Nature ecology & evolution最新文献

{"title":"Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene programme in bat wing development","authors":"Magdalena Schindler, Christian Feregrino, Silvia Aldrovandi, Bai-Wei Lo, Anna A. Monaco, Alessa R. Ringel, Ariadna E. Morales, Tobias Zehnder, Rose Yinghan Behncke, Juliane Glaser, Alexander Barclay, Guillaume Andrey, Bjørt K. Kragesteen, René Hägerling, Stefan A. Haas, Martin Vingron, Igor Ulitsky, Marc A. Marti-Renom, Julio Hechavarria, Nicolas Fasel, Michael Hiller, Darío G. Lupiáñez, Stefan Mundlos, Francisca M. Real","doi":"10.1038/s41559-025-02780-x","DOIUrl":"10.1038/s41559-025-02780-x","url":null,"abstract":"Bats are the only mammals capable of self-powered flight, an evolutionary innovation based on the transformation of forelimbs into wings. The bat wing is characterized by an extreme elongation of the second to fifth digits with a wing membrane called the chiropatagium connecting them. Here we investigated the developmental and cellular origin of this structure by comparing bat and mouse limbs using omics tools and single-cell analyses. Despite the substantial morphological differences between the species, we observed an overall conservation of cell populations and gene expression patterns including interdigital apoptosis. Single-cell analyses of micro-dissected embryonic chiropatagium identified a specific fibroblast population, independent of apoptosis-associated interdigital cells, as the origin of this tissue. These distal cells express a conserved gene programme including the transcription factors MEIS2 and TBX3, which are commonly known to specify and pattern the early proximal limb. Transgenic ectopic expression of MEIS2 and TBX3 in mouse distal limb cells resulted in the activation of genes expressed during wing development and phenotypic changes related to wing morphology, such as the fusion of digits. Our results elucidate fundamental molecular mechanisms of bat wing development and illustrate how drastic morphological changes can be achieved through repurposing of existing developmental programmes during evolution. Single-cell comparison of developing bat and mouse limbs reveals conservation of cell populations and gene expression patterns, and suggests repurposing of genes involved in proximal limb development for wing evolution.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 9","pages":"1626-1642"},"PeriodicalIF":13.9,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41559-025-02780-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144639824","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 next generation of colour pattern genomics","authors":"Nidal Karagic, Claudius F. Kratochwil","doi":"10.1038/s41559-025-02816-2","DOIUrl":"10.1038/s41559-025-02816-2","url":null,"abstract":"Convolutional neural networks and genetic association analysis decode the evolution of colour pattern diversity and its underlying complex genetic architecture in the Trinidadian guppy.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 9","pages":"1554-1555"},"PeriodicalIF":13.9,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144639823","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 regulatory networks and essential transcription factors for de novo-originated genes","authors":"Junhui Peng, Bing-Jun Wang, Nicolas Svetec, Li Zhao","doi":"10.1038/s41559-025-02747-y","DOIUrl":"10.1038/s41559-025-02747-y","url":null,"abstract":"The regulation of gene expression is crucial for the functional integration of evolutionarily young genes, particularly those that emerge de novo. However, the regulatory programmes governing the expression of de novo genes remain unknown. To address this, we applied computational methods to single-cell RNA sequencing data, identifying key transcription factors probably instrumental in regulating de novo genes. We found that transcription factors do not have the same propensity for regulating de novo genes; some transcription factors regulate more de novo genes than others. Leveraging genetic and genomic tools in Drosophila, we further examined the role of two key transcription factors, achintya and vismay, and the regulatory architecture of new genes. Our findings identify key transcription factors associated with the expression of de novo genes and highlight how transcription factors, and possibly their duplications, are linked to the expressional regulation of de novo genes. A combination of computational methods applied to single-cell RNA sequencing data and genetic experiments shows that a small number of transcription factors are involved in the regulation of many de novo genes in Drosophila melanogaster.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 8","pages":"1487-1498"},"PeriodicalIF":13.9,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144622365","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":"Combining science and policy for a unified global soil biodiversity observatory","authors":"J. Jacob Parnell, Peter de Ruiter, Carlos Guerra, Luca Montanarella, Natalia Rodriguez Eugenio, Talita Ferreira, Maria Elizabeth F. Correia, Cintia C. Niva, Ederson C. Jesus, Maria Inês L. Oliveira, Luiz Fernando S. Antunes, Lucília M. Parron, Marcia R. Coelho, Guilherme M. Chaer, Juaci V. Malaquias, Ozanival Dario D. Silva, Ieda C. Mendes, Zoë Lindo, Jeff Battigelli, Gian Luca Bagnara, Rosalina González, Rosa M. Poch, Diana H. Wall, Leena Vilonen, Giulio Malorgio, Carlos Barreto, Monica Kobayashi, Rosa Cuevas-Corona, George G. Brown","doi":"10.1038/s41559-025-02754-z","DOIUrl":"10.1038/s41559-025-02754-z","url":null,"abstract":"The effective conservation of soil biodiversity and ecosystem services in the face of global-change threats requires improvements in national monitoring. We outline the Global Soil Biodiversity Observatory, an initiative that aims to develop standardized indicators and enhance national monitoring capacities to support evidence-based policymaking and facilitate global assessments.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 8","pages":"1302-1306"},"PeriodicalIF":13.9,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144622236","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 role of plasmid copy number and mutation rate in evolutionary outcomes","authors":"Alexander ‘Olek’ Pisera, Chang C. Liu","doi":"10.1038/s41559-025-02792-7","DOIUrl":"10.1038/s41559-025-02792-7","url":null,"abstract":"Multicopy plasmids are widespread in nature and compose a common strategy for spreading beneficial traits across microbes. However, the role of plasmids in supporting the evolution of encoded genes remains underexplored due to challenges in experimentally manipulating key parameters such as plasmid copy number and mutation rate. Here we developed a strategy for controlling copy number in the plasmid-based Saccharomyces cerevisiae continuous evolution system, OrthoRep, and used our resulting capabilities to investigate the evolution of a conditionally essential gene under varying copy number and mutation rate conditions. Our results show that low copy number facilitated the faster enrichment of beneficial alleles whereas high copy number promoted robustness through the maintenance of allelic diversity. High copy number also slowed the removal of deleterious mutations and increased the fraction of non-functional alleles that could hitchhike during evolution. This study highlights the nuanced relationships between plasmid copy number, mutation rate and evolutionary outcomes, providing insights into the adaptive dynamics of genes encoded on multicopy plasmids and nominating OrthoRep as a versatile tool for studying plasmid evolution. In an experimental multicopy plasmid evolution system that allows manipulation of mutation rate and copy number, low copy number promoted enrichment of beneficial alleles whereas high copy number maintained allelic diversity.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 9","pages":"1694-1704"},"PeriodicalIF":13.9,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144622239","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":"Water-use efficiency driven by water savings","authors":"Jürgen Knauer","doi":"10.1038/s41559-025-02793-6","DOIUrl":"10.1038/s41559-025-02793-6","url":null,"abstract":"Analysis of land–atmosphere water and CO2 fluxes suggests that reduced water use by vegetation, rather than increased carbon uptake, is the driving factor behind the well-documented increase in vegetation water-use efficiency in response to rising atmospheric CO2.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 9","pages":"1548-1549"},"PeriodicalIF":13.9,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144603559","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":"Partitioning how biodiversity brings stability","authors":"Frank Pennekamp","doi":"10.1038/s41559-025-02803-7","DOIUrl":"10.1038/s41559-025-02803-7","url":null,"abstract":"A theoretical approach quantifies the drivers of community variability in simulated and natural plant communities, which sheds light on the mechanisms that underlie biodiversity–ecosystem stability relationships.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 10","pages":"1761-1762"},"PeriodicalIF":13.9,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144603397","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 water loss rather than increased photosynthesis controls CO2-enhanced water-use efficiency","authors":"Weiwei Zhan, Xu Lian, Jiangong Liu, Jisu Han, Yu Huang, Hao Yang, Chunhui Zhan, Alexander J. Winkler, Pierre Gentine","doi":"10.1038/s41559-025-02761-0","DOIUrl":"10.1038/s41559-025-02761-0","url":null,"abstract":"Numerous leaf-level experiments suggest that plant intrinsic water-use efficiency (iWUE) increases under elevated CO2 because of reduced stomatal conductance and enhanced photosynthesis. However, it remains elusive whether this response can be extrapolated to the ecosystem scale, because confounding factors and compensating feedbacks are often involved in ecosystem iWUE variations. Here we develop a machine learning-based framework to disentangle the ecosystem-scale CO2 effects on iWUE and its two components, canopy conductance (Gc) and gross primary productivity (GPP), based on global networks of long-term eddy covariance observations. Our results show widespread CO2-induced enhancement of iWUE across diverse ecosystems, driven predominantly by Gc reduction rather than GPP stimulation. Moreover, three divergent response types are identified across the studied ecosystems, based on the strength and significance of CO2-driven Gc reduction and GPP enhancement, indicating spatially non-uniform responses to rising CO2. Nutrient supply, water availability and biome types are found to be critical factors regulating this spatial heterogeneity. Overall, our study provides observational insights into ecosystem-scale CO2 fertilization effects. Such understandings are essential to inform terrestrial biosphere models for better projections of carbon and water cycles given the intensified changing climate in a CO2-rich future. A machine learning approach using long-term observations of eddy covariance finds that the increase in plant intrinsic water-use efficiency under higher CO2 levels, across diverse ecosystems, is driven primarily by reduction in canopy conductance, rather than by stimulation of gross primary productivity.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 9","pages":"1571-1584"},"PeriodicalIF":13.9,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144603567","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":"Stabilizing effects of biodiversity arise from species-specific dynamics rather than interspecific interactions in grasslands","authors":"Bo Meng, Mingyu Luo, Michel Loreau, Pubin Hong, Dylan Craven, Nico Eisenhauer, Forest Isbell, Maowei Liang, Daniel Reuman, Brian Wilsey, Jasper van Ruijven, Lei Zhao, Shaopeng Wang","doi":"10.1038/s41559-025-02787-4","DOIUrl":"10.1038/s41559-025-02787-4","url":null,"abstract":"Although numerous studies have demonstrated a positive relationship between biodiversity and ecosystem stability, that is low temporal variability in ecosystem functions, the role of interspecific interactions in driving this relationship remains elusive. Here we develop a partitioning framework to disentangle the effects of interspecific interactions on ecosystem variability from those of interaction-independent processes. Applying this framework to competition models and biodiversity experiments in European and North American grasslands, we find that species-specific dynamics observable in monocultures (for example, environmental responses or demographic stochasticity), rather than interspecific interactions observable only in mixtures, explain much of the stabilizing effects of biodiversity on ecosystems. The weak net effect of interspecific interactions results from two counter-balancing effects: an interaction-driven increase in average species variability and an interaction-driven decrease in average species synchrony. We also find that interspecific interactions contributing to higher ecosystem functioning tend to reduce ecosystem variability. Our study provides a systematic empirical assessment of the role of interspecific interactions in shaping grassland ecosystem stability, challenging traditional assumptions about their importance and highlighting species-specific dynamics as the primary mechanism underlying the pervasive biodiversity–stability relationship. The role of interspecific interactions in biodiversity–ecosystem stability relationships is unclear. Here the authors develop a theoretical approach and show that empirical diversity–stability relationships in grasslands are best explained by species-specific dynamics rather than by interspecific interactions.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 10","pages":"1837-1847"},"PeriodicalIF":13.9,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144603566","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":"Methane fuel for sea spiders","authors":"Walter Andriuzzi","doi":"10.1038/s41559-025-02820-6","DOIUrl":"10.1038/s41559-025-02820-6","url":null,"abstract":"","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 8","pages":"1308-1308"},"PeriodicalIF":13.9,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144603558","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}