Nature ecology & evolution最新文献

{"title":"Genomic architecture of rapid adaptation illustrated by biological invasions","authors":"Thomas Brazier, Claire Mérot","doi":"10.1038/s41559-025-02774-9","DOIUrl":"10.1038/s41559-025-02774-9","url":null,"abstract":"Genomic and phenotypic analysis of a global invasive plant pinpoints large-effect haplotype blocks involved in parallel local adaptation and invasion success across continents, underscoring a contribution of putative structural variants to rapid evolution.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 8","pages":"1317-1318"},"PeriodicalIF":13.9,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144578008","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":"Haploblocks contribute to parallel climate adaptation following global invasion of a cosmopolitan plant","authors":"Paul Battlay, Brandon T. Hendrickson, Jonas I. Mendez-Reneau, James S. Santangelo, Lucas J. Albano, Jonathan Wilson, Aude E. Caizergues, Nevada King, Adriana Puentes, Amelia Tudoran, Cyrille Violle, Francois Vasseur, Courtney M. Patterson, Michael Foster, Caitlyn Stamps, Simon G. Innes, Rémi Allio, Fabio Angeoletto, Daniel N. Anstett, Julia Anstett, Anna Bucharova, Mattheau S. Comerford, Santiago David, Mohsen Falahati-Anbaran, William Godsoe, César González-Lagos, Pedro E. Gundel, Glen Ray Hood, Christian Lampei, Carlos Lara, Adrián Lázaro-Lobo, Deleon Silva Leandro, Thomas J. S. Merritt, Nora Mitchell, Mitra Mohammadi Bazargani, Angela Moles, Maureen Murúa, Juraj Paule, Vera Pfeiffer, Joost A. M. Raeymaekers, Diana J. Rennison, Rodrigo S. Rios, Jennifer K. Rowntree, Adam C. Schneider, Kaitlin Stack Whitney, Ítalo Tamburrino, Acer VanWallendael, Paul Y. Kim, Rob W. Ness, Marc T. J. Johnson, Kathryn A. Hodgins, Nicholas J. Kooyers","doi":"10.1038/s41559-025-02751-2","DOIUrl":"10.1038/s41559-025-02751-2","url":null,"abstract":"The role of rapid adaptation during species invasions has historically been minimized with the assumption that introductions consist of few colonists and limited genetic diversity. While overwhelming evidence suggests that rapid adaptation is more prevalent than originally assumed, the demographic and adaptive processes underlying successful invasions remain unresolved. Here we leverage a large whole-genome sequence dataset to investigate the relative roles of colonization history and adaptation during the worldwide invasion of the forage crop, Trifolium repens (Fabaceae). We show that introduced populations encompass high levels of genetic variation with little evidence of bottlenecks. Independent colonization histories on different continents are evident from genome-wide population structure. Five haploblocks—large haplotypes with limited recombination—on three chromosomes exist as standing genetic variation within the native and introduced ranges and exhibit strong signatures of parallel climate-associated adaptation across continents. Field experiments in the native and introduced ranges demonstrate that three of the haploblocks strongly affect fitness and exhibit patterns of selection consistent with local adaptation across each range. Our results provide strong evidence that large-effect structural variants contribute substantially to rapid and parallel adaptation of an introduced species throughout the world. Whole-genome sequences and field experiments focusing on the global invasive forage crop, Trifolium repens, show high levels of genetic variation across continents and parallel signatures of selection in five haploblocks.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 8","pages":"1441-1455"},"PeriodicalIF":13.9,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41559-025-02751-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144578014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The length of time series affects patterns of species synchrony","authors":"","doi":"10.1038/s41559-025-02778-5","DOIUrl":"10.1038/s41559-025-02778-5","url":null,"abstract":"Using theoretical and empirical analyses, we demonstrate that species synchrony itself and its relationships with species diversity and competition strength could exhibit opposite patterns in short versus long time series. This finding challenges the implicit assumption in ecological studies that observational length should not qualitatively alter patterns of interest.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 8","pages":"1321-1322"},"PeriodicalIF":13.9,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144564965","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":"Functional replacement of ancestral antibacterial secretion system in a bacterial plant pathogen","authors":"Chloé Peduzzi, Jules Butchacas, François Nikis, Nathaniel Heiden, Marcus V. Merfa, Manon Martin, Veronica Roman-Reyna, Jonathan M. Jacobs, Ralf Koebnik, Claude Bragard","doi":"10.1038/s41559-025-02773-w","DOIUrl":"10.1038/s41559-025-02773-w","url":null,"abstract":"Two distinct molecular machineries, T4SS and T6SS, have been found within the order Xanthomonadales to be involved in outcompeting other bacterial species through the secretion of toxic effector proteins. However, the ecological and evolutionary basis leading xanthomonads to evolve two secretion systems with such similar functions remain unclear. Here we show that Xanthomonas translucens (Xt) lineages have switched from an X-T4SS-mediated to T6SS-i4-mediated bacterial killing strategy. T6SS-i4 was only found in Xt strains lacking X-T4SS and vice versa, resulting in a patchy distribution of the two nanoweapons along the Xt phylogeny. Using genetic and fluorescence-based methods, we demonstrated that X-T4SS and T6SS-i4 are crucial for interbacterial competition in Xt, but not Xt T6SS-i3. Combined comparative genetic and phylogenetic analyses further revealed that the X-T4SS gene clusters have been subject to degradation and had several loss events, while T6SS-i4 was inserted through independent gain events. Overall, this research supports the ancestral state of X-T4SS and provides new insights into the mechanisms promoting Xt survival within their ecological niches. The bacterial plant pathogen genus Xanthomonas uses two distinct secretion systems for antibacterial competition. Here the authors show that some Xanthomonas lineages have switched from the ancestral X-T4SS state to T6SS-i4 despite the functional similarity of the systems, with X-T4SS gene clusters subject to degradation and loss and T6SS-i4-encoding sequences inserted through independent gains.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 8","pages":"1393-1404"},"PeriodicalIF":13.9,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144564964","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":"Palaeolithic people returned north earlier than expected","authors":"","doi":"10.1038/s41559-025-02722-7","DOIUrl":"10.1038/s41559-025-02722-7","url":null,"abstract":"Climatic conditions from the northwestern European margins indicate that warmer summer conditions after the last cold glacial period existed there around 15,200 years ago. The presence of prey species in this landscape, combined with warmer summer conditions, presented an environment that supported the reoccupation of these northern marginal latitudes by Late Upper Palaeolithic humans.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 7","pages":"1096-1097"},"PeriodicalIF":13.9,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144547062","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":"Leprosy in the Americas before Columbus","authors":"Charlotte A. Roberts","doi":"10.1038/s41559-025-02790-9","DOIUrl":"10.1038/s41559-025-02790-9","url":null,"abstract":"Mycobacterium lepromatosis genomes associated with 4,000-year-old human skeletons in Chile establish an American origin for this causal agent of leprosy (also known as Hansen’s disease), and point to different evolutionary trajectories and transmission pathways for M. lepromatosis and its sister pathogen Mycobacterium leprae.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 9","pages":"1550-1551"},"PeriodicalIF":13.9,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144547061","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":"Stepwise evolution of placental cell types","authors":"Eulalie Liorzou, Camille Berthelot","doi":"10.1038/s41559-025-02768-7","DOIUrl":"10.1038/s41559-025-02768-7","url":null,"abstract":"Single-cell analysis of placental transcriptomes across species reveals the evolutionary divergence and crosstalk of maternal and fetal cell types during early mammalian evolution.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 8","pages":"1315-1316"},"PeriodicalIF":13.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144520448","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":"Deep learning reveals the complex genetic architecture of male guppy colouration","authors":"Wouter van der Bijl, Jacelyn J. Shu, Versara S. Goberdhan, Linley M. Sherin, Changfu Jia, Maria Cortazar-Chinarro, Alberto Corral-Lopez, Judith E. Mank","doi":"10.1038/s41559-025-02781-w","DOIUrl":"10.1038/s41559-025-02781-w","url":null,"abstract":"The extraordinary variation in male guppy (Poecilia reticulata) colouration is a powerful model for studying the interplay of natural and sexual selection. However, the complexity of this variation has hampered the high-resolution characterization and determination of the genetic architecture underlying male guppy colour and clouded our understanding of how this exceptional level of diversity is maintained. Here we identify the heritability and genetic basis of male colour variation using convolutional neural networks for high-resolution phenotyping coupled with selection experiments, controlled pedigrees and whole-genome resequencing for a genome-wide association study of colour traits. Our phenotypic and genomic results converge to show that colour patterning in guppies is a combination of many heritable features, each with a largely independent genetic architecture spanning the entire genome. Autosomally inherited ornaments are polygenic, with significant contributions from loci involved in neural crest cell migration. Unusually, the results of our genome-wide association study suggest that gene duplicates from the autosomes to the Y chromosome are responsible for much of the sex-linked variation in colour in guppies, providing a potential mechanism for the maintenance of variation of this classic model trait. Guppy colouration is a very diverse trait under natural and sexual selection. Using a combination of high-resolution phenotyping and genomic analysis, the authors reveal the genetic architecture of this complex trait.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 9","pages":"1614-1625"},"PeriodicalIF":13.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144520499","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":"More realistic plankton simulation models will improve projections of ocean ecosystem responses to global change","authors":"Kevin J. Flynn, Angus Atkinson, John Beardall, John A. Berges, Maarten Boersma, Christophe Brunet, Albert Calbet, Dave A. Caron, Hans G. Dam, Patricia M. Glibert, Per Juel Hansen, Peng Jin, Christian Lønborg, Daniel J. Mayor, Susanne Menden-Deuer, Thomas Mock, Margaret R. Mulholland, David M. Needham, Luca Polimene, Alex J. Poulton, Carol Robinson, Sebastian D. Rokitta, Björn Rost, Enric Saiz, David J. Scanlan, Katrin Schmidt, Evelyn Sherr, Diane K. Stoecker, Camilla Svensen, Stefan Thiele, Tron F. Thingstad, Selina Våge","doi":"10.1038/s41559-025-02788-3","DOIUrl":"10.1038/s41559-025-02788-3","url":null,"abstract":"Plankton models form the core of marine ecosystem simulators, with uses from regional resource and ecosystem management to climate change projections. In this Perspective, we suggest that stronger alignment of models with empirical knowledge about plankton physiology, diversity and trophic roles will improve model utility and the reliability of their outputs regarding biodiversity, ecophysiology, trophic dynamics and biogeochemistry. We recommend key steps to resolve the disconnect between empirical research and simulation models accounting for well-established plankton processes with an aim to increase the utility of such models for applied uses. A central challenge is characterizing the complexity of plankton diversity and activity in ways that are amenable to model incorporation. We argue that experts in empirical science are best placed to advise the development of next-generation models to address these challenges, and we propose a series of actions to achieve that engagement, including involvement of these experts in the design and exploitation of plankton digital twins. Plankton models have crucial applications in ecosystem management and climate change projections. This Perspective suggests that stronger alignment of plankton models with empirical knowledge is needed and recommends steps to close the gap between empirical research and modelling.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 9","pages":"1562-1570"},"PeriodicalIF":13.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144520497","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":"Cell type and cell signalling innovations underlying mammalian pregnancy","authors":"Daniel J. Stadtmauer, Silvia Basanta, Jamie D. Maziarz, Alison G. Cole, Gülay Dagdas, Gilbecca Rae Smith, Frank van Breukelen, Mihaela Pavličev, Günter P. Wagner","doi":"10.1038/s41559-025-02748-x","DOIUrl":"10.1038/s41559-025-02748-x","url":null,"abstract":"How fetal and maternal cell types have co-evolved to enable mammalian placentation poses a unique evolutionary puzzle. Here we integrate and compare single-cell transcriptomes from six species bracketing therian mammal diversity: opossum (a marsupial), Malagasy common tenrec (an afrotherian), mouse and guinea pig (rodents), and macaque and human (primates). We identify a conserved transcriptomic signature of invasive trophoblast across eutherians, probably representing a cell type family that radiated with the evolution of haemochorial placentation. In the maternal stroma, comparative analysis reveals that the endocrine decidual cell evolved from an immunomodulatory predecidual cell type retained in Tenrec and resembling early human decidua. Fetal and maternal cell signalling shows a pronounced tendency towards disambiguation—the exclusive expression of ligands by only one partner—although few ligand–receptor pairs follow an escalatory arms race dynamic. Finally, we reconstruct the uteroplacental cell–cell communication networks of extinct mammalian ancestors, identifying signalling innovations and widespread integration of fetal trophoblast and maternal decidual cells into signalling networks. Together, these results reveal a dynamic history of cell type innovation and co-evolution at the fetal–maternal interface. Single-cell transcriptomes from the fetal–maternal interface of six species of mammals reveal a conserved gene expression signature of invasive trophoblast, stepwise evolution of decidual stromal cell types and co-evolutionary patterns in cell–cell signalling.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 8","pages":"1469-1486"},"PeriodicalIF":13.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41559-025-02748-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144520498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}