Nature ecology & evolution最新文献

{"title":"Cross-kingdom comparative genomics reveal the metabolic potential of fungi for lignin turnover in deadwood","authors":"Teeratas Kijpornyongpan, Eugene Kuatsjah, Evan Komp, James E. Evans, Francisco Javier Ruiz-Dueñas, Davinia Salvachúa","doi":"10.1038/s41559-025-02785-6","DOIUrl":"10.1038/s41559-025-02785-6","url":null,"abstract":"Deadwood is a major carbon source in forests, and yet the fate of this carbon remains a gap in our understanding of global carbon cycling. Lignin, the most recalcitrant biopolymer in wood, is mainly decayed through extracellular enzymatic and chemical processes initiated by white-rot fungi. However, the intracellular conversion of lignin decay products has been overlooked in the fungal kingdom. Here we integrate comparative genomic and phylogenetic analyses to understand the distribution and evolution of enzymes responsible for modifying lignin-related aromatic compounds—such as decarboxylases, hydroxylases, dioxygenases and other downstream ring-cleavage enzymes—that funnel carbon to central metabolism across the bacterial and the fungal kingdoms. We demonstrate that specific fungal lineages conserve these enzyme families, and that the abilities to enzymatically depolymerize lignin and catabolize lignin-related aromatic compounds are not necessarily coupled. Our analyses also reveal an expanded substrate specificity of aromatic ring-cleavage enzymes during fungal evolution, as well as a clade of extracellular enzymes among them, broadening the spatial range of these biochemical capabilities. Together, our results highlight a large diversity of fungal enzymes and hosts that warrant further investigation for inclusion into carbon cycling models and biotechnological applications for the conversion of aromatic compounds. This study uses comparative genomics and phylogenetics to analyse the distribution and evolution of key enzymes involved in the catabolism of lignin-related aromatic compounds in the bacterial and fungal kingdoms.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 9","pages":"1599-1613"},"PeriodicalIF":13.9,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41559-025-02785-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144586651","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":"Pervasive but biome-dependent relationship between fragmentation and resilience in forests","authors":"Yongxian Su, Chaoqun Zhang, Alessandro Cescatti, Kailiang Yu, Philippe Ciais, Taylor Smith, Jiali Shang, Jofre Carnicer, Jane Liu, Jing Ming Chen, Julia K. Green, Jianping Wu, Guillermo E. Ponce-Campos, Yongguang Zhang, Zhiyan Zuo, Jinbao Liao, Jianping Wu, Raffaele Lafortezza, Kai Yan, Xueqin Yang, Liyang Liu, Jiashun Ren, Wenping Yuan, Xiuzhi Chen, Chaoyang Wu, Weiqi Zhou","doi":"10.1038/s41559-025-02776-7","DOIUrl":"10.1038/s41559-025-02776-7","url":null,"abstract":"The relationship between landscape fragmentation and vegetation resilience is uncertain. Here we use multiple satellite-based tree cover data and vegetation indices to quantify the apparent effects of fragmentation on global forest resilience and potential mechanisms thereof. We measure fragmentation as edge density, patch density and mean patch area of tree cover patches, and measure resilience as one-lag temporal autocorrelation of vegetation indices. We find a statistically significant (P < 0.05) fragmentation–resilience relationship in about 77% of fragmented forests, but the direction varies across biomes. In tropical and temperate forests, fragmentation is linked to increased local temperature and atmospheric dryness, resulting in a negative fragmentation–resilience relationship. Conversely, in boreal forests, fragmentation is associated with decreased atmospheric dryness and enhanced light resource, thereby increasing forest resilience. Our results reconcile competing hypotheses and highlight the importance of accounting for fragmentation when predicting shifts in ecosystem resilience under disturbances. These findings also suggest the necessity of biome-targeted forest management strategies for climate change mitigation and adaptation. Human-driven forest fragmentation could have major impacts on ecosystem functioning. This global analysis shows that the relationship between fragmentation and vegetation resilience in forests may differ depending on bioclimatic region and local environmental conditions.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 9","pages":"1670-1684"},"PeriodicalIF":13.9,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144578018","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":"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":"Summer warmth between 15,500 and 15,000 years ago enabled human repopulation of the northwest European margin","authors":"I. P. Matthews, A. P. Palmer, I. Candy, C. Francis, A. M. Abrook, P. C. Lincoln, S. P. E. Blockley, S. Engels, A. MacLeod, R. A. Staff, W. Z. Hoek, J. Burton","doi":"10.1038/s41559-025-02712-9","DOIUrl":"10.1038/s41559-025-02712-9","url":null,"abstract":"High-magnitude decadal to centennial-scale abrupt changes in climate had a transformative effect on many past human populations. However, our understanding of these human/climate relationships is limited because robust tests of these linkages require region-specific quantified palaeoclimatic data with sufficient chronological precision to permit comparisons to the archaeological record. Here we present new high-resolution palaeoclimatic data and combine these with radiocarbon inventories of archaeological and faunal material, to test the relationship between abrupt warming and the ability of humans to rapidly repopulate the northwest margins of Europe (>50° N and encompassing the area of Britain, Ireland, the surrounding islands and the North Sea basin) after regional abandonment during the Last Glacial Maximum. We address the timing of this process and the relevance of the abrupt climate changes recorded in the Greenland ice cores. We use the IntCal20 radiocarbon calibration curve to show that the earliest human repopulation in this region occurred up to 500 years before the climate of Greenland warmed. However, our analyses show that parts of the northwest European margin had already experienced substantial summer warming by this time, probably driven by changes of sea-ice area in the eastern North Atlantic. The associated warming influenced the distribution of key hunter-gatherer prey species such as reindeer, which were a key resource for humans. Accordingly, this study highlights asynchrony in seasonal warming across the North Atlantic region during the last deglaciation and shows that this asynchrony permitted human exploitation of northwest European margin paraglacial landscapes by ~15,200 years before the present. The authors use the latest radiocarbon calibration curve and new local palaeoclimatic and palaeoenvironmental records from Britain to show that humans repopulated the northwest European margin between 15,500 and 15,000 years ago, supported by local summer warmth occurring earlier than previously thought.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 7","pages":"1179-1192"},"PeriodicalIF":13.9,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41559-025-02712-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144533141","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":"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}