Pub Date : 2025-01-02DOI: 10.1038/s41559-024-02605-3
Hong Yang, Defu Liu, Henglin Xiao, Julian R. Thompson, Roger J. Flower, Heang Sophal, Tomos Avent
{"title":"Better plans are needed for mitigating the ecological impacts of Cambodia''s Funan Techo Canal","authors":"Hong Yang, Defu Liu, Henglin Xiao, Julian R. Thompson, Roger J. Flower, Heang Sophal, Tomos Avent","doi":"10.1038/s41559-024-02605-3","DOIUrl":"10.1038/s41559-024-02605-3","url":null,"abstract":"","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 2","pages":"185-186"},"PeriodicalIF":13.9,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142911810","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 : 2025-01-02DOI: 10.1038/s41559-024-02603-5
Pengcheng He, Qing Ye, Kailiang Yu, Xiaorong Liu, Hui Liu, Xingyun Liang, Shidan Zhu, Han Wang, Junhua Yan, Ying-Ping Wang, Ian J. Wright
Wind is an important ecological factor for plants as it can increase evapotranspiration and cause dehydration. However, the impact of wind on plant hydraulics at a global scale remains unclear. Here we compiled plant key hydraulic traits, including water potential at 50% loss of hydraulic conductivity (P50), xylem-specific hydraulic conductivity (KS), leaf area to sapwood area ratio (AL/AS) and conduit diameter (D) with 2,786 species-at-site combinations across 1,922 woody species at 469 sites worldwide and analysed their correlations with wind speed. Even with other climatic factors controlled (for example, moisture index, temperature and vapour pressure deficit), wind speed clearly affected plant hydraulics; for example, on average, species from windier sites constructed sapwood with smaller D and lower KS that was more resilient to drought (more negative P50), deploying less leaf total area for a given sapwood cross-section. Species with these traits may be at an advantage under future climates with higher wind speeds. A global analysis of hydraulic traits in 1,922 woody plant species shows that wind speed has substantial effects on key traits related to plant water transport, independently of other climatic factors.
{"title":"Relationship between wind speed and plant hydraulics at the global scale","authors":"Pengcheng He, Qing Ye, Kailiang Yu, Xiaorong Liu, Hui Liu, Xingyun Liang, Shidan Zhu, Han Wang, Junhua Yan, Ying-Ping Wang, Ian J. Wright","doi":"10.1038/s41559-024-02603-5","DOIUrl":"10.1038/s41559-024-02603-5","url":null,"abstract":"Wind is an important ecological factor for plants as it can increase evapotranspiration and cause dehydration. However, the impact of wind on plant hydraulics at a global scale remains unclear. Here we compiled plant key hydraulic traits, including water potential at 50% loss of hydraulic conductivity (P50), xylem-specific hydraulic conductivity (KS), leaf area to sapwood area ratio (AL/AS) and conduit diameter (D) with 2,786 species-at-site combinations across 1,922 woody species at 469 sites worldwide and analysed their correlations with wind speed. Even with other climatic factors controlled (for example, moisture index, temperature and vapour pressure deficit), wind speed clearly affected plant hydraulics; for example, on average, species from windier sites constructed sapwood with smaller D and lower KS that was more resilient to drought (more negative P50), deploying less leaf total area for a given sapwood cross-section. Species with these traits may be at an advantage under future climates with higher wind speeds. A global analysis of hydraulic traits in 1,922 woody plant species shows that wind speed has substantial effects on key traits related to plant water transport, independently of other climatic factors.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 2","pages":"273-281"},"PeriodicalIF":13.9,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142911815","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 : 2025-01-02DOI: 10.1038/s41559-024-02619-x
Brian D. Inouye
Two analyses of large global datasets of terrestrial phenological events document earlier spring activity in most species, but also large differences linked to phylogenetic history, trophic level and local differences in climate patterns.
{"title":"Spring comes earlier but not equally among species","authors":"Brian D. Inouye","doi":"10.1038/s41559-024-02619-x","DOIUrl":"10.1038/s41559-024-02619-x","url":null,"abstract":"Two analyses of large global datasets of terrestrial phenological events document earlier spring activity in most species, but also large differences linked to phylogenetic history, trophic level and local differences in climate patterns.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 2","pages":"192-193"},"PeriodicalIF":13.9,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142911801","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 : 2024-12-27DOI: 10.1038/s41559-024-02596-1
Joseph D. Orkin, Lukas F. K. Kuderna, Núria Hermosilla-Albala, Claudia Fontsere, Megan L. Aylward, Mareike C. Janiak, Nicole Andriaholinirina, Patricia Balaresque, Mary E. Blair, Jean-Luc Fausser, Ivo Glynne Gut, Marta Gut, Matthew W. Hahn, R. Alan Harris, Julie E. Horvath, Christine Keyser, Andrew C. Kitchener, Minh D. Le, Esther Lizano, Stefan Merker, Tilo Nadler, George H. Perry, Clément J. Rabarivola, Linett Rasmussen, Muthuswamy Raveendran, Christian Roos, Dong Dong Wu, Alphonse Zaramody, Guojie Zhang, Dietmar Zinner, Luca Pozzi, Jeffrey Rogers, Kyle Kai-How Farh, Tomas Marques Bonet
Ecological variation and anthropogenic landscape modification have had key roles in the diversification and extinction of mammals in Madagascar. Lemurs represent a radiation with more than 100 species, constituting roughly one-fifth of the primate order. Almost all species of lemurs are threatened with extinction, but little is known about their genetic diversity and demographic history. Here, we analyse high-coverage genome-wide resequencing data from 162 unique individuals comprising 50 species of Lemuriformes, including multiple individuals from most species. Genomic diversity varies widely across the infraorder and yet is broadly consistent among individuals within species. We show widespread introgression in multiple genera and generally high levels of genomic diversity likely resulting from allele sharing that occurred during periods of connectivity and fragmentation during climatic shifts. We find distinct patterns of demographic history in lemurs across the ecogeographic regions of Madagascar within the last million years. Within the past 2,000 years, lemurs underwent major declines in effective population size that corresponded to the timing of human population expansion in Madagascar. In multiple regions of the island, we identified chronological trajectories of inbreeding that are consistent across genera and species, suggesting localized effects of human activity. Our results show how the extraordinary diversity of these long-neglected, endangered primates has been influenced by ecological and anthropogenic factors. Analysis of the genomes of 50 species of Lemuriformes shows high levels of genomic diversity, likely due to allele sharing, as well as population declines and inbreeding patterns resulting from ecological factors and human impacts in Madagascar.
{"title":"Ecological and anthropogenic effects on the genomic diversity of lemurs in Madagascar","authors":"Joseph D. Orkin, Lukas F. K. Kuderna, Núria Hermosilla-Albala, Claudia Fontsere, Megan L. Aylward, Mareike C. Janiak, Nicole Andriaholinirina, Patricia Balaresque, Mary E. Blair, Jean-Luc Fausser, Ivo Glynne Gut, Marta Gut, Matthew W. Hahn, R. Alan Harris, Julie E. Horvath, Christine Keyser, Andrew C. Kitchener, Minh D. Le, Esther Lizano, Stefan Merker, Tilo Nadler, George H. Perry, Clément J. Rabarivola, Linett Rasmussen, Muthuswamy Raveendran, Christian Roos, Dong Dong Wu, Alphonse Zaramody, Guojie Zhang, Dietmar Zinner, Luca Pozzi, Jeffrey Rogers, Kyle Kai-How Farh, Tomas Marques Bonet","doi":"10.1038/s41559-024-02596-1","DOIUrl":"10.1038/s41559-024-02596-1","url":null,"abstract":"Ecological variation and anthropogenic landscape modification have had key roles in the diversification and extinction of mammals in Madagascar. Lemurs represent a radiation with more than 100 species, constituting roughly one-fifth of the primate order. Almost all species of lemurs are threatened with extinction, but little is known about their genetic diversity and demographic history. Here, we analyse high-coverage genome-wide resequencing data from 162 unique individuals comprising 50 species of Lemuriformes, including multiple individuals from most species. Genomic diversity varies widely across the infraorder and yet is broadly consistent among individuals within species. We show widespread introgression in multiple genera and generally high levels of genomic diversity likely resulting from allele sharing that occurred during periods of connectivity and fragmentation during climatic shifts. We find distinct patterns of demographic history in lemurs across the ecogeographic regions of Madagascar within the last million years. Within the past 2,000 years, lemurs underwent major declines in effective population size that corresponded to the timing of human population expansion in Madagascar. In multiple regions of the island, we identified chronological trajectories of inbreeding that are consistent across genera and species, suggesting localized effects of human activity. Our results show how the extraordinary diversity of these long-neglected, endangered primates has been influenced by ecological and anthropogenic factors. Analysis of the genomes of 50 species of Lemuriformes shows high levels of genomic diversity, likely due to allele sharing, as well as population declines and inbreeding patterns resulting from ecological factors and human impacts in Madagascar.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 1","pages":"42-56"},"PeriodicalIF":13.9,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142888218","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 : 2024-12-23DOI: 10.1038/s41559-024-02588-1
The diversity of a tropical forest plant community is stably maintained and species coexist because each species limits its population size through negative frequency-dependent demographic responses.
{"title":"The diversity of a tropical plant community is stably maintained by deterministic processes","authors":"","doi":"10.1038/s41559-024-02588-1","DOIUrl":"10.1038/s41559-024-02588-1","url":null,"abstract":"The diversity of a tropical forest plant community is stably maintained and species coexist because each species limits its population size through negative frequency-dependent demographic responses.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 2","pages":"194-195"},"PeriodicalIF":13.9,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142874563","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 : 2024-12-23DOI: 10.1038/s41559-024-02617-z
April E. Reside, Josie Carwardine, Michelle Ward, Chuanji Yong, Ruben Venegas Li, Andrew Rogers, Brendan A. Wintle, Jennifer Silcock, John Woinarski, Mark Lintermans, Gary Taylor, Anna F. V. Pintor, James E. M. Watson
Accounting for the cost of repairing the degradation of Earth’s biosphere is critical to guide conservation and sustainable development decisions. Yet the costs of repairing nature through the recovery of a continental suite of threatened species across their range have never been calculated. We estimated the cost of in situ recovery of nationally listed terrestrial and freshwater threatened species (n = 1,657) across the megadiverse continent of Australia by combining the spatially explicit costs of all strategies required to address species-specific threats. Individual species recovery required up to 12 strategies (mean 2.3), predominantly habitat retention and restoration, and the management of fire and invasive species. The estimated costs of maximizing threatened species recovery across Australia varied from AU$0–$12,626 per ha, depending on the species, threats and context of each location. The total cost of implementing all strategies to recover threatened species in their in situ habitat across Australia summed to an estimated AU$583 billion per year, with management of invasive weeds making up 81% of the total cost. This figure, at 25% of Australia’s GDP, does not represent a realistic biodiversity conservation budget, but needs to be accounted for when weighing up decisions that lead to further costly degradation of Australia’s natural heritage.
{"title":"The cost of recovering Australia’s threatened species","authors":"April E. Reside, Josie Carwardine, Michelle Ward, Chuanji Yong, Ruben Venegas Li, Andrew Rogers, Brendan A. Wintle, Jennifer Silcock, John Woinarski, Mark Lintermans, Gary Taylor, Anna F. V. Pintor, James E. M. Watson","doi":"10.1038/s41559-024-02617-z","DOIUrl":"https://doi.org/10.1038/s41559-024-02617-z","url":null,"abstract":"<p>Accounting for the cost of repairing the degradation of Earth’s biosphere is critical to guide conservation and sustainable development decisions. Yet the costs of repairing nature through the recovery of a continental suite of threatened species across their range have never been calculated. We estimated the cost of in situ recovery of nationally listed terrestrial and freshwater threatened species (<i>n</i> = 1,657) across the megadiverse continent of Australia by combining the spatially explicit costs of all strategies required to address species-specific threats. Individual species recovery required up to 12 strategies (mean 2.3), predominantly habitat retention and restoration, and the management of fire and invasive species. The estimated costs of maximizing threatened species recovery across Australia varied from AU$0–$12,626 per ha, depending on the species, threats and context of each location. The total cost of implementing all strategies to recover threatened species in their in situ habitat across Australia summed to an estimated AU$583 billion per year, with management of invasive weeds making up 81% of the total cost. This figure, at 25% of Australia’s GDP, does not represent a realistic biodiversity conservation budget, but needs to be accounted for when weighing up decisions that lead to further costly degradation of Australia’s natural heritage.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"24 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142874269","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 : 2024-12-23DOI: 10.1038/s41559-024-02600-8
Alex Slavenko, Natalie Cooper, Shai Meiri, Gopal Murali, Daniel Pincheira-Donoso, Gavin H. Thomas
Sexual size dimorphism (SSD) is highly prevalent in nature. Several hypotheses aim to explain its evolution including sexual selection, differential equilibrium and ecological niche divergence. Disentangling the causal mechanism behind the evolution of SSD is challenging, as selection arising from multiple pressures on fitness may act simultaneously to generate observed patterns. Here, we use phylogenetic comparative methods to study the evolution of SSD across tetrapods globally. We estimate directional changes in body size evolution, and compare the number, phylogenetic position and magnitude of size changes between sexes. We find evidence that directional changes in size associated with SSD are typically more common in males—even in lineages where females are larger. However, underlying mechanisms differ among lineages—whereas SSD in amphibians becomes more male-biased with greater increases in male size and mammalian SSD becomes more female-biased with greater decreases in male size. Thus, differing mechanisms of directional body size evolution across sexes are essential to explain observed SSD patterns.
{"title":"Evolution of sexual size dimorphism in tetrapods is driven by varying patterns of sex-specific selection on size","authors":"Alex Slavenko, Natalie Cooper, Shai Meiri, Gopal Murali, Daniel Pincheira-Donoso, Gavin H. Thomas","doi":"10.1038/s41559-024-02600-8","DOIUrl":"https://doi.org/10.1038/s41559-024-02600-8","url":null,"abstract":"<p>Sexual size dimorphism (SSD) is highly prevalent in nature. Several hypotheses aim to explain its evolution including sexual selection, differential equilibrium and ecological niche divergence. Disentangling the causal mechanism behind the evolution of SSD is challenging, as selection arising from multiple pressures on fitness may act simultaneously to generate observed patterns. Here, we use phylogenetic comparative methods to study the evolution of SSD across tetrapods globally. We estimate directional changes in body size evolution, and compare the number, phylogenetic position and magnitude of size changes between sexes. We find evidence that directional changes in size associated with SSD are typically more common in males—even in lineages where females are larger. However, underlying mechanisms differ among lineages—whereas SSD in amphibians becomes more male-biased with greater increases in male size and mammalian SSD becomes more female-biased with greater decreases in male size. Thus, differing mechanisms of directional body size evolution across sexes are essential to explain observed SSD patterns.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"31 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142874271","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 : 2024-12-23DOI: 10.1038/s41559-024-02579-2
David M. DeFilippis, Joseph A. LaManna, Stefan A. Schnitzer
Testing the extent to which ecological communities are structured by deterministic (niche-based) assembly processes, resulting in predictable species abundance and composition, is a fundamental goal of ecology. Here we use a 10-year dataset of 55,156 lianas comprising 86 species in an old-growth tropical forest in Panama to test whether community assembly is consistent with niche-based assembly processes. We find that species diversity and community composition was maintained because species conformed to four general requirements of coexistence theory: (1) species have negative conspecific frequency-dependent feedback that control their local population size; (2) species have a stronger negative effect on their own population than that of heterospecifics; (3) the equilibrium frequencies of species correspond to their relative abundance; and (4) species have positive invasibility. These results indicate that coexistence through deterministic niche-based processes controls local population sizes and prevents any one species from displacing others. Rare species persisted because particularly strong negative feedbacks maintained them at their relatively low equilibrium abundances, thus preventing them from going extinct. Furthermore, we show that it is necessary to use population demography to test coexistence theory because stem mortality alone does not reflect species demography. These findings have broad implications for species coexistence and diversity maintenance in tropical forests and possibly other ecosystems. Ecological communities may arise through distinct assembly processes, which are difficult to disentangle. Here the authors show that deterministic niche-based, not neutral dispersal, assembly processes explain the vast majority of the structure of a tropical forest liana community.
{"title":"Frequency-dependent assembly processes determine the coexistence and relative abundance of tropical plant species","authors":"David M. DeFilippis, Joseph A. LaManna, Stefan A. Schnitzer","doi":"10.1038/s41559-024-02579-2","DOIUrl":"10.1038/s41559-024-02579-2","url":null,"abstract":"Testing the extent to which ecological communities are structured by deterministic (niche-based) assembly processes, resulting in predictable species abundance and composition, is a fundamental goal of ecology. Here we use a 10-year dataset of 55,156 lianas comprising 86 species in an old-growth tropical forest in Panama to test whether community assembly is consistent with niche-based assembly processes. We find that species diversity and community composition was maintained because species conformed to four general requirements of coexistence theory: (1) species have negative conspecific frequency-dependent feedback that control their local population size; (2) species have a stronger negative effect on their own population than that of heterospecifics; (3) the equilibrium frequencies of species correspond to their relative abundance; and (4) species have positive invasibility. These results indicate that coexistence through deterministic niche-based processes controls local population sizes and prevents any one species from displacing others. Rare species persisted because particularly strong negative feedbacks maintained them at their relatively low equilibrium abundances, thus preventing them from going extinct. Furthermore, we show that it is necessary to use population demography to test coexistence theory because stem mortality alone does not reflect species demography. These findings have broad implications for species coexistence and diversity maintenance in tropical forests and possibly other ecosystems. Ecological communities may arise through distinct assembly processes, which are difficult to disentangle. Here the authors show that deterministic niche-based, not neutral dispersal, assembly processes explain the vast majority of the structure of a tropical forest liana community.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 2","pages":"249-260"},"PeriodicalIF":13.9,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142874270","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 : 2024-12-16DOI: 10.1038/s41559-024-02622-2
Vaishali Bhaumik, Ajith Kumar, Jayashree Ratnam
The inaugural Indian Wildlife Ecology Conference took place on 14–16 June 2024. We talked to the co-conveners of this conference, Ajith Kumar and Jayashree Ratnam, about how the event fostered connections among Indian wildlife ecologists, and their future plans.
{"title":"Indian wildlife ecology comes of age","authors":"Vaishali Bhaumik, Ajith Kumar, Jayashree Ratnam","doi":"10.1038/s41559-024-02622-2","DOIUrl":"10.1038/s41559-024-02622-2","url":null,"abstract":"The inaugural Indian Wildlife Ecology Conference took place on 14–16 June 2024. We talked to the co-conveners of this conference, Ajith Kumar and Jayashree Ratnam, about how the event fostered connections among Indian wildlife ecologists, and their future plans.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 2","pages":"187-189"},"PeriodicalIF":13.9,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142825067","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 : 2024-12-13DOI: 10.1038/s41559-024-02591-6
Rémi Tournebize, Lounès Chikhi
Genomic and ancient DNA data have revolutionized palaeoanthropology and our vision of human evolution, with indisputable landmarks like the sequencing of Neanderthal and Denisovan genomes. Yet, using genetic data to identify, date and quantify evolutionary events—such as ancient bottlenecks or admixture—is not straightforward, as inferences may depend on model assumptions. In the last two decades, the idea that Neanderthals and members of the Homo sapiens lineage interbred has gained momentum. From the status of unlikely theory, it has reached consensus among human evolutionary biologists. This theory is mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure, despite its widespread occurrence and the fact that, when ignored, population structure can lead to the inference of spurious demographic events. We simulated genomic data under a structured and admixture-free model of human evolution, and found that all the tested admixture approaches identified long Neanderthal fragments in our simulated genomes and an admixture event that never took place. We also observed that several published admixture models failed to predict important empirical diversity or admixture statistics, and that we could identify several scenarios from our structured model that better predicted these statistics jointly. Using a simulated time series of ancient DNA, the structured scenarios could also predict the trajectory of the empirical D statistics. Our results suggest that models accounting for population structure are fundamental to improve our understanding of human evolution, and that admixture between Neanderthals and H. sapiens needs to be re-evaluated in the light of structured models. Beyond the Neanderthal case, we argue that ancient hybridization events, which are increasingly documented in many species, including with other hominins, may also benefit from such re-evaluation. Simulating a metapopulation of human evolution without Neanderthal introgression into Homo sapiens still identifies Neanderthal fragments in simulated genomes, and an admixture event that never took place. This indicates that population structure must be accounted for in human evolutionary genomics and that putative ancient hybridization events should be reinterpreted in this light.
基因组和古 DNA 数据彻底改变了古人类学和我们对人类进化的认识，尼安德特人和丹尼索瓦人基因组测序等里程碑事件无可争议。然而，利用基因数据来识别、确定进化事件（如远古瓶颈或混杂）的时间和数量并不简单，因为推论可能取决于模型假设。在过去的二十年里，尼安德特人与智人血统成员杂交的观点得到了越来越多的支持。它从一种不太可能的理论，发展成为人类进化生物学家的共识。支持这一理论的主要是统计方法，这些方法依赖于最小化或忽略种群结构的人口统计模型，尽管种群结构广泛存在，而且忽略种群结构会导致推断出虚假的人口统计事件。我们在一个结构化和无混杂的人类进化模型下模拟了基因组数据，发现所有测试过的混杂方法都在我们模拟的基因组中发现了长尼安德特人片段，以及从未发生过的混杂事件。我们还观察到，一些已发表的混杂模型未能预测重要的经验多样性或混杂统计数据，而我们可以从我们的结构化模型中找出几种情况，更好地共同预测这些统计数据。利用古 DNA 的模拟时间序列，结构化方案还能预测经验 D 统计量的轨迹。我们的研究结果表明，考虑种群结构的模型对于提高我们对人类进化的理解至关重要，尼安德特人与智人之间的混杂需要根据结构化模型重新评估。除了尼安德特人之外，我们还认为，在许多物种（包括与其他类人猿）中被越来越多地记录下来的古代杂交事件也可能从这种重新评估中受益。
{"title":"Ignoring population structure in hominin evolutionary models can lead to the inference of spurious admixture events","authors":"Rémi Tournebize, Lounès Chikhi","doi":"10.1038/s41559-024-02591-6","DOIUrl":"10.1038/s41559-024-02591-6","url":null,"abstract":"Genomic and ancient DNA data have revolutionized palaeoanthropology and our vision of human evolution, with indisputable landmarks like the sequencing of Neanderthal and Denisovan genomes. Yet, using genetic data to identify, date and quantify evolutionary events—such as ancient bottlenecks or admixture—is not straightforward, as inferences may depend on model assumptions. In the last two decades, the idea that Neanderthals and members of the Homo sapiens lineage interbred has gained momentum. From the status of unlikely theory, it has reached consensus among human evolutionary biologists. This theory is mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure, despite its widespread occurrence and the fact that, when ignored, population structure can lead to the inference of spurious demographic events. We simulated genomic data under a structured and admixture-free model of human evolution, and found that all the tested admixture approaches identified long Neanderthal fragments in our simulated genomes and an admixture event that never took place. We also observed that several published admixture models failed to predict important empirical diversity or admixture statistics, and that we could identify several scenarios from our structured model that better predicted these statistics jointly. Using a simulated time series of ancient DNA, the structured scenarios could also predict the trajectory of the empirical D statistics. Our results suggest that models accounting for population structure are fundamental to improve our understanding of human evolution, and that admixture between Neanderthals and H. sapiens needs to be re-evaluated in the light of structured models. Beyond the Neanderthal case, we argue that ancient hybridization events, which are increasingly documented in many species, including with other hominins, may also benefit from such re-evaluation. Simulating a metapopulation of human evolution without Neanderthal introgression into Homo sapiens still identifies Neanderthal fragments in simulated genomes, and an admixture event that never took place. This indicates that population structure must be accounted for in human evolutionary genomics and that putative ancient hybridization events should be reinterpreted in this light.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 2","pages":"225-236"},"PeriodicalIF":13.9,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142815758","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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