Global climate change has increased concerns regarding biodiversity loss.However,many key conservation issues still required further research,including demographic history,deleterious mutation load,adaptive evolution,...Global climate change has increased concerns regarding biodiversity loss.However,many key conservation issues still required further research,including demographic history,deleterious mutation load,adaptive evolution,and putative introgression.Here we generated the first chromosome-level genome of the endangered Chinese hazelnut,Corylus chinensis,and compared the genomic signatures with its sympatric widespread C.kwechowensis-C yunnanensis complex.We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation.Population genomics revealed that both C.chinensis and the C.kwechowensis-C.yunnanensis complex had diverged into two genetic lineages,forming a consistent pattern of southwestern-northern differentiation.Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene,whereas the widespread northern lineages have remained stable(C.chinensis) or have even recovered from population bottlenecks(C.kwechowensis-C.yunnanensis complex) during the Quaternary.Compared with C.kwechowensis-C. yunnanensis complex,C.chinensis showed significantly lower genomic diversity and higher inbreeding level.However,C.chinensis carried significantly fewer deleterious mutations than C.kwechowensis-C. yunnanensis complex,as more effective purging selection reduced the accumulation of homozygous variants.We also detected signals of positive selection and adaptive introgression in different lineages,which facilitated the accumulation of favorable variants and formation of local adaptation.Hence,both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C.chinensis.Overall,our study provides critical insights into lineage differentiation,local adaptation,and the potential for future recovery of endangered trees.展开更多
The Chinese pangolin(Manis pentadactyla,MP)has been extensively exploited and is now on the brink of extinction,but its population structure,evolutionary history,and adaptive potential are unclear.Here,we analyzed 94 ...The Chinese pangolin(Manis pentadactyla,MP)has been extensively exploited and is now on the brink of extinction,but its population structure,evolutionary history,and adaptive potential are unclear.Here,we analyzed 94 genomes from three subspecies of the Chinese pangolin and identified three distinct genetic clusters(MPA,MPB,and MPC),with MPB further divided into MPB1 and MPB2 subpopulations.The divergence of these populations was driven by past climate change.For MPB2 and MPC,recent human activities have caused dramatic population decline and small population size as well as increased inbreeding,but not decrease in genomic variation and increase in genetic load probably due to strong gene flow;therefore,it is crucial to strengthen in situ habitat management for these two populations.By contrast,although human activities have a milder impact on MPA,it is at high risk of extinction due to long-term contraction and isolation,and genetic rescue is urgently needed.MPB1 exhibited a relatively healthy population status and can potentially serve as a source population.Overall,our findings provide novel insights into the conservation of the Chinese pangolin and biogeography of the mammals of eastern Asia.展开更多
Bumblebees are a genus of pollinators(Bombus)that play important roles in natural ecosystem and agricultural production.Several bumblebee species have been recorded as under population decline,and the proportion of sp...Bumblebees are a genus of pollinators(Bombus)that play important roles in natural ecosystem and agricultural production.Several bumblebee species have been recorded as under population decline,and the proportion of species experiencing popula-tion decline within subgenus Thoracobombus is higher than average.Bombus opulentus is 1 species in Thoracobombus,but little is known about its recent population dynamics.Here,we employed conservation genomics methods to investigate the population dynam-ics of B.opulentus during the recent past and identify the likely environmental factors that may cause population decline.Firstly,we placed the scaffold-level of B.opulentus ref-erence genome sequence onto chromosome-level using Hi-C technique.Then,based on this reference genome and whole-genome resequencing data for 51 B.opulentus samples,we reconstructed the population structure and effective population size(Ne)trajectories of B.opulentus and identified genes that were under positive selection.Our results revealed that the collected B.opulentus samples could be divided into 2 populations,and 1 of them experienced a recent population decline;the declining population also exhibited lower ge-netic diversity and higher inbreeding levels.Genes related to high-temperature tolerance,immune response,and detoxication showed signals of positive selection in the declining population,suggesting that climate warming and pathogen/pesticide exposures may con-tribute to the decline of this B.opulentus population.Taken together,our study provided insights into the demography of B.opulentus populations and highlighted that popula-tions of the same bumblebee species could have contrasting Ne trajectories and population decline could be caused by a combination of various stressors.展开更多
Endangered species generally have small populations with low genetic diversity and a high genetic load.Thuja sutchuenensis is an endangered conifer endemic to southwestern China.It was once considered extinct in the w...Endangered species generally have small populations with low genetic diversity and a high genetic load.Thuja sutchuenensis is an endangered conifer endemic to southwestern China.It was once considered extinct in the wild,but in 1999 was rediscovered.However,little is known about its genetic load.We collected 67 individuals from five wild,isolated T.sutchuenensis populations,and used 636,151 SNPs to analyze the level of genetic diversity and genetic load in T.sutchuenensis to delineate the conservation units of T.sutchuenensis,based on whole transcriptome sequencing data,as well as target capture sequencing data.We found that populations of T.sutchuenensis could be divided into three groups.These groups had low levels genetic diversity and were moderately genetically differentiated.Our findings also indicate that T.sutchuenensis suffered two severe bottlenecks around the Last Glaciation Period and Last Glacial Maximum.Among Thuja species,T.sutchuenensis presented the lowest genetic load and hence might have purged deleterious mutations efficiently through purifying selection.However,distribution of fitness effects analysis indicated a high extinction risk for T.sutchuenensis.Multiple lines of evidence identified three management units for T.sutchuenensis.Although T.sutchuenensis possesses a low genetic load,low genetic diversity,suboptimal fitness,and anthropogenic pressures all present an extinction risk for this rare conifer.This might also hold true for many endangered plant species in the mountains all over the world.展开更多
Understanding genome-wide diversity,inbreeding,and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience.Howe...Understanding genome-wide diversity,inbreeding,and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience.However,these effects are rarely studied in limestone karst plants.Here,we re-sequenced the nuclear genomes of 62 individuals of the Begonia masoniana complex(B.liuyanii,B.longgangensis,B.masoniana and B.variegata)and investigated genomic divergence and genetic load for these four species.Our analyses revealed four distinct clusters corresponding to each species within the complex.Notably,there was only limited admixture between B.liuyanii and B.longgangensis occurring in overlapping geographic regions.All species experienced historical bottlenecks during the Pleistocene,which were likely caused by glacial climate fluctuations.We detected an asymmetric historical gene flow between group pairs within this timeframe,highlighting a distinctive pattern of interspecific divergence attributable to karst geographic isolation.We found that isolated populations of B.masoniana have limited gene flow,the smallest recent population size,the highest inbreeding coefficients,and the greatest accumulation of recessive deleterious mutations.These findings underscore the urgency to prioritize conservation efforts for these isolated population.This study is among the first to disentangle the genetic differentiation and specific demographic history of karst Begonia plants at the whole-genome level,shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of inbreeding.Moreover,our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.展开更多
Pangolins(Pholidota,Manidae)are classified as an evolutionarily distinct and globally endangered mammal due to their unique morphology(nail-like scales and a myrmecophagous diet)and being the victim of heavy poaching ...Pangolins(Pholidota,Manidae)are classified as an evolutionarily distinct and globally endangered mammal due to their unique morphology(nail-like scales and a myrmecophagous diet)and being the victim of heavy poaching and worldwide trafficking.As such,pangolins serve as a textbook example for studying the special phenotypic evolutionary adaptations and conservation genetics of an endangered species.Recent years have demonstrated significant advancements in the fields of molecular genetics and genomics,which have translated to a series of important research achievements and breakthroughs concerning the evolution and conservation genetics of pangolins.This review comprehensively presents the hitherto advances in phylogeny,adaptive evolution,conservation genetics,and conservation genomics that are related to pangolins,which will provide an ample understanding of their diversity,molecular adaptation mechanisms,and evolutionary potentials.In addition,we highlight the priority of investigating species/population diversity among pangolins and suggest several avenues of research that are highly relevant for future pangolin conservation.展开更多
Conservation genetics and genomics are two independent disciplines that focus on using new techniques in genetics and genomics to solve problems in conservation biology. During the past two decades,conservation geneti...Conservation genetics and genomics are two independent disciplines that focus on using new techniques in genetics and genomics to solve problems in conservation biology. During the past two decades,conservation genetics and genomics have experienced rapid progress. Here, we summarize the research advances in the conservation genetics and genomics of threatened vertebrates(e.g., carnivorans, primates, ungulates, cetaceans, avians, amphibians and reptiles) in China. First, we introduce the concepts of conservation genetics and genomics and their development. Second, we review the recent advances in conservation genetics research, including noninvasive genetics and landscape genetics. Third, we summarize the progress in conservation genomics research, which mainly focuses on resolving genetic problems relevant to conservation such as genetic diversity, genetic structure, demographic history, and genomic evolution and adaptation. Finally, we discuss the future directions of conservation genetics and genomics.展开更多
Living fossils are evidence of long-term sustained ecological success.However,whether living fossils have little molecular changes remains poorly known,particularly in plants.Here,we have introduced a novel method tha...Living fossils are evidence of long-term sustained ecological success.However,whether living fossils have little molecular changes remains poorly known,particularly in plants.Here,we have introduced a novel method that integrates phylogenomic,comparative genomic,and ecological niche modeling analyses to investigate the rate of molecular evolution of Eupteleaceae,a Cretaceous relict angiosperm family endemic to East Asia.We assembled a high-quality chromosome-level nuclear genome,and the chloroplast and mitochondrial genomes of a member of Eupteleaceae(Euptelea pleiosperma).Our results show that Eupteleaceae is most basal in Ranunculales,the earliest-diverging order in eudicots,and shares an ancient whole-genome duplication event with the other Ranunculales.We document that Eupteleaceae has the slowest rate of molecular changes in the observed angiosperms.The unusually low rate of molecular evolution of Eupteleaceae across all three independent inherited genomes and genes within each of the three genomes is in association with its conserved genome architecture,ancestral woody habit,and conserved niche requirements.Our findings reveal the evolution and adaptation of living fossil plants through large-scale environmental change and also provide new insights into early eudicot diversification.展开更多
基金supported by the National Natural Science Foundation of China(Grant No.32101541)the National Key R&D Program of China(Grant No.2022YFD2200400).
文摘Global climate change has increased concerns regarding biodiversity loss.However,many key conservation issues still required further research,including demographic history,deleterious mutation load,adaptive evolution,and putative introgression.Here we generated the first chromosome-level genome of the endangered Chinese hazelnut,Corylus chinensis,and compared the genomic signatures with its sympatric widespread C.kwechowensis-C yunnanensis complex.We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation.Population genomics revealed that both C.chinensis and the C.kwechowensis-C.yunnanensis complex had diverged into two genetic lineages,forming a consistent pattern of southwestern-northern differentiation.Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene,whereas the widespread northern lineages have remained stable(C.chinensis) or have even recovered from population bottlenecks(C.kwechowensis-C.yunnanensis complex) during the Quaternary.Compared with C.kwechowensis-C. yunnanensis complex,C.chinensis showed significantly lower genomic diversity and higher inbreeding level.However,C.chinensis carried significantly fewer deleterious mutations than C.kwechowensis-C. yunnanensis complex,as more effective purging selection reduced the accumulation of homozygous variants.We also detected signals of positive selection and adaptive introgression in different lineages,which facilitated the accumulation of favorable variants and formation of local adaptation.Hence,both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C.chinensis.Overall,our study provides critical insights into lineage differentiation,local adaptation,and the potential for future recovery of endangered trees.
基金supported by the Major Program of the Natural Science Foundation of Jiangxi Province of China(20233ACB209001)Guangdong Basic and Applied Basic Research Foundation(2022A1515111016)+1 种基金Science and Technology Department of Guangdong Province(2021QN02H103)Natural Resources Affairs Management-Ecological Forestry Construction Special Project of Forestry Administration of Guangdong Province(SLYJ2023B4002,SLYJ2023B4003,SLYJ2023B4005)。
文摘The Chinese pangolin(Manis pentadactyla,MP)has been extensively exploited and is now on the brink of extinction,but its population structure,evolutionary history,and adaptive potential are unclear.Here,we analyzed 94 genomes from three subspecies of the Chinese pangolin and identified three distinct genetic clusters(MPA,MPB,and MPC),with MPB further divided into MPB1 and MPB2 subpopulations.The divergence of these populations was driven by past climate change.For MPB2 and MPC,recent human activities have caused dramatic population decline and small population size as well as increased inbreeding,but not decrease in genomic variation and increase in genetic load probably due to strong gene flow;therefore,it is crucial to strengthen in situ habitat management for these two populations.By contrast,although human activities have a milder impact on MPA,it is at high risk of extinction due to long-term contraction and isolation,and genetic rescue is urgently needed.MPB1 exhibited a relatively healthy population status and can potentially serve as a source population.Overall,our findings provide novel insights into the conservation of the Chinese pangolin and biogeography of the mammals of eastern Asia.
基金This work was supported by the National Natural Science Foundation of China(Grant numbers 32270445 and 31971397)the Support Project of High-level Teachers in Beijing Municipal Universities in the Period of 14th Fiveyear Plan(Grant number BPHR20220114)the Central Public-interest Scientific Institution Basal Research Fund(Grant numbers Y2019XK13 and Y2021XK16).
文摘Bumblebees are a genus of pollinators(Bombus)that play important roles in natural ecosystem and agricultural production.Several bumblebee species have been recorded as under population decline,and the proportion of species experiencing popula-tion decline within subgenus Thoracobombus is higher than average.Bombus opulentus is 1 species in Thoracobombus,but little is known about its recent population dynamics.Here,we employed conservation genomics methods to investigate the population dynam-ics of B.opulentus during the recent past and identify the likely environmental factors that may cause population decline.Firstly,we placed the scaffold-level of B.opulentus ref-erence genome sequence onto chromosome-level using Hi-C technique.Then,based on this reference genome and whole-genome resequencing data for 51 B.opulentus samples,we reconstructed the population structure and effective population size(Ne)trajectories of B.opulentus and identified genes that were under positive selection.Our results revealed that the collected B.opulentus samples could be divided into 2 populations,and 1 of them experienced a recent population decline;the declining population also exhibited lower ge-netic diversity and higher inbreeding levels.Genes related to high-temperature tolerance,immune response,and detoxication showed signals of positive selection in the declining population,suggesting that climate warming and pathogen/pesticide exposures may con-tribute to the decline of this B.opulentus population.Taken together,our study provided insights into the demography of B.opulentus populations and highlighted that popula-tions of the same bumblebee species could have contrasting Ne trajectories and population decline could be caused by a combination of various stressors.
基金This study was financially supported by National Natural Science Foundation of China(grant No.U20A2080,31622015)the Institutional Research Fund from Sichuan University(2021SCUNL102)Fundamental Research Fund for the Central Universities of China(SCU 2021D006,SCU 2022D003).
文摘Endangered species generally have small populations with low genetic diversity and a high genetic load.Thuja sutchuenensis is an endangered conifer endemic to southwestern China.It was once considered extinct in the wild,but in 1999 was rediscovered.However,little is known about its genetic load.We collected 67 individuals from five wild,isolated T.sutchuenensis populations,and used 636,151 SNPs to analyze the level of genetic diversity and genetic load in T.sutchuenensis to delineate the conservation units of T.sutchuenensis,based on whole transcriptome sequencing data,as well as target capture sequencing data.We found that populations of T.sutchuenensis could be divided into three groups.These groups had low levels genetic diversity and were moderately genetically differentiated.Our findings also indicate that T.sutchuenensis suffered two severe bottlenecks around the Last Glaciation Period and Last Glacial Maximum.Among Thuja species,T.sutchuenensis presented the lowest genetic load and hence might have purged deleterious mutations efficiently through purifying selection.However,distribution of fitness effects analysis indicated a high extinction risk for T.sutchuenensis.Multiple lines of evidence identified three management units for T.sutchuenensis.Although T.sutchuenensis possesses a low genetic load,low genetic diversity,suboptimal fitness,and anthropogenic pressures all present an extinction risk for this rare conifer.This might also hold true for many endangered plant species in the mountains all over the world.
基金supported by Key-Area Research and Development Program of Guangdong Province(Grant No.2022B1111230001)National Natural Science Foundation of China(31860048).
文摘Understanding genome-wide diversity,inbreeding,and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience.However,these effects are rarely studied in limestone karst plants.Here,we re-sequenced the nuclear genomes of 62 individuals of the Begonia masoniana complex(B.liuyanii,B.longgangensis,B.masoniana and B.variegata)and investigated genomic divergence and genetic load for these four species.Our analyses revealed four distinct clusters corresponding to each species within the complex.Notably,there was only limited admixture between B.liuyanii and B.longgangensis occurring in overlapping geographic regions.All species experienced historical bottlenecks during the Pleistocene,which were likely caused by glacial climate fluctuations.We detected an asymmetric historical gene flow between group pairs within this timeframe,highlighting a distinctive pattern of interspecific divergence attributable to karst geographic isolation.We found that isolated populations of B.masoniana have limited gene flow,the smallest recent population size,the highest inbreeding coefficients,and the greatest accumulation of recessive deleterious mutations.These findings underscore the urgency to prioritize conservation efforts for these isolated population.This study is among the first to disentangle the genetic differentiation and specific demographic history of karst Begonia plants at the whole-genome level,shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of inbreeding.Moreover,our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.
文摘Pangolins(Pholidota,Manidae)are classified as an evolutionarily distinct and globally endangered mammal due to their unique morphology(nail-like scales and a myrmecophagous diet)and being the victim of heavy poaching and worldwide trafficking.As such,pangolins serve as a textbook example for studying the special phenotypic evolutionary adaptations and conservation genetics of an endangered species.Recent years have demonstrated significant advancements in the fields of molecular genetics and genomics,which have translated to a series of important research achievements and breakthroughs concerning the evolution and conservation genetics of pangolins.This review comprehensively presents the hitherto advances in phylogeny,adaptive evolution,conservation genetics,and conservation genomics that are related to pangolins,which will provide an ample understanding of their diversity,molecular adaptation mechanisms,and evolutionary potentials.In addition,we highlight the priority of investigating species/population diversity among pangolins and suggest several avenues of research that are highly relevant for future pangolin conservation.
基金funded by Chinese Academy of Sciences (XDB31000000 and QYZDY-SSW-SMC019)Ministry of Science and Technology (2016YFC0503200)the National Natural Science Foundation of China (Nos.91531302 and 31670386)
文摘Conservation genetics and genomics are two independent disciplines that focus on using new techniques in genetics and genomics to solve problems in conservation biology. During the past two decades,conservation genetics and genomics have experienced rapid progress. Here, we summarize the research advances in the conservation genetics and genomics of threatened vertebrates(e.g., carnivorans, primates, ungulates, cetaceans, avians, amphibians and reptiles) in China. First, we introduce the concepts of conservation genetics and genomics and their development. Second, we review the recent advances in conservation genetics research, including noninvasive genetics and landscape genetics. Third, we summarize the progress in conservation genomics research, which mainly focuses on resolving genetic problems relevant to conservation such as genetic diversity, genetic structure, demographic history, and genomic evolution and adaptation. Finally, we discuss the future directions of conservation genetics and genomics.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31030000)the National Natural Science Foundation of China(32170210,32170238,31770231,31770233)+2 种基金the Science,Technology,and Innovation Commission of Shenzhen Municipality of China(RCYX20200714114538196)K.C.Wong Education Foundation(GJTD-2020-05)Innovation Program of Chinese Academy of Agricultural Sciences。
文摘Living fossils are evidence of long-term sustained ecological success.However,whether living fossils have little molecular changes remains poorly known,particularly in plants.Here,we have introduced a novel method that integrates phylogenomic,comparative genomic,and ecological niche modeling analyses to investigate the rate of molecular evolution of Eupteleaceae,a Cretaceous relict angiosperm family endemic to East Asia.We assembled a high-quality chromosome-level nuclear genome,and the chloroplast and mitochondrial genomes of a member of Eupteleaceae(Euptelea pleiosperma).Our results show that Eupteleaceae is most basal in Ranunculales,the earliest-diverging order in eudicots,and shares an ancient whole-genome duplication event with the other Ranunculales.We document that Eupteleaceae has the slowest rate of molecular changes in the observed angiosperms.The unusually low rate of molecular evolution of Eupteleaceae across all three independent inherited genomes and genes within each of the three genomes is in association with its conserved genome architecture,ancestral woody habit,and conserved niche requirements.Our findings reveal the evolution and adaptation of living fossil plants through large-scale environmental change and also provide new insights into early eudicot diversification.
