Nature ecology & evolution最新文献_第7页

Archived natural DNA samplers reveal four decades of biodiversity change across the tree of life 存档的自然DNA样本揭示了四十年来整个生命之树的生物多样性变化

IF 13.9 1区生物学

Nature ecology & evolution Pub Date : 2025-08-01 DOI: 10.1038/s41559-025-02812-6

Isabelle Junk, Julian Hans, Benoît Perez-Lamarque, Manuel Stothut, Sven Weber, Elisabeth Gold, Caroline Schubert, Alice Schumacher, Nina Schmitt, Anja Melcher, Martin Paulus, Roland Klein, Diana Teubner, Jan Koschorreck, Susan Kennedy, Hélène Morlon, Henrik Krehenwinkel

{"title":"Archived natural DNA samplers reveal four decades of biodiversity change across the tree of life","authors":"Isabelle Junk, Julian Hans, Benoît Perez-Lamarque, Manuel Stothut, Sven Weber, Elisabeth Gold, Caroline Schubert, Alice Schumacher, Nina Schmitt, Anja Melcher, Martin Paulus, Roland Klein, Diana Teubner, Jan Koschorreck, Susan Kennedy, Hélène Morlon, Henrik Krehenwinkel","doi":"10.1038/s41559-025-02812-6","DOIUrl":"10.1038/s41559-025-02812-6","url":null,"abstract":"Detecting the imprints of global environmental change on biological communities is a paramount task for ecological research. But a lack of standardized long-term biomonitoring data prevents a deeper understanding of biodiversity change in the Anthropocene. Novel sources of data for analysing biodiversity change across time and space are urgently needed. By metabarcoding highly standardized biota samples from a long-term pollution monitoring archive in Germany, we here analyse four decades of community diversity for tens of thousands of species across the tree of life. The archived samples—tree leaves, marine macroalgae, and marine and limnic mussels—represent natural community DNA samplers, preserving a taxonomically diverse imprint of their associated biodiversity at the time of collection. We find no evidence for universal diversity declines at the local scale. Instead, a gradual compositional turnover emerges as a universal pattern of temporal biodiversity change in Germany’s terrestrial and aquatic ecosystems. This turnover results in biotic homogenization in most terrestrial and marine communities. Limnic communities, in contrast, rather differentiate across space, probably due to the immigration of different invasive species into different sites. Our study highlights the immense promise of alternative sample sources to provide standardized time series data of biodiversity change in the Anthropocene. This study explores four decades of biodiversity change across the tree of life in Germany’s terrestrial and aquatic ecosystems by sequencing standardized biota samples from a long-term pollution monitoring archive.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 10","pages":"1873-1884"},"PeriodicalIF":13.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41559-025-02812-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144756552","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}

引用次数: 0

Cryptic phenotypic variation emerges rapidly during the adaptive evolution of a carbapenemase 在碳青霉烯酶的适应性进化过程中，隐性表型变异迅速出现

IF 16.8 1区生物学

Nature ecology & evolution Pub Date : 2025-07-30 DOI: 10.1038/s41559-025-02804-6

Laura Dabos, Inssaf Nedjari, Alejandro Couce

{"title":"Cryptic phenotypic variation emerges rapidly during the adaptive evolution of a carbapenemase","authors":"Laura Dabos, Inssaf Nedjari, Alejandro Couce","doi":"10.1038/s41559-025-02804-6","DOIUrl":"https://doi.org/10.1038/s41559-025-02804-6","url":null,"abstract":"<p>Interactions among beneficial mutations (that is, epistasis) are often strong enough to direct adaptation through alternative mutational paths. Although alternative solutions should display similar fitness under the primary selective conditions, their properties across secondary environments may differ widely. The extent to which these cryptic differences are to be expected is largely unknown, despite their importance—for example, in identifying exploitable collateral sensitivities among mutations conferring antibiotic resistance. Here we use directed evolution to characterize the diversity of mutational paths through which the prevalent carbapenemase <i>Klebsiella pneumoniae</i> carbapenemase-2 can evolve high activity against the clinically relevant antibiotic ceftazidime, an initially poor substrate. We identified 40 different substitutions—including many that are common in clinical settings—spread among 18 different mutational trajectories. Initial mutations determined four major groups into which the trajectories can be classified, a signature of strong epistasis. Despite similar final ceftazidime resistance, groups diverged markedly across multiple phenotypic dimensions, from molecular traits, such as in-cell stability and catalytic efficiency, to macroscopic traits, such as growth rate and activity against other β-lactam antibiotics. Our results indicate that cryptic yet consequential phenotypic differences can accumulate rapidly under strong selection, unpredictably shaping the long-term success of resistance enzymes in their journey across hosts and environments.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"97 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144736840","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}

引用次数: 0

Ecological and hydroclimatic determinants of vegetation water-use strategies 植被用水策略的生态和水文气候决定因素

IF 13.9 1区生物学

Nature ecology & evolution Pub Date : 2025-07-29 DOI: 10.1038/s41559-025-02810-8

Bryn E. Morgan, Ryoko Araki, Anna T. Trugman, Kelly K. Caylor

{"title":"Ecological and hydroclimatic determinants of vegetation water-use strategies","authors":"Bryn E. Morgan, Ryoko Araki, Anna T. Trugman, Kelly K. Caylor","doi":"10.1038/s41559-025-02810-8","DOIUrl":"10.1038/s41559-025-02810-8","url":null,"abstract":"Vegetation responses to soil moisture limitation play a key role in land–atmosphere interactions and are a major source of uncertainty in future projections of the global water and carbon cycles. Vegetation water-use strategies—that is, how plants regulate transpiration rates as the soil dries—are highly dynamic across space and time, presenting a major challenge to inferring ecosystem responses to water limitation. Here we show that, when aggregated globally, water-use strategies derived from point-based soil moisture observations exhibit emergent patterns across and within climates and vegetation types along a spectrum of aggressive to conservative responses to water limitation. Water use becomes more conservative, declining more rapidly as the soil dries, as mean annual precipitation increases and as woody cover increases from grasslands to savannahs to forests. We embed this empirical synthesis within an ecohydrological framework to show that key ecological (leaf area) and hydroclimatic (aridity) factors driving demand for water explain up to 77% of the variance in water-use strategies within ecosystem types. All biomes respond to ecological and hydroclimatic demand by shifting towards more aggressive water-use strategies. However, woodlands reach a threshold beyond which water use becomes increasingly conservative, probably reflecting the greater hydraulic risk and cost of tissue damage associated with sustaining high transpiration rates under water limitation for trees than grasses. These findings highlight the importance of characterizing the dynamic nature of vegetation water-use strategies to improve predictions of ecosystem responses to climate change. Vegetation responses to water limitation are difficult to predict due to large variation across space and time. A new analysis of global soil moisture dynamics reveals that water-use strategies vary systematically by vegetation type in response to ecological and climatic conditions.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 10","pages":"1791-1799"},"PeriodicalIF":13.9,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719404","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}

引用次数: 0

Speciation in 3D 三维物种形成

IF 13.9 1区生物学

Nature ecology & evolution Pub Date : 2025-07-29 DOI: 10.1038/s41559-025-02834-0

Vera Domingues

引用次数: 0

Mines aren’t on the maps 地雷不在地图上

IF 13.9 1区生物学

Nature ecology & evolution Pub Date : 2025-07-29 DOI: 10.1038/s41559-025-02833-1

Marian Turner

引用次数: 0

Restoration outcomes are compromised by a lack of diverse native seed supply 由于缺乏多样化的本地种子供应，恢复结果受到影响

IF 13.9 1区生物学

Nature ecology & evolution Pub Date : 2025-07-29 DOI: 10.1038/s41559-025-02825-1

Rachael V. Gallagher

引用次数: 0

Breathing room for diving lice 给潜水虱子喘息的空间

IF 13.9 1区生物学

Nature ecology & evolution Pub Date : 2025-07-29 DOI: 10.1038/s41559-025-02832-2

Vaishali Bhaumik

引用次数: 0

Lagged precipitation effects on plant production across terrestrial biomes 滞后降水对陆地生物群系植物生产的影响

IF 13.9 1区生物学

Nature ecology & evolution Pub Date : 2025-07-28 DOI: 10.1038/s41559-025-02806-4

Lei He, Jian Wang, Drew M. P. Peltier, François Ritter, Philippe Ciais, Josep Peñuelas, Jingfeng Xiao, Thomas W. Crowther, Xing Li, Jian-Sheng Ye, Takehiro Sasaki, Chenghu Zhou, Zhao-Liang Li

{"title":"Lagged precipitation effects on plant production across terrestrial biomes","authors":"Lei He, Jian Wang, Drew M. P. Peltier, François Ritter, Philippe Ciais, Josep Peñuelas, Jingfeng Xiao, Thomas W. Crowther, Xing Li, Jian-Sheng Ye, Takehiro Sasaki, Chenghu Zhou, Zhao-Liang Li","doi":"10.1038/s41559-025-02806-4","DOIUrl":"10.1038/s41559-025-02806-4","url":null,"abstract":"Precipitation effects on plant carbon uptake extend beyond immediate timeframes, reflecting temporal lags between rainfall and plant growth. Mechanisms and relative importance of such lagged effects are expected to vary across ecosystems. Here we draw on an extensive collections of productivity proxies from long-term ground measurements, satellite observations and model simulations to show that preceding-year precipitation exerts a comparable influence on plant productivity to current-year precipitation. Statistically supported lagged precipitation effects are detected in 13.4%–19.7% of the grids depending on the data source. In these sites, preceding-year precipitation positively controls current-year plant productivity in water-limited areas, while negative effects occur in some wet regions, such as tropical forests. While aridity emerges as the main driver of this spatial variability, machine learning-based spatial attribution also indicates interactions among plant traits, climatic conditions and soil properties. We also show that soil water dynamics, plant phenology and foliar structure might mediate lagged precipitation effects across time. Our findings highlight the role of preceding-year precipitation in global plant productivity. Precipitation is a key driver of plant growth. Here the authors integrate ground-based observations, remote sensing and process-based models to disentangle the relative contribution of preceding-year and current-year precipitation on plant productivity and identify its predictors across biomes.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 10","pages":"1800-1811"},"PeriodicalIF":13.9,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144715563","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}

引用次数: 0

The structure of an ancient genotype–phenotype map shaped the functional evolution of a protein family 一个古老的基因型-表型图谱的结构塑造了一个蛋白质家族的功能进化

IF 13.9 1区生物学

Nature ecology & evolution Pub Date : 2025-07-25 DOI: 10.1038/s41559-025-02777-6

Santiago Herrera-Álvarez, Jaeda E. J. Patton, Joseph W. Thornton

{"title":"The structure of an ancient genotype–phenotype map shaped the functional evolution of a protein family","authors":"Santiago Herrera-Álvarez, Jaeda E. J. Patton, Joseph W. Thornton","doi":"10.1038/s41559-025-02777-6","DOIUrl":"10.1038/s41559-025-02777-6","url":null,"abstract":"Mutations are more likely to produce some phenotypes than others, but the causal role of these production propensities in the evolution of phenotypic diversity remains unclear. There are two major challenges: it is difficult to separate the effect of the genotype–phenotype (GP) map from that of natural selection when analysing natural diversity, and most extant phenotypes evolved long ago in species whose GP maps cannot be recovered. Here, using two reconstructed ancestral transcription factors that are closely related but differ in function, we created libraries containing all possible amino acid combinations at historically variable sites in the proteins’ DNA binding interface (the genotypes) and measured their capacity to specifically bind DNA elements containing all possible combinations of nucleotides at historically variable sites (the phenotypes). The ancestral GP maps were strongly anisotropic (the distribution of phenotypes encoded by genotypes is highly non-uniform) and heterogeneous (the phenotypes accessible around each genotype vary greatly among genotypes), but the extent and direction of these properties differed substantially between the maps. In both cases, these properties steered evolution towards the lineage-specific phenotypes that evolved during history. Our findings establish that ancient properties of the GP relationship were causal factors in the evolutionary process that produced present-day patterns of functional conservation and diversity. A combination of ancestral reconstruction and deep mutational scanning to examine the genotype–phenotype maps of steroid receptors shows that the properties of ancestral genotype–phenotype maps determine the lineage-specific evolution of DNA specificity.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 9","pages":"1656-1669"},"PeriodicalIF":13.9,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144701793","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}

引用次数: 0

Citrus reticulata (mandarin) 柑橘（柑桔）

IF 13.9 1区生物学

Nature ecology & evolution Pub Date : 2025-07-25 DOI: 10.1038/s41559-025-02822-4

Qiang Xu

引用次数: 0