Pygmy lorises are arboreal primates primarily found in forest environments across Southeast Asia(Nekaris 2014).Theyhave a diverse diet,including plant secretions,nectar,fruits,invertebrates,tree bark,and bird eggs.All...Pygmy lorises are arboreal primates primarily found in forest environments across Southeast Asia(Nekaris 2014).Theyhave a diverse diet,including plant secretions,nectar,fruits,invertebrates,tree bark,and bird eggs.All 9 known speciesof pygmy lorises are listed as globally endangered species(Nekaris 2014).Pygmy lorises exhibit a range of unique phenotypic characteristics rarely seen among primates.展开更多
While methodology for determining the mode of evolution in coding sequences has been well established,evaluation of adaptation events in emerging types of phenotype data needs further development.Here,we propose an an...While methodology for determining the mode of evolution in coding sequences has been well established,evaluation of adaptation events in emerging types of phenotype data needs further development.Here,we propose an analysis framework(expression variance decomposition,EVaDe)for comparative single-cell expression data based on phenotypic evolution theory.After decomposing the gene expression variance into separate components,we use two strategies to identify genes exhibiting large between-taxon expression divergence and small within-cell-type expression noise in certain cell types,attributing this pattern to putative adaptive evolution.In a dataset of primate prefrontal cortex,we find that such humanspecific key genes enrich with neurodevelopment-related functions,while most other genes exhibit neutral evolution patterns.Specific neuron types are found to harbor more of these key genes than other cell types,thus likely to have experienced more extensive adaptation.Reassuringly,at the molecular sequence level,the key genes are significantly associated with the rapidly evolving conserved non-coding elements.An additional case analysis comparing the naked mole-rat(NMR)with the mouse suggests that innateimmunity-related genes and cell types have undergone putative expression adaptation in NMR.Overall,the EVaDe framework may effectively probe adaptive evolution mode in single-cell expression data.展开更多
Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary biology.The use of genomic data has greatly advanced our understandings on this ...Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary biology.The use of genomic data has greatly advanced our understandings on this issue,as well as other aspects of evolutionary biology,including molecular adaptation,speciation,and even conservation of endangered species.Despite the well-recognized advantages,usages of genomic data are still limited to non-mammal vertebrate groups,partly due to the difficulties in assembling large or highly heterozygous genomes.Although this is particularly the case for amphibians,nonetheless,several comparative and population genomic analyses have shed lights into the speciation and adaptation processes of amphibians in a complex landscape,giving a promising hope for a wider application of genomics in the previously believed challenging groups of organisms.At the same time,these pioneer studies also allow us to realize numerous challenges in studying the molecular adaptations and/or phenotypic evolutionary mechanisms of amphibians.In this review,we first summarize the recent progresses in the study of adaptive evolution of amphibians based on genomic data,and then we give perspectives regarding how to effectively identify key pathways underlying the evolution of complex traits in the genomic era,as well as directions for future research.展开更多
Male frogs emit stereotypical advertisement calls to attractmates and deter conspecific rivals.The evolution of these calls is thought to be linked to anatomical constraints and the acoustic characteristics of their s...Male frogs emit stereotypical advertisement calls to attractmates and deter conspecific rivals.The evolution of these calls is thought to be linked to anatomical constraints and the acoustic characteristics of their surroundings.The acoustic adaptation hypothesis(AAH)posits that species evolve calls that maximize propagation distance and reduce signal degradation in the environmentwhere they are emitted.We applied phylogenetic comparative analyses to study the association of body size,vegetation density,type of aquatic ecosystem,and calling site on the evolution of acoustic traits in Cophomantini,a large radiation of Neotropical treefrogs(Hylidae).We obtained and analyzed body size,acoustic,and habitat data from a total of 112 species(58%of Cophomantini),using themost inclusive available phylogeny.We found a significant negative correlation between peak frequency,body size,and calling site,but contrary to the predictions of the AAH,we did not find support for associations among call traits and environmental characteristics.Although spectral allometry is explained by an anatomical constraint,it could also be maintained by female choice.We recommend that future studies strive to incorporate factors such as female mate preferences,eavesdropping by predators or parasites,and genetic drift.展开更多
基金supported by the Shaanxi FundamentalScience Research Project for Chemistry&Biology(grant no.22JHQ049)Basic Research Program of Natural Sciencesof Shaanxi Province(2019JM-339).
文摘Pygmy lorises are arboreal primates primarily found in forest environments across Southeast Asia(Nekaris 2014).Theyhave a diverse diet,including plant secretions,nectar,fruits,invertebrates,tree bark,and bird eggs.All 9 known speciesof pygmy lorises are listed as globally endangered species(Nekaris 2014).Pygmy lorises exhibit a range of unique phenotypic characteristics rarely seen among primates.
文摘While methodology for determining the mode of evolution in coding sequences has been well established,evaluation of adaptation events in emerging types of phenotype data needs further development.Here,we propose an analysis framework(expression variance decomposition,EVaDe)for comparative single-cell expression data based on phenotypic evolution theory.After decomposing the gene expression variance into separate components,we use two strategies to identify genes exhibiting large between-taxon expression divergence and small within-cell-type expression noise in certain cell types,attributing this pattern to putative adaptive evolution.In a dataset of primate prefrontal cortex,we find that such humanspecific key genes enrich with neurodevelopment-related functions,while most other genes exhibit neutral evolution patterns.Specific neuron types are found to harbor more of these key genes than other cell types,thus likely to have experienced more extensive adaptation.Reassuringly,at the molecular sequence level,the key genes are significantly associated with the rapidly evolving conserved non-coding elements.An additional case analysis comparing the naked mole-rat(NMR)with the mouse suggests that innateimmunity-related genes and cell types have undergone putative expression adaptation in NMR.Overall,the EVaDe framework may effectively probe adaptive evolution mode in single-cell expression data.
基金This study was supported by the National Natural Science Foundation of China(31671326,31871275)the Highlevel Talent Introduction Program of Yunnan University to Y.B.S。
文摘Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary biology.The use of genomic data has greatly advanced our understandings on this issue,as well as other aspects of evolutionary biology,including molecular adaptation,speciation,and even conservation of endangered species.Despite the well-recognized advantages,usages of genomic data are still limited to non-mammal vertebrate groups,partly due to the difficulties in assembling large or highly heterozygous genomes.Although this is particularly the case for amphibians,nonetheless,several comparative and population genomic analyses have shed lights into the speciation and adaptation processes of amphibians in a complex landscape,giving a promising hope for a wider application of genomics in the previously believed challenging groups of organisms.At the same time,these pioneer studies also allow us to realize numerous challenges in studying the molecular adaptations and/or phenotypic evolutionary mechanisms of amphibians.In this review,we first summarize the recent progresses in the study of adaptive evolution of amphibians based on genomic data,and then we give perspectives regarding how to effectively identify key pathways underlying the evolution of complex traits in the genomic era,as well as directions for future research.
基金supported by Conselho Nacional de Desenvolvimento Cientifico e Tecnologico(CNPq,ref.140815/2018-0)Society of Systematic Biology(SSB-GSRA 2018)+6 种基金Programa para el Desarrollo de la Ciencias Basicas(PEDECIBA)Fundacao de Amparo a Pesquisa do Estado do Rio Grande do Sul(FAPERGS,23/2551-0001938-8)Maxwell/hanrahan FoundationFonds voor Wetenschappelijk Onderzoek(FWO12A7614N and FWO12A7617N)Marie Skłodowska-Curie Actions(MSCA,101022238/HOSTILE)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo(FAPESP,#2018/18473-6 and#2022/02789-0)Junta de Andalucia(EMERGIA20_38444).
文摘Male frogs emit stereotypical advertisement calls to attractmates and deter conspecific rivals.The evolution of these calls is thought to be linked to anatomical constraints and the acoustic characteristics of their surroundings.The acoustic adaptation hypothesis(AAH)posits that species evolve calls that maximize propagation distance and reduce signal degradation in the environmentwhere they are emitted.We applied phylogenetic comparative analyses to study the association of body size,vegetation density,type of aquatic ecosystem,and calling site on the evolution of acoustic traits in Cophomantini,a large radiation of Neotropical treefrogs(Hylidae).We obtained and analyzed body size,acoustic,and habitat data from a total of 112 species(58%of Cophomantini),using themost inclusive available phylogeny.We found a significant negative correlation between peak frequency,body size,and calling site,but contrary to the predictions of the AAH,we did not find support for associations among call traits and environmental characteristics.Although spectral allometry is explained by an anatomical constraint,it could also be maintained by female choice.We recommend that future studies strive to incorporate factors such as female mate preferences,eavesdropping by predators or parasites,and genetic drift.
