Pub Date : 2026-01-07DOI: 10.1038/s41559-025-02941-y
Marta S. Magri, Danila Voronov, Saoirse Foley, Pedro Manuel Martínez-García, Martin Franke, Gregory A. Cary, José M. Santos-Pereira, Claudia Cuomo, Manuel Fernández-Moreno, Marta Portela, Alejandro Gil-Galvez, Rafael D. Acemel, Periklis Paganos, Carolyn Ku, Jovana Ranđelović, Maria Lorenza Rusciano, Panos N. Firbas, José Luis Gómez-Skarmeta, Veronica F. Hinman, Maria Ina Arnone, Ignacio Maeso
Despite the growing abundance of sequenced animal genomes, we only have detailed knowledge of regulatory organization for a handful of lineages, particularly flies and vertebrates. These two taxa show contrasting trends in the molecular mechanisms of 3D chromatin organization and long-term evolutionary dynamics of cis-regulatory element (CRE) conservation. Here we study the evolution and organization of the regulatory genome of echinoderms, a lineage whose phylogenetic position and relatively slow molecular evolution have proven particularly useful for evolutionary studies. We generated new reference genome assemblies for two species belonging to two different echinoderm classes: the purple sea urchin Strongylocentrotus purpuratus and the bat sea star Patiria miniata using PacBio and HiC data and characterize their 3D chromatin architecture. We show that these echinoderms have TAD-like domains that, such as in flies, do not seem to be associated with CTCF motif orientation. We systematically profiled CREs during sea star and sea urchin development using ATAC-seq, comparing their regulatory logic and dynamics over multiple developmental stages. Finally, our analysis of sea urchin and sea star CRE evolution across multiple evolutionary distances and timescales showed several thousand elements conserved for hundreds of millions of years, revealing a vertebrate-like pattern of CRE evolution that probably constitutes an ancestral property of the regulatory evolution of animals. Analysis of the 3D chromatin architecture and cis-regulatory elements in a sea urchin and a sea star reveals mechanisms of 3D chromatin organization in echinoderms and the long-term evolutionary dynamics of cis-regulatory elements in animals.
{"title":"Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes","authors":"Marta S. Magri, Danila Voronov, Saoirse Foley, Pedro Manuel Martínez-García, Martin Franke, Gregory A. Cary, José M. Santos-Pereira, Claudia Cuomo, Manuel Fernández-Moreno, Marta Portela, Alejandro Gil-Galvez, Rafael D. Acemel, Periklis Paganos, Carolyn Ku, Jovana Ranđelović, Maria Lorenza Rusciano, Panos N. Firbas, José Luis Gómez-Skarmeta, Veronica F. Hinman, Maria Ina Arnone, Ignacio Maeso","doi":"10.1038/s41559-025-02941-y","DOIUrl":"10.1038/s41559-025-02941-y","url":null,"abstract":"Despite the growing abundance of sequenced animal genomes, we only have detailed knowledge of regulatory organization for a handful of lineages, particularly flies and vertebrates. These two taxa show contrasting trends in the molecular mechanisms of 3D chromatin organization and long-term evolutionary dynamics of cis-regulatory element (CRE) conservation. Here we study the evolution and organization of the regulatory genome of echinoderms, a lineage whose phylogenetic position and relatively slow molecular evolution have proven particularly useful for evolutionary studies. We generated new reference genome assemblies for two species belonging to two different echinoderm classes: the purple sea urchin Strongylocentrotus purpuratus and the bat sea star Patiria miniata using PacBio and HiC data and characterize their 3D chromatin architecture. We show that these echinoderms have TAD-like domains that, such as in flies, do not seem to be associated with CTCF motif orientation. We systematically profiled CREs during sea star and sea urchin development using ATAC-seq, comparing their regulatory logic and dynamics over multiple developmental stages. Finally, our analysis of sea urchin and sea star CRE evolution across multiple evolutionary distances and timescales showed several thousand elements conserved for hundreds of millions of years, revealing a vertebrate-like pattern of CRE evolution that probably constitutes an ancestral property of the regulatory evolution of animals. Analysis of the 3D chromatin architecture and cis-regulatory elements in a sea urchin and a sea star reveals mechanisms of 3D chromatin organization in echinoderms and the long-term evolutionary dynamics of cis-regulatory elements in animals.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"10 2","pages":"355-371"},"PeriodicalIF":13.9,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145908003","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}
Pub Date : 2026-01-05DOI: 10.1038/s41559-025-02965-4
Jeroen Ingels, Daniel Leduc, Ailish Ullmann, Ashley Rowden
New studies that document the effect of polymetallic nodule mining vehicles on deep-sea biodiversity suggest that keeping up with technological innovations will be key to more realistic impact assessments of deep-sea mining.
{"title":"Assessing mining impacts in the deep sea","authors":"Jeroen Ingels, Daniel Leduc, Ailish Ullmann, Ashley Rowden","doi":"10.1038/s41559-025-02965-4","DOIUrl":"10.1038/s41559-025-02965-4","url":null,"abstract":"New studies that document the effect of polymetallic nodule mining vehicles on deep-sea biodiversity suggest that keeping up with technological innovations will be key to more realistic impact assessments of deep-sea mining.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"10 2","pages":"172-174"},"PeriodicalIF":13.9,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145903427","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}
Pub Date : 2026-01-05DOI: 10.1038/s41559-025-02944-9
Global climate change has the potential to shift the roles and prevalence of mutualisms, including the positive interactions between plants and microorganisms. A combination of field surveys and common garden experiments has revealed a paradox: fungal mutualists promote long-term, range-wide population persistence of their host plants, especially under drought, yet are selected against by interannual climate variability.
{"title":"Climate variability disrupts crucial plant–fungal mutualisms","authors":"","doi":"10.1038/s41559-025-02944-9","DOIUrl":"10.1038/s41559-025-02944-9","url":null,"abstract":"Global climate change has the potential to shift the roles and prevalence of mutualisms, including the positive interactions between plants and microorganisms. A combination of field surveys and common garden experiments has revealed a paradox: fungal mutualists promote long-term, range-wide population persistence of their host plants, especially under drought, yet are selected against by interannual climate variability.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"10 2","pages":"179-180"},"PeriodicalIF":13.9,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145902726","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}
Pub Date : 2026-01-05DOI: 10.1038/s41559-025-02952-9
Lucio Biancari, Gastón R. Oñatibia, Yoann Le Bagousse-Pinguet, Nicolas Gross, Laura Yahdjian, Martín R. Aguiar, Hugo Saiz, David J. Eldridge, Enrique Valencia, Xoaquín Moreira, Victoria Ochoa, Beatriz Gozalo, Sergio Asensio, César Plaza, Emilio Guirado, Miguel García-Gómez, Juan J. Gaitán, Jaime Martínez-Valderrama, Betty J. Mendoza, Fernando T. Maestre
Understanding the mechanisms that shape ecosystem resistance to increasing livestock grazing pressure, a major driver of land degradation, is essential for predicting its impacts and informing sustainable land management strategies. This issue is particularly relevant in drylands, which host half of the world’s livestock production and are highly vulnerable to desertification caused by overgrazing. Here we conduct a standardized field survey across 73 dryland sites in 25 countries to simultaneously evaluate how climatic, edaphic, vegetation and grazing-related factors influence ecosystem resistance—defined here as the capacity to maintain vegetation cover under increasing grazing pressure. We found that increasing grazing pressure reduced vegetation cover in 80% of sites, with an average decline of 35%. Plant species richness emerged as the strongest predictor of ecosystem resistance, with higher richness associated with lower vegetation cover loss. Functional trait data indicated that this positive effect was mainly explained by complementarity in trait values among plants, rather than by functional redundancy. Our results indicate that conserving plant diversity is key to strengthening ecosystem resistance and sustaining dryland functioning under intensifying grazing pressure. Grazing affects plant diversity, but plant diversity in turn may modulate the effect of grazing on the plant community. This global analysis explores the association between plant species richness and plant cover resistance to grazing intensity in drylands.
{"title":"Plant diversity enhances ecosystem resistance to increasing grazing pressure in global drylands","authors":"Lucio Biancari, Gastón R. Oñatibia, Yoann Le Bagousse-Pinguet, Nicolas Gross, Laura Yahdjian, Martín R. Aguiar, Hugo Saiz, David J. Eldridge, Enrique Valencia, Xoaquín Moreira, Victoria Ochoa, Beatriz Gozalo, Sergio Asensio, César Plaza, Emilio Guirado, Miguel García-Gómez, Juan J. Gaitán, Jaime Martínez-Valderrama, Betty J. Mendoza, Fernando T. Maestre","doi":"10.1038/s41559-025-02952-9","DOIUrl":"10.1038/s41559-025-02952-9","url":null,"abstract":"Understanding the mechanisms that shape ecosystem resistance to increasing livestock grazing pressure, a major driver of land degradation, is essential for predicting its impacts and informing sustainable land management strategies. This issue is particularly relevant in drylands, which host half of the world’s livestock production and are highly vulnerable to desertification caused by overgrazing. Here we conduct a standardized field survey across 73 dryland sites in 25 countries to simultaneously evaluate how climatic, edaphic, vegetation and grazing-related factors influence ecosystem resistance—defined here as the capacity to maintain vegetation cover under increasing grazing pressure. We found that increasing grazing pressure reduced vegetation cover in 80% of sites, with an average decline of 35%. Plant species richness emerged as the strongest predictor of ecosystem resistance, with higher richness associated with lower vegetation cover loss. Functional trait data indicated that this positive effect was mainly explained by complementarity in trait values among plants, rather than by functional redundancy. Our results indicate that conserving plant diversity is key to strengthening ecosystem resistance and sustaining dryland functioning under intensifying grazing pressure. Grazing affects plant diversity, but plant diversity in turn may modulate the effect of grazing on the plant community. This global analysis explores the association between plant species richness and plant cover resistance to grazing intensity in drylands.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"10 2","pages":"258-266"},"PeriodicalIF":13.9,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145902722","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}
Pub Date : 2026-01-05DOI: 10.1038/s41559-025-02943-w
Vicki W. Li, Joshua C. Fowler, Aaron S. David, Sharon Y. Strauss, Christopher A. Searcy, Michelle E. Afkhami
Understanding how species interactions impact population dynamics and long-term persistence over broad temporal and spatial scales is crucial for predicting species distributions and responses to global change. Here we investigate how microbial mutualisms can promote long-term and range-wide population persistence of plants, particularly by ameliorating drought stress. We integrate range-wide field surveys of ~90 grass host populations spanning 13 years with demographic modelling based on 6-year common garden experiments conducted across the host range. We found that mutualistic fungal endophytes (genus Epichloë) promote population-level persistence and growth of their native host grass (Bromus laevipes) across its distribution, with non-mutualistic populations four times more likely to go locally extinct. However, endophyte prevalence declined eightfold more in historically mutualistic populations that experienced high climate variability. This demonstrates that mutualisms can underpin population persistence and buffer hosts against environmental stress but may themselves be vulnerable to global change, with concerning implications for long-term population viability and, ultimately, species distributions under an increasingly uncertain climate. Microbial mutualists could affect plant population persistence under climate change. Here the authors show that fungal endophytes contribute to the population persistence of a grass species by ameliorating drought stress but are more likely to disappear locally under climate variability.
{"title":"Climate variability disrupts microbial mutualism-driven population persistence","authors":"Vicki W. Li, Joshua C. Fowler, Aaron S. David, Sharon Y. Strauss, Christopher A. Searcy, Michelle E. Afkhami","doi":"10.1038/s41559-025-02943-w","DOIUrl":"10.1038/s41559-025-02943-w","url":null,"abstract":"Understanding how species interactions impact population dynamics and long-term persistence over broad temporal and spatial scales is crucial for predicting species distributions and responses to global change. Here we investigate how microbial mutualisms can promote long-term and range-wide population persistence of plants, particularly by ameliorating drought stress. We integrate range-wide field surveys of ~90 grass host populations spanning 13 years with demographic modelling based on 6-year common garden experiments conducted across the host range. We found that mutualistic fungal endophytes (genus Epichloë) promote population-level persistence and growth of their native host grass (Bromus laevipes) across its distribution, with non-mutualistic populations four times more likely to go locally extinct. However, endophyte prevalence declined eightfold more in historically mutualistic populations that experienced high climate variability. This demonstrates that mutualisms can underpin population persistence and buffer hosts against environmental stress but may themselves be vulnerable to global change, with concerning implications for long-term population viability and, ultimately, species distributions under an increasingly uncertain climate. Microbial mutualists could affect plant population persistence under climate change. Here the authors show that fungal endophytes contribute to the population persistence of a grass species by ameliorating drought stress but are more likely to disappear locally under climate variability.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"10 2","pages":"221-231"},"PeriodicalIF":13.9,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145903428","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}
Pub Date : 2026-01-02DOI: 10.1038/s41559-025-02950-x
Gabriel Maturani Barrile
Zooming in at fine spatial scales reveals that pathogens spread through close contact can produce striking variation in infection rates among groups of host animals just metres apart, which drives hidden epidemics and population collapse.
{"title":"Hidden outbreaks in an amphibian pandemic","authors":"Gabriel Maturani Barrile","doi":"10.1038/s41559-025-02950-x","DOIUrl":"10.1038/s41559-025-02950-x","url":null,"abstract":"Zooming in at fine spatial scales reveals that pathogens spread through close contact can produce striking variation in infection rates among groups of host animals just metres apart, which drives hidden epidemics and population collapse.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"10 2","pages":"167-168"},"PeriodicalIF":13.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145892711","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}
Pub Date : 2026-01-02DOI: 10.1038/s41559-025-02918-x
By disentangling the mechanisms that underpin changes in community biomass, we show that local arthropod biomass declines are overwhelmingly associated with species losses, independent of which species are lost and with only minor contributions of abundance change. High plant diversity and low land-use intensity mitigate arthropod biomass declines and community homogenization.
{"title":"When local arthropod biomass declines, every species counts","authors":"","doi":"10.1038/s41559-025-02918-x","DOIUrl":"10.1038/s41559-025-02918-x","url":null,"abstract":"By disentangling the mechanisms that underpin changes in community biomass, we show that local arthropod biomass declines are overwhelmingly associated with species losses, independent of which species are lost and with only minor contributions of abundance change. High plant diversity and low land-use intensity mitigate arthropod biomass declines and community homogenization.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"10 1","pages":"24-25"},"PeriodicalIF":13.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145892840","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}
Pub Date : 2026-01-02DOI: 10.1038/s41559-025-02915-0
A Europe‑wide survey of 10,000 respondents shows strong backing for the recovery of wolves, lynx and bears, as well as opposition to hunting and culling, but also shows that a majority opposes any further population growth. Many respondents remain neutral, which indicates that large carnivore recovery is far less polarizing than commonly portrayed.
{"title":"Europeans like wolves, lynx and bears and oppose hunting them but do not want more of these animals","authors":"","doi":"10.1038/s41559-025-02915-0","DOIUrl":"10.1038/s41559-025-02915-0","url":null,"abstract":"A Europe‑wide survey of 10,000 respondents shows strong backing for the recovery of wolves, lynx and bears, as well as opposition to hunting and culling, but also shows that a majority opposes any further population growth. Many respondents remain neutral, which indicates that large carnivore recovery is far less polarizing than commonly portrayed.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"10 1","pages":"22-23"},"PeriodicalIF":13.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145892699","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}
Pub Date : 2026-01-02DOI: 10.1038/s41559-025-02925-y
By leveraging a spatially representative dataset that comprises more than 300,000 trees from 3,396 natural forest plots, we fill crucial knowledge gaps regarding fine-grained spatial patterns, driving mechanisms and the future potential of tree species richness and structural diversity in China’s natural forests.
{"title":"Fine-grained mapping of forest diversity in China","authors":"","doi":"10.1038/s41559-025-02925-y","DOIUrl":"10.1038/s41559-025-02925-y","url":null,"abstract":"By leveraging a spatially representative dataset that comprises more than 300,000 trees from 3,396 natural forest plots, we fill crucial knowledge gaps regarding fine-grained spatial patterns, driving mechanisms and the future potential of tree species richness and structural diversity in China’s natural forests.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"10 1","pages":"20-21"},"PeriodicalIF":13.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145892707","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}
Pub Date : 2026-01-02DOI: 10.1038/s41559-025-02920-3
Population genomic data from five species of brood parasitic birds, representing three independent origins of the trait, enabled the identification of shared signatures of natural selection reflecting repeated adaptation in species with this lifestyle. This repeated signal of adaptation is present in particular in genes involved in spermatogenesis and neural development.
{"title":"Repeated adaptation in sperm-related and neuronal genes in brood parasitic birds","authors":"","doi":"10.1038/s41559-025-02920-3","DOIUrl":"10.1038/s41559-025-02920-3","url":null,"abstract":"Population genomic data from five species of brood parasitic birds, representing three independent origins of the trait, enabled the identification of shared signatures of natural selection reflecting repeated adaptation in species with this lifestyle. This repeated signal of adaptation is present in particular in genes involved in spermatogenesis and neural development.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"10 1","pages":"26-27"},"PeriodicalIF":13.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145892851","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}
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