Pub Date : 2024-11-27DOI: 10.1038/s41559-024-02586-3
Elizabeth Christina Miller, Rose Faucher, Pamela B. Hart, Melissa Rincón-Sandoval, Aintzane Santaquiteria, William T. White, Carole C. Baldwin, Masaki Miya, Ricardo Betancur-R, Luke Tornabene, Kory Evans, Dahiana Arcila
Colonization of a novel habitat is often followed by phenotypic diversification in the wake of ecological opportunity. However, some habitats should be inherently more constraining than others if the challenges of that environment offer few evolutionary solutions. We examined this push-and-pull on macroevolutionary diversification following habitat transitions in the anglerfishes (Lophiiformes). We constructed a phylogeny with extensive sampling (1,092 loci and ~38% of species), combined with three-dimensional phenotypic data from museum specimens. We used these datasets to examine the tempo and mode of phenotypic diversification. The deep-sea pelagic anglerfishes originated from a benthic ancestor and shortly after experienced rapid lineage diversification rates. This transition incurred shifts towards larger jaws, smaller eyes and a more laterally compressed body plan. Despite these directional trends, this lineage still evolved high phenotypic disparity in body, skull and jaw shapes. In particular, bathypelagic anglerfishes show high variability in body elongation, while benthic anglerfishes are constrained around optimal shapes. Within this radiation, phenotypic evolution was concentrated among recently diverged lineages, notably those that deviated from the archetypical globose body plan. Taken together, these results demonstrate that spectacular evolutionary radiations can unfold even within environments with few ecological resources and demanding physiological challenges.
{"title":"Reduced evolutionary constraint accompanies ongoing radiation in deep-sea anglerfishes","authors":"Elizabeth Christina Miller, Rose Faucher, Pamela B. Hart, Melissa Rincón-Sandoval, Aintzane Santaquiteria, William T. White, Carole C. Baldwin, Masaki Miya, Ricardo Betancur-R, Luke Tornabene, Kory Evans, Dahiana Arcila","doi":"10.1038/s41559-024-02586-3","DOIUrl":"https://doi.org/10.1038/s41559-024-02586-3","url":null,"abstract":"<p>Colonization of a novel habitat is often followed by phenotypic diversification in the wake of ecological opportunity. However, some habitats should be inherently more constraining than others if the challenges of that environment offer few evolutionary solutions. We examined this push-and-pull on macroevolutionary diversification following habitat transitions in the anglerfishes (Lophiiformes). We constructed a phylogeny with extensive sampling (1,092 loci and ~38% of species), combined with three-dimensional phenotypic data from museum specimens. We used these datasets to examine the tempo and mode of phenotypic diversification. The deep-sea pelagic anglerfishes originated from a benthic ancestor and shortly after experienced rapid lineage diversification rates. This transition incurred shifts towards larger jaws, smaller eyes and a more laterally compressed body plan. Despite these directional trends, this lineage still evolved high phenotypic disparity in body, skull and jaw shapes. In particular, bathypelagic anglerfishes show high variability in body elongation, while benthic anglerfishes are constrained around optimal shapes. Within this radiation, phenotypic evolution was concentrated among recently diverged lineages, notably those that deviated from the archetypical globose body plan. Taken together, these results demonstrate that spectacular evolutionary radiations can unfold even within environments with few ecological resources and demanding physiological challenges.</p>","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"1 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142718171","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 : 2024-11-25DOI: 10.1038/s41559-024-02594-3
Laura Andrea Barrero Guevara, Sarah C. Kramer, Tobias Kurth, Matthieu Domenech de Cellès
A pressing question resulting from global warming is how climate change will affect infectious diseases. Answering this question requires research into the effects of weather on the population dynamics of transmission and infection; elucidating these effects, however, has proved difficult due to the challenges of assessing causality from the predominantly observational data available in epidemiological research. Here we show how concepts from causal inference—the sub-field of statistics aiming at inferring causality from data—can guide that research. Through a series of case studies, we illustrate how such concepts can help assess study design and strategically choose a study’s location, evaluate and reduce the risk of bias, and interpret the multifaceted effects of meteorological variables on transmission. More broadly, we argue that interdisciplinary approaches based on explicit causal frameworks are crucial for reliably estimating the effect of weather and accurately predicting the consequences of climate change. A series of case studies is used to illustrate how concepts from causal interference can be used to guide research into the effects of weather on the transmission and population dynamics of infectious diseases.
{"title":"Causal inference concepts can guide research into the effects of climate on infectious diseases","authors":"Laura Andrea Barrero Guevara, Sarah C. Kramer, Tobias Kurth, Matthieu Domenech de Cellès","doi":"10.1038/s41559-024-02594-3","DOIUrl":"10.1038/s41559-024-02594-3","url":null,"abstract":"A pressing question resulting from global warming is how climate change will affect infectious diseases. Answering this question requires research into the effects of weather on the population dynamics of transmission and infection; elucidating these effects, however, has proved difficult due to the challenges of assessing causality from the predominantly observational data available in epidemiological research. Here we show how concepts from causal inference—the sub-field of statistics aiming at inferring causality from data—can guide that research. Through a series of case studies, we illustrate how such concepts can help assess study design and strategically choose a study’s location, evaluate and reduce the risk of bias, and interpret the multifaceted effects of meteorological variables on transmission. More broadly, we argue that interdisciplinary approaches based on explicit causal frameworks are crucial for reliably estimating the effect of weather and accurately predicting the consequences of climate change. A series of case studies is used to illustrate how concepts from causal interference can be used to guide research into the effects of weather on the transmission and population dynamics of infectious diseases.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 2","pages":"349-363"},"PeriodicalIF":13.9,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41559-024-02594-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142696704","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}
Pub Date : 2024-11-22DOI: 10.1038/s41559-024-02587-2
Zeeshan A. Syed, R. Antonio Gomez, Kirill Borziak, Amaar Asif, Abelard S. Cong, Patrick. M. O’Grady, Bernard Y. Kim, Anton Suvorov, Dmitri A. Petrov, Stefan Lüpold, Peter Wengert, Caitlin McDonough-Goldstein, Yasir H. Ahmed-Braimah, Steve Dorus, Scott Pitnick
Our understanding of animal ornaments and the mating preferences driving their exaggeration is limited by knowledge of their genetics. Post-copulatory sexual selection is credited with the rapid evolution of female sperm-storage organ morphology and corresponding sperm quality traits across diverse taxa. In Drosophila, the mechanisms by which longer flagella convey an advantage in the competition among sperm for limited storage space in the female, and by which female sperm-storage organ morphology biases fertilization in favour of longer sperm have been resolved. However, the evolutionary genetics underlying this model post-copulatory ornament and preference system have remained elusive. Here we combined comparative analyses of 149 Drosophila species, a genome-wide association study in Drosophila melanogaster and molecular evolutionary analysis of ~9,400 genes to elucidate how sperm and female sperm-storage organ length co-evolved into one of nature’s most extreme ornaments and preferences. Our results reveal a diverse repertoire of pleiotropic genes linking sperm length and seminal receptacle length expression to central nervous system development and sensory biology. Sperm length development appears condition-dependent and is governed by conserved hormonal (insulin/insulin-like growth factor) and developmental (including Notch and Fruitless) pathways. Central developmental pathway genes, including Notch, also comprised the majority of a restricted set of genes contributing to both intraspecific and interspecific variation in sperm length. Our findings support ‘good genes’ models of female preference evolution. A comparative analysis of morphological data across 149 species of Drosophilidae shows that sperm length in males has co-evolved with the length of the sperm-storage organ in females. Combining a genome-wide association study of these traits in Drosophila melanogaster with molecular evolutionary analyses of the genomes of 15 Drosophila species, the authors find that the genetic architecture underlying sperm length is associated with indirect genetic benefits in females, providing support for the ‘good genes’ hypothesis.
{"title":"Genomics of a sexually selected sperm ornament and female preference in Drosophila","authors":"Zeeshan A. Syed, R. Antonio Gomez, Kirill Borziak, Amaar Asif, Abelard S. Cong, Patrick. M. O’Grady, Bernard Y. Kim, Anton Suvorov, Dmitri A. Petrov, Stefan Lüpold, Peter Wengert, Caitlin McDonough-Goldstein, Yasir H. Ahmed-Braimah, Steve Dorus, Scott Pitnick","doi":"10.1038/s41559-024-02587-2","DOIUrl":"10.1038/s41559-024-02587-2","url":null,"abstract":"Our understanding of animal ornaments and the mating preferences driving their exaggeration is limited by knowledge of their genetics. Post-copulatory sexual selection is credited with the rapid evolution of female sperm-storage organ morphology and corresponding sperm quality traits across diverse taxa. In Drosophila, the mechanisms by which longer flagella convey an advantage in the competition among sperm for limited storage space in the female, and by which female sperm-storage organ morphology biases fertilization in favour of longer sperm have been resolved. However, the evolutionary genetics underlying this model post-copulatory ornament and preference system have remained elusive. Here we combined comparative analyses of 149 Drosophila species, a genome-wide association study in Drosophila melanogaster and molecular evolutionary analysis of ~9,400 genes to elucidate how sperm and female sperm-storage organ length co-evolved into one of nature’s most extreme ornaments and preferences. Our results reveal a diverse repertoire of pleiotropic genes linking sperm length and seminal receptacle length expression to central nervous system development and sensory biology. Sperm length development appears condition-dependent and is governed by conserved hormonal (insulin/insulin-like growth factor) and developmental (including Notch and Fruitless) pathways. Central developmental pathway genes, including Notch, also comprised the majority of a restricted set of genes contributing to both intraspecific and interspecific variation in sperm length. Our findings support ‘good genes’ models of female preference evolution. A comparative analysis of morphological data across 149 species of Drosophilidae shows that sperm length in males has co-evolved with the length of the sperm-storage organ in females. Combining a genome-wide association study of these traits in Drosophila melanogaster with molecular evolutionary analyses of the genomes of 15 Drosophila species, the authors find that the genetic architecture underlying sperm length is associated with indirect genetic benefits in females, providing support for the ‘good genes’ hypothesis.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 2","pages":"336-348"},"PeriodicalIF":13.9,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142684379","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 : 2024-11-22DOI: 10.1038/s41559-024-02578-3
Joao A. Ascensao, Kristen Lok, Oskar Hallatschek
Large stochastic population abundance fluctuations are ubiquitous across the tree of life, impacting the predictability and outcomes of population dynamics. It is generally thought that abundance fluctuations with a Taylor’s law exponent of two do not strongly impact evolution. However, we argue that such abundance fluctuations can lead to substantial genotype frequency fluctuations if different genotypes in a population experience these fluctuations asynchronously. By serially diluting mixtures of two closely related Escherichia coli strains, we show that such asynchrony can occur, leading to giant frequency fluctuations that far exceed expectations from genetic drift. We develop an effective model explaining that the abundance fluctuations arise from correlated offspring numbers between individuals, and the large frequency fluctuations result from (even slight) decoupling in offspring number correlations between genotypes. The model quantitatively predicts the observed abundance and frequency fluctuation scaling. Initially close trajectories diverge exponentially, suggesting that chaotic dynamics may underpin the excess frequency fluctuations. Our findings suggest that decoupling noise is also present in mixed-genotype Saccharomyces cerevisiae populations. Theoretical analyses demonstrate that decoupling noise can strongly influence evolutionary outcomes, in a manner distinct from genetic drift. Given the generic nature of these frequency fluctuations, we expect them to be widespread across biological populations. Based on a combination of experiments and modelling, this study shows large stochastic fluctuations in genotype frequencies caused by intrinsic and extrinsic factors, with implications for population dynamics and evolution.
{"title":"Asynchronous abundance fluctuations can drive giant genotype frequency fluctuations","authors":"Joao A. Ascensao, Kristen Lok, Oskar Hallatschek","doi":"10.1038/s41559-024-02578-3","DOIUrl":"10.1038/s41559-024-02578-3","url":null,"abstract":"Large stochastic population abundance fluctuations are ubiquitous across the tree of life, impacting the predictability and outcomes of population dynamics. It is generally thought that abundance fluctuations with a Taylor’s law exponent of two do not strongly impact evolution. However, we argue that such abundance fluctuations can lead to substantial genotype frequency fluctuations if different genotypes in a population experience these fluctuations asynchronously. By serially diluting mixtures of two closely related Escherichia coli strains, we show that such asynchrony can occur, leading to giant frequency fluctuations that far exceed expectations from genetic drift. We develop an effective model explaining that the abundance fluctuations arise from correlated offspring numbers between individuals, and the large frequency fluctuations result from (even slight) decoupling in offspring number correlations between genotypes. The model quantitatively predicts the observed abundance and frequency fluctuation scaling. Initially close trajectories diverge exponentially, suggesting that chaotic dynamics may underpin the excess frequency fluctuations. Our findings suggest that decoupling noise is also present in mixed-genotype Saccharomyces cerevisiae populations. Theoretical analyses demonstrate that decoupling noise can strongly influence evolutionary outcomes, in a manner distinct from genetic drift. Given the generic nature of these frequency fluctuations, we expect them to be widespread across biological populations. Based on a combination of experiments and modelling, this study shows large stochastic fluctuations in genotype frequencies caused by intrinsic and extrinsic factors, with implications for population dynamics and evolution.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 1","pages":"166-179"},"PeriodicalIF":13.9,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142684378","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 : 2024-11-20DOI: 10.1038/s41559-024-02571-w
Yoav Mathov, Malka Nissim-Rafinia, Chen Leibson, Nir Galun, Tomas Marques-Bonet, Arye Kandel, Meir Liebergal, Eran Meshorer, Liran Carmel
Genome-wide premortem DNA methylation patterns can be computationally reconstructed from high-coverage DNA sequences of ancient samples. Because DNA methylation is more conserved across species than across tissues, and ancient DNA is typically extracted from bones and teeth, previous works utilizing ancient DNA methylation maps focused on studying evolutionary changes in the skeletal system. Here we suggest that DNA methylation patterns in one tissue may, under certain conditions, be informative on DNA methylation patterns in other tissues of the same individual. Using the fact that tissue-specific DNA methylation builds up during embryonic development, we identified the conditions that allow for such cross-tissue inference and devised an algorithm that carries it out. We trained the algorithm on methylation data from extant species and reached high precisions of up to 0.92 for validation datasets. We then used the algorithm on archaic humans, and identified more than 1,850 positions for which we were able to observe differential DNA methylation in prefrontal cortex neurons. These positions are linked to hundreds of genes, many of which are involved in neural functions such as structural and developmental processes. Six positions are located in the neuroblastoma breaking point family (NBPF) gene family, which probably played a role in human brain evolution. The algorithm we present here allows for the examination of epigenetic changes in tissues and cell types that are absent from the palaeontological record, and therefore provides new ways to study the evolutionary impacts of epigenetic changes. The authors show that DNA methylation patterns in one tissue can inform on those in another, under certain conditions, and devise an algorithm that allows identification of differential DNA methylation. They applied it to an archaic human dataset, revealing information about human brain evolution in the absence of preserved brain tissue.
全基因组的死前DNA甲基化模式可以从古代样本的高覆盖率DNA序列中计算重建。由于 DNA 甲基化在不同物种间比不同组织间更为保守，而古代 DNA 通常是从骨骼和牙齿中提取的，因此之前利用古代 DNA 甲基化图谱的研究主要集中在研究骨骼系统的进化变化上。在这里，我们提出，在某些条件下，一个组织的 DNA 甲基化模式可能对同一个体其他组织的 DNA 甲基化模式有参考价值。利用组织特异性 DNA 甲基化在胚胎发育过程中形成的事实，我们确定了进行这种跨组织推断的条件，并设计了一种算法来进行推断。我们在现存物种的甲基化数据上对算法进行了训练，验证数据集的精确度高达 0.92。然后，我们在古人类身上使用了该算法，并确定了 1850 多个位置，在这些位置上，我们可以观察到前额叶皮层神经元的 DNA 甲基化差异。这些位置与数百个基因相关联，其中许多涉及神经功能，如结构和发育过程。其中六个位置位于神经母细胞瘤断裂点家族（NBPF）基因家族，该家族可能在人类大脑进化过程中扮演了重要角色。我们在这里介绍的算法可以研究古生物记录中没有的组织和细胞类型的表观遗传变化，因此为研究表观遗传变化对进化的影响提供了新的方法。
{"title":"Inferring DNA methylation in non-skeletal tissues of ancient specimens","authors":"Yoav Mathov, Malka Nissim-Rafinia, Chen Leibson, Nir Galun, Tomas Marques-Bonet, Arye Kandel, Meir Liebergal, Eran Meshorer, Liran Carmel","doi":"10.1038/s41559-024-02571-w","DOIUrl":"10.1038/s41559-024-02571-w","url":null,"abstract":"Genome-wide premortem DNA methylation patterns can be computationally reconstructed from high-coverage DNA sequences of ancient samples. Because DNA methylation is more conserved across species than across tissues, and ancient DNA is typically extracted from bones and teeth, previous works utilizing ancient DNA methylation maps focused on studying evolutionary changes in the skeletal system. Here we suggest that DNA methylation patterns in one tissue may, under certain conditions, be informative on DNA methylation patterns in other tissues of the same individual. Using the fact that tissue-specific DNA methylation builds up during embryonic development, we identified the conditions that allow for such cross-tissue inference and devised an algorithm that carries it out. We trained the algorithm on methylation data from extant species and reached high precisions of up to 0.92 for validation datasets. We then used the algorithm on archaic humans, and identified more than 1,850 positions for which we were able to observe differential DNA methylation in prefrontal cortex neurons. These positions are linked to hundreds of genes, many of which are involved in neural functions such as structural and developmental processes. Six positions are located in the neuroblastoma breaking point family (NBPF) gene family, which probably played a role in human brain evolution. The algorithm we present here allows for the examination of epigenetic changes in tissues and cell types that are absent from the palaeontological record, and therefore provides new ways to study the evolutionary impacts of epigenetic changes. The authors show that DNA methylation patterns in one tissue can inform on those in another, under certain conditions, and devise an algorithm that allows identification of differential DNA methylation. They applied it to an archaic human dataset, revealing information about human brain evolution in the absence of preserved brain tissue.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 1","pages":"153-165"},"PeriodicalIF":13.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41559-024-02571-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142673415","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}
Pub Date : 2024-11-18DOI: 10.1038/s41559-024-02570-x
Shan Pei, Pengbo Yu, Jayna Raghwani, Yuxin Wang, Ziyan Liu, Yidan Li, Yanchao Cheng, Qiushi Lin, Chuliang Song, Guha Dharmarajan, Christina L. Faust, Yunyu Tian, Yiting Xu, Yilin Liang, Jianhui Qu, Jing Wei, Shen Li, Tongjun Zhang, Chaofeng Ma, Nita Bharti, Bernard Cazelles, Ruifu Yang, Oliver G. Pybus, Andrew P. Dobson, Nils Chr. Stenseth, Huaiyu Tian
Anthropogenic land-use change is an important driver of global biodiversity loss and threatens public health through biological interactions. Understanding these landscape–ecological effects at local scales will help achieve the United Nations Sustainable Development Goals by balancing urbanization, biodiversity and the spread of infectious diseases. Here, we address this knowledge gap by analysing a 43-year-long monthly dataset (1980–2022) of synanthropic rodents in Central China during intensive land-use change. We observed a notable increase in the mean patch size, coinciding with a substantial change in rodent community composition and a marked decline in rodent diversity; eight of the nine local rodent species experienced near-extirpation. Our analysis reveals that these irregular species replacements can be attributed to the effect of land consolidation on species competition among rodents, favouring striped field mice, a critical reservoir host of Hantaan virus (HTNV). Consequently, land consolidation has facilitated the proliferation of striped field mice and increased the prevalence of HTNV among them. This study highlights the importance of considering both direct and indirect effects of anthropogenic activities in the management of biodiversity and public health. A 43-year dataset of rodents in the Hu region of China reveals how urbanization-induced changes to land-use configuration affect rodent community composition, including benefitting striped field mice, the primary local hosts of the zoonotic pathogen Hantaan virus.
{"title":"Anthropogenic land consolidation intensifies zoonotic host diversity loss and disease transmission in human habitats","authors":"Shan Pei, Pengbo Yu, Jayna Raghwani, Yuxin Wang, Ziyan Liu, Yidan Li, Yanchao Cheng, Qiushi Lin, Chuliang Song, Guha Dharmarajan, Christina L. Faust, Yunyu Tian, Yiting Xu, Yilin Liang, Jianhui Qu, Jing Wei, Shen Li, Tongjun Zhang, Chaofeng Ma, Nita Bharti, Bernard Cazelles, Ruifu Yang, Oliver G. Pybus, Andrew P. Dobson, Nils Chr. Stenseth, Huaiyu Tian","doi":"10.1038/s41559-024-02570-x","DOIUrl":"10.1038/s41559-024-02570-x","url":null,"abstract":"Anthropogenic land-use change is an important driver of global biodiversity loss and threatens public health through biological interactions. Understanding these landscape–ecological effects at local scales will help achieve the United Nations Sustainable Development Goals by balancing urbanization, biodiversity and the spread of infectious diseases. Here, we address this knowledge gap by analysing a 43-year-long monthly dataset (1980–2022) of synanthropic rodents in Central China during intensive land-use change. We observed a notable increase in the mean patch size, coinciding with a substantial change in rodent community composition and a marked decline in rodent diversity; eight of the nine local rodent species experienced near-extirpation. Our analysis reveals that these irregular species replacements can be attributed to the effect of land consolidation on species competition among rodents, favouring striped field mice, a critical reservoir host of Hantaan virus (HTNV). Consequently, land consolidation has facilitated the proliferation of striped field mice and increased the prevalence of HTNV among them. This study highlights the importance of considering both direct and indirect effects of anthropogenic activities in the management of biodiversity and public health. A 43-year dataset of rodents in the Hu region of China reveals how urbanization-induced changes to land-use configuration affect rodent community composition, including benefitting striped field mice, the primary local hosts of the zoonotic pathogen Hantaan virus.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 1","pages":"99-110"},"PeriodicalIF":13.9,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142665286","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 : 2024-11-18DOI: 10.1038/s41559-024-02584-5
Claire S. Teitelbaum
Four decades of data on rodent species composition and hantavirus prevalence across a changing urban–agricultural landscape demonstrate that long-term data are key for understanding links between biodiversity loss and disease dynamics
{"title":"Species diversity links land consolidation to rodent disease","authors":"Claire S. Teitelbaum","doi":"10.1038/s41559-024-02584-5","DOIUrl":"10.1038/s41559-024-02584-5","url":null,"abstract":"Four decades of data on rodent species composition and hantavirus prevalence across a changing urban–agricultural landscape demonstrate that long-term data are key for understanding links between biodiversity loss and disease dynamics","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 1","pages":"17-18"},"PeriodicalIF":13.9,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142665283","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 : 2024-11-15DOI: 10.1038/s41559-024-02580-9
Jayden E. Engert, Penny van Oosterzee
Australia has proposed a legislated market for biodiversity based on an existing carbon credits scheme which generates Australian carbon credit units (ACCU) from land-based projects. This provides a unique opportunity to assess the potential for markets to benefit biodiversity. We assessed the extent to which projects under the ACCU scheme overlap potential threatened species habitat, compared that to overlap afforded by protected areas, and compared the ability of different project types to deliver potential benefits to species most impacted by habitat loss. Projects are primarily located in low-cost, marginal arid lands, a pattern that reflects that of the protected area estate. Projects are smaller and fewer in number in more productive lands close to human populations. These lands also overlap most threatened species habitat, hence those species most in need of habitat restoration are the least likely to have their habitat restored under the ACCU scheme. Projects, however, do overlap the geographic range of 32% of the 1,660 threatened species assessed, including for 275 species with <17% of their range in protected areas. Biodiversity markets must incentivize actions in areas of high biodiversity value underpinned by regulations that align with national priorities for biodiversity conservation. An assessment of the Australian carbon credit units scheme finds that most current projects under the scheme overlap the habitats of few threatened species. The findings generate lessons for the planned development of a national biodiversity market based on the ACCU scheme.
{"title":"Limits to the ability of carbon farming projects to deliver benefits for threatened species","authors":"Jayden E. Engert, Penny van Oosterzee","doi":"10.1038/s41559-024-02580-9","DOIUrl":"10.1038/s41559-024-02580-9","url":null,"abstract":"Australia has proposed a legislated market for biodiversity based on an existing carbon credits scheme which generates Australian carbon credit units (ACCU) from land-based projects. This provides a unique opportunity to assess the potential for markets to benefit biodiversity. We assessed the extent to which projects under the ACCU scheme overlap potential threatened species habitat, compared that to overlap afforded by protected areas, and compared the ability of different project types to deliver potential benefits to species most impacted by habitat loss. Projects are primarily located in low-cost, marginal arid lands, a pattern that reflects that of the protected area estate. Projects are smaller and fewer in number in more productive lands close to human populations. These lands also overlap most threatened species habitat, hence those species most in need of habitat restoration are the least likely to have their habitat restored under the ACCU scheme. Projects, however, do overlap the geographic range of 32% of the 1,660 threatened species assessed, including for 275 species with <17% of their range in protected areas. Biodiversity markets must incentivize actions in areas of high biodiversity value underpinned by regulations that align with national priorities for biodiversity conservation. An assessment of the Australian carbon credit units scheme finds that most current projects under the scheme overlap the habitats of few threatened species. The findings generate lessons for the planned development of a national biodiversity market based on the ACCU scheme.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"9 1","pages":"134-141"},"PeriodicalIF":13.9,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142637053","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 : 2024-11-13DOI: 10.1038/s41559-024-02577-4
Simon Aubé, Christian R. Landry
Experiments in budding yeast reveal how the effects of mutations on phenotype and fitness vary across environments.
芽殖酵母的实验揭示了突变对表型和适应性的影响在不同环境下的差异。
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Pub Date : 2024-11-13DOI: 10.1038/s41559-024-02582-7
Mohammad A. Siddiq, Fabien Duveau, Patricia J. Wittkopp
The environment influences how an organism’s genotype determines its phenotype and how this phenotype affects its fitness. Here, to better understand this dual role of environment in the production and selection of phenotypic variation, we determined genotype–phenotype–fitness relationships for mutant strains of Saccharomyces cerevisiae in four environments. Specifically, we measured how promoter mutations of the metabolic gene TDH3 modified expression level and affected growth for four different carbon sources. In each environment, we observed a clear relationship between TDH3 expression level and fitness, but this relationship differed among environments. Mutations with similar effects on expression in different environments often had different effects on fitness and vice versa. Such environment-specific relationships between phenotype and fitness can shape the evolution of phenotypic plasticity. We also found that mutations disrupting binding sites for transcription factors had more variable effects on expression among environments than those disrupting the TATA box, which is part of the core promoter. However, mutations with the most environmentally variable effects on fitness were located in the TATA box, because of both the lack of plasticity of TATA box mutations and environment-specific fitness functions. This observation suggests that mutations affecting different molecular mechanisms contribute unequally to regulatory sequence evolution in changing environments. Measuring how mutations in the promoter of a metabolic gene modified its expression level and affected growth of Saccharomyces cerevisiae in four environments, the authors show that the effects of mutations on gene expression and the relationships between expression levels and fitness vary among environments.
{"title":"Plasticity and environment-specific relationships between gene expression and fitness in Saccharomyces cerevisiae","authors":"Mohammad A. Siddiq, Fabien Duveau, Patricia J. Wittkopp","doi":"10.1038/s41559-024-02582-7","DOIUrl":"10.1038/s41559-024-02582-7","url":null,"abstract":"The environment influences how an organism’s genotype determines its phenotype and how this phenotype affects its fitness. Here, to better understand this dual role of environment in the production and selection of phenotypic variation, we determined genotype–phenotype–fitness relationships for mutant strains of Saccharomyces cerevisiae in four environments. Specifically, we measured how promoter mutations of the metabolic gene TDH3 modified expression level and affected growth for four different carbon sources. In each environment, we observed a clear relationship between TDH3 expression level and fitness, but this relationship differed among environments. Mutations with similar effects on expression in different environments often had different effects on fitness and vice versa. Such environment-specific relationships between phenotype and fitness can shape the evolution of phenotypic plasticity. We also found that mutations disrupting binding sites for transcription factors had more variable effects on expression among environments than those disrupting the TATA box, which is part of the core promoter. However, mutations with the most environmentally variable effects on fitness were located in the TATA box, because of both the lack of plasticity of TATA box mutations and environment-specific fitness functions. This observation suggests that mutations affecting different molecular mechanisms contribute unequally to regulatory sequence evolution in changing environments. Measuring how mutations in the promoter of a metabolic gene modified its expression level and affected growth of Saccharomyces cerevisiae in four environments, the authors show that the effects of mutations on gene expression and the relationships between expression levels and fitness vary among environments.","PeriodicalId":18835,"journal":{"name":"Nature ecology & evolution","volume":"8 12","pages":"2184-2194"},"PeriodicalIF":13.9,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41559-024-02582-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142601079","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}
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