1934 is resurrected as a valid species herein in a new combination, Lestrolepisphilippina. Lestrolepisnigroventralis Ho, Tsai & Li is recognized as a junior synonym of L.japonica herein. Revised diagnostic characteristics for both L.japonica and L.philippina are provided, along with comments on related names to verify their nomenclatural status.},
}

@article {pmid39682651,
year = {2024},
author = {Wiggins, TJ and Peng, R and Bushnell, RV and Tobin, JK and MacLeod, DA and Du, K and Tobin, GJ and Dollery, SJ},
title = {Instrument-Free Point-of-Care Diagnostic for Leishmania Parasites.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {14},
number = {23},
pages = {},
doi = {10.3390/diagnostics14232744},
pmid = {39682651},
issn = {2075-4418},
abstract = {BACKGROUND/OBJECTIVE: Leishmaniasis is the second deadliest parasitic disease in the world, after malaria, with an estimated 1.6 million new cases each year. While cutaneous leishmaniasis can result in permanent scars from lesions after treatment, the mucocutaneous and visceral diseases can result in life-altering and life-threatening complications. Accurate species diagnosis is critical for treatment and follow-up, and while PCR-based diagnostics can provide sensitive parasite detection and species identification, they are slow, expensive, and not suitable for low-resource settings. In this publication, we describe our efforts to develop a simple, affordable, and instrument-free Leishmania DNA diagnostic that can be used in both high-tech settings and the field.

METHODS: Computational biology was utilized to design region-targeted RPA oligos and the corresponding CRISPR guides for the detection of all Leishmania species as well as the specific identification of L. (V.) panamensis as a predictor of mucocutaneous disease. Then, we executed systematic approaches for parasite lysis, RPA amplification of DNA, and fluorescent CRISPR crRNA detection.

RESULTS: We have demonstrated the ability to detect single-digit parasites without compromising the specificity in identifying single species as the proof of concept for a point-of-care diagnostic. Individual assays were carried out in succession, culminating in an unquenched fluorescent signal quantifiable over negative control.

CONCLUSIONS: The described work is the foundation which will be implemented into a three-track [all Leishmania, mucocutaneous or visceral only, and a human positive control] assay that we plan to utilize in a Funnel Adapted Sensing Tube (FAST) single use, instrument-free, and affordable diagnostic.},
}

@article {pmid39656776,
year = {2024},
author = {Schmidt, SA and Schmiedel, U and Carstens, F and Rau, AL and Rudolph-Bartsch, B},
title = {Diversity on a small scale - phylogeography of the locally endemic dwarf succulent genus Oophytum (Aizoaceae) in the Knersvlakte of South Africa.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcae207},
pmid = {39656776},
issn = {1095-8290},
abstract = {BACKGROUND AND AIMS: Oophytum (Aizoaceae) is a locally endemic genus of the extremely fast evolving subfamily Ruschioideae and consists of only two formally accepted species (O. nanum and O. oviforme). Both species are leaf-succulent dwarf shrubs and habitat specialists on quartz fields in the Knersvlakte, a renowned biodiversity hotspot in the arid winter-rainfall Succulent Karoo Biome of South Africa. Quartz fields present specialised patchy habitats with an island-like distribution in the landscape. Oophytum oviforme grows in the south-western part, whereas O. nanum covers most of the remaining Knersvlakte. These species co-occur in a small area but within different quartz islands. We investigated the effects of the patchy distribution, environmental conditions and potential effects of paleoclimatic changes on the genetics of Oophytum.

METHODS: Phylogenetic and population genetic analyses of 35 populations of the genus, covering its entire distribution area, were conducted using four cpDNA markers and an AFLP dataset. These were combined with environmental data via a principal component analysis and comparative heatmap analyses.

KEY RESULTS: The genetic pattern of the Oophytum metapopulation is a tripartite division with a northern, central and western group. This geographical pattern does not correspond to the two-species concept of Oophytum. Only the western O. oviforme populations form a monophyletic lineage, whereas the central populations of O. oviforme are genetic hybrids of O. nanum populations. The highly restricted gene flow often resulted in private gene pools with very low genetic diversity, in contrast to the hybrid gene pools of the central and edge populations.

CONCLUSIONS: Oophytum is an exceptional example of an extremely fast-evolving genus that illustrates the high speciation rate of the Ruschioideae and their success as one of the leading plant groups of the drought-prone succulent Karoo Biome. The survival strategy of these dwarf quartz-field endemics is an interplay of adaptation to diverse island habitats, highly restricted gene flow, occasional long-distance dispersal, migration, founder effects and hybridisation events within a small and restricted area caused by glacial and interglacial changing climate conditions from Pleistocene up to Present. These findings have important implications for future conservation management strategies.},
}

@article {pmid39663807,
year = {2024},
author = {Krasnov, BR and Stanko, M and Vinarski, MV and Korallo-Vinarskaya, NP and Khokhlova, IS},
title = {Variation of functional diversity structure measured as combined species dominance, functional diversity, and functional redundancy in two taxa of ectoparasitic arthropods at two spatial scales: host-associated, ecological, and geographic effects.},
journal = {Parasitology},
volume = {},
number = {},
pages = {1-10},
doi = {10.1017/S0031182024001483},
pmid = {39663807},
issn = {1469-8161},
support = {548/23//Israel Science Foundation/ ; },
abstract = {The functional diversity structure of a community can be represented as a combination of three additive components (species dominance D, functional redundancy R, and functional diversity Q) (DRQ approach in which different facets of functional differences between species are considered simultaneously). We applied this concept to assemblages of fleas and gamasid mites parasitic on small mammals at continental (across regions of the Palearctic) and regional (across sampling sites in Slovakia) scales and asked: What are the relative effects of host species, biome/habitat type, and geographic locality on the DRQ composition of a parasite assemblage? At the continental scale, regions were partitioned according to predominant biome or geographic position in a continental section. At the regional scale, sampling sites were partitioned according to habitat type or geographic locality. We tested for differences in the functional diversity structure (measured as the DRQ composition) of an ectoparasite assemblage (a) within a host species between biomes/habitat types or continental sections/localities and (b) between host species within a biome/habitat type or a continental section/locality. At both scales, the functional diversity structure of both flea and mite assemblages differed mainly between host species within a biome/habitat or geographic regions/locations, whereas differences in the DRQ composition between biomes/habitats or geographic regions/locations were only detected in a few host species. We compare our results with the results of earlier studies and conclude that the DRQ approach has an advantage over a single diversity metric and allows a better understanding of spatial variation in different facets of ectoparasite diversity.},
}

@article {pmid39658503,
year = {2024},
author = {Wang, Z and Dong, X and Chen, Y and Wang, C},
title = {Quadruplex DNA hybrid catalysts for enantioselective reactions.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {},
number = {},
pages = {e202400909},
doi = {10.1002/cbic.202400909},
pmid = {39658503},
issn = {1439-7633},
abstract = {Beyond the pivotal genetic roles of DNA, its duplex structures as chiral scaffolds interacting with metal complexes give rise to DNA hybrid catalysts for a set of aqueous-phase enantioselective reactions. Besides DNA duplex, DNA quadruplexes including G-quadruplex and i-motif show tunable structures with variable non-canonical base pairs. In this concept, based on the interaction between metal species and DNA, we classify the constructing strategies of quadruplex DNA hybrid catalysts into supramolecular, covalent and coordinative modes. Furthermore, we analyze the relationship between DNA quadruplexes and their enantioselective catalytic performance. Finally, we summarize the current challenges and prospect the future directions in DNA-based enantioselective catalysis.},
}

@article {pmid39646234,
year = {2024},
author = {Lee, GE and Li, H},
title = {A taxonomic review of Thiotricha Meyrick, 1886 (Lepidoptera, Gelechiidae, Thiotrichinae) from China, with descriptions of 84 new species.},
journal = {Zootaxa},
volume = {5449},
number = {1},
pages = {1-222},
doi = {10.11646/zootaxa.5449.1.1},
pmid = {39646234},
issn = {1175-5334},
mesh = {Animals ; Male ; Female ; China ; *Animal Distribution ; *Moths/anatomy & histology/classification ; Body Size ; Organ Size ; Animal Structures/anatomy & histology/growth & development ; },
abstract = {Thiotricha Meyrick, 1886 is a large and morphologically diverse genus in the subfamily Thiotrichinae of the family Gelechiidae. The distribution is mainly concentrated in the Old World, but only 14 species were previously known in China. In this study, we reviewed Chinese Thiotricha and examined related species distributed in Korea, Japan, Cambodia and Vietnam. As a result, 84 new species are described in the genus: T. apicispinea sp. nov., T. fasciaria sp. nov., T. atralata sp. nov., T. lativalva sp. nov., T. gracilis sp. nov., T. vittata sp. nov., T. minuta sp. nov., T. albida sp. nov., T. ateriguttata sp. nov., T. parvunca sp. nov., T. eborinicosta sp. nov., T. lacrimiformis sp. nov., T. umbrosidorsa sp. nov., T. asymmetricijuxta sp. nov., T. lunata sp. nov., T. spatulativalva sp. nov., T. uncaticula sp. nov., T. curtisacca sp. nov., T. candidipalpa sp. nov., T. spinesigna sp. nov., T. angusteproducta sp. nov., T. cornuata sp. nov., T. crassiflagella sp. nov., T. minorirugata sp. nov., T. tridentata sp. nov., T. digitiprojecta sp. nov., T. truncata sp. nov., T. peniticoncava sp. nov., T. brevissima sp. nov., T. confluens sp. nov., T. rosatorna sp. nov., T. cochlearis sp. nov., T. albimaculata sp. nov., T. rufimarginata sp. nov., T. deltaloba sp. nov., T. roseapicalis sp. nov., T. jianfengensis sp. nov., T. grandimacula sp. nov., T. latistriata sp. nov., T. contracta sp. nov., T. projecta sp. nov., T. duristria sp. nov., T. robustiseta sp. nov., T. setangulata sp. nov., T. macularis sp. nov., T. vittaticosta sp. nov., T. lineata sp. nov., T. albalata sp. nov., T. disciformis sp. nov., T. rhombiformis sp. nov., T. semota sp. nov., T. karsholti sp. nov., T. wufengensis sp. nov., T. angustifasciata sp. nov., T. anthracina sp. nov., T. longisigna sp. nov., T. cultriformis sp. nov., T. vivida sp. nov., T. magnalata sp. nov., T. rotundata sp. nov., T. guizhouensis sp. nov., T. bicolor sp. nov., T. simplex sp. nov., T. globularis sp. nov., T. xizangensis sp. nov., T. ferruginea sp. nov., T. rosebasis sp. nov., T. nullisigna sp. nov., T. nigrimaculata sp. nov., T. asymmetricosta sp. nov., T. aurea sp. nov., T. lata sp. nov., T. emarginata sp. nov., T. pediformis sp. nov., T. curviciliaris sp. nov., T. recticiliaris sp. nov., T. parvimaculata sp. nov., T. apicidisca sp. nov., T. villosa sp. nov., T. flaviterminata sp. nov., T. hamatisigna sp. nov., T. acicularis sp. nov., T. rosegrammica sp. nov. and T. canimaculata sp. nov. Sixteen species are reported from China for the first time: T. attenuata Omelko, 1993, T. prunifolivora Ueda & Fujiwara, 2005, T. albicephalata Walia & Wadhawan, 2005, T. rhodomicta Meyrick, 1918, T. scioplecta Meyrick, 1918, T. polyaula Meyrick, 1918, T. poecilopa (Meyrick, 1918), T. scatebrosa (Meyrick, 1918), T. clinopeda Meyrick, 1918, T. oxygramma Meyrick, 1918, T. hoplomacha Meyrick, 1908, T. embolarcha Meyrick, 1929, T. hexanesa Meyrick, 1929, T. acrantha Meyrick, 1908, T. scotaea Meyrick, 1908 and T. pyrphora Meyrick, 1918. Four new combinations are proposed: T. barathrota (Meyrick, 1918) comb. nov., T. leucochalca (Meyrick, 1918) comb. nov., T. poecilopa (Meyrick, 1918) comb. nov. and T. scatebrosa (Meyrick, 1918) comb. nov. Based on examination of the type specimens, T. synodonta Meyrick, 1936 is synonymized with T. trichoma. Also, we divide Chinese Thiotricha into four species groups, the subocellea-group, the pontifera-group, the confluens-group and the pancratiastis-group, based on the morphology and the molecular data. Eight species are grouped into another species group (the lata-group) based only on the morphological similarities, but the generic placement of this group needs to be re-evaluated since their morphological traits do not fit well into the generic concept. Fourteen species remain unplaced, and some species such as T. dissobola Meyrick, 1935 and T. pyrphora do not show the typical characteristics of Thiotricha, suggesting that further critical reassessment is also required for the species on the basis of additional morphological and molecular evidence. In this study, a total of 110 species are finally recognized as a result of a taxonomic study on Chinese Thiotricha. Photographs of adults and genitalia are provided for all studied taxa as well as related type specimens deposited in NHMUK and MGBA.},
}

Animals
Male
Female
China
*Animal Distribution
*Moths/anatomy & histology/classification
Body Size
Organ Size
Animal Structures/anatomy & histology/growth & development

@article {pmid39646070,
year = {2024},
author = {Bick, A and Oberrisser, P and Bastrop, R},
title = {Redescription of Manayunkia caspica Annenkova, 1929 and M. danubialis Băcescu, 1944 n. comb. (Fabriciidae, Sabellida, Polychaeta).},
journal = {Zootaxa},
volume = {5477},
number = {4},
pages = {445-464},
doi = {10.11646/zootaxa.5477.4.3},
pmid = {39646070},
issn = {1175-5334},
mesh = {Animals ; *Polychaeta/classification/anatomy & histology ; Female ; Male ; *Animal Distribution ; *Ecosystem ; Organ Size ; Body Size ; Animal Structures/anatomy & histology/growth & development ; Phylogeny ; },
abstract = {The spread of the subspecies M. caspica danubialis Băcescu, 1944, which has been found in the Danube since 1944, into the upper section of the Danube as far as Austria was the reason for describing the characters of this species and comparing it with the nominotypical subspecies M. caspica caspica Annenkova, 1929, which lives in the Caspian Sea. Both subspecies are similar in the most important diagnostic characters, such as the number of branches of the radioles and the presence and number of pseudospatulate chaetae on thoracic chaetigers. However, they differ in other, less conspicuous characters, such as the number of thoracic uncini and the length of chaetigers. But these characters vary depending on the size of the specimens. Both subspecies inhabit completely different habitats. Based on the ecological species concept, the spatially and ecologically separated populations are regarded as distinct species, M. caspica, and M. danubialis n. comb. The occurrence of transitional uncini in both species and the presence of a brood chamber in the females of M. caspica are described for the first time. The structure of the radiolar crown is also described for both species. A molecular barcode for M. danubialis n. comb., a 654 base pair fragment of cytochrome c oxidase I is presented, allowing a fast and simple identification of this species by using a robust PCR/sequencing approach.},
}

Animals
*Polychaeta/classification/anatomy & histology
Female
Male
*Animal Distribution
*Ecosystem
Organ Size
Body Size
Animal Structures/anatomy & histology/growth & development
Phylogeny

@article {pmid39645780,
year = {2024},
author = {Beard, JJ and Beaulieu, F and Knee, W and Gotoh, T},
title = {The six-spotted spider mite, Eotetranychus sexmaculatus (Riley) (Trombidiformes: Tetranychidae) in Australia, New Zealand, Japan and USA: a revised morphological and molecular-based concept, synonyms, and related species.},
journal = {Zootaxa},
volume = {5432},
number = {3},
pages = {349-378},
doi = {10.11646/zootaxa.5432.3.2},
pmid = {39645780},
issn = {1175-5334},
mesh = {Animals ; Male ; Female ; *Tetranychidae/anatomy & histology/classification/genetics ; New Zealand ; Australia ; Japan ; United States ; Phylogeny ; Animal Distribution ; Animal Structures/anatomy & histology/growth & development ; Body Size ; Organ Size ; },
abstract = {Based on morphological and molecular evidence, Eotetranychus asiaticus Ehara is confirmed as a junior synonym of E. sexmaculatus (Riley). Eotetranychus queenslandicus Manson differs to E. sexmaculatus in some morphological characters states, and currently there is insufficient evidence to confirm if it is also a junior synonym. We therefore propose that it remains a valid species until fresh material can be collected from the type host (Codiaeum variegatum (L.) A.Juss.; Euphorbiaceae) in the type location (Freshwater, Queensland, Australia) for molecular analysis and further comparisons. Eotetranychus sexmaculatus is confirmed as present in Australia and New Zealand. Our analyses indicate that specimens identified as E. sexmaculatus from avocado (Persea americana Mill.; Lauraceae) in Western Australia and New Zealand, and specimens of E. asiaticus from the type host (Ficus erecta Thunb.; Moraceae) and type location (Tomigusuku, Okinawa, Japan) are conspecific with specimens of E. sexmaculatus recently collected from the type host (Citrus sp.; Rutaceae) and type location (Florida, USA), with 0-3.6% divergence in a fragment (451 bp) of cytochrome oxidase subunit I (COI), and 0-0.3% in the ribosomal internal transcribed spacer II (ITS2) gene. Herein we redefine E. sexmaculatus, providing a revised diagnosis, notes on leg chaetotaxy, and variation in the shape of the aedeagus-which is a keystone feature critical for determining species boundaries of spider mite species that have males. Our findings also reinforce the potential of the eupathidion on the palptarsus suζ (i.e. the spinneret) for species diagnoses.},
}

Animals
Male
Female
*Tetranychidae/anatomy & histology/classification/genetics
New Zealand
Australia
Japan
United States
Phylogeny
Animal Distribution
Animal Structures/anatomy & histology/growth & development
Body Size
Organ Size

@article {pmid39639304,
year = {2024},
author = {Ma, ZS},
title = {Species specificity and specificity diversity (SSD) framework: a novel method for detecting the unique and enriched species associated with disease by leveraging the microbiome heterogeneity.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {283},
pmid = {39639304},
issn = {1741-7007},
mesh = {*Species Specificity ; *Microbiota ; Humans ; Biodiversity ; },
abstract = {BACKGROUND: Differentiating the microbiome changes associated with diseases is challenging but critically important. Majority of existing efforts have been focused on a community level, but the discerning power of community or holistic metrics such as diversity analysis seems limited. This prompts many researchers to believe that the promise should be downward to species or even strain level-effectively and efficiently identifying unique or enriched species in diseased microbiomes with statistical rigor. Nevertheless, virtually, all species-level approaches such as differential abundance and differential network analysis methods exclusively rely on species abundances without considering species distribution information, while it can be said that distribution is equally, if not more, important than abundance in shaping the spatiotemporal heterogeneity of community compositions.

RESULTS: Here, we fill the gap by developing a novel framework-species specificity and specificity diversity (SSD)-that synthesizes both abundance and distribution information to differentiate microbiomes, at both species and community scales, under different environmental gradients such as the healthy and diseased treatments. The proposed SSD framework consists of three essential elements. The first is species specificity (SS), a concept that reincarnates the traditional specialist-generalist continuum and is defined by Mariadassou et al. (Ecol Lett 18:974-82, 2015). The SS synthesizes a species' local prevalence (distribution) and global abundance information and attaches specificity measure to each species in a specific habitat (e.g., healthy or diseased treatment). The second element is a new concept to introduce here, the (species) specificity diversity (SD), which is inspired by traditional species (abundance) diversity in community ecology and measures the diversity of specificity (a proxy for metacommunity heterogeneity, essentially) with Renyi's entropy. The third element is a pair of statistical tests based on the principle of permutation tests.

CONCLUSIONS: The SSD framework can (i) identify and catalogue lists of unique species (US), significantly enriched species (ES) in each treatment based on SS and specificity permutation (SP) test and (ii) measure the holistic differences between assemblages (or treatments) based on SD and specificity diversity permutation (SDP) test. Both capacities can be enabling technologies for general comparative microbiome research including risk assessment, diagnosis, and treatment of microbiome-associated diseases.},
}

*Species Specificity
*Microbiota
Humans
Biodiversity

@article {pmid39628484,
year = {2024},
author = {Manjunathachar, HV and Kumar, B and Parthasarathi, BC and Chigure, GM and Saravanan, BC and Sankar, M and Harish, DR and de la Fuente, J and Ghosh, S},
title = {Cocktail vaccine for the management of Hyalomma anatolicum and Rhipicephalus microplus.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1471317},
pmid = {39628484},
issn = {1664-3224},
mesh = {Animals ; *Rhipicephalus/immunology ; *Tick Infestations/prevention & control/immunology/veterinary ; Rats ; Cattle ; Female ; Ixodidae/immunology ; Vaccines/immunology ; Ferritins ; Vaccines, Combined/immunology/administration & dosage ; Vaccination/methods ; Tick Control/methods ; Male ; Antigens/immunology ; },
abstract = {INTRODUCTION: Globally, ticks rank second only to mosquitoes as vectors of deadly pathogens affecting humans and first in transmitting animal pathogens, presenting a significant challenge to human wellness and sustainability of livestock-based industries. Traditional tick control via chemical acaricides impacts on the environment and has led to the emergence of multi-acaricide-resistant tick populations. Use of immunoprophylactic, along with other components of integrated tick management, holds the potential to mitigate tick infestations in a sustainable manner. To control multi-species tick infestations, the concept of a cocktail vaccine comprising of more than one antigens has emerged as a viable solution due to the inconsistent efficacy of single antigen-based immunization protocol.

METHODS: In this study, a dual antigen cocktail immunization protocol was developed targeting ferritin2 (FER2) and tropomyosin (TPM) proteins, which are associated with ticks' essential cellular and physiological functions, like blood iron homeostasis and muscle contractions.

RESULTS: Dual gene silencing of FER2 and TPM genes in Hyalomma anatolicum resulted in a 75.3% reduction in infested ticks, a 95.4% decrease in egg masses, and a complete loss of egg hatching when compared to control ticks. Microscopically, an altered ovarian cellular architecture, marked by vacuolation and reduced nucleus-to-cytoplasmic ratio were noted in the gene knocked down ticks. An immunization with cocktails of 300 µg dose of each protein, rHaFER2 and rHaTPM was standardized in a rat model and was used to immunize cross-bred (Bos indicus x B. taurus) male cattle with Montanide ISA 50V2 adjuvant on days 0, 28, and 49. A significant (p < 0.001) IgG and IgG2 antibody response was observed in the immunized animals with high IgG levels sustained until day 119 post-primary immunization, showing a 4.1-fold increase over the pre-immunization period. The animals were challenged with larvae and adults of H. anatolicum and larvae of Rhipicephalus microplus. Immunization with the cocktail antigen resulted an efficacy of 70% and 76% against H. anatolicum larvae and adults, respectively, and 54% against R. microplus infestations. Compared to single-antigen immunization, the immunization with cocktail antigens demonstrated higher protection against R. microplus and H. anatolicum ticks. The results advance the development of cocktail vaccines to control multiple tick species.},
}

Animals
*Rhipicephalus/immunology
*Tick Infestations/prevention & control/immunology/veterinary
Rats
Cattle
Female
Ixodidae/immunology
Vaccines/immunology
Ferritins
Vaccines, Combined/immunology/administration & dosage
Vaccination/methods
Tick Control/methods
Male
Antigens/immunology

@article {pmid39603011,
year = {2024},
author = {Li, W and Li, W and He, H and Wang, M and Wu, L and Yang, Y and Tu, P and Liu, W and Song, Y},
title = {Spatial-resolved metabolome imaging of petals for Forsythia viridissima and Jasminum nudiflorum using online extraction (OLE) coupled to LC-Qtof-MS.},
journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences},
volume = {1250},
number = {},
pages = {124385},
doi = {10.1016/j.jchromb.2024.124385},
pmid = {39603011},
issn = {1873-376X},
abstract = {MS imaging (MSI) is a powerful technique for investigating the spatial distribution of metabolites in complex biological samples. However, due to the absence of liquid chromatography (LC) separation in routine MSI analysis, matrix effect is obvious and isomers identification remains challenging. To overcome these shortcomings of classical MSI tools (e.g., DESI-MSI and MALDI-MSI) for isomer differentiation and insufficient datapoints for quantification, online extraction-liquid chromatogram-hybrid triple quadrupole-time-of-flight mass spectrometry (OLE-LC-Qtof-MS) platform has been developed for spatial metabolome. As a proof-of-concept, two species flowers namely Forsythia viridissima (FV) and Jasminum nudiflorum (JN) that bloom in early spring were collected, dried, and cut into small pieces (1.0 mm × 1.0 mm). All pieces successively underwent OLE-LC-Qtof-MS measurements. As a result, 46 and 41 metabolites were observed and identified from FV and JN petals, respectively. Particularly, each compound corresponded to a chromatographic peak and isomeric differentiation was achieved amongst a set of chlorogenic acid derivatives. The peak areas of high intensity metabolites were aligned and combined within either species. The datasets were individually converted into heatmaps for all compounds, 87 ones in total, and each grid of any heatmap was assigned to the original location in the petal. Then, the spatial-resolved distribution style of each compound crossing the petal was reflected by the re-organized heatmap bearing the petal shape. As expected, regio-specific occurrence and accumulation were observed for several compounds, particularly among the chlorogenic acid isomers. Above all, OLE-LC-Qtof-MS is an alternative tool for spatial-resolved metabolome attributing to the advantages of isomeric separation and reliable quantification.},
}

@article {pmid39602495,
year = {2024},
author = {Nishigaki, K},
title = {Discoveries by the genome profiling, symbolic powers of non-next generation sequencing methods.},
journal = {Briefings in functional genomics},
volume = {},
number = {},
pages = {},
doi = {10.1093/bfgp/elae047},
pmid = {39602495},
issn = {2041-2657},
abstract = {Next-generation sequencing and other sequencing approaches have made significant progress in DNA analysis. However, there are indispensable advantages in the nonsequencing methods. They have their justifications such as being speedy, cost-effective, multi-applicable, and straightforward. Among the nonsequencing methods, the genome profiling method is worthy of reviewing because of its high potential. This article first reviews its basic properties, highlights the key concept of species identification dots (spiddos), and then summarizes its various applications.},
}

@article {pmid39585232,
year = {2024},
author = {Tsang, CC and Zhao, C and Liu, Y and Lin, KPK and Tang, JYM and Cheng, KO and Chow, FWN and Yao, W and Chan, KF and Poon, SNL and Wong, KYC and Zhou, L and Mak, OTN and Lee, JCY and Zhao, S and Ngan, AHY and Wu, AKL and Fung, KSC and Que, TL and Teng, JLL and Schnieders, D and Yiu, SM and Lau, SKP and Woo, PCY},
title = {Automatic identification of clinically important Aspergillus species by artificial intelligence-based image recognition: proof-of-concept study.},
journal = {Emerging microbes & infections},
volume = {},
number = {},
pages = {2434573},
doi = {10.1080/22221751.2024.2434573},
pmid = {39585232},
issn = {2222-1751},
abstract = {While morphological examination is the most widely used for Aspergillus identification in clinical laboratories, PCR-sequencing and MALDI-TOF MS are emerging technologies in more financially-competent laboratories. However, mycological expertise, molecular biologists and/or expensive equipment are needed for these. Recently, artificial intelligence (AI), especially image recognition, is being increasingly employed in medicine for fast and automated disease diagnosis. We explored the potential utility of AI in identifying Aspergillus species. In this proof-of-concept study, using 2,813, 2,814 and 1,240 images from four clinically important Aspergillus species for training, validation and testing, respectively; the performances and accuracies of automatic Aspergillus identification using colonial images by three different convolutional neural networks were evaluated. Results demonstrated that ResNet-18 outperformed Inception-v3 and DenseNet-121 and is the best algorithm of choice because it made the fewest misidentifications (n = 8) and possessed the highest testing accuracy (99.35%). Images showing more unique morphological features were more accurately identified. AI-based image recognition using colonial images is a promising technology for Aspergillus identification. Given its short turn-around-time, minimal demand of expertise, low reagent/equipment costs and user-friendliness, it has the potential to serve as a routine laboratory diagnostic tool after the database is further expanded.},
}

@article {pmid39563522,
year = {2024},
author = {Stern, N and Leidig, J and Wolffe, G},
title = {Proof of Concept: Autonomous Machine Vision Software for Botanical Identification.},
journal = {Journal of AOAC International},
volume = {},
number = {},
pages = {},
doi = {10.1093/jaoacint/qsae091},
pmid = {39563522},
issn = {1944-7922},
abstract = {BACKGROUND: HPTLC is a widely used and accepted technique for identification of botanicals. Current best practices involve subjective comparison of HPTLC-generated images between test samples and certified botanical reference materials based on specific bands.

OBJECTIVE: This research was designed to evaluate the potential of cutting-edge machine vision-based machine learning techniques to automate identification of botanicals using native HPTLC image data.

METHOD: HPTLC images from Ginger and its closely related species and common adulterants were used to create large, synthetic datasets using a deep conditional generative adversarial network. This synthetic dataset was used to train and validate a deep convolutional neural network capable of automatically identifying new HPTLC image data. Performance of both neural networks was evaluated over time using appropriate loss functions as an indicator of their progress during learning. Validation of the overall system was measured via the accuracy of the learned model when applied to real HPTLC data.

RESULTS: The machine vision system was able to generate realistic synthetic HPTLC images that were successfully used to train a deep convolutional neural network. The resulting learned model achieved high-accuracy identification from HPTLC images corresponding to Ginger and six other related species.

CONCLUSIONS: A proof-of-concept HPTLC image-based machine vision system for the identification of botanicals was proven to be feasible and a fully working prototype was validated for several species related to Ginger.

HIGHLIGHTS: This use of an autonomous machine-vision system for botanical identification removed the subjectivity inherent to human-based evaluation. The learned model also accurately evaluated botanical HPTLC images significantly faster than its human counterpart, which could save both time and resources.},
}

@article {pmid39552431,
year = {2024},
author = {Torres-Nieves, GM and López-Hernández, DD and Locke, SA},
title = {Genomic characterization of a new species of Pseudoparacreptotrema (Digenea: Allocreadiidae) from Puerto Rico, with comments on the biogeography of the genus.},
journal = {Journal of helminthology},
volume = {98},
number = {},
pages = {e72},
doi = {10.1017/S0022149X24000567},
pmid = {39552431},
issn = {1475-2697},
mesh = {Animals ; *Trematoda/genetics/classification/anatomy & histology/isolation & purification ; Puerto Rico ; *Phylogeny ; *Trematode Infections/parasitology/veterinary ; DNA, Helminth/genetics ; RNA, Ribosomal, 28S/genetics ; Smegmamorpha/parasitology ; Fish Diseases/parasitology ; Genome, Mitochondrial ; Phylogeography ; DNA, Ribosomal/genetics ; Genome, Helminth ; Genomics ; },
abstract = {In this study, we describe a new species of Pseudoparacreptotrema (Allocreadiidae) from the mugilid Dajaus monticola collected in western Puerto Rico, where no allocreadiid has previously been reported, bringing the number of species in this genus to seven (five in D. monticola, two in Profundulus spp.). The new parasite species is distinguished from congeners by its overall size, oral-to-ventral sucker size ratio, pharynx size, cirrus sac, and oral lobe morphology, and by 0.64%-3.45% divergence in a 1019-bp alignment of 28S. We build on prior suggestions that the current concept of P. agonostomi likely includes multiple species and provide the first mitochondrial data (whole mitochondrial genome) as well as the complete nuclear rDNA array from Pseudoparacreptotrema to facilitate future phylogenetic work. Within the Allocreadiidae, phylogenetic analysis of mitochondrial genomes and 28S provides conflicting topologies for the placement of Pseudoparacreptotrema and Allocreadium. The 28S phylogeny of six species of Pseudoparacreptotrema resembles that of four lineages of D. monticola in that in both host and parasite, Pacific coastal lineages branch earliest, and a Caribbean lineage is more recently evolved.},
}

Animals
*Trematoda/genetics/classification/anatomy & histology/isolation & purification
Puerto Rico
*Phylogeny
*Trematode Infections/parasitology/veterinary
DNA, Helminth/genetics
RNA, Ribosomal, 28S/genetics
Smegmamorpha/parasitology
Fish Diseases/parasitology
Genome, Mitochondrial
Phylogeography
DNA, Ribosomal/genetics
Genome, Helminth
Genomics

@article {pmid39530692,
year = {2024},
author = {Muñoz-Castro, AR},
title = {Bonding Interaction Within Concentric Structural Layers in Gold Superatoms. The Concentric Bond.},
journal = {Chemphyschem : a European journal of chemical physics and physical chemistry},
volume = {},
number = {},
pages = {e202400892},
doi = {10.1002/cphc.202400892},
pmid = {39530692},
issn = {1439-7641},
abstract = {Ligand-protected gold clusters display a rich structural diversity, featuring remarkable structures such as Au25(SR)18, Au55(PPh3)12Cl6, and CuAu144(SR)603+, involving a central core composed of consecutive layers. The respective Au@Au12, Au@Au12@Au42, and Cu@Au12@Au42@Au60cores with concentric structural layers enable a variable bonding/antibonding character between the electronic shells ascribed to each layer. Here, we rationalize the bonding within concentric structural layers in order to gain a further understanding of the related bonding patterns in such species. The proposed bonding concept differs from the classical situation in adjacent atoms, now being considered between concentric shells and, thus, coined as the concentric bond. From this approach, the bonding/antibonding character of each concentric shell is evaluated, and its contribution to the overall bonding is discussed. The concentric bond enables building a clear picture of the bonding acting in the overall cluster under the superatom concept. Such an approach expands the understanding of multi-layered cluster cores and is useful to further rationalize the bonding situation in metallic nanostructures.},
}

@article {pmid39503946,
year = {2024},
author = {Lehtonen, S},
title = {Seeking the first phylogenetic method-Edvard A. Vainio (1853-1929) and his troubled endeavour towards a natural lichen classification in the late nineteenth century Finland.},
journal = {History and philosophy of the life sciences},
volume = {46},
number = {4},
pages = {37},
pmid = {39503946},
issn = {1742-6316},
mesh = {*Phylogeny ; *Lichens/classification ; History, 19th Century ; Finland ; History, 20th Century ; Classification/methods ; },
abstract = {Edvard August Vainio was a world-renowned Finnish lichenologist. In Finland, however, he was a controversial person due to his strong pro-Finnish political views. Equally disputed was his opinion that systematics should be based on evolutionary theory and phylogenetic thinking. Vainio was familiar with the ideas of the early German phylogeneticists-especially those of Carl Wilhelm von Nägeli - and, applying them, aimed to create an exact method for building a natural classification of lichens already at the end of the nineteenth century. In this respect, Vainio was a true pioneer, as no actual phylogenetic method had yet been developed. In the general spirit of the time, Vainio focused on finding the ancestors of species and other taxa by comparing primitive and derived features of homologous characters. However, Vainio already understood the concept of sister groups in 1880, the identification of which is the basis of all modern phylogenetic research. Nevertheless, the distinctive method developed by Vainio was not so much focused on the construction of a phylogenetic tree, but on revealing the origin of species through the differentiation and fixation of their polymorphic variation. Indeed, Vainio's species concept is surprisingly similar to the phylogenetic species concepts presented a hundred years later. Although in many ways progressive, Vainio's views did not influence the development of phylogenetics more widely, but his discussions are nevertheless a valuable source to understanding the early development of phylogenetic theory.},
}

*Phylogeny
*Lichens/classification
History, 19th Century
Finland
History, 20th Century
Classification/methods

@article {pmid39480207,
year = {2024},
author = {Blyden, K and Thomas, J and Emami-Naeini, P and Fashina, T and Conrady, CD and Albini, TA and Carag, J and Yeh, S},
title = {Emerging Infectious Diseases and the Eye: Ophthalmic Manifestations, Pathogenesis, and One Health Perspectives.},
journal = {International ophthalmology clinics},
volume = {64},
number = {4},
pages = {39-54},
pmid = {39480207},
issn = {1536-9617},
mesh = {Humans ; *Communicable Diseases, Emerging/virology ; Eye Diseases/etiology/virology ; Animals ; Eye Infections/virology ; },
abstract = {Infectious diseases may lead to ocular complications including uveitis, an ocular inflammatory condition with potentially sight-threatening sequelae, and conjunctivitis, inflammation of the conjunctiva. Emerging infectious pathogens with known ocular findings include Ebola virus, Zika virus, Avian influenza virus, Nipah virus, severe acute respiratory syndrome coronaviruses, and Dengue virus. Re-emerging pathogens with ocular findings include Toxoplasma gondii and Plasmodium species that lead to malaria. The concept of One Health involves a collaborative and interdisciplinary approach to achieve optimal health outcomes by combining human, animal, and environmental health factors. This approach examines the interconnected and often complex human-pathogen-intermediate host interactions in infectious diseases that may also result in ocular disease, including uveitis and conjunctivitis. Through a comprehensive review of the literature, we review the ophthalmic findings of emerging infectious diseases, pathogenesis, and One Health perspectives that provide further insight into the disease state. While eye care providers and vision researchers may often focus on key local aspects of disease process and management, additional perspective on host-pathogen-reservoir life cycles and transmission considerations, including environmental factors, may offer greater insight to improve outcomes for affected individuals and stakeholders.},
}

Humans
*Communicable Diseases, Emerging/virology
Eye Diseases/etiology/virology
Animals
Eye Infections/virology

@article {pmid39468698,
year = {2024},
author = {Bouvarel, L and Liu, D and Zheng, C},
title = {Visualizing genomic evolution in Caenorhabditis through WormSynteny.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1009},
pmid = {39468698},
issn = {1471-2164},
support = {Excellent Young Scientists Fund for Hong Kong and Macau, 32122002//National Natural Science Foundation of China/ ; GRF 17107021, GRF 17106322, GRF 17105523, and CRF C7026-20G//Research Grants Council, University Grants Committee/ ; HMRF 09201426//Health Bureau/ ; },
mesh = {Animals ; *Synteny ; *Evolution, Molecular ; *Caenorhabditis/genetics ; Genomics/methods ; Gene Duplication ; Caenorhabditis elegans/genetics ; Software ; Genome, Helminth ; Phylogeny ; Sequence Alignment ; },
abstract = {Understanding the syntenic relationships among genomes is crucial to elucidate the genomic mechanisms that drive the evolution of species. The nematode Caenorhabditis is a good model for studying genomic evolution due to the well-established biology of Caenorhabditis elegans and the availability of > 50 genomes in the genus. However, effective alignment of more than ten species in Caenorhabditis has not been conducted before, and there is currently no tool to visualize the synteny of more than two species. In this study, we used Progressive Cactus, a recently developed multigenome aligner, to align the genomes of eleven Caenorhabditis species. Through the progressive alignment, we reconstructed nine ancestral genomes, analyzed the mutational types that cause genomic rearrangement during speciation, and found that insertion and duplication are the major driving forces for genome expansion. Dioecious species appear to expand their genomes more than androdioecious species. We then built an online interactive app called WormSynteny to visualize the syntenic relationship among the eleven species. Users can search the alignment dataset using C. elegans query sequences, construct synteny plots at different genomic scales, and use a set of options to control alignment output and plot presentation. We showcased the use of WormSynteny to visualize the syntenic conservation of one-to-one orthologues among species, tandem and dispersed gene duplication in C. elegans, and the evolution of exon and intron structures. Importantly, the integration of orthogroup information with synteny linkage in WormSynteny allows the easy visualization of conserved genomic blocks and disruptive rearrangement. In conclusion, WormSynteny provides immediate access to the syntenic relationships among the most widely used Caenorhabditis species and can facilitate numerous comparative genomics studies. This pilot study with eleven species also serves as a proof-of-concept to a more comprehensive larger-scale analysis using hundreds of nematode genomes, which is expected to reveal mechanisms that drive genomic evolution in the Nematoda phylum. Finally, the WormSynteny software provides a generalizable solution for visualizing the output of Progressive Cactus with interactive graphics, which would be useful for a broad community of genome researchers.},
}

Animals
*Synteny
*Evolution, Molecular
*Caenorhabditis/genetics
Genomics/methods
Gene Duplication
Caenorhabditis elegans/genetics
Software
Genome, Helminth
Phylogeny
Sequence Alignment

@article {pmid39464388,
year = {2024},
author = {Arndt, SS and van der Staay, FJ and Goerlich, VC},
title = {Near and Dear? If animal welfare concepts do not apply to species at a great phylogenetic distance from humans, what concepts might serve as alternatives?.},
journal = {Animal welfare (South Mimms, England)},
volume = {33},
number = {},
pages = {e38},
pmid = {39464388},
issn = {2054-1538},
abstract = {A wide range of animal taxa, including vertebrates and invertebrates, are controlled or kept by humans. They may be used as pets, for recreation, sport and hobbies, as working animals, as producers of animal-derived (food) products or as biomedical models in research. There is a need for clear guidance on the treatment of animals, regardless of their phylogenetic distance from humans. Current animal welfare concepts, which emphasise animal sentience and the ability of animals to experience negative or positive mental states, are limited in scope to a small proportion of the animal kingdom, as the vast majority of species are (currently) thought to lack sentience. We discuss four options for addressing the question of which basic concept(s) could be used to derive guidelines for the treatment of animal species, sentient or non-sentient: (1) alternative concepts tailored to specific groups of species; (2) 'welfare' concepts not presupposing sentience; (3) the precautionary principle; or (4) the concept of animal integrity. Since questions regarding the appropriate treatment of animals, including species with a large phylogenetic distance from humans, have an ethical/moral dimension, we also address who counts morally and how much, and how animals should be treated given their moral status. We suggest that the concept of animal integrity, possibly complemented and extended by the concept of habitat/ecosystem integrity, is suitable for application to all species. However, a current concept of animal welfare should serve as the primary basis for guidance on how to treat species that are sentient and capable of experiencing emotions.},
}

@article {pmid39402017,
year = {2024},
author = {Waldock, C and Wegscheider, B and Josi, D and Calegari, BB and Brodersen, J and Jardim de Queiroz, L and Seehausen, O},
title = {Deconstructing the geography of human impacts on species' natural distribution.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8852},
pmid = {39402017},
issn = {2041-1723},
mesh = {Animals ; *Biodiversity ; *Conservation of Natural Resources ; *Fishes ; Humans ; Switzerland ; *Geography ; Ecosystem ; Endangered Species/statistics & numerical data ; Artificial Intelligence ; Fresh Water ; Anthropogenic Effects ; Animal Distribution ; },
abstract = {It remains unknown how species' populations across their geographic range are constrained by multiple coincident natural and anthropogenic environmental gradients. Conservation actions are likely undermined without this knowledge because the relative importance of the multiple anthropogenic threats is not set within the context of the natural determinants of species' distributions. We introduce the concept of a species 'shadow distribution' to address this knowledge gap, using explainable artificial intelligence to deconstruct the environmental building blocks of current species distributions. We assess shadow distributions for multiple threatened freshwater fishes in Switzerland which indicated how and where species respond negatively to threats - with negative threat impacts covering 88% of locations inside species' environmental niches leading to a 25% reduction in environmental suitability. Our findings highlight that conservation of species' geographic distributions is likely insufficient when biodiversity mapping is based on species distribution models, or threat mapping, without also quantifying species' expected or shadow distributions. Overall, we show how priority actions for nature's recovery can be identified and contextualised within the multiple natural constraints on biodiversity to better meet national and international biodiversity targets.},
}

Animals
*Biodiversity
*Conservation of Natural Resources
*Fishes
Humans
Switzerland
*Geography
Ecosystem
Endangered Species/statistics & numerical data
Artificial Intelligence
Fresh Water
Anthropogenic Effects
Animal Distribution

@article {pmid39398478,
year = {2024},
author = {Brukental, H and Doron-Faigenboim, A and Bar-Ya'akov, I and Harel-Beja, R and Trainin, T and Hatib, K and Aharon, S and Azoulay-Shemer, T and Holland, D},
title = {Exploring the wild almond, Prunus arabica (Olivier), as a genetic source for almond breeding.},
journal = {Tree genetics & genomes},
volume = {20},
number = {5},
pages = {37},
pmid = {39398478},
issn = {1614-2942},
abstract = {UNLABELLED: During the process of almond (Prunus dulcis) domestication, essential traits, which gave plants the plasticity for facing unstable environmental conditions, were lost. In general, the domestication process often narrows the natural genetic diversity. Modern selections (i.e., breeding programs) dramatically accelerated this genetic bottleneck trend to a few successful almond cultivars, which are presently the founders of most commercial cultivars worldwide. The concept of utilizing wild species as a source for important traits and for the enrichment of the gene pool was deeply discussed in previous studies. However, in almonds and other Prunus species, deliberate utilization of wild species as a genetic resource for breeding programs is quite rare. To address these significant challenges, we generated an interspecific F1 population between the Israeli almond cultivar Um el Fahem (UEF) and a specimen of a local wild almond species, Prunus arabica (P. arabica), originating from the Judea desert. This interspecific F1 population possesses high phenotypic variability, and sixteen segregating traits were phenotyped. Among the segregating traits, we were able to genetically associate six agriculturally important traits, such as leaf chlorophyll content (LCC), flower size, and fruit size. The alleles for Self-Compatibility (SC) and kernel bitterness were previously mapped in almond and were reexamined on the background of the distinctive wild genetic material of P. arabica. Finally, phenotypic interactions between traits were suggested, such as rootstock perimeter and canopy area that were positively correlated with total yield in the F1 population. This study is a first step towards developing a well-characterized almond interspecies genetic population. The availability of such a genetic tool with detailed phenotypic analysis is crucial to address and explore the profound influence of almond wild species in Prunus genetic research and breeding. By using the interspecific population as the infrastructure, we show the advantages and importance of utilizing wild relatives.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11295-024-01668-4.},
}

@article {pmid39386977,
year = {2024},
author = {Ortiz-Morazán, AS and Moncada, MM and Escobar, D and Cabrera-Moreno, LA and Fontecha, G},
title = {Coevolutionary Analysis of the Pfs47-P47Rec Complex: A Bioinformatics Approach.},
journal = {Bioinformatics and biology insights},
volume = {18},
number = {},
pages = {11779322241284223},
pmid = {39386977},
issn = {1177-9322},
abstract = {BACKGROUND: The ability to predict and comprehend molecular interactions offers significant insights into the biological functions of proteins. The interaction between surface protein 47 of Plasmodium falciparum (Pfs47) and receptor of the protein 47 (P47Rec) has attracted increased attention due to their role in parasite evasion of the mosquito immune system and the concept of geographical coevolution between species. The aims of this study were as follows: to apply a bioinformatics approach to investigate the interaction between Pfs47 and P47Rec proteins and to identify the potential binding sites, protein orientations and receptor specificity sites concerning the geographical origins of the vectors and the parasite.

METHODS: Public sequences of the pfs47 and p47rec genes were downloaded and subsequently filtered to predict functional and structural annotations of the Pfs47-P47Rec complex. Phylogenetic analyses of both proteins were carried out. In addition, the p47Rec gene was subjected to sequencing and subsequent analysis in 2 distinct Anopheles species collected in Honduras.

RESULTS: The examination of motifs reveals a significant degree of conservation in pfs47, suggesting that Pfs47 might have undergone recent evolutionary development and adaptation. Structural models and docking analyses supported the theory of selectivity of Plasmodium falciparum strains towards their vectors in diverse geographical regions. A detailed description of the putative interaction between the Pfs47-P47Rec complex is shown.

CONCLUSIONS: The study identifies coevolutionary patterns between P47Rec and Pfs47 related to the speciation and geographic dispersion of Anopheles species and Plasmodium falciparum, with Pfs47 evolving more recently than P47Rec. This suggests a link between the parasite's adaptability and existing anopheline species across different regions. P47Rec likely has a cytoplasmic localization due to its lack of membrane attachment elements. However, these findings are based on simulations and require validation through methods like cryo-electron microscopy. A significant limitation is the scarcity of sequences in global databases, which restricts precise interaction modelling. Further research with diverse parasite isolates and anopheline species is recommended to enhance understanding of these proteins' structure and interaction.},
}

@article {pmid39364037,
year = {2024},
author = {Burbrink, FT and Myers, EA and Pyron, RA},
title = {Understanding species limits through the formation of phylogeographic lineages.},
journal = {Ecology and evolution},
volume = {14},
number = {10},
pages = {e70263},
pmid = {39364037},
issn = {2045-7758},
abstract = {The outcomes of speciation across organismal dimensions (e.g., ecological, genetic, phenotypic) are often assessed using phylogeographic methods. At one extreme, reproductively isolated lineages represent easily delimitable species differing in many or all dimensions, and at the other, geographically distinct genetic segments introgress across broad environmental gradients with limited phenotypic disparity. In the ambiguous gray zone of speciation, where lineages are genetically delimitable but still interacting ecologically, it is expected that these lineages represent species in the context of ontology and the evolutionary species concept when they are maintained over time with geographically well-defined hybrid zones, particularly at the intersection of distinct environments. As a result, genetic structure is correlated with environmental differences and not space alone, and a subset of genes fail to introgress across these zones as underlying genomic differences accumulate. We present a set of tests that synthesize species delimitation with the speciation process. We can thereby assess historical demographics and diversification processes while understanding how lineages are maintained through space and time by exploring spatial and genome clines, genotype-environment interactions, and genome scans for selected loci. Employing these tests in eight lineage-pairs of snakes in North America, we show that six pairs represent 12 "good" species and that two pairs represent local adaptation and regional population structure. The distinct species pairs all have the signature of divergence before or near the mid-Pleistocene, often with low migration, stable hybrid zones of varying size, and a subset of loci showing selection on alleles at the hybrid zone corresponding to transitions between distinct ecoregions. Locally adapted populations are younger, exhibit higher migration, and less ecological differentiation. Our results demonstrate that interacting lineages can be delimited using phylogeographic and population genetic methods that properly integrate spatial, temporal, and environmental data.},
}

@article {pmid39351611,
year = {2024},
author = {Singer, SD and Mukthar, MM and Subedi, U and Poudel, H and Chen, G and Foroud, N and Chatterton, S},
title = {CRISPR/Cas-Mediated Gene Editing in Plant Immunity and Its Potential for the Future Development of Fungal, Oomycete, and Bacterial Pathogen-Resistant Pulse Crops.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15174},
pmid = {39351611},
issn = {1365-3040},
support = {//The authors are grateful for the financial support provided by Agriculture and Agri-Food Canada, the S-CAP ASC-06 Pulse Cluster, Saskatchewan Agriculture Development Fund and Beef Cattle Research Council./ ; },
abstract = {Pulses provide myriad health benefits and are advantageous in an environmental context as a result of their leguminous nature. However, phytopathogenic fungi, oomycetes and bacteria pose a substantial threat to pulse production, at times leading to crop failure. Unfortunately, existing disease management strategies often provide insufficient control, and there is a clear need for the development of new pulse cultivars with durable and broad-spectrum disease resistance. CRISPR/Cas-mediated gene editing has proven its potential for rapidly enhancing disease resistance in many plant species. However, this tool has only very recently been applied in pulse species, and never in the context of plant immunity. In this review, we examine the recent successful utilization of this technology in pulse species for proof-of-concept or the improvement of other traits. In addition, we consider various genes that have been edited in other plant species to reduce susceptibility to pathogens, and discuss current knowledge regarding their roles in pulses. Given the functional conservation of the selected genes across diverse plant species, there is a high likelihood that their editing would elicit similar effects in non-oilseed grain legumes, thus providing a suite of potential targets for CRISPR/Cas-mediated gene editing to promote pulse crop productivity in coming years.},
}

@article {pmid39336608,
year = {2024},
author = {Ballester-Torres, I and Nedeljković, Z and Aguado-Aranda, P and Vujić, A and Marcos-García, MÁ and Ricarte, A},
title = {Resolving the Taxonomy of Mountain Syrphidae (Diptera) in the Iberian Peninsula: The Species Group of Cheilosia melanura Becker, 1894.},
journal = {Insects},
volume = {15},
number = {9},
pages = {},
pmid = {39336608},
issn = {2075-4450},
support = {PGC2018-095851-A-C65//Ministerio de Ciencia, Innovación y Universidades/ ; C04.I01.P01.02.05//European Union/ ; },
abstract = {The largest genus of Palaearctic Syrphidae, Cheilosia Meigen, 1822 (Syrphidae: Rhingiini), is currently under revision in the Ibero-Balearic region (Iberian Peninsula + Balearic Islands). Prior to this study, various species groups with putative phylogenetic support were defined for this genus of complex taxonomy. The group of Cheilosia melanura Becker, 1894 includes species distributed all over Europe, with some of these species being similar each other in both morphology and genetics. After recent fieldwork in different Iberian localities and consultation of entomological collections, a new species from Sierra Nevada (Granada, Spain) was uncovered, described, and illustrated. Data on diagnostic characters, intraspecific variability, and adult biology were also provided. Maximum likelihood analyses of the fragment "C" of the 5' end of the cytochrome c oxydase subunit I (COI-5') and complete COI-5' were performed to explore and support morphological species concepts within the group. The Spanish-endemic Cheilosia andalusiaca Torp Pedersen, 1971 is recognised here to be part of the C. melanura group based both on morphological and molecular evidence. Cheilosia carbonaria Egger, 1860 and Cheilosia cynocephala Loew, 1840 from the Iberian Peninsula are reported for the first time based on specimens originating in the Spanish Pyrenees. An identification key for the Iberian species of the C. melanura group is provided.},
}

@article {pmid39336088,
year = {2024},
author = {Ross, AT and Stauffer, JR},
title = {Morphological Analysis of a New Species of Micropterus (Teleostei: Centrarchidae) from Lake Erie, PA, USA.},
journal = {Biology},
volume = {13},
number = {9},
pages = {},
pmid = {39336088},
issn = {2079-7737},
support = {Pen04584//Penn State Agriculture Experiment/ ; },
abstract = {This previously undescribed species of Micropterus is described from collections in Lake Erie. The species was first recognized by the tri-colored tail of juveniles. This tri-colored tail, the presence of bold parallel lines ventral to the lateral band, and scales in the inter-radial membranes of the dorsal fin distinguish it from Micropterus nigricans. The large mouth that extends past the eye distinguishes it from Micropterus punctulatus.},
}

@article {pmid39286928,
year = {2024},
author = {Giustiniano, M},
title = {Isonitrile Photochemistry: A Functional Group Class Coming in from the Cold.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e202402350},
doi = {10.1002/chem.202402350},
pmid = {39286928},
issn = {1521-3765},
abstract = {Starting from a historical background that acknowledges isonitriles as a neglected class of compounds due to their unpleasant smell and hardly controlled reaction conditions with open shell species, the present concept article aims at highlighting the seeds of the modern isonitrile photochemistry. Representative essential transformations achieved via either UV light irradiation or radical initiators at high temperatures are brought into play to draw a parallel with the current literature relying on the exploitation of visible light photochemical methods. Such a comparison points out the potential of this enabling technology to further expand the scope of isonitrile chemistry and the unmet challenges which makes it a very stimulating field.},
}

@article {pmid39227900,
year = {2024},
author = {Muñoz-Castro, AR},
title = {Beyond The Sphere. Au20(PR3)8 as a Spherical Aromatic Cuboctahedron Cluster.},
journal = {Chemistry, an Asian journal},
volume = {},
number = {},
pages = {e202400670},
doi = {10.1002/asia.202400670},
pmid = {39227900},
issn = {1861-471X},
abstract = {The icosahedral Au135+ core is a recurrent building block in ligand-protected gold clusters involving an 8-cluster electron 1S21P6 electronic shell. Such a prototypical structure enables a spherical aromatic behavior as given by long-range magnetic shielding. Recently, the Au20(tBu3P)8 cluster featuring a contrasting cuboctahedral core with formally neutral gold atoms appears as a novel core architecture with the potential to be considered as another potential building block towards functional nanostructures. Here, we explore the ligand-core interaction and spherical aromatic characteristics of Au20(tBu3P)8, in order to provide a direct connection to classical icosahedral spherical aromatic compounds, now involving a cuboctahedral core structure. Such characteristics suggest rationalization of their robustness in terms of certain electron counts, enabling a shielding cone property in ligand-protected metallic clusters, which favors bridging organic and inorganic planar/spherical aromatic species towards the unification of the aromaticity concept and designing guidelines for further achievements.},
}

@article {pmid39209587,
year = {2024},
author = {Limborg, MT and Winther-Have, CS and Morueta-Holme, N and Gilbert, MTP and Rasmussen, JA},
title = {The overlooked biodiversity loss.},
journal = {Trends in ecology & evolution},
volume = {39},
number = {10},
pages = {889-891},
doi = {10.1016/j.tree.2024.08.001},
pmid = {39209587},
issn = {1872-8383},
mesh = {*Biodiversity ; *Extinction, Biological ; Ecosystem ; Host Microbial Interactions ; Conservation of Natural Resources ; Biological Coevolution ; Microbiota ; Animals ; },
abstract = {As most life-forms exist as holobionts, reduction of host-level biodiversity drives parallel habitat losses to their host-adapted microorganisms. The holobiont concept helps us to understand how species are habitats for - often ignored - coevolved microorganisms also worthy of conservation. Indeed, loss of host-associated microbial biodiversity may accelerate the extinction risks of their host.},
}

*Biodiversity
*Extinction, Biological
Ecosystem
Host Microbial Interactions
Conservation of Natural Resources
Biological Coevolution
Microbiota
Animals

@article {pmid39204634,
year = {2024},
author = {Bakalin, VA and Vilnet, AA and Klimova, KG and Nguyen, VS and Choi, SS},
title = {Gottschelia (Gottscheliaceae, Marchantiophyta) in Indochina.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {16},
pages = {},
pmid = {39204634},
issn = {2223-7747},
support = {122040800088-5//Botanical Garden Institute research project "Bryophytes and lichens of Pacific Asia: taxonomy, floristic composition, patterns of species distribution"/ ; IEBR ĐT.5-24//Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology/ ; NIE-A-2023-01//National Eco-system Survey of the National Institute of Ecology/ ; },
abstract = {Gottschelia, collected for the first time in Indochina, inspired an attempt to review the genus phylogeny to identify a more precise position of Indochinese plants. The genetic distance between African and Asian populations of G. schizopleura sensu lato was confirmed. The two groups should be treated as different species. A new combination, G. microphylla comb. nov., has been proposed for Asian plants. Aside from molecular genetics, distinguishing this species from the presumable strictly African G. schizopleura is also possible by morphological characteristics, as well as by its distribution. At the same time, at least three groups are distinguished among Asian haplotypes of G. microphylla, each of which can be interpreted as a species or, at least, subspecies. A morphological description, intravital photographs of the general habitat, and details of the morphological structures are provided. The position of Gottschelia in the phylogenetic schema of Jungermanniales does not allow us to attribute it to any of the known families and forces us to describe a new family, Gottscheliaceae, which is phylogenetically somewhat related to the Chaetophyllopsidaceae re-evaluated here and very different from Gottscheliaceae morphologically.},
}

@article {pmid39181786,
year = {2024},
author = {Lin, C and Lu, Y and Miao, J and Ma, Z and Choi, Y and Yang, Y and Dong, C and Shen, J and Park, JH and Zhang, K},
title = {Quasi-homogeneous photoelectrochemical organic transformations for tunable products and 100% conversion ratio.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2024.08.014},
pmid = {39181786},
issn = {2095-9281},
abstract = {Photoelectrochemical (PEC) organic transformation at the anode coupled with cathodic H2 generation is a potentially rewarding strategy for efficient solar energy utilization. Nevertheless, achieving the full conversion of organic substrates with exceptional product selectivity remains a formidable hurdle in the context of heterogeneous catalysis at the solid/liquid interface. Here, we put forward a quasi-homogeneous catalysis concept by using the reactive oxygen species (ROS), such as ·OH, H2O2 and SO4[•-], as a charge transfer mediator instead of direct heterogeneous catalysis at the solid/liquid interface. In the context of glycerol oxidation, all ROS exhibited a preference for first-order reaction kinetics. These ROS, however, showcased distinct oxidation mechanisms, offering a range of advantages such as ∼ 100 % conversion ratios and the flexibility to tune the resulting products. Glycerol oxidative formic acid with Faradaic efficiency (FE) of 81.2 % was realized by the H2O2 and ·OH, while SO4[•-] was preferably for glycerol conversion to C3 products like glyceraldehyde and dihydroxyacetone with a total FE of about 80 %. Strikingly, the oxidative coupling of methane to ethanol was successfully achieved in our quasi-homogeneous system, yielding a remarkable production rate of 12.27 μmol h[-1] and an impressive selectivity of 92.7 %. This study is anticipated to pave the way for novel approaches in steering solar-driven organic conversions by manipulating ROS to attain desired products and conversion ratios.},
}

@article {pmid39152781,
year = {2024},
author = {Cui, J and Yang, Y and Zhang, Y and Yang, X and Liu, Y and Tan, J and Wu, S and Liu, Z},
title = {Luminescence performance and antioxidant properties of selenium carbon dots prepared from selenium-hyperaccumulating plants.},
journal = {Luminescence : the journal of biological and chemical luminescence},
volume = {39},
number = {8},
pages = {e4867},
doi = {10.1002/bio.4867},
pmid = {39152781},
issn = {1522-7243},
support = {21565013//National Science Foundation of China/ ; PT082204//Hubei Engineering Research Center of Selenium Food Nutrition and Health Intelligent Technology/ ; PT082305//Hubei Engineering Research Center of Selenium Food Nutrition and Health Intelligent Technology/ ; Q20221906//Science and Technology Plan Research Project of Hubei Education Department/ ; OIR202304Z//Hubei Provincial Clinical Medical Research Center for Nephropathy/ ; },
mesh = {*Selenium/chemistry ; *Carbon/chemistry ; *Quantum Dots/chemistry ; *Antioxidants/chemistry/pharmacology ; *Luminescence ; Humans ; Reactive Oxygen Species/metabolism ; Plants/chemistry/metabolism ; },
abstract = {Heteroatom doping has become an important method to enhance the performance of traditional carbon dots in modern times. Selenium (Se) is a nonmetallic trace element with excellent redox properties and is therefore essential for health. Previous studies have mainly used pure chemicals as selenium sources to prepare selenium-doped carbon dots (Se-CDs), but the precursor pure chemicals have the disadvantages of being expensive, difficult to obtain, toxic, and having low fluorescence yields of the synthesised Se-CDs. Fortunately, our team achieved successful synthesis of selenium carbon dots, exhibiting excellent luminescence and biocompatibility through a one-step hydrothermal method using selenium-enriched natural plant Cardamine, as an alternative to selenium chemicals. This approach aims to address the limitations and high costs associated with Se-CDs precursors. Electron spin resonance spectroscopy (ESR) and cellular antioxidant tests have confirmed the protective ability of Se-CDs against oxidative damage induced by excessive reactive oxygen species (ROS). A new concept and method for synthesizing selenium carbon dots on the basis of biomass, a rationale for the antioxidant effects on human health, and a wide range of development and application possibilities were offered in this work.},
}

*Selenium/chemistry
*Carbon/chemistry
*Quantum Dots/chemistry
*Antioxidants/chemistry/pharmacology
*Luminescence
Humans
Reactive Oxygen Species/metabolism
Plants/chemistry/metabolism

@article {pmid39114565,
year = {2024},
author = {van Achterberg, C and Shaw, MR and Fernandez-Triana, J and Quicke, DLJ},
title = {Resolution of the Aleiodesseriatus (Herrich-Schäffer, 1838)-aggregate in the western Palaearctic (Hymenoptera, Braconidae, Rogadinae), with description of a new species.},
journal = {ZooKeys},
volume = {1208},
number = {},
pages = {241-258},
pmid = {39114565},
issn = {1313-2989},
abstract = {Two European species are recognised and characterised within the traditional Aleiodesseriatus species concept, based initially on DNA barcoding but with supporting, although slight and sometimes unreliable, morphological differences. Aleiodespseudoseriatus sp. nov. is described and a neotype is designated for Rogasseriatus Herrich-Schäffer, 1838. Specimens from the Russian Far East were also DNA barcoded and were found to belong to a new species distinct from the two European taxa. The two European species were found to use different lithosiine hosts.},
}

@article {pmid39091844,
year = {2024},
author = {Pan, B and Bruno, M and Macfarlan, TS and Akera, T},
title = {Meiosis-specific decoupling of the pericentromere from the kinetochore.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39091844},
issn = {2692-8205},
support = {ZIA HD008933/ImNIH/Intramural NIH HHS/United States ; ZIA HL006249/ImNIH/Intramural NIH HHS/United States ; },
abstract = {The primary constriction site of the M-phase chromosome is an established marker for the kinetochore position, often used to determine the karyotype of each species. Underlying this observation is the concept that the kinetochore is spatially linked with the pericentromere where sister-chromatids are most tightly cohered. Here, we found an unconventional pericentromere specification with sister chromatids mainly cohered at a chromosome end, spatially separated from the kinetochore in Peromyscus mouse oocytes. This distal locus enriched cohesin protectors, such as the Chromosomal Passenger Complex (CPC) and PP2A, at a higher level compared to its centromere/kinetochore region, acting as the primary site for sister-chromatid cohesion. Chromosomes with the distal cohesion site exhibited enhanced cohesin protection at anaphase I compared to those without it, implying that these distal cohesion sites may have evolved to ensure sister-chromatid cohesion during meiosis. In contrast, mitotic cells enriched CPC only near the kinetochore and the distal locus was not cohered between sister chromatids, suggesting a meiosis-specific mechanism to protect cohesin at this distal locus. We found that this distal locus corresponds to an additional centromeric satellite block, located far apart from the centromeric satellite block that builds the kinetochore. Several Peromyscus species carry chromosomes with two such centromeric satellite blocks. Analyses on three Peromyscus species revealed that the internal satellite consistently assembles the kinetochore in both mitosis and meiosis, whereas the distal satellite selectively enriches cohesin protectors in meiosis to promote sister-chromatid cohesion at that site. Thus, our study demonstrates that pericentromere specification is remarkably flexible and can control chromosome segregation in a cell-type and context dependent manner.},
}

@article {pmid39091691,
year = {2024},
author = {Orizar, IDS and Repetti, SI and Lewandowska, AM},
title = {Phytoplankton stoichiometry along the salinity gradient under limited nutrient and light supply.},
journal = {Journal of plankton research},
volume = {46},
number = {4},
pages = {387-397},
pmid = {39091691},
issn = {0142-7873},
abstract = {Ongoing climate warming alters precipitation and water column stability, leading to salinity and nutrient supply changes in the euphotic zone of many coastal ecosystems and semi-enclosed seas. Changing salinity and nutrient conditions affect phytoplankton physiology by altering elemental ratios of carbon (C), nitrogen (N) and phosphorus (P). This study aimed to understand how salinity stress and resource acquisition affect phytoplankton stoichiometry. We incubated a phytoplankton polyculture composed of 10 species under different light, inorganic nutrient ratio and salinity levels. At the end of the incubation period, we measured particulate elemental composition (C, N and P), chlorophyll a and species abundances. The phytoplankton polyculture, dominated by Phaeodactylum tricornutum, accumulated more particulate organic carbon (POC) with increasing salinity. The low POC and low particulate C:N and C:P ratios toward 0 psu suggest that the hypoosmotic conditions highly affected primary production. The relative abundance of different species varied with salinity, and some species grew faster under low nutrient supply. Still, the dominant diatom regulated the overall POC of the polyculture, following the classic concept of the foundation species.},
}

@article {pmid39083124,
year = {2024},
author = {Hashimoto, A and Shibata, S and Hirooka, Y and Ohkuma, M},
title = {Phylogenetic and morphological re-evaluation of Camptophora.},
journal = {Antonie van Leeuwenhoek},
volume = {117},
number = {1},
pages = {109},
pmid = {39083124},
issn = {1572-9699},
support = {21K15155//JSPS KAKENHI/ ; 19H05689//JSPS KAKENHI/ ; FY 2023 Incentive Research Projects//Competitive Program for Creative Science and Technology, RIKEN Science Council, RIKEN Scientists' Assembly Steering Committee/ ; },
mesh = {*Phylogeny ; *DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Spores, Fungal/genetics/cytology/classification ; Sequence Analysis, DNA ; Plant Leaves/microbiology ; RNA Polymerase II/genetics ; Ascomycota/genetics/classification ; Tubulin/genetics ; },
abstract = {The genetic variety and habitats of Camptophora species, generally known as black yeast, have not been clarified. In this study, we re-evaluated Camptophora based on morphological observations and phylogenetic analyses. Because prior investigations on Camptophora only included a few strains/specimens, 24 Camptophora-related strains were newly obtained from 13 leaf samples of various plant species to redefine the genetic and species concepts of Camptophora. Their molecular phylogenetic relationships were examined using small subunit nuclear ribosomal DNA (nSSU, 18S rDNA), the internal transcribed spacer (ITS) rDNA operon, the large subunit nuclear ribosomal DNA (LSU, 28S rDNA), β-tubulin, the second largest subunit of RNA polymerase II (rpb2), and mitochondrial small subunit DNA (mtSSU). Single- and multi-locus analyses using nSSU-ITS-LSU-rpb2-mtSSU revealed a robust phylogenetic relationship among Camptophora species within Chaetothyriaceae. Camptophora species could be distinguished from other chaetothyriaceous genera by their snake-shaped conidia with microcyclic conidiation and loosely interwoven mycelial masses. Based on the results of phylogenetic analyses, two undescribed lineages were recognized, and Ca. schimae was excluded from the genus. ITS sequence comparison with environmental DNA sequences revealed that the distribution of the genus is restricted to the Asia-Pacific region. Camptophora has been isolated or detected from abrupt sources, and this was attributed to its microcycle. The mechanisms driving genetic diversity within species are discussed with respect to their phyllosphere habitats.},
}

*Phylogeny
*DNA, Fungal/genetics
DNA, Ribosomal/genetics
DNA, Ribosomal Spacer/genetics
Spores, Fungal/genetics/cytology/classification
Sequence Analysis, DNA
Plant Leaves/microbiology
RNA Polymerase II/genetics
Ascomycota/genetics/classification
Tubulin/genetics

@article {pmid39047818,
year = {2024},
author = {Sheehy, J and Kerr, S and Bell, M and Porter, J},
title = {Adaptive stacked species distribution modelling: Novel approaches to large scale quantification of blue carbon to support marine management.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {174993},
doi = {10.1016/j.scitotenv.2024.174993},
pmid = {39047818},
issn = {1879-1026},
abstract = {This study introduces a novel concept of 'Adaptively Stacked' Species Distribution Models (AS-SDMs) to predict blue carbon habitat distribution, abundance, carbon stocks, and carbon sequestration potential in Orkney. AS-SDMs are built from Weighted Boosted Regression Trees (WBRTs) that adaptively stack blue carbon sediment thickness, sediment carbon content, and sequestration potential to predicted abundance. A novel method to describe substrate types by relative inputs of mud, sand, and gravel is detailed that better characterises the determining factors of seagrass, maerl, and horse mussel abundance. This study also introduces a novel use of indexes to mitigate double counting issues of mixed species distribution models. Seagrass, maerl, horse mussel, and mixed seagrass and maerl (SGM) habitats are estimated to cover a maximum area of 657 km[2] in Orkney, have a total sediment carbon stock of 16 Mt. C, and sequester 6000 t C yr[-1]. Applying a conservative threshold of 50 % abundance to habitat predictions, six key potential areas of blue carbon offset projects are identified. These areas cover just over 9 km[2], have a total carbon stock of 330,000 t C, and sequester 330 t C yr[-1]. When applied to UK carbon credit value, assuming integration with voluntary markets and compliance with accreditation criteria, the habitats in these areas have a potential value of £24.5 million. If applied as annual values, these areas have carbon stocks with a potential value of £0.93 million yr[-1] and a carbon sequestration potential value of £24,000 yr[-1].},
}

@article {pmid39045499,
year = {2024},
author = {Wellenbeck, A and Fehrmann, L and Feilhauer, H and Schmidtlein, S and Misof, B and Hein, N},
title = {Discriminating woody species assemblages from National Forest Inventory data based on phylogeny in Georgia.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11569},
pmid = {39045499},
issn = {2045-7758},
abstract = {Classifications of forest vegetation types and characterization of related species assemblages are important analytical tools for mapping and diversity monitoring of forest communities. The discrimination of forest communities is often based on β-diversity, which can be quantified via numerous indices to derive compositional dissimilarity between samples. This study aims to evaluate the applicability of unsupervised classification for National Forest Inventory data from Georgia by comparing two cluster hierarchies. We calculated the mean basal area per hectare for each woody species across 1059 plot observations and quantified interspecies distances for all 87 species. Following an unspuervised cluster analysis, we compared the results derived from the species-neutral dissimilarity (Bray-Curtis) with those based on the Discriminating Avalanche dissimilarity, which incorporates interspecies phylogenetic variation. Incorporating genetic variation in the dissimilarity quantification resulted in a more nuanced discrimination of woody species assemblages and increased cluster coherence. Favorable statistics include the total number of clusters (23 vs. 20), mean distance within clusters (0.773 vs. 0.343), and within sum of squares (344.13 vs. 112.92). Clusters derived from dissimilarities that account for genetic variation showed a more robust alignment with biogeographical units, such as elevation and known habitats. We demonstrate that the applicability of unsupervised classification of species assemblages to large-scale forest inventory data strongly depends on the underlying quantification of dissimilarity. Our results indicate that by incorporating phylogenetic variation, a more precise classification aligned with biogeographic units is attained. This supports the concept that the genetic signal of species assemblages reflects biogeographical patterns and facilitates more precise analyses for mapping, monitoring, and management of forest diversity.},
}

@article {pmid39040508,
year = {2024},
author = {Cook, TM and Biswas, E and Aboobucker, SI and Dutta, S and Lübberstedt, T},
title = {A cell-based fluorescent system and statistical framework to detect meiosis-like induction in plants.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1386274},
pmid = {39040508},
issn = {1664-462X},
abstract = {Genetic gains made by plant breeders are limited by generational cycling rates and flowering time. Several efforts have been made to reduce the time to switch from vegetative to reproductive stages in plants, but these solutions are usually species-specific and require flowering. The concept of in vitro nurseries is that somatic plant cells can be induced to form haploid cells that have undergone recombination (creating artificial gametes), which can then be used for cell fusion to enable breeding in a Petri dish. The induction of in vitro meiosis, however, is the largest current bottleneck to in vitro nurseries. To help overcome this, we previously described a high-throughput, bi-fluorescent, single cell system in Arabidopsis thaliana, which can be used to test the meiosis-like induction capabilities of candidate factors. In this present work, we validated the system using robust datasets (>4M datapoints) from extensive simulated meiosis induction tests. Additionally, we determined false-detection rates of the fluorescent cells used in this system as well as the ideal tissue source for factor testing.},
}

@article {pmid39036421,
year = {2024},
author = {Takahata, T},
title = {Development of ocular dominance columns across rodents and other species: revisiting the concept of critical period plasticity.},
journal = {Frontiers in neural circuits},
volume = {18},
number = {},
pages = {1402700},
pmid = {39036421},
issn = {1662-5110},
mesh = {Animals ; *Dominance, Ocular/physiology ; *Neuronal Plasticity/physiology ; Visual Cortex/physiology/growth & development ; Rats ; Species Specificity ; Rodentia/physiology ; Humans ; Critical Period, Psychological ; Visual Pathways/physiology/growth & development ; Primary Visual Cortex/physiology ; Rats, Long-Evans ; },
abstract = {The existence of cortical columns, regarded as computational units underlying both lower and higher-order information processing, has long been associated with highly evolved brains, and previous studies suggested their absence in rodents. However, recent discoveries have unveiled the presence of ocular dominance columns (ODCs) in the primary visual cortex (V1) of Long-Evans rats. These domains exhibit continuity from layer 2 through layer 6, confirming their identity as genuine ODCs. Notably, ODCs are also observed in Brown Norway rats, a strain closely related to wild rats, suggesting the physiological relevance of ODCs in natural survival contexts, although they are lacking in albino rats. This discovery has enabled researchers to explore the development and plasticity of cortical columns using a multidisciplinary approach, leveraging studies involving hundreds of individuals-an endeavor challenging in carnivore and primate species. Notably, developmental trajectories differ depending on the aspect under examination: while the distribution of geniculo-cortical afferent terminals indicates matured ODCs even before eye-opening, consistent with prevailing theories in carnivore/primate studies, examination of cortical neuron spiking activities reveals immature ODCs until postnatal day 35, suggesting delayed maturation of functional synapses which is dependent on visual experience. This developmental gap might be recognized as 'critical period' for ocular dominance plasticity in previous studies. In this article, I summarize cross-species differences in ODCs and geniculo-cortical network, followed by a discussion on the development, plasticity, and evolutionary significance of rat ODCs. I discuss classical and recent studies on critical period plasticity in the venue where critical period plasticity might be a component of experience-dependent development. Consequently, this series of studies prompts a paradigm shift in our understanding of species conservation of cortical columns and the nature of plasticity during the classical critical period.},
}

Animals
*Dominance, Ocular/physiology
*Neuronal Plasticity/physiology
Visual Cortex/physiology/growth & development
Rats
Species Specificity
Rodentia/physiology
Humans
Critical Period, Psychological
Visual Pathways/physiology/growth & development
Primary Visual Cortex/physiology
Rats, Long-Evans

@article {pmid39031059,
year = {2024},
author = {Zhou, H and Hu, W and Zhang, J and Ma, T and Liu, X and Yan, J},
title = {A Lateral Flow Biosensor Based on Isothermal Amplification for Visual Identification of Species and Sex from Bloodstain.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.4c01623},
pmid = {39031059},
issn = {1520-6882},
abstract = {The prompt species identification from biological samples at a crime scene can rapidly filter out truly valuable biometric information for subsequent personal identification. Meanwhile, early sex determination can assist in narrowing the pool of suspects. However, the current methods for forensic DNA analysis, particularly in point-of-care scenarios, are often limited by the intricate equipment for signal generation and the laborious procedure for DNA purification. The present study introduces a novel portable lateral flow biosensor that possesses extraction-free and anti-aerosol characteristics for on-site determination of species and sex. The bloodstain can be directly submitted to loop-mediated isothermal amplification (LAMP) for the analysis of both mitochondrial and nuclear DNA. The incorporation of a lateral flow device with gold magnetic nanoparticle probes allows for visual interpretation of results through colorimetric signals while also preventing interference on result judgment from pigments such as hemoglobin. Carryover contamination, which is a disharmonious factor in LAMP, especially as the inherent contradiction derived from uncapping in the lateral flow strategy, has been effectively addressed through the integration of uracil DNA glycosylase without compromising the isothermy throughout the process. As a proof-of-concept experiment, species and sex can be accurately identified within 40 min from trace bloodstains amidst significant background interference by targeting cytochrome b and Y-chromosomal amelogenin. Furthermore, the single-blind study revealed a concordance rate of up to 100% in both simulative degraded and true dated bloodstains. This suggests that this biosensor has the potential to be utilized in forensic DNA analysis at crime scenes.},
}

@article {pmid39003615,
year = {2024},
author = {Chen, Z and Chen, Y and Shi, L and Li, X and Xu, G and Zeng, X and Zheng, X and Qi, Z and Zhang, K and Li, J and Zhang, S and Zhao, Z and Zhang, Y},
title = {Directional Construction of the Highly Stable Active-Site Ensembles at Sub-2 nm to Enhance Catalytic Activity and Selectivity.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {36},
number = {35},
pages = {e2405733},
doi = {10.1002/adma.202405733},
pmid = {39003615},
issn = {1521-4095},
support = {2022YFB4201804//National Key Research and Development Program of China/ ; 22378377//National Natural Science Foundation of China/ ; 22078311//National Natural Science Foundation of China/ ; 2108085J09//Science Fund for Distinguished Young Scholars of Anhui Province/ ; },
abstract = {Precise control over the size, species, and breakthrough of the activity-selectivity trade-off are great challenges for sub-nano non-noble metal catalysts. Here, for the first time, a "multiheteroatom induced SMSI + in situ P activation" strategy that enables high stability and effective construction of sub-2 nm metal sites for optimizing selective hydrogenation performance is developed. It is synthesized the smallest metal phosphide clusters (<2 nm) including from unary to ternary non-noble metal systems, accompanied by unprecedented thermal stability. In the proof-of-concept demonstration, further modulation of size and species results in the creation of a sub-2 nm site platform, directionally achieving single atom (Ni1), Ni1+metal cluster (Ni1+Nin), or novel Ni1+metal phosphide cluster synergistic sites (Ni1+Ni2Pn), respectively. Based on thorough structure and mechanism investigation, it is found the Ni1+Ni2Pn site is motivated to achieve electronic structure self-optimizing through synergistic SMSI and site coupling effect. Therefore, it speeds up the substrate adsorption-desorption kinetics in semihydrogenation of alkyne and achieves superior catalytic activity that is 56 times higher than the Ni1 site under mild conditions. Compared to traditional active sites, this may represent the highly effective integration of atom utilization, thermal stability, and favorable site requirements for chemisorption properties and reactivities of substrates.},
}

@article {pmid38980817,
year = {2024},
author = {Moreno, AA and Tully, TN and Liu, CC and Heatley, JJ},
title = {Reference Interval Creation for Symmetric Dimethylarginine (SDMA) in Healthy Hispaniolan Amazon Parrots (Amazona ventralis) and Quaker Parrots (Myiopsitta monachus).},
journal = {Journal of avian medicine and surgery},
volume = {38},
number = {2},
pages = {83-90},
doi = {10.1647/AVIANMS-D-24-00003},
pmid = {38980817},
issn = {1082-6742},
mesh = {Animals ; Reference Values ; Male ; *Arginine/analogs & derivatives/blood ; Female ; *Parrots/blood ; Amazona/blood ; Biomarkers/blood ; },
abstract = {Renal disease is often identified as a cause of morbidity and mortality in avian patients. However, currently, early antemortem detection of renal disease in avian patients is difficult. Anatomical and physiological differences between mammals and birds mean the use of commonly employed diagnostic testing (ie, measurement of blood urea nitrogen [BUN] and serum creatinine, urinalysis, and ultrasonography) are either nondiagnostic or difficult to achieve. Symmetric dimethylarginine (SDMA) is considered a more sensitive marker for renal disease in humans, dogs, and cats. However, SDMA has not yet been assessed for diagnostic use in any psittacine species. In this study, we establish reference ranges for SDMA in both Hispaniolan Amazon parrots (Amazona ventralis, HAP) and Quaker parrots (Myiopsitta monachus, QP). Blood was collected from 23 Amazon parrots and 32 Quaker parrots maintained in research facilities. Measurement of SDMA through a commercially available immunoassay (IA-SDMA) as well as creatinine, BUN, uric acid, phosphorus, calcium, sodium, potassium, and chloride were determined through IDEXX Laboratories. Plasma SDMA concentrations ranged from 6 to 15 µg/dL and 3 to 15 µg/dL for the HAP and QP, respectively. Sex was a confounding factor for the QP population, but sex did not have a significant effect on SDMA for the HAP population. No significant correlations were identified between SDMA concentrations and other parameters in either psittacine species. Our results show proof of concept for the IA-SDMA and provide reference intervals for SDMA in HAP and QP. Further investigation is required to determine the validity of this assay and the predictive power of SDMA in the detection of renal impairment for parrots and other common companion birds.},
}

Animals
Reference Values
Male
*Arginine/analogs & derivatives/blood
Female
*Parrots/blood
Amazona/blood
Biomarkers/blood

@article {pmid38933688,
year = {2024},
author = {Carlisle, JD and Smith, KT and Beck, JL and Murphy, MA and Chalfoun, AD},
title = {Beyond overlap: Considering habitat preference and fitness outcomes in the umbrella species concept.},
journal = {Animal conservation},
volume = {27},
number = {2},
pages = {212-225},
pmid = {38933688},
issn = {1367-9430},
support = {P20 GM103432/GM/NIGMS NIH HHS/United States ; },
abstract = {Umbrella species and other surrogate-species approaches to conservation provide an appealing framework to extend the reach of conservation efforts beyond single species. For the umbrella species concept to be effective, populations of multiple species of concern must persist in areas protected on behalf of the umbrella species. Most assessments of the concept, however, focus exclusively on geographic overlap among umbrella and background species, and not measures that affect population persistence (e.g., habitat quality or fitness). We quantified the congruence between the habitat preferences and nesting success of a high-profile umbrella species (greater sage-grouse, Centrocercus urophasianus, hereafter "sage-grouse"), and three sympatric species of declining songbirds (Brewer's sparrow Spizella breweri, sage thasher Oreoscoptes montanus, and vesper sparrow Pooecetes gramineus) in central Wyoming, USA during 2012 - 2013. We used machine-learning methods to create data-driven predictions of sage-grouse nest-site selection and nest survival probabilities by modeling field-collected sage-grouse data relative to habitat attributes. We then used field-collected songbird data to assess whether high-quality sites for songbirds aligned with those of sage-grouse. Nest sites selected by songbirds did not coincide with sage-grouse nesting preferences, with the exception that Brewer's sparrows preferred similar nest sites to sage-grouse in 2012. Moreover, the areas that produced higher rates of songbird nest survival were unrelated to those for sage-grouse. Our findings suggest that management actions at local scales that prioritize sage-grouse nesting habitat will not necessarily enhance the reproductive success of sagebrush-associated songbirds. Measures implemented to conserve sage-grouse and other purported umbrella species at broad spatial scales likely overlap the distribution of many species, however, broad-scale overlap may not translate to fine-scale conservation benefit beyond the umbrella species itself. The maintenance of microhabitat heterogeneity important for a diversity of species of concern will be critical for a more-holistic application of the umbrella species concept.},
}

@article {pmid38930806,
year = {2024},
author = {Scopel, JM and Medeiros-Neves, B and Teixeira, HF and Brazil, NT and Bordignon, SAL and Diz, FM and Morrone, FB and Almeida, RN and Cassel, E and von Poser, GL and Vargas, RMF},
title = {Supercritical Carbon Dioxide Extraction of Coumarins from the Aerial Parts of Pterocaulon polystachyum.},
journal = {Molecules (Basel, Switzerland)},
volume = {29},
number = {12},
pages = {},
pmid = {38930806},
issn = {1420-3049},
mesh = {*Coumarins/chemistry/isolation & purification/pharmacology ; *Carbon Dioxide/chemistry ; *Plant Extracts/chemistry/pharmacology/isolation & purification ; Humans ; *Chromatography, Supercritical Fluid/methods ; Plant Components, Aerial/chemistry ; Cell Line, Tumor ; Cell Survival/drug effects ; Antineoplastic Agents, Phytogenic/pharmacology/chemistry/isolation & purification ; },
abstract = {Pterocaulon polystachyum is a species of pharmacological interest for providing volatile and non-volatile extracts with antifungal and amebicidal properties. The biological activities of non-volatile extracts may be related to the presence of coumarins, a promising group of secondary metabolites. In the present study, leaves and inflorescences previously used for the extraction of essential oils instead of being disposed of were subjected to extraction with supercritical CO2 after pretreatment with microwaves. An experimental design was followed to seek the best extraction condition with the objective function being the maximum total extract. Pressure and temperature were statistically significant factors, and the optimal extraction condition was 240 bar, 60 °C, and pretreatment at 30 °C. The applied mathematical models showed good adherence to the experimental data. The extracts obtained by supercritical CO2 were analyzed and the presence of coumarins was confirmed. The extract investigated for cytotoxicity against bladder tumor cells (T24) exhibited significant reduction in cell viability at concentrations between 6 and 12 μg/mL. The introduction of green technology, supercritical extraction, in the exploration of P. polystachyum as a source of coumarins represents a paradigm shift with regard to previous studies carried out with this species, which used organic solvents. Furthermore, the concept of circular bioeconomy was applied, i.e., the raw material used was the residue of a steam-distillation process. Therefore, the approach used here is in line with the sustainable exploitation of native plants to obtain extracts rich in coumarins with cytotoxic potential against cancer cells.},
}

*Coumarins/chemistry/isolation & purification/pharmacology
*Carbon Dioxide/chemistry
*Plant Extracts/chemistry/pharmacology/isolation & purification
Humans
*Chromatography, Supercritical Fluid/methods
Plant Components, Aerial/chemistry
Cell Line, Tumor
Cell Survival/drug effects
Antineoplastic Agents, Phytogenic/pharmacology/chemistry/isolation & purification

@article {pmid38926575,
year = {2024},
author = {Waddle, AW and Clulow, S and Aquilina, A and Sauer, EL and Kaiser, SW and Miller, C and Flegg, JA and Campbell, PT and Gallagher, H and Dimovski, I and Lambreghts, Y and Berger, L and Skerratt, LF and Shine, R},
title = {Hotspot shelters stimulate frog resistance to chytridiomycosis.},
journal = {Nature},
volume = {631},
number = {8020},
pages = {344-349},
pmid = {38926575},
issn = {1476-4687},
mesh = {Animals ; *Anura/immunology/microbiology/physiology ; Body Temperature/immunology/physiology/radiation effects ; *Chytridiomycota/immunology/pathogenicity/physiology ; *Disease Resistance/immunology/physiology/radiation effects ; Ecosystem ; *Endangered Species ; *Mycoses/veterinary/microbiology/immunology ; *Refugium ; Sunlight ; Animals, Wild/immunology/microbiology/physiology ; Introduced Species ; },
abstract = {Many threats to biodiversity cannot be eliminated; for example, invasive pathogens may be ubiquitous. Chytridiomycosis is a fungal disease that has spread worldwide, driving at least 90 amphibian species to extinction, and severely affecting hundreds of others[1-4]. Once the disease spreads to a new environment, it is likely to become a permanent part of that ecosystem. To enable coexistence with chytridiomycosis in the field, we devised an intervention that exploits host defences and pathogen vulnerabilities. Here we show that sunlight-heated artificial refugia attract endangered frogs and enable body temperatures high enough to clear infections, and that having recovered in this way, frogs are subsequently resistant to chytridiomycosis even under cool conditions that are optimal for fungal growth. Our results provide a simple, inexpensive and widely applicable strategy to buffer frogs against chytridiomycosis in nature. The refugia are immediately useful for the endangered species we tested and will have broader utility for amphibian species with similar ecologies. Furthermore, our concept could be applied to other wildlife diseases in which differences in host and pathogen physiologies can be exploited. The refugia are made from cheap and readily available materials and therefore could be rapidly adopted by wildlife managers and the public. In summary, habitat protection alone cannot protect species that are affected by invasive diseases, but simple manipulations to microhabitat structure could spell the difference between the extinction and the persistence of endangered amphibians.},
}

Animals
*Anura/immunology/microbiology/physiology
Body Temperature/immunology/physiology/radiation effects
*Chytridiomycota/immunology/pathogenicity/physiology
*Disease Resistance/immunology/physiology/radiation effects
Ecosystem
*Endangered Species
*Mycoses/veterinary/microbiology/immunology
*Refugium
Sunlight
Animals, Wild/immunology/microbiology/physiology
Introduced Species

@article {pmid38898619,
year = {2024},
author = {Leal-Bertioli, SCM and de Blas, FJ and Carolina Chavarro, M and Simpson, CE and Valls, JFM and Tallury, SP and Moretzsohn, MC and Custodio, AR and Thomas Stalker, H and Seijo, G and Bertioli, DJ},
title = {Relationships of the wild peanut species, section Arachis: A resource for botanical classification, crop improvement, and germplasm management.},
journal = {American journal of botany},
volume = {111},
number = {6},
pages = {e16357},
doi = {10.1002/ajb2.16357},
pmid = {38898619},
issn = {1537-2197},
mesh = {*Arachis/genetics/classification ; *Crops, Agricultural/genetics ; *Phylogeny ; Genome, Plant ; Seed Bank ; Genotype ; },
abstract = {PREMISE: Wild species are strategic sources of valuable traits to be introduced into crops through hybridization. For peanut, the 33 currently described wild species in the section Arachis are particularly important because of their sexual compatibility with the domesticated species, Arachis hypogaea. Although numerous wild accessions are carefully preserved in seed banks, their morphological similarities pose challenges to routine classification.

METHODS: Using a high-density array, we genotyped 272 accessions encompassing all diploid species in section Arachis. Detailed relationships between accessions and species were revealed through phylogenetic analyses and interpreted using the expertise of germplasm collectors and curators.

RESULTS: Two main groups were identified: one with A genome species and the other with B, D, F, G, and K genomes. Species groupings generally showed clear boundaries. Structure within groups was informative, for instance, revealing the history of the proto-domesticate A. stenosperma. However, some groupings suggested multiple sibling species. Others were polyphyletic, indicating the need for taxonomic revision. Annual species were better defined than perennial ones, revealing limitations in applying classical and phylogenetic species concepts to the genus. We suggest new species assignments for several accessions.

CONCLUSIONS: Curated by germplasm collectors and curators, this analysis of species relationships lays the foundation for future species descriptions, classification of unknown accessions, and germplasm use for peanut improvement. It supports the conservation and curation of current germplasm, both critical tasks considering the threats to the genus posed by habitat loss and the current restrictions on new collections and germplasm transfer.},
}

*Arachis/genetics/classification
*Crops, Agricultural/genetics
*Phylogeny
Genome, Plant
Seed Bank
Genotype