Nature ecology & evolution最新文献

{"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":"https://doi.org/10.1038/s41559-025-02747-y","url":null,"abstract":"<p>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 <i>Drosophila</i>, we further examined the role of two key transcription factors, <i>achintya</i> and <i>vismay</i>, 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.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"23 1","pages":""},"PeriodicalIF":16.8,"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":"https://doi.org/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":"34 1","pages":""},"PeriodicalIF":16.8,"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":"https://doi.org/10.1038/s41559-025-02792-7","url":null,"abstract":"<p>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 <i>Saccharomyces cerevisiae</i> 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.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"23 1","pages":""},"PeriodicalIF":16.8,"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":"https://doi.org/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":"106 1","pages":""},"PeriodicalIF":16.8,"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":"https://doi.org/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":"12 1","pages":""},"PeriodicalIF":16.8,"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":"https://doi.org/10.1038/s41559-025-02761-0","url":null,"abstract":"<p>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.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"145 1","pages":""},"PeriodicalIF":16.8,"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":"https://doi.org/10.1038/s41559-025-02787-4","url":null,"abstract":"<p>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.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"37 1","pages":""},"PeriodicalIF":16.8,"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":"https://doi.org/10.1038/s41559-025-02820-6","url":null,"abstract":"<p>Deep-sea exploration has revealed the existence of ecosystems that are not powered by photosynthesis. For example, microorganisms that are able to metabolize hydrocarbons emitted from methane seeps form the basis of food webs that can comprise hundreds of animal species. Now, a study published in <i>Proceedings of the National Academy of Sciences USA</i> shows that some sea spiders (from the class Pycnogonida) harness the chemical energy of methane seeps by feeding on chemoautotrophic bacteria that live on their exoskeleton. During oceanographic expeditions off the coasts in California and Alaska, Dal Bó and colleagues collected specimens of three species of sea spiders known only from methane seeps. Through sequencing analyses and microscopic observations, they found abundant and diverse methanotrophic and methylotrophic bacteria living on the sea spider bodies. This association is more than skin deep: isotopic labelling experiments and subsequent single-cell imaging and analyses of digestive tissues showed that the sea spiders assimilate methane-derived carbon by consuming the methane-oxidizing bacteria. The presence of the bacteria also on the egg sacs carried by adult males suggests that these invertebrates pass on their microbial symbionts to their offspring. Beside putting sea spiders in the company of the hairy-chested yeti crab among the animals known to farm specialized bacteria on their own bodies, Dal Bó and colleagues’ discovery showcases how much there is still to discover about the life forms and ecosystems of the ocean depths.</p><p><b>Original reference:</b> <i>Proc. Natl Acad. Sci. USA</i> <b>122</b>, e2501422122 (2025)</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"93 1","pages":""},"PeriodicalIF":16.8,"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}

{"title":"Bates’ many contributions","authors":"","doi":"10.1038/s41559-025-02807-3","DOIUrl":"https://doi.org/10.1038/s41559-025-02807-3","url":null,"abstract":"Henry Walter Bates gave the first known scientific account of mimicry in biological systems. To mark the bicentenary of his birth, we present a collection of content that reflects on his life and legacy.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"47 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144594182","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":"Human contributions to global soundscapes are less predictable than the acoustic rhythms of wildlife","authors":"Panu Somervuo, Tomas Roslin, Brian L. Fisher, Bess Hardwick, Deirdre Kerdraon, Dimby Raharinjanahary, Eric Tsiriniaina Rajoelison, Patrik Lauha, Lukas Griem, Petteri Lehikoinen, Pekka Niittynen, Esko Piirainen, Markus Lumme, Ville-Matti Riihikoski, Orlando Acevedo-Charry, Solny A. Adalsteinsson, Maaz Ahmad, Sandra Alcobia, Jón Aldará, Nigel R. Andrew, Sten Anslan, Alexandre Antonelli, Julieta Soledad Arena, Santiago Arroyo Almeida, Ines Aster, Hannu Autto, Anahi Aviles Gamboa, Joaquín Baixeras, Mario Baldauf, Rosario Balestrieri, Gaia Giedre Banelyte, Adrian Barrett, Pedro Beja, Thomas Olof Berg, Benjamin Bergerot, Elizabeth G. Biro, Pedro G. Blendinger, Loïc Bollache, Magda Bou Dagher Kharrat, Stephane Boyer, Erika Bridell, Martyn Brotherson, Leslie Robert Brown, Hannah L. Buckley, Erika Buscardo, Nokuphila Buthelezi, Luciano Cagnolo, Alice Calvente, Giovanni Capobianco, Laura Carreón-Palau, Suzanne Carriere, Bradley S. Case, Jenyu Chang, Juan Matías Chaparro, Chi-Ling Chen, Christine Chicoine, Madeleine Christensson, Francisco Collado Rosique, William Colom Montero, Ricardo do Sacramento da Fonseca, Luís P. Da Silva, Anamaria Dal Molin, Tad Dallas, Maria Carla de Francesco, Jorge Arturo Del Ángel-Rodríguez, Ricardo Díaz-Delgado, Thomas Dirnböck, Ika Djukic, Philile Dladla, Jeremías Domínguez Masciale, Thiago Dorigo, Errol Douwes, Torbjørn Ekrem, Helena Enderskog, Charlotta Erefur, Muhammad Fahad, Mohsen Falahati-Anbaran, Arielle Farrell, Gabriel Ferland, Emanuele Ferrari, Axa Figueiredo, Fernando Forero, Inga Freiberga, Andrea Frosch-Radivo, Luis Alberto Ganchozo Intriago, Laura Garzoli, Paola Giacomotti, Andros T. Gianuca, Olivier Gilg, Vladimir Gilg, Fanney Gísladóttir, Ryan Glowacki, Brigitte Gottsberger, Jocelyn Gregoire, Elli Groner, Patrícia Guedes, Aimee Michelle Guile, Peter Haase, Fazal Hadi, Magdalena Haidegger, Leivur Janus Hansen, Lars Holst Hansen, Reid Harrop, Harald Havnås, David Herrera Báez, Chris C. Y. Ho, Denise Hohenbühel, Marketa Houska Tahadlova, Jari Hänninen, Linda Höglund, Kolbrún Í Haraldsstovu, Elise Imbeau, Jasmin Inkinen, Masae Iwamoto Ishihara, Abigail C. Jackson, Gunnar Jansson, Rohit Jha, Gerald Kager, Rhea Kahale, Oula Kalttopää, Elizabeth Wanjiru Karai, Dave Karlsson, Andrea Kaus-Thiel, Asghar Khan, Qaisar Khan, Keishi Kimoto, Shadrack Chumo Kipngetich, Clemens Klante, Leif Klemedtsson, Mårten Klinth, Janne Koskinen, Matti Kotakorpi, Agnes-Katharina Kreiling, Irmgard Krisai-Greilhuber, Erik Kristensen, Sebastian König, Silke Langenheder, Kalevi Laurila, Pascaline Le Gouar, Nicolas Lecomte, Erin Lecomte, Paula Moraes Leitman, Jorge L. León-Cortés, Daijiang Li, John Loehr, Carlos Lopez-Vaamonde, Mehsen Makari, Gabriela Giselle Mangini, Michael Maroschek, Vanessa A. Mata, Shunsuke Matsuoka, Thais Mazzafera, Paul G. McDonald, Laura Meinert, Mayra Meléndez-González, Angela M. Mendoza-Henao, Sebastien Moreau, Jérôme Moreau, Jesper Mosbacher, Esteban Moyer, Anna Mrazova, Samantha Mteshane, Nancy Wangari Mungai, Gema Muñoz Herraiz, Andrea Murillo-Vázquez, Simona Musazzi, Marko Mutanen, Jörg Müller, Rebeca Navarro Canales, Monica Ndlovu, Annegret Nicolai, Armin Niessner, Jenni Nordén, Paweł Nowak, Erin O’Connell, Arianna Orru, Thomas Pagnon, Yurani Nayive Pantoja-Diaz, Mikko Pentinsaari, Sebastian Pilloni, Adrian Pinder, Thiago A. Pinheiro, Sergei Põlme, Luke L. Powell, Gisela Pröll, Paola Pulido-Santacruz, Enrique Queralt, Mark Tristan Quilantang, Kirsty Quinlan, Ricardo Ramirez, Juha Rankinen, Micaela Del Valle Rasino, Rui Rebelo, Wolfram Remmers, Franziska Retz, Evelin Reyes, Gonzalo Rivas Torres, Hanna M. K. Rogers, Inês T. Rosário, Sidney Rosário Da Rosàrio da Costa, Tobias Rütting, Johannes Sahlstén, Carole Saliba, Teppo Salmirinne, Katerina Sam, Douglas Santos, Margarida Santos-Reis, Michel Sawan, Benjamin Schattanek-Wiesmair, Pauliina Schiestl-Aalto, Niels Martin Schmidt, Sebastian Seibold, Rupert Seidl, Linda Seifert, Malibongwe Sithole, Elise Sivault, Jessica Smart, Ireneusz Smerczyński, Ayaka Soda, Renata S. Sousa-Lima, Angela Stanisci, Margaret C. Stanley, Daleen Steenkamp, Elisa Stengel, Stefan Stoll, Willem Maartin Strauss, Elisabeth Stur, Maija Sujala, Janne Sundell, Jónína Svavarsdóttir, Leho Tedersoo, Saana Tepsa, Maor Tiko Tikochinsky, Esa-Pekka Tuominen, Stefanie Tweraser, Catalina Ulloa Espinosa, Joni Uusitalo, Mikko Vallinmäki, Fabrice Vannier, Abigail Varela, Emma Vatka, Silja Veikkolainen, Karl Vernes, Phillip C. Watts, Per Weslien, Ciara Wirth, Jana Helga Wisniewski, Amanda B. Young, Robyn Övergaard, Otso Ovaskainen","doi":"10.1038/s41559-025-02786-5","DOIUrl":"https://doi.org/10.1038/s41559-025-02786-5","url":null,"abstract":"<p>Across the world, human (anthropophonic) sounds add to sounds of biological (biophonic) and geophysical (geophonic) origin, with human contributions including both speech and technophony (sounds of technological devices). To characterize society’s contribution to the global soundscapes, we used passive acoustic recorders at 139 sites across 6 continents, sampling both urban green spaces and nearby pristine sites continuously for 3 years in a paired design. Recordings were characterized by bird species richness and by 14 complementary acoustic indices. By relating each index to seasonal, diurnal, climatic and anthropogenic factors, we show here that latitude, time of day and day of year each predict a substantial proportion of variation in key metrics of biophony—whereas anthropophony (speech and traffic) show less predictable patterns. Compared to pristine sites, the soundscape of urban green spaces is more dominated by technophony and less diverse in terms of acoustic energy across frequencies and time steps, with less instances of quiet. We conclude that the global soundscape is formed from a highly predictable rhythm in biophony, with added noise from geophony and anthropophony. At urban sites, animals experience an increasingly noisy background of sound, which poses challenges to efficient communication.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"11 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144586652","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}