Environmental temperature serves as a major driver of adaptive changes in wild organisms.To discover the mechanisms underpinning cold tolerance in domestic animals,we sequenced the genomes of 28 cattle from warm and c...Environmental temperature serves as a major driver of adaptive changes in wild organisms.To discover the mechanisms underpinning cold tolerance in domestic animals,we sequenced the genomes of 28 cattle from warm and cold areas across China.By characterizing the population structure and demographic history,we identified two genetic clusters,i.e.,northern and southern groups,as well as a common historic population peak at 30 kilo years ago.Genomic scan of cold-tolerant breeds determined potential candidate genes in the thermogenesis-related pathways that were under selection.Specifically,functional analysis identified a substitution of PRDM16(p.P779 L)in northern cattle,which maintains brown adipocyte formation by boosting thermogenesis-related gene expression,indicating a vital role of this gene in cold tolerance.These findings provide a basis for genetic variation in domestic cattle shaped by environmental temperature and highlight the role of reverse mutation in livestock species.展开更多
Many bird species are specialized to live in the broadleaved,evergreen forests in the mountain regions in Southeast Asia.These mountain habitats are not continuously distributed as the different mountain areas are sep...Many bird species are specialized to live in the broadleaved,evergreen forests in the mountain regions in Southeast Asia.These mountain habitats are not continuously distributed as the different mountain areas are separated by lowlands,which has restricted gene flow and thus contributed to the high biological diversity in this region.The degree of connectivity between mountain areas has fluctuated with the Pleistocene glacial cycles,being largest during the glaciations when the mountain forests spread to lower elevations.Here we study how the intermittent periods of restricted gene flow and connectivity between the populations of five montane species of babblers(Aves,Timaliidae)in Vietnam may be traced in their genomes.The results suggest that the babbler species in the Central Highlands have been isolated from their sister-populations in northern Vietnam for between ca.585 and 380 ky.For two species with populations in both the Central Highlands and the Da Lat region,we found that these split at more or less the same time(440–340 kya).We also found a significant statistical correlation between the time of the splits of these populations and the lowest altitude at which they are known to occur(no similar correlation was found with the geographic distances between populations).The populations in northern Vietnam show higher genetic variation than their counterparts in South-Central Vietnam,supporting the postulate that smaller populations may have lower genetic variation than larger.In accordance with this,we found the lowest genetic variation in the two species with the smallest populations in the Central Highlands.These two populations also show low levels of genomic heterozygosity.Our results show that the south-central populations of the studied babbler species are genetically distinct from their sister-populations in northern Vietnam,providing additional argument for the long-term protection of the evergreen mountain forests in Southeast Asia.展开更多
Horseshoe bats(genus Rhinolophus,family Rhinolophidae)represent an important group within chiropteran phylogeny due to their distinctive traits,including constant high-frequency echolocation,rapid karyotype evolution,...Horseshoe bats(genus Rhinolophus,family Rhinolophidae)represent an important group within chiropteran phylogeny due to their distinctive traits,including constant high-frequency echolocation,rapid karyotype evolution,and unique immune system.Advances in evolutionary biology,supported by high-quality reference genomes and comprehensive whole-genome data,have significantly enhanced our understanding of species origins,speciation mechanisms,adaptive evolutionary processes,and phenotypic diversity.However,genomic research and understanding of the evolutionary patterns of Rhinolophus are severely constrained by limited data,with only a single published genome of R.ferrumequinum currently available.In this study,we constructed a high-quality chromosome-level reference genome for the intermediate horseshoe bat(R.affinis).Comparative genomic analyses revealed potential genetic characteristics associated with virus tolerance in Rhinolophidae.Notably,we observed expansions in several immune-related gene families and identified various genes functionally associated with the SARS-CoV-2 signaling pathway,DNA repair,and apoptosis,which displayed signs of rapid evolution.In addition,we observed an expansion of the major histocompatibility complex class II(MHC-II)region and a higher copy number of the HLA-DQB2 gene in horseshoe bats compared to other chiropteran species.Based on whole-genome resequencing and population genomic analyses,we identified multiple candidate loci(e.g.,GLI3)associated with variations in echolocation call frequency across R.affinis subspecies.This research not only expands our understanding of the genetic characteristics of the Rhinolophus genus but also establishes a valuable foundation for future research.展开更多
In recent years, advances in high-throughput sequencing technique and capacity of big data analysis have facilitated genomics research in many species. Genome sequencing, single nucleotide polymorphism （SNPs） identi...In recent years, advances in high-throughput sequencing technique and capacity of big data analysis have facilitated genomics research in many species. Genome sequencing, single nucleotide polymorphism （SNPs） identification and population transcriptomics are conducive to understanding the evolutionary progress and regulatory mechanisms of genes related to adaptive traits in organisms, which poses great significance to the theoretical research and productive practice. Fur- thermore, population genomics of marine fishes can deepen the understanding of important microevolution events, such as genetic differentiation, hybridization and speciation. Therefore, the related research contributes to better understanding of the evolutionary process of marine organisms and provides theoretical evidences for the development of aquaculture industry and nmnagement and protection of marine fishery resources.展开更多
Body size is the most important economic trait for animal production and breeding.Several hundreds of loci have been reported to be associated with growth trait and body weight in chickens.The loci are mapped to large...Body size is the most important economic trait for animal production and breeding.Several hundreds of loci have been reported to be associated with growth trait and body weight in chickens.The loci are mapped to large genomic regions due to the low density and limited number of genetic markers in previous studies.Herein,we employed comparative population genomics to identify genetic basis underlying the small body size of Yuanbao chicken(a famous ornamental chicken)based on 89 whole genomes.The most significant signal was mapped to the BMP10 gene,whose expression was upregulated in the Yuanbao chicken.Overexpression of BMP10 induced a significant decrease in body length by inhibiting angiogenic vessel development in zebrafish.In addition,three other loci on chromosomes 1,2,and 24 were also identified to be potentially involved in the development of body size.Our results provide a paradigm shift in identification of novel loci controlling body size variation,availing a fast and efficient strategy.These loci,particularly BMP10,add insights into ongoing research of the evolution of body size under artificial selection and have important implications for future chicken breeding.展开更多
Population genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial...Population genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial and environmental context of their study region （e.g., geographical distance, average sea surface temperature, average salinity）. We contend that a more nuanced and considered approach to quantifying seascape dynamics and patterns can strengthen population genomic investigations and help identify spatial, temporal, and environmental factors associated with differing selective regimes or demographic histories. Nevertheless, approaches for quantifying marine landscapes are complicated. Characteristic features of the marine environment, including pelagic living in flowing water （experienced by most marine taxa at some point in their life cycle）, require a well-designed spatial-temporal sampling strategy and analysis. Many genetic summary statistics used to describe populations may be inappropriate for marine species with large population sizes, large species ranges, stochastic recruitment, and asymmetrical gene flow. Finally, statistical approaches for testing associations between seascapes and population genomic patterns are still maturing with no single approach able to capture all relevant considerations. None of these issues are completely unique to marine systems and therefore similar issues and solutions will be shared for many organisms regardless of habitat. Here, we outline goals and spatial approaches for land- scape genomics with an emphasis on marine systems and review the growing empirical literature on seascape genomics. We review established tools and approaches and highlight promising new strategies to overcome select issues including a strategy to spatially optimize sampling. Despite the many challenges, we argue that marine systems may be especially well suited for identifying candidate genomic regions under environmentally mediated selection and that seascape genomic approaches are especially useful for identifying robust locus-by-environment associations.展开更多
Prevailing concerns on mountainous biodiversity are concentrated on the impacts of climate change at higher elevations. However, the lower elevations are facing additional human disturbance and are expected to suffer ...Prevailing concerns on mountainous biodiversity are concentrated on the impacts of climate change at higher elevations. However, the lower elevations are facing additional human disturbance and are expected to suffer from higher extinction risk but have attracted less conservation attention. Here, we employed population genomics to compare extinction risk two common songbirds—the Vinous-throated Parrotbill (Sinosuthora webbiana) and the Rufous-capped Babbler (Cyanoderma ruficeps)—at lower and higher elevations on the Taiwan island. As the result, we observed decreased genetic diversity and increased genetic load and thus elevated extinction risk in the low-elevation populations of both birds in the eastern slope of the Central Mountains on the Taiwan island. In contrast, genetic-load patterns of both birds in the western slope might be confused by substantial gene flow across lower and higher elevations. These results, on the one hand, call for conservation efforts to lower elevations in mountains and, on the other hand, highlight the importance of population connection in maintaining population viability under impending global change.展开更多
Physiological adaptation of tree shrews(Tupaia belangeri)to changing environmental temperature has been re-ported in detail.However,the T.belangeri origin(mainland or island),population history,and adaptation to histo...Physiological adaptation of tree shrews(Tupaia belangeri)to changing environmental temperature has been re-ported in detail.However,the T.belangeri origin(mainland or island),population history,and adaptation to histor-ical climate change remain largely unknown or controversial.Here,for thefirst time,we sequenced the simplified genome of 134 T.belangeri individuals from 12 populations in China and further resequenced one individual from each population.Using population genomic approaches,wefirst observed considerable genetic variation in T.be-langeri.Moreover,T.belangeri populations formed obvious genetic structure and reflected different demographic histories;they generally exhibited high genetic diversity,although the isolated populations had relatively low ge-netic diversity.The results presented in this study indicate that T.b.modesta and T.b.tonquinia were separated recently and with a similar population dynamics.Second,physical barriers rather than distance were the driving factors of divergence,and environmental heterogeneity may play an important role in genetic differentiation in T.belangeri.Moreover,our analyses highlight the role of historical global climates in the T.belangeri population dynamics and indicate that the decrease of the T.belangeri population size may be due to the low temperature.Finally,we identified the olfaction-associated adaptive genes between different altitude populations and found that olfactory-related genes of high-altitude populations were selectively eliminated.Our study provides demographic history knowledge of T.belangeri;their adaption history offers new insights into their evolution and adaptation,and provides valuable baseline information for conservation measures.展开更多
The evolutionary and functional features of RNA editing are well studied in mammals,cephalopods,and insects,but not in birds.Here,we integrated transcriptomic and whole-genomic analyses to exhaustively characterize th...The evolutionary and functional features of RNA editing are well studied in mammals,cephalopods,and insects,but not in birds.Here,we integrated transcriptomic and whole-genomic analyses to exhaustively characterize the expansive repertoire of adenosine-to-inosine(A-to-I)RNA editing sites(RESs)in the chicken.In addition,we investigated the evolutionary status of the chicken editome as a potential mechanism of domestication.We detected the lowest editing level in the liver of chickens,compared to muscles in humans,and found higher editing activity and specificity in the brain than in non-neural tissues,consistent with the brain’s functional complexity.To a certain extent,specific editing activity may account for the specific functions of tissues.Our results also revealed that sequences critical to RES secondary structures remained conserved within avian evolution.Furthermore,the RNA editome was shaped by purifying selection during chicken domestication and most RESs may have served as a selection pool for a few functional RESs involved in chicken domestication,including evolution of nervous and immune systems.Regulation of RNA editing in chickens by adenosine deaminase acting on RNA(ADAR)enzymes may be affected by non-ADAR factors whose expression levels changed widely after ADAR knockdown.Collectively,we provide comprehensive lists of candidate RESs and non-ADAR-editing regulators in the chicken,thus contributing to our current understanding of the functions and evolution of RNA editing in animals.展开更多
Recombinant inbred lines(RILs) serve as powerful tools for genetic mapping.RILs are obtained by crossing two inbred lines followed by repeated selfing or sib-mating to create a set of new
The fungal order Botryosphaeriales includes numerous ecologically and economically important plant-associated taxa,yet its genomic diversity and evolutionary mechanisms remain poorly understood.Here,we present high-qu...The fungal order Botryosphaeriales includes numerous ecologically and economically important plant-associated taxa,yet its genomic diversity and evolutionary mechanisms remain poorly understood.Here,we present high-quality de novo genome assemblies for three representative species—Botryosphaeria dothidea,Neofusicoccum parvum,and Phyllosticta capitalensis—and perform integrative analyses using comparative genomics,population genetics,and pan-genome frameworks.Pathogenic species(B.dothidea and N.parvum)exhibit significant expansions in gene families related to membrane transport and metabolism,suggesting enhanced adaptability and virulence potential.Selective sweep analyses highlight population-level divergence in metabolic and stress-response pathways,reflecting natural selection in host and environmental adaptation.Cross-species pan-genome comparisons of six Phyllosticta species reveal a conserved core genome,dynamic gene family turnover,and extensive horizontal gene transfer from bacterial,and archaeal sources—potentially driving ecological diversification.Furthermore,effector proteins display striking domain variation across genera,particularly in regions associated with host cell wall targeting,indicating convergent strategies for host adaptation.Together,these findings provide comprehensive insights into the genomic evolution,adaptation,and virulence mechanisms of Botryosphaeriales fungi,laying a foundation for future studies on plant–fungal interactions.展开更多
Cooperative breeding is a sophisticated altruistic social behavior that helps social animals to adapt to harsh environments.The Tibetan ground tit,Pseudopodoces humilis,is a high-altitude bird endemic to the Tibetan p...Cooperative breeding is a sophisticated altruistic social behavior that helps social animals to adapt to harsh environments.The Tibetan ground tit,Pseudopodoces humilis,is a high-altitude bird endemic to the Tibetan plateau.Recently,it has become an exciting system for studying the evolution of facultative cooperative breeding.To test for molecular adaptations associated with cooperative breeding,we resequenced the whole genome of ground tits from 6 wild populations that display remarkable variation in the frequency of cooperative breeding.Population structure analyses showed that the 6 populations were divided into 4 lineages,which is congruent with the major geographical distribution of the sampling sites.Using genome-wide selective sweep analysis,we identified putative positively selected genes(PSGs)in groups of tits that displayed high and low cooperative breeding rates.The total number of PSGs varied from 146 to 722 in high cooperative breeding rate populations,and from 272 to 752 in low cooperative breeding rate populations.Functional enrichment analysis of these PSGs identified several significantly enriched ontologies related to oxytocin signaling,estrogen signaling,and insulin secretion.PSGs involved in these functional ontologies suggest that molecular adaptations in hormonal regulation may have played important roles in shaping the evolution of cooperative breeding in the ground tit.Taken together,our study provides candidate genes and functional ontologies involved in molecular adaptations associated with cooperative breeding in Tibetan ground tits,and calls for a better understanding of the genetic roles in the evolution of cooperative breeding.展开更多
The identification and understanding of cryptic intraspecific evolutionary units(lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species.However...The identification and understanding of cryptic intraspecific evolutionary units(lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species.However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a “living fossil” dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range.Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.展开更多
Identifying targets of positive selection in farm animals has, until recently, been frustratingly slow, relying on the analysis of individual candidate genes. Genomics, however, has provided the necessary resources to...Identifying targets of positive selection in farm animals has, until recently, been frustratingly slow, relying on the analysis of individual candidate genes. Genomics, however, has provided the necessary resources to systematically interrogate the entire genome for signatures of selection. This review described important recent results derived from the application of genome-wide scan to the study of genetic changes in farm animals. These included findings of regions of the genome that showed breed differentiation, evidence of selective sweeps within individual genomes and signatures of demographic events. Particular attention is focused on the study of the implications for domestication. To date, sixteen genome-wide scans for recent or ongoing positive selection have been performed in farm animals. A key challenge is to begin synthesizing these newly constructed maps of selection into a coherent narrative of animal breed evolutionary history and derive a deeper mechanistic understanding of how animal populations improve or evolve. The major insights from the surveyed studies are highlighted and directions for future study are suggested.展开更多
Island species/populations are characterized by evolutionary uniqueness and a high degree of endemism and extinction.The conservation and restoration of island species/populations have become the most challenging and ...Island species/populations are characterized by evolutionary uniqueness and a high degree of endemism and extinction.The conservation and restoration of island species/populations have become the most challenging and urgent issues in biodiversity conservation.Chinese pangolin in Taiwan island(Manis pentadactyla pentadactyla)is a well-known,critically endangered,and island-endemic Chinese pangolin subspecies,which has been the focus of conservation concern.Here,we first generated large-scale population genomics data for the Chinese pangolin in Taiwan to address its population structure,demographic history,the genomic consequences of population declines,and survival potential.We revealed that the Chinese pangolin in Taiwan originated in southeast China and was differentiated into Northern and nonNorthern populations due to the isolation of the Xueshan and Central Mountain Ranges,proposing to treat them as separate conservation units.The southeast of Taiwan island acted as a refuge for this Chinese pangolin subspecies during the Last Glacial Maximum.The Northern population had experienced a more severe bottleneck and isolation than the non-Northern population,which corresponded to the estimated current lower genetic diversity,higher inbreeding,and genetic load of the Northern population.The modeling results revealed that the Northern population is more seriously affected by climate change than the non-Northern population,which highlights that climate change poses a substantial threat to island biodiversity.The simulation results indicate that the Northern population needs a higher population growth rate to achieve evolutionary potential equal to the non-Northern population over the next 100 years,deserving conservation prioritization.This study enhances the understanding of genetic background,conservation status,and future prospects for Chinese pangolin in Taiwan,as well as the genetic consequences of a small and isolated island population.展开更多
基金supported by the General Program(Major Research Plan)of National Natural Science Foundation of China(92057208)National Key Research and Development Program of China(2018YFD0501702)+4 种基金Youth Program of the National Natural Science Foundation of China(31900830)National Natural Science Foundation of China(81770834)Jilin Provincial Development and Reform Commission Budget Capital Construction Fund Project(2018M640182)111 Project(D20034)China Postdoctoral Science Foundation Funded Project(2018M640182 to J.L.)。
文摘Environmental temperature serves as a major driver of adaptive changes in wild organisms.To discover the mechanisms underpinning cold tolerance in domestic animals,we sequenced the genomes of 28 cattle from warm and cold areas across China.By characterizing the population structure and demographic history,we identified two genetic clusters,i.e.,northern and southern groups,as well as a common historic population peak at 30 kilo years ago.Genomic scan of cold-tolerant breeds determined potential candidate genes in the thermogenesis-related pathways that were under selection.Specifically,functional analysis identified a substitution of PRDM16(p.P779 L)in northern cattle,which maintains brown adipocyte formation by boosting thermogenesis-related gene expression,indicating a vital role of this gene in cold tolerance.These findings provide a basis for genetic variation in domestic cattle shaped by environmental temperature and highlight the role of reverse mutation in livestock species.
基金This work was supported by the Swedish Research Council(grant no.621-2017-3693 to PE).
文摘Many bird species are specialized to live in the broadleaved,evergreen forests in the mountain regions in Southeast Asia.These mountain habitats are not continuously distributed as the different mountain areas are separated by lowlands,which has restricted gene flow and thus contributed to the high biological diversity in this region.The degree of connectivity between mountain areas has fluctuated with the Pleistocene glacial cycles,being largest during the glaciations when the mountain forests spread to lower elevations.Here we study how the intermittent periods of restricted gene flow and connectivity between the populations of five montane species of babblers(Aves,Timaliidae)in Vietnam may be traced in their genomes.The results suggest that the babbler species in the Central Highlands have been isolated from their sister-populations in northern Vietnam for between ca.585 and 380 ky.For two species with populations in both the Central Highlands and the Da Lat region,we found that these split at more or less the same time(440–340 kya).We also found a significant statistical correlation between the time of the splits of these populations and the lowest altitude at which they are known to occur(no similar correlation was found with the geographic distances between populations).The populations in northern Vietnam show higher genetic variation than their counterparts in South-Central Vietnam,supporting the postulate that smaller populations may have lower genetic variation than larger.In accordance with this,we found the lowest genetic variation in the two species with the smallest populations in the Central Highlands.These two populations also show low levels of genomic heterozygosity.Our results show that the south-central populations of the studied babbler species are genetically distinct from their sister-populations in northern Vietnam,providing additional argument for the long-term protection of the evergreen mountain forests in Southeast Asia.
基金supported by the China Postdoctoral Science Foundation(2022M722020)to Z.L.Key Project of Scientific Research Program of Shaanxi Provincial Education Department(23JY020)to Z.L.+5 种基金Natural Science Basic Research Program of Shaanxi(2024JCYBMS-152)to Z.L.Key Projects of Shaanxi University of Technology(SLGKYXM2302)to Z.L.Opening Foundation of Shaanxi University of Technology(SLGPT2019KF02-02)to Z.L.Natural Science Basic Research Program of Shaanxi(2020JM-280)to G.L.Fundamental Research Funds for the Central Universities(GK201902008)to G.LNational Natural Science Foundation of China(31570378)to X.M.
文摘Horseshoe bats(genus Rhinolophus,family Rhinolophidae)represent an important group within chiropteran phylogeny due to their distinctive traits,including constant high-frequency echolocation,rapid karyotype evolution,and unique immune system.Advances in evolutionary biology,supported by high-quality reference genomes and comprehensive whole-genome data,have significantly enhanced our understanding of species origins,speciation mechanisms,adaptive evolutionary processes,and phenotypic diversity.However,genomic research and understanding of the evolutionary patterns of Rhinolophus are severely constrained by limited data,with only a single published genome of R.ferrumequinum currently available.In this study,we constructed a high-quality chromosome-level reference genome for the intermediate horseshoe bat(R.affinis).Comparative genomic analyses revealed potential genetic characteristics associated with virus tolerance in Rhinolophidae.Notably,we observed expansions in several immune-related gene families and identified various genes functionally associated with the SARS-CoV-2 signaling pathway,DNA repair,and apoptosis,which displayed signs of rapid evolution.In addition,we observed an expansion of the major histocompatibility complex class II(MHC-II)region and a higher copy number of the HLA-DQB2 gene in horseshoe bats compared to other chiropteran species.Based on whole-genome resequencing and population genomic analyses,we identified multiple candidate loci(e.g.,GLI3)associated with variations in echolocation call frequency across R.affinis subspecies.This research not only expands our understanding of the genetic characteristics of the Rhinolophus genus but also establishes a valuable foundation for future research.
基金Supported by Project of Offshore Fishery Resources Assessment of Ministry of Agriculture(HX15K06)Project of Fishery Germplasm Resources Protection of Shandong Province(HX15K11)
文摘In recent years, advances in high-throughput sequencing technique and capacity of big data analysis have facilitated genomics research in many species. Genome sequencing, single nucleotide polymorphism （SNPs） identification and population transcriptomics are conducive to understanding the evolutionary progress and regulatory mechanisms of genes related to adaptive traits in organisms, which poses great significance to the theoretical research and productive practice. Fur- thermore, population genomics of marine fishes can deepen the understanding of important microevolution events, such as genetic differentiation, hybridization and speciation. Therefore, the related research contributes to better understanding of the evolutionary process of marine organisms and provides theoretical evidences for the development of aquaculture industry and nmnagement and protection of marine fishery resources.
基金supported by grants from the National Natural Science Foundation of China(91331104)the 973 Program(2013CB835200,2013CB835204)Bureau of Science and Technology of Yunnan Province(2015FA026)。
文摘Body size is the most important economic trait for animal production and breeding.Several hundreds of loci have been reported to be associated with growth trait and body weight in chickens.The loci are mapped to large genomic regions due to the low density and limited number of genetic markers in previous studies.Herein,we employed comparative population genomics to identify genetic basis underlying the small body size of Yuanbao chicken(a famous ornamental chicken)based on 89 whole genomes.The most significant signal was mapped to the BMP10 gene,whose expression was upregulated in the Yuanbao chicken.Overexpression of BMP10 induced a significant decrease in body length by inhibiting angiogenic vessel development in zebrafish.In addition,three other loci on chromosomes 1,2,and 24 were also identified to be potentially involved in the development of body size.Our results provide a paradigm shift in identification of novel loci controlling body size variation,availing a fast and efficient strategy.These loci,particularly BMP10,add insights into ongoing research of the evolution of body size under artificial selection and have important implications for future chicken breeding.
文摘Population genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial and environmental context of their study region （e.g., geographical distance, average sea surface temperature, average salinity）. We contend that a more nuanced and considered approach to quantifying seascape dynamics and patterns can strengthen population genomic investigations and help identify spatial, temporal, and environmental factors associated with differing selective regimes or demographic histories. Nevertheless, approaches for quantifying marine landscapes are complicated. Characteristic features of the marine environment, including pelagic living in flowing water （experienced by most marine taxa at some point in their life cycle）, require a well-designed spatial-temporal sampling strategy and analysis. Many genetic summary statistics used to describe populations may be inappropriate for marine species with large population sizes, large species ranges, stochastic recruitment, and asymmetrical gene flow. Finally, statistical approaches for testing associations between seascapes and population genomic patterns are still maturing with no single approach able to capture all relevant considerations. None of these issues are completely unique to marine systems and therefore similar issues and solutions will be shared for many organisms regardless of habitat. Here, we outline goals and spatial approaches for land- scape genomics with an emphasis on marine systems and review the growing empirical literature on seascape genomics. We review established tools and approaches and highlight promising new strategies to overcome select issues including a strategy to spatially optimize sampling. Despite the many challenges, we argue that marine systems may be especially well suited for identifying candidate genomic regions under environmentally mediated selection and that seascape genomic approaches are especially useful for identifying robust locus-by-environment associations.
基金supported by the National Natural Science Foundation of China (32170440 and 31772437)the West Light Foundation of the Chinese Academy of Sciencesthe Yunnan Applied Basic Research Project (202401AS070078)
文摘Prevailing concerns on mountainous biodiversity are concentrated on the impacts of climate change at higher elevations. However, the lower elevations are facing additional human disturbance and are expected to suffer from higher extinction risk but have attracted less conservation attention. Here, we employed population genomics to compare extinction risk two common songbirds—the Vinous-throated Parrotbill (Sinosuthora webbiana) and the Rufous-capped Babbler (Cyanoderma ruficeps)—at lower and higher elevations on the Taiwan island. As the result, we observed decreased genetic diversity and increased genetic load and thus elevated extinction risk in the low-elevation populations of both birds in the eastern slope of the Central Mountains on the Taiwan island. In contrast, genetic-load patterns of both birds in the western slope might be confused by substantial gene flow across lower and higher elevations. These results, on the one hand, call for conservation efforts to lower elevations in mountains and, on the other hand, highlight the importance of population connection in maintaining population viability under impending global change.
基金financially supported by the National Natural Scientific Foundation of China(Grant No.32160254)Natural Scientific Foundation of China(Grant No.31760118)+1 种基金Yunnan Ten Thousand Talents Plan Young&Elite Talents Project(YNWR-QNRC-2019-047)Yunnan Provincial Middle-Young Academic and Technical Leader candidate(2019HB013).
文摘Physiological adaptation of tree shrews(Tupaia belangeri)to changing environmental temperature has been re-ported in detail.However,the T.belangeri origin(mainland or island),population history,and adaptation to histor-ical climate change remain largely unknown or controversial.Here,for thefirst time,we sequenced the simplified genome of 134 T.belangeri individuals from 12 populations in China and further resequenced one individual from each population.Using population genomic approaches,wefirst observed considerable genetic variation in T.be-langeri.Moreover,T.belangeri populations formed obvious genetic structure and reflected different demographic histories;they generally exhibited high genetic diversity,although the isolated populations had relatively low ge-netic diversity.The results presented in this study indicate that T.b.modesta and T.b.tonquinia were separated recently and with a similar population dynamics.Second,physical barriers rather than distance were the driving factors of divergence,and environmental heterogeneity may play an important role in genetic differentiation in T.belangeri.Moreover,our analyses highlight the role of historical global climates in the T.belangeri population dynamics and indicate that the decrease of the T.belangeri population size may be due to the low temperature.Finally,we identified the olfaction-associated adaptive genes between different altitude populations and found that olfactory-related genes of high-altitude populations were selectively eliminated.Our study provides demographic history knowledge of T.belangeri;their adaption history offers new insights into their evolution and adaptation,and provides valuable baseline information for conservation measures.
基金supported by the National Natural Science Foundation of China(32100342,U1902204,31771415,31801054)Bureau of Science and Technology of Yunnan Province(2015FA026)+1 种基金Youth Innovation Promotion AssociationWest Light Foundation of CAS(Y902401081)。
文摘The evolutionary and functional features of RNA editing are well studied in mammals,cephalopods,and insects,but not in birds.Here,we integrated transcriptomic and whole-genomic analyses to exhaustively characterize the expansive repertoire of adenosine-to-inosine(A-to-I)RNA editing sites(RESs)in the chicken.In addition,we investigated the evolutionary status of the chicken editome as a potential mechanism of domestication.We detected the lowest editing level in the liver of chickens,compared to muscles in humans,and found higher editing activity and specificity in the brain than in non-neural tissues,consistent with the brain’s functional complexity.To a certain extent,specific editing activity may account for the specific functions of tissues.Our results also revealed that sequences critical to RES secondary structures remained conserved within avian evolution.Furthermore,the RNA editome was shaped by purifying selection during chicken domestication and most RESs may have served as a selection pool for a few functional RESs involved in chicken domestication,including evolution of nervous and immune systems.Regulation of RNA editing in chickens by adenosine deaminase acting on RNA(ADAR)enzymes may be affected by non-ADAR factors whose expression levels changed widely after ADAR knockdown.Collectively,we provide comprehensive lists of candidate RESs and non-ADAR-editing regulators in the chicken,thus contributing to our current understanding of the functions and evolution of RNA editing in animals.
文摘Recombinant inbred lines(RILs) serve as powerful tools for genetic mapping.RILs are obtained by crossing two inbred lines followed by repeated selfing or sib-mating to create a set of new
基金supported by the Biological Breeding-Major Projects(2023ZD04076)the Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province(Grant No.U1812401)+1 种基金the National Natural Science Foundation of China(Grant No.31600032)the Start-Up Funding from the Chengdu Institute of Biology,Chinese Academy of Sciences.
文摘The fungal order Botryosphaeriales includes numerous ecologically and economically important plant-associated taxa,yet its genomic diversity and evolutionary mechanisms remain poorly understood.Here,we present high-quality de novo genome assemblies for three representative species—Botryosphaeria dothidea,Neofusicoccum parvum,and Phyllosticta capitalensis—and perform integrative analyses using comparative genomics,population genetics,and pan-genome frameworks.Pathogenic species(B.dothidea and N.parvum)exhibit significant expansions in gene families related to membrane transport and metabolism,suggesting enhanced adaptability and virulence potential.Selective sweep analyses highlight population-level divergence in metabolic and stress-response pathways,reflecting natural selection in host and environmental adaptation.Cross-species pan-genome comparisons of six Phyllosticta species reveal a conserved core genome,dynamic gene family turnover,and extensive horizontal gene transfer from bacterial,and archaeal sources—potentially driving ecological diversification.Furthermore,effector proteins display striking domain variation across genera,particularly in regions associated with host cell wall targeting,indicating convergent strategies for host adaptation.Together,these findings provide comprehensive insights into the genomic evolution,adaptation,and virulence mechanisms of Botryosphaeriales fungi,laying a foundation for future studies on plant–fungal interactions.
基金supported in part by the National Natural Science Foundation of China(31672272,31722051)Fundamental Research Funds for the Central Universities(2042021kf0217)+3 种基金Natural Science Foundation of the Hubei Province(2019CFA075)Plateau Ecology Youth Innovative Fund of Wuhan University(to H.Z.)X.L.was supported by the National Natural Science Foundation of China(31830085)Second Tibetan Plateau Scientific Expedition and Research program(2019QZKK0501).
文摘Cooperative breeding is a sophisticated altruistic social behavior that helps social animals to adapt to harsh environments.The Tibetan ground tit,Pseudopodoces humilis,is a high-altitude bird endemic to the Tibetan plateau.Recently,it has become an exciting system for studying the evolution of facultative cooperative breeding.To test for molecular adaptations associated with cooperative breeding,we resequenced the whole genome of ground tits from 6 wild populations that display remarkable variation in the frequency of cooperative breeding.Population structure analyses showed that the 6 populations were divided into 4 lineages,which is congruent with the major geographical distribution of the sampling sites.Using genome-wide selective sweep analysis,we identified putative positively selected genes(PSGs)in groups of tits that displayed high and low cooperative breeding rates.The total number of PSGs varied from 146 to 722 in high cooperative breeding rate populations,and from 272 to 752 in low cooperative breeding rate populations.Functional enrichment analysis of these PSGs identified several significantly enriched ontologies related to oxytocin signaling,estrogen signaling,and insulin secretion.PSGs involved in these functional ontologies suggest that molecular adaptations in hormonal regulation may have played important roles in shaping the evolution of cooperative breeding in the ground tit.Taken together,our study provides candidate genes and functional ontologies involved in molecular adaptations associated with cooperative breeding in Tibetan ground tits,and calls for a better understanding of the genetic roles in the evolution of cooperative breeding.
基金supported by the Second Tibetan Plateau Scientific Expedition and Research program (No. 2019QZKK0502)Strategic Priority Research Program of Chinese Academy of Sciences (No. XDB31010300)+1 种基金Fundamental Research Funds for the Central UniversitiesInternational Collaboration 111 Program (BP0719040)。
文摘The identification and understanding of cryptic intraspecific evolutionary units(lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species.However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a “living fossil” dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range.Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.
基金Support for this work was provided by the Inner Mongolia Autonomous Region(2010ZD11)the National Natural Science Foundation of China(30960246,31260538)the Key Projects in the National Science&Technology Pillar Program(30960242011BAD28B05)
文摘Identifying targets of positive selection in farm animals has, until recently, been frustratingly slow, relying on the analysis of individual candidate genes. Genomics, however, has provided the necessary resources to systematically interrogate the entire genome for signatures of selection. This review described important recent results derived from the application of genome-wide scan to the study of genetic changes in farm animals. These included findings of regions of the genome that showed breed differentiation, evidence of selective sweeps within individual genomes and signatures of demographic events. Particular attention is focused on the study of the implications for domestication. To date, sixteen genome-wide scans for recent or ongoing positive selection have been performed in farm animals. A key challenge is to begin synthesizing these newly constructed maps of selection into a coherent narrative of animal breed evolutionary history and derive a deeper mechanistic understanding of how animal populations improve or evolve. The major insights from the surveyed studies are highlighted and directions for future study are suggested.
基金supported by the National Natural Science Foundation of China(32470527,32160130)Xingdian Talent Fund Project of Yunnan Province,Basic Research of Yunnan Province(202301AT070185)+2 种基金Joint Funding of the Yunnan Provincial Science and Technology Department and Yunnan University(202401BF070001-018)Wildlife Protection Administration of Hainan Province,Scientific Research and Innovation Project of Postgraduate Students in the Academic Degree of Yunnan University(KC-23234049)Central Government Guidance Fund for the Development of Local Science and Technology(202407AB110004)。
文摘Island species/populations are characterized by evolutionary uniqueness and a high degree of endemism and extinction.The conservation and restoration of island species/populations have become the most challenging and urgent issues in biodiversity conservation.Chinese pangolin in Taiwan island(Manis pentadactyla pentadactyla)is a well-known,critically endangered,and island-endemic Chinese pangolin subspecies,which has been the focus of conservation concern.Here,we first generated large-scale population genomics data for the Chinese pangolin in Taiwan to address its population structure,demographic history,the genomic consequences of population declines,and survival potential.We revealed that the Chinese pangolin in Taiwan originated in southeast China and was differentiated into Northern and nonNorthern populations due to the isolation of the Xueshan and Central Mountain Ranges,proposing to treat them as separate conservation units.The southeast of Taiwan island acted as a refuge for this Chinese pangolin subspecies during the Last Glacial Maximum.The Northern population had experienced a more severe bottleneck and isolation than the non-Northern population,which corresponded to the estimated current lower genetic diversity,higher inbreeding,and genetic load of the Northern population.The modeling results revealed that the Northern population is more seriously affected by climate change than the non-Northern population,which highlights that climate change poses a substantial threat to island biodiversity.The simulation results indicate that the Northern population needs a higher population growth rate to achieve evolutionary potential equal to the non-Northern population over the next 100 years,deserving conservation prioritization.This study enhances the understanding of genetic background,conservation status,and future prospects for Chinese pangolin in Taiwan,as well as the genetic consequences of a small and isolated island population.
