Nature ecology & evolution最新文献

{"title":"Global decoupling of functional and phylogenetic diversity in plant communities","authors":"Georg J. A. Hähn, Gabriella Damasceno, Esteban Alvarez-Davila, Isabelle Aubin, Marijn Bauters, Erwin Bergmeier, Idoia Biurrun, Anne D. Bjorkman, Gianmaria Bonari, Zoltán Botta-Dukát, Juan A. Campos, Andraž Čarni, Milan Chytrý, Renata Ćušterevska, André Luís de Gasper, Michele De Sanctis, Jürgen Dengler, Jiri Dolezal, Mohamed A. El-Sheikh, Manfred Finckh, Antonio Galán-de-Mera, Emmanuel Garbolino, Hamid Gholizadeh, Valentin Golub, Sylvia Haider, Mohamed Z. Hatim, Bruno Hérault, Jürgen Homeier, Ute Jandt, Florian Jansen, Anke Jentsch, Jens Kattge, Michael Kessler, Larisa Khanina, Holger Kreft, Filip Küzmič, Jonathan Lenoir, Jesper Erenskjold Moeslund, Ladislav Mucina, Alireza Naqinezhad, Jalil Noroozi, Aaron Pérez-Haase, Oliver L. Phillips, Valério D. Pillar, Gonzalo Rivas-Torres, Eszter Ruprecht, Brody Sandel, Marco Schmidt, Ute Schmiedel, Stefan Schnitzer, Franziska Schrodt, Urban Šilc, Ben Sparrow, Maria Sporbert, Zvjezdana Stančić, Ben Strohbach, Jens-Christian Svenning, Cindy Q. Tang, Zhiyao Tang, Alexander Christian Vibrans, Cyrille Violle, Donald Waller, Desalegn Wana, Hua-Feng Wang, Timothy Whitfeld, Georg Zizka, Francesco Maria Sabatini, Helge Bruelheide","doi":"10.1038/s41559-024-02589-0","DOIUrl":"https://doi.org/10.1038/s41559-024-02589-0","url":null,"abstract":"<p>Plant communities are composed of species that differ both in functional traits and evolutionary histories. As species’ functional traits partly result from their individual evolutionary history, we expect the functional diversity of communities to increase with increasing phylogenetic diversity. This expectation has only been tested at local scales and generally for specific growth forms or specific habitat types, for example, grasslands. Here we compare standardized effect sizes for functional and phylogenetic diversity among 1,781,836 vegetation plots using the global sPlot database. In contrast to expectations, we find functional diversity and phylogenetic diversity to be only weakly and negatively correlated, implying a decoupling between these two facets of diversity. While phylogenetic diversity is higher in forests and reflects recent climatic conditions (1981 to 2010), functional diversity tends to reflect recent and past climatic conditions (21,000 years ago). The independent nature of functional and phylogenetic diversity makes it crucial to consider both aspects of diversity when analysing ecosystem functioning and prioritizing conservation efforts.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"21 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142760222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental filtering, not dispersal history, explains global patterns of phylogenetic turnover in seed plants at deep evolutionary timescales","authors":"Lirong Cai, Holger Kreft, Pierre Denelle, Amanda Taylor, Dylan Craven, Wayne Dawson, Franz Essl, Mark van Kleunen, Jan Pergl, Petr Pyšek, Marten Winter, Francisco J. Cabezas, Viktoria Wagner, Pieter B. Pelser, Jan J. Wieringa, Patrick Weigelt","doi":"10.1038/s41559-024-02599-y","DOIUrl":"https://doi.org/10.1038/s41559-024-02599-y","url":null,"abstract":"<p>Environmental filtering and dispersal history limit plant distributions and affect biogeographical patterns, but how their relative importance varies across evolutionary timescales is unresolved. Phylogenetic beta diversity quantifies dissimilarity in evolutionary relatedness among assemblages and might help resolve the ecological and biogeographical mechanisms structuring biodiversity. Here, we examined the effects of environmental dissimilarity and geographical distance on phylogenetic and taxonomic turnover for ~270,000 seed plant species globally and across evolutionary timescales. We calculated past and present dispersal barriers using palaeogeographical reconstructions and calculated geographical linear and least-cost distances, accounting for dispersal over water, mountains or areas with unsuitable climates. Environmental dissimilarity and geographical distance jointly explained most of the deviance in taxonomic (up to 86.4%) and phylogenetic turnover (65.6%). While environmental dissimilarity consistently showed strongly positive effects, the effect of geographical distance on phylogenetic turnover was less pronounced further back in evolutionary time. Past physiogeographical barriers explained a relatively low amount of the variation across all timescales, with a slight peak at intermediate timescales (20–50 Myr <span>bp</span>). Our results suggest that while old lineages have generally dispersed widely, the imprint of environmental filtering on range expansion persists, providing insights into biogeographical and evolutionary processes underlying global biodiversity patterns.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"65 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142742446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reduced evolutionary constraint accompanies ongoing radiation in deep-sea anglerfishes","authors":"Elizabeth Christina Miller, Rose Faucher, Pamela B. Hart, Melissa Rincón-Sandoval, Aintzane Santaquiteria, William T. White, Carole C. Baldwin, Masaki Miya, Ricardo Betancur-R, Luke Tornabene, Kory Evans, Dahiana Arcila","doi":"10.1038/s41559-024-02586-3","DOIUrl":"https://doi.org/10.1038/s41559-024-02586-3","url":null,"abstract":"<p>Colonization of a novel habitat is often followed by phenotypic diversification in the wake of ecological opportunity. However, some habitats should be inherently more constraining than others if the challenges of that environment offer few evolutionary solutions. We examined this push-and-pull on macroevolutionary diversification following habitat transitions in the anglerfishes (Lophiiformes). We constructed a phylogeny with extensive sampling (1,092 loci and ~38% of species), combined with three-dimensional phenotypic data from museum specimens. We used these datasets to examine the tempo and mode of phenotypic diversification. The deep-sea pelagic anglerfishes originated from a benthic ancestor and shortly after experienced rapid lineage diversification rates. This transition incurred shifts towards larger jaws, smaller eyes and a more laterally compressed body plan. Despite these directional trends, this lineage still evolved high phenotypic disparity in body, skull and jaw shapes. In particular, bathypelagic anglerfishes show high variability in body elongation, while benthic anglerfishes are constrained around optimal shapes. Within this radiation, phenotypic evolution was concentrated among recently diverged lineages, notably those that deviated from the archetypical globose body plan. Taken together, these results demonstrate that spectacular evolutionary radiations can unfold even within environments with few ecological resources and demanding physiological challenges.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"1 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142718171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Causal inference concepts can guide research into the effects of climate on infectious diseases","authors":"Laura Andrea Barrero Guevara, Sarah C. Kramer, Tobias Kurth, Matthieu Domenech de Cellès","doi":"10.1038/s41559-024-02594-3","DOIUrl":"https://doi.org/10.1038/s41559-024-02594-3","url":null,"abstract":"<p>A pressing question resulting from global warming is how climate change will affect infectious diseases. Answering this question requires research into the effects of weather on the population dynamics of transmission and infection; elucidating these effects, however, has proved difficult due to the challenges of assessing causality from the predominantly observational data available in epidemiological research. Here we show how concepts from causal inference—the sub-field of statistics aiming at inferring causality from data—can guide that research. Through a series of case studies, we illustrate how such concepts can help assess study design and strategically choose a study’s location, evaluate and reduce the risk of bias, and interpret the multifaceted effects of meteorological variables on transmission. More broadly, we argue that interdisciplinary approaches based on explicit causal frameworks are crucial for reliably estimating the effect of weather and accurately predicting the consequences of climate change.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"256 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142696704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomics of a sexually selected sperm ornament and female preference in Drosophila","authors":"Zeeshan A. Syed, R. Antonio Gomez, Kirill Borziak, Amaar Asif, Abelard S. Cong, Patrick. M. O’Grady, Bernard Y. Kim, Anton Suvorov, Dmitri A. Petrov, Stefan Lüpold, Peter Wengert, Caitlin McDonough-Goldstein, Yasir H. Ahmed-Braimah, Steve Dorus, Scott Pitnick","doi":"10.1038/s41559-024-02587-2","DOIUrl":"https://doi.org/10.1038/s41559-024-02587-2","url":null,"abstract":"<p>Our understanding of animal ornaments and the mating preferences driving their exaggeration is limited by knowledge of their genetics. Post-copulatory sexual selection is credited with the rapid evolution of female sperm-storage organ morphology and corresponding sperm quality traits across diverse taxa. In <i>Drosophila</i>, the mechanisms by which longer flagella convey an advantage in the competition among sperm for limited storage space in the female, and by which female sperm-storage organ morphology biases fertilization in favour of longer sperm have been resolved. However, the evolutionary genetics underlying this model post-copulatory ornament and preference system have remained elusive. Here we combined comparative analyses of 149 <i>Drosophila</i> species, a genome-wide association study in <i>Drosophila</i> <i>melanogaster</i> and molecular evolutionary analysis of ~9,400 genes to elucidate how sperm and female sperm-storage organ length co-evolved into one of nature’s most extreme ornaments and preferences. Our results reveal a diverse repertoire of pleiotropic genes linking sperm length and seminal receptacle length expression to central nervous system development and sensory biology. Sperm length development appears condition-dependent and is governed by conserved hormonal (insulin/insulin-like growth factor) and developmental (including <i>Notch</i> and <i>Fruitless</i>) pathways. Central developmental pathway genes, including <i>Notch</i>, also comprised the majority of a restricted set of genes contributing to both intraspecific and interspecific variation in sperm length. Our findings support ‘good genes’ models of female preference evolution.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"71 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142684379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Asynchronous abundance fluctuations can drive giant genotype frequency fluctuations","authors":"Joao A. Ascensao, Kristen Lok, Oskar Hallatschek","doi":"10.1038/s41559-024-02578-3","DOIUrl":"https://doi.org/10.1038/s41559-024-02578-3","url":null,"abstract":"<p>Large stochastic population abundance fluctuations are ubiquitous across the tree of life, impacting the predictability and outcomes of population dynamics. It is generally thought that abundance fluctuations with a Taylor’s law exponent of two do not strongly impact evolution. However, we argue that such abundance fluctuations can lead to substantial genotype frequency fluctuations if different genotypes in a population experience these fluctuations asynchronously. By serially diluting mixtures of two closely related <i>Escherichia coli</i> strains, we show that such asynchrony can occur, leading to giant frequency fluctuations that far exceed expectations from genetic drift. We develop an effective model explaining that the abundance fluctuations arise from correlated offspring numbers between individuals, and the large frequency fluctuations result from (even slight) decoupling in offspring number correlations between genotypes. The model quantitatively predicts the observed abundance and frequency fluctuation scaling. Initially close trajectories diverge exponentially, suggesting that chaotic dynamics may underpin the excess frequency fluctuations. Our findings suggest that decoupling noise is also present in mixed-genotype <i>Saccharomyces cerevisiae</i> populations. Theoretical analyses demonstrate that decoupling noise can strongly influence evolutionary outcomes, in a manner distinct from genetic drift. Given the generic nature of these frequency fluctuations, we expect them to be widespread across biological populations.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"115 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142684378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inferring DNA methylation in non-skeletal tissues of ancient specimens","authors":"Yoav Mathov, Malka Nissim-Rafinia, Chen Leibson, Nir Galun, Tomas Marques-Bonet, Arye Kandel, Meir Liebergal, Eran Meshorer, Liran Carmel","doi":"10.1038/s41559-024-02571-w","DOIUrl":"https://doi.org/10.1038/s41559-024-02571-w","url":null,"abstract":"<p>Genome-wide premortem DNA methylation patterns can be computationally reconstructed from high-coverage DNA sequences of ancient samples. Because DNA methylation is more conserved across species than across tissues, and ancient DNA is typically extracted from bones and teeth, previous works utilizing ancient DNA methylation maps focused on studying evolutionary changes in the skeletal system. Here we suggest that DNA methylation patterns in one tissue may, under certain conditions, be informative on DNA methylation patterns in other tissues of the same individual. Using the fact that tissue-specific DNA methylation builds up during embryonic development, we identified the conditions that allow for such cross-tissue inference and devised an algorithm that carries it out. We trained the algorithm on methylation data from extant species and reached high precisions of up to 0.92 for validation datasets. We then used the algorithm on archaic humans, and identified more than 1,850 positions for which we were able to observe differential DNA methylation in prefrontal cortex neurons. These positions are linked to hundreds of genes, many of which are involved in neural functions such as structural and developmental processes. Six positions are located in the neuroblastoma breaking point family (NBPF) gene family, which probably played a role in human brain evolution. The algorithm we present here allows for the examination of epigenetic changes in tissues and cell types that are absent from the palaeontological record, and therefore provides new ways to study the evolutionary impacts of epigenetic changes.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"18 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142673415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anthropogenic land consolidation intensifies zoonotic host diversity loss and disease transmission in human habitats","authors":"Shan Pei, Pengbo Yu, Jayna Raghwani, Yuxin Wang, Ziyan Liu, Yidan Li, Yanchao Cheng, Qiushi Lin, Chuliang Song, Guha Dharmarajan, Christina L. Faust, Yunyu Tian, Yiting Xu, Yilin Liang, Jianhui Qu, Jing Wei, Shen Li, Tongjun Zhang, Chaofeng Ma, Nita Bharti, Bernard Cazelles, Ruifu Yang, Oliver G. Pybus, Andrew P. Dobson, Nils Chr. Stenseth, Huaiyu Tian","doi":"10.1038/s41559-024-02570-x","DOIUrl":"https://doi.org/10.1038/s41559-024-02570-x","url":null,"abstract":"<p>Anthropogenic land-use change is an important driver of global biodiversity loss and threatens public health through biological interactions. Understanding these landscape–ecological effects at local scales will help achieve the United Nations Sustainable Development Goals by balancing urbanization, biodiversity and the spread of infectious diseases. Here, we address this knowledge gap by analysing a 43-year-long monthly dataset (1980–2022) of synanthropic rodents in Central China during intensive land-use change. We observed a notable increase in the mean patch size, coinciding with a substantial change in rodent community composition and a marked decline in rodent diversity; eight of the nine local rodent species experienced near-extirpation. Our analysis reveals that these irregular species replacements can be attributed to the effect of land consolidation on species competition among rodents, favouring striped field mice, a critical reservoir host of Hantaan virus (HTNV). Consequently, land consolidation has facilitated the proliferation of striped field mice and increased the prevalence of HTNV among them. This study highlights the importance of considering both direct and indirect effects of anthropogenic activities in the management of biodiversity and public health.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"18 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142665286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Species diversity links land consolidation to rodent disease","authors":"Claire S. Teitelbaum","doi":"10.1038/s41559-024-02584-5","DOIUrl":"https://doi.org/10.1038/s41559-024-02584-5","url":null,"abstract":"Four decades of data on rodent species composition and hantavirus prevalence across a changing urban–agricultural landscape demonstrate that long-term data are key for understanding links between biodiversity loss and disease dynamics","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"12 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142665283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Limits to the ability of carbon farming projects to deliver benefits for threatened species","authors":"Jayden E. Engert, Penny van Oosterzee","doi":"10.1038/s41559-024-02580-9","DOIUrl":"https://doi.org/10.1038/s41559-024-02580-9","url":null,"abstract":"<p>Australia has proposed a legislated market for biodiversity based on an existing carbon credits scheme which generates Australian carbon credit units (ACCU) from land-based projects. This provides a unique opportunity to assess the potential for markets to benefit biodiversity. We assessed the extent to which projects under the ACCU scheme overlap potential threatened species habitat, compared that to overlap afforded by protected areas, and compared the ability of different project types to deliver potential benefits to species most impacted by habitat loss. Projects are primarily located in low-cost, marginal arid lands, a pattern that reflects that of the protected area estate. Projects are smaller and fewer in number in more productive lands close to human populations. These lands also overlap most threatened species habitat, hence those species most in need of habitat restoration are the least likely to have their habitat restored under the ACCU scheme. Projects, however, do overlap the geographic range of 32% of the 1,660 threatened species assessed, including for 275 species with &lt;17% of their range in protected areas. Biodiversity markets must incentivize actions in areas of high biodiversity value underpinned by regulations that align with national priorities for biodiversity conservation.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"15 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142637053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}