Nature ecology & evolution最新文献

{"title":"Identification of old coding regions disproves the hominoid de novo status of genes","authors":"Evgeny Leushkin, Henrik Kaessmann","doi":"10.1038/s41559-024-02513-6","DOIUrl":"10.1038/s41559-024-02513-6","url":null,"abstract":"","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"8 10","pages":"1826-1830"},"PeriodicalIF":13.9,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142073321","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":"The genetic architecture of repeated local adaptation to climate in distantly related plants","authors":"James R. Whiting, Tom R. Booker, Clément Rougeux, Brandon M. Lind, Pooja Singh, Mengmeng Lu, Kaichi Huang, Michael C. Whitlock, Sally N. Aitken, Rose L. Andrew, Justin O. Borevitz, Jeremy J. Bruhl, Timothy L. Collins, Martin C. Fischer, Kathryn A. Hodgins, Jason A. Holliday, Pär K. Ingvarsson, Jasmine K. Janes, Momena Khandaker, Daniel Koenig, Julia M. Kreiner, Antoine Kremer, Martin Lascoux, Thibault Leroy, Pascal Milesi, Kevin D. Murray, Tanja Pyhäjärvi, Christian Rellstab, Loren H. Rieseberg, Fabrice Roux, John R. Stinchcombe, Ian R. H. Telford, Marco Todesco, Jaakko S. Tyrmi, Baosheng Wang, Detlef Weigel, Yvonne Willi, Stephen I. Wright, Lecong Zhou, Sam Yeaman","doi":"10.1038/s41559-024-02514-5","DOIUrl":"10.1038/s41559-024-02514-5","url":null,"abstract":"Closely related species often use the same genes to adapt to similar environments. However, we know little about why such genes possess increased adaptive potential and whether this is conserved across deeper evolutionary lineages. Adaptation to climate presents a natural laboratory to test these ideas, as even distantly related species must contend with similar stresses. Here, we re-analyse genomic data from thousands of individuals from 25 plant species as diverged as lodgepole pine and Arabidopsis (~300 Myr). We test for genetic repeatability based on within-species associations between allele frequencies in genes and variation in 21 climate variables. Our results demonstrate significant statistical evidence for genetic repeatability across deep time that is not expected under randomness, identifying a suite of 108 gene families (orthogroups) and gene functions that repeatedly drive local adaptation to climate. This set includes many orthogroups with well-known functions in abiotic stress response. Using gene co-expression networks to quantify pleiotropy, we find that orthogroups with stronger evidence for repeatability exhibit greater network centrality and broader expression across tissues (higher pleiotropy), contrary to the ‘cost of complexity’ theory. These gene families may be important in helping wild and crop species cope with future climate change, representing important candidates for future study. Analysis of genomic data from 25 distantly related plant species shows signatures of selection on the same gene families and functions that repeatedly contributed to local adaptation to climate.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"8 10","pages":"1933-1947"},"PeriodicalIF":13.9,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41559-024-02514-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142073324","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":"Reply to: Identification of old coding regions disproves the hominoid de novo status of genes","authors":"Chunfu Xiao, Fan Mo, Yingfei Lu, Qi Xiao, Chao Yao, Ting Li, Jianhuan Qi, Xiaoge Liu, Jia-Yu Chen, Li Zhang, Tiannan Guo, Baoyang Hu, Ni A. An, Chuan-Yun Li","doi":"10.1038/s41559-024-02515-4","DOIUrl":"10.1038/s41559-024-02515-4","url":null,"abstract":"","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"8 10","pages":"1831-1834"},"PeriodicalIF":13.9,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142073323","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":"Spatial bias in the fossil record affects understanding of human evolution","authors":"","doi":"10.1038/s41559-024-02524-3","DOIUrl":"10.1038/s41559-024-02524-3","url":null,"abstract":"Using modern mammals as analogues, we investigate how spatial bias in the early human fossil record probably influences understanding of human evolution. Our results suggest that the environmental and fossil records from palaeoanthropological hotspots are probably missing aspects of environmental and anatomical variation.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"8 11","pages":"2016-2017"},"PeriodicalIF":13.9,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142021981","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":"Tripartite origin of the chordate brain","authors":"Jacob M. Musser","doi":"10.1038/s41559-024-02528-z","DOIUrl":"10.1038/s41559-024-02528-z","url":null,"abstract":"A survey of Amphioxus cell types reveals ancient neurosecretory cells and multiple developmental origins of the chordate brain.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"8 10","pages":"1782-1783"},"PeriodicalIF":13.9,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142007489","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":"Spatial sampling bias influences our understanding of early hominin evolution in eastern Africa","authors":"W. Andrew Barr, Bernard Wood","doi":"10.1038/s41559-024-02522-5","DOIUrl":"10.1038/s41559-024-02522-5","url":null,"abstract":"The eastern branch of the Eastern African Rift System (EARS) is the source of a large proportion of the early hominin fossil record, but it covers a tiny fraction (ca. 1%) of the continent. Here we investigate how this mismatch between where fossils are preserved and where hominins probably lived may influence our ability to understand early hominin evolution, using extant mammals as analogues. We show that the eastern branch of the EARS is not an environmentally representative sample of the full species range for nearly all extant rift-dwelling mammals. Likewise, when we investigate published morphometric datasets for extant cercopithecine primates, evidence from the eastern branch alone fails to capture major portions of continental-scale cercopithecine cranial morphospace. We suggest that extant rift-dwelling species should be used as analogues to place confidence intervals on hominin habitat reconstructions. Furthermore, given the north–south orientation of the eastern branch of the EARS, morphoclines that are not aligned along this major north–south axis are likely to be poorly sampled by sites in the eastern branch. There is a pressing need for research on the geography of early hominin morphoclines to estimate how morphologically representative the hominin fossil sample from the eastern branch may be. The Eastern African Rift System (EARS) is a key location for the hominin fossil record, but the fact that it samples a narrow section of the continent has long been known. The authors tackle this known (but largely unaddressed) bias by sampling the distribution and morphospace of extant mammals in the rift, showing that the eastern branch of the EARS fails to capture the full range of diversity and morphology. This approach could be helpful to place confidence intervals on extinct habitat reconstructions, controlling for spatial bias.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"8 11","pages":"2113-2120"},"PeriodicalIF":13.9,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142007491","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":"Author Correction: Widening global variability in grassland biomass since the 1980s","authors":"Andrew S. MacDougall, Ellen Esch, Qingqing Chen, Oliver Carroll, Colin Bonner, Timothy Ohlert, Matthias Siewert, John Sulik, Anna K. Schweiger, Elizabeth T. Borer, Dilip Naidu, Sumanta Bagchi, Yann Hautier, Peter Wilfahrt, Keith Larson, Johan Olofsson, Elsa Cleland, Ranjan Muthukrishnan, Lydia O’Halloran, Juan Alberti, T. Michael Anderson, Carlos A. Arnillas, Jonathan D. Bakker, Isabel C. Barrio, Lori Biederman, Elizabeth H. Boughton, Lars A. Brudvig, Martin Bruschetti, Yvonne Buckley, Miguel N. Bugalho, Marc W. Cadotte, Maria C. Caldeira, Jane A. Catford, Carla D’Antonio, Kendi Davies, Pedro Daleo, Christopher R. Dickman, Ian Donohue, Mary Ellyn DuPre, Kenneth Elgersma, Nico Eisenhauer, Anu Eskelinen, Catalina Estrada, Philip A. Fay, Yanhao Feng, Daniel S. Gruner, Nicole Hagenah, Sylvia Haider, W. Stanley Harpole, Erika Hersch-Green, Anke Jentsch, Kevin Kirkman, Johannes M. H. Knops, Lauri Laanisto, Lucíola S. Lannes, Ramesh Laungani, Ariuntsetseg Lkhagva, Petr Macek, Jason P. Martina, Rebecca L. McCulley, Brett Melbourne, Rachel Mitchell, Joslin L. Moore, John W. Morgan, Taofeek O. Muraina, Yujie Niu, Meelis Pärtel, Pablo L. Peri, Sally A. Power, Jodi N. Price, Suzanne M. Prober, Zhengwei Ren, Anita C. Risch, Nicholas G. Smith, Grégory Sonnier, Rachel J. Standish, Carly J. Stevens, Michelle Tedder, Pedro Tognetti, G. F. (Ciska) Veen, Risto Virtanen, Glenda M. Wardle, Elizabeth Waring, Amelia A. Wolf, Laura Yahdjian, Eric W. Seabloom","doi":"10.1038/s41559-024-02538-x","DOIUrl":"10.1038/s41559-024-02538-x","url":null,"abstract":"","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"8 10","pages":"2003-2003"},"PeriodicalIF":13.9,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41559-024-02538-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142004848","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":"Loss of sex in brown algae","authors":"Christoph R. Haag","doi":"10.1038/s41559-024-02497-3","DOIUrl":"10.1038/s41559-024-02497-3","url":null,"abstract":"An analysis of phenotypic and genomic changes that accompany the loss of sex in brown algae reveals shared features with transitions to asexuality in animals and plants.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"8 10","pages":"1786-1787"},"PeriodicalIF":13.9,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141991811","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":"Single-cell analysis of the amphioxus hepatic caecum and vertebrate liver reveals genetic mechanisms of vertebrate liver evolution","authors":"Baosheng Wu, Wenjie Xu, Kunjin Wu, Ye Li, Mingliang Hu, Chenguang Feng, Chenglong Zhu, Jiangmin Zheng, Xinxin Cui, Jing Li, Deqian Fan, Fenghua Zhang, Yuxuan Liu, Jinping Chen, Chang Liu, Guang Li, Qiang Qiu, Kai Qu, Wen Wang, Kun Wang","doi":"10.1038/s41559-024-02510-9","DOIUrl":"10.1038/s41559-024-02510-9","url":null,"abstract":"The evolution of the vertebrate liver is a prime example of the evolution of complex organs, yet the driving genetic factors behind it remain unknown. Here we study the evolutionary genetics of liver by comparing the amphioxus hepatic caecum and the vertebrate liver, as well as examining the functional transition within vertebrates. Using in vivo and in vitro experiments, single-cell/nucleus RNA-seq data and gene knockout experiments, we confirm that the amphioxus hepatic caecum and vertebrate liver are homologous organs and show that the emergence of ohnologues from two rounds of whole-genome duplications greatly contributed to the functional complexity of the vertebrate liver. Two ohnologues, kdr and flt4, play an important role in the development of liver sinusoidal endothelial cells. In addition, we found that liver-related functions such as coagulation and bile production evolved in a step-by-step manner, with gene duplicates playing a crucial role. We reconstructed the genetic footprint of the transfer of haem detoxification from the liver to the spleen during vertebrate evolution. Together, these findings challenge the previous hypothesis that organ evolution is primarily driven by regulatory elements, underscoring the importance of gene duplicates in the emergence and diversification of a complex organ. Comparative analysis of single-cell data from the amphioxus hepatic caecum and the liver of several vertebrates shows how genome duplication contributes to cellular diversification and functional complexity of the vertebrate liver.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"8 10","pages":"1972-1990"},"PeriodicalIF":13.9,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141991934","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":"Gene duplication contributes to liver evolution","authors":"Francisca Hervas-Sotomayor, Florent Murat","doi":"10.1038/s41559-024-02509-2","DOIUrl":"10.1038/s41559-024-02509-2","url":null,"abstract":"A cross-species analysis reveals how whole genome duplication underlies the cellular diversification of the vertebrate liver.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"8 10","pages":"1788-1789"},"PeriodicalIF":13.9,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141991932","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}