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
Inbreeding increases genome homozygosity within populations,which can exacerbate inbreeding depression by exposing homozygous deleterious alleles that are responsible for declines in fitness traits.In small population...Inbreeding increases genome homozygosity within populations,which can exacerbate inbreeding depression by exposing homozygous deleterious alleles that are responsible for declines in fitness traits.In small populations,genetic purging that occurs under the pressure of natural selection acts as an opposing force,contributing to a reduction of deleterious alleles.Both inbreeding and genetic purging are paramount in the field of conservation genomics.The Amur tiger(Panthera tigris altaica)lives in small populations in the forests of Northeast Asia and is among the most endangered animals on the planet.Using genome-wide assessment and comparison,we reveal substantially higher and more extensive inbreeding in wild Amur tigers(F_(ROH)=0.50)than in captive individuals(F_(ROH)=0.24).However,a relatively reduced number of lossof-function mutations in wild Amur tigers is observed compared to captive individuals,indicating genetic purging of inbreeding load with relatively large-effect alleles.The higher ratio of homozygous mutation load and number of fixed damaging alleles in the wild population indicates a less-efficient genetic purging,with purifying selection also contributing to this process.These findings provide valuable insights for the future conservation of Amur tigers.展开更多
Preserving genetic diversity is crucial for the long-term survival of wild plant species,yet many remain at risk of genetic erosion due to small population sizes and habitat fragmentation.Here,we present a comparative...Preserving genetic diversity is crucial for the long-term survival of wild plant species,yet many remain at risk of genetic erosion due to small population sizes and habitat fragmentation.Here,we present a comparative genomic study of the critically endangered Oreocharis esquirolii(Gesneriaceae)and its widespread congener O.maximowiczii.We assembled and annotated chromosome-level reference genomes for both species and generated whole-genome resequencing data from 28 O.esquirolii and 79 O.maximowiczii individuals.Our analyses reveal substantially lower genetic diversity and higher inbreeding in O.esquirolii,despite its overall reduced mutational burden.Notably,O.esquirolii exhibits an elevated proportion of strongly deleterious mutations relative to O.maximowiczii,suggesting that limited opportunities for purging have allowed these variants to accumulate.These contrasting genomic profileslikely reflectdivergent demographic histories,with O.esquirolii having experienced severe bottlenecks and protracted population decline.Collectively,our findingshighlight the critically endangered status of O.esquirolii,characterized by diminished genetic diversity,pronounced inbreeding,and reduced ability to eliminate deleterious alleles.This study provides valuable genomic resources for the Gesneriaceae family and underscores the urgent need for targeted conservation measures,including habitat protection and ex situ preservation efforts,to mitigate the extinction risk facing O.esquirolii and potentially other threatened congeners.展开更多
Mitochondrial DNA（mt DNA） variation has been implicated in many common complex diseases, but inconsistent and contradicting results are common. Here we introduce a novel mutational load hypothesis, which also consid...Mitochondrial DNA（mt DNA） variation has been implicated in many common complex diseases, but inconsistent and contradicting results are common. Here we introduce a novel mutational load hypothesis, which also considers the collective effect of mainly rare variants, utilising the Mut Pred Program.We apply this new methodology to investigate the possible role of mt DNA in two cardiovascular disease（CVD） phenotypes（hypertension and hyperglycaemia）, within a two-population cohort（n = 363; mean age 45 ± 9 yrs）. Very few studies have looked at African mt DNA variation in the context of complex disease, and none using complete sequence data in a well-phenotyped cohort. As such, our study will also extend our knowledge of African mt DNA variation, with complete sequences of Southern Africans being especially under-represented. The cohort showed prevalence rates for hypertension（58.6%） and prediabetes（44.8%）. We could not identify a statistically significant role for mt DNA variation in association with hypertension or hyperglycaemia in our cohort. However, we are of the opinion that the method described will find wide application in the field, being especially useful for cohorts from multiple locations or with a variety of mt DNA lineages, where the traditional haplogroup association method has been particularly likely to generate spurious results in the context of association with common complex disease.展开更多
Evaluating the genetic status of threatened species is an essential task in conservation genetics.However,the genetic status of threatened species has been mostly evaluated through techniques that fail to estimate gen...Evaluating the genetic status of threatened species is an essential task in conservation genetics.However,the genetic status of threatened species has been mostly evaluated through techniques that fail to estimate genetic diversity at the whole genomic level.Next generation sequencing can meet this demand,but high quality samples such as blood or muscle tissues are required.However,it is difficult to collect such samples from threatened species because sampling work may impact their health.Therefore,it is essential to design a workflow to evaluate the whole genomic status of threatened species using non-destructive sampling.Even though non-destructive sampling has been used in traditional barcoding technique,the barcoding technique cannot evaluate the whole genomic status.Brown Eared Pheasant(Crossoptilon mantchuricum)is an endangered species,with captive populations maintained in Taiyuan Zoo,China,and Europe.However,the genetic diversity,inbreeding pattern,and mutation load of these two populations are unclear.To uncover the genetic status of these two captive populations,we applied 2b-RAD technology to evaluate the genomic status of these populations using feathers as samples.The feathers could be collected by non-destructive sampling.The results indicate that the Taiyuan Zoo population has a lower genetic diversity and higher inbreeding coefficient than the European population.The Taiyuan Zoo population has lethal mutations when homozygous.The current project uses a non-destructive sampling technique to evaluate the whole genomic status of the two captive populations,providing a paradigm for conservation genetics,which will facilitate the development of conservation biology.展开更多
According to current theoretical predictions, any deleterious mutations that reduce nonsexual fitness may have a negative influence on mating success. This means that sexual selection may remove deleterious mutations ...According to current theoretical predictions, any deleterious mutations that reduce nonsexual fitness may have a negative influence on mating success. This means that sexual selection may remove deleterious mutations from the populations. Males of good genetic quality should be more successful in mating, compared to the males of lower genetic quality. As mating success is a condition dependent trait, large fractions of the genome may be a target of sexual selection and many behavioral traits are likely to be condition dependent. We manipulated the genetic quality of Drosophila subobscura males by inducing mutations with ionizing radiation and observed the effects of the obtained heterozygous mutations on male mating behavior： courtship occurrence, courtship latency, mating occurrence, latency to mating and duration of mating. We found possible effects of mutations. Females mated more frequently with male progeny of nonirradiated males and that these males courted females faster compared to the male progeny of irradiated males. Our findings indicate a possible important role of sexual selection in purging deleterious mutations.展开更多
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.
基金supported by the Fundamental Research Funds for the Central Universities of China(2572022DQ03)the National Natural Science Foundation of China(32170517)+2 种基金the Guangdong Provincial Key Laboratory of Genome Read and Write(2017B030301011)the Start-up Scientific Foundation of Northeast Forestry University(60201524043)supported by China National GeneBank(CNGB).
文摘Inbreeding increases genome homozygosity within populations,which can exacerbate inbreeding depression by exposing homozygous deleterious alleles that are responsible for declines in fitness traits.In small populations,genetic purging that occurs under the pressure of natural selection acts as an opposing force,contributing to a reduction of deleterious alleles.Both inbreeding and genetic purging are paramount in the field of conservation genomics.The Amur tiger(Panthera tigris altaica)lives in small populations in the forests of Northeast Asia and is among the most endangered animals on the planet.Using genome-wide assessment and comparison,we reveal substantially higher and more extensive inbreeding in wild Amur tigers(F_(ROH)=0.50)than in captive individuals(F_(ROH)=0.24).However,a relatively reduced number of lossof-function mutations in wild Amur tigers is observed compared to captive individuals,indicating genetic purging of inbreeding load with relatively large-effect alleles.The higher ratio of homozygous mutation load and number of fixed damaging alleles in the wild population indicates a less-efficient genetic purging,with purifying selection also contributing to this process.These findings provide valuable insights for the future conservation of Amur tigers.
基金supported by National Key R&D Program of China(2024YFF1307400)Guangdong S&T Program(2022B1111230001).
文摘Preserving genetic diversity is crucial for the long-term survival of wild plant species,yet many remain at risk of genetic erosion due to small population sizes and habitat fragmentation.Here,we present a comparative genomic study of the critically endangered Oreocharis esquirolii(Gesneriaceae)and its widespread congener O.maximowiczii.We assembled and annotated chromosome-level reference genomes for both species and generated whole-genome resequencing data from 28 O.esquirolii and 79 O.maximowiczii individuals.Our analyses reveal substantially lower genetic diversity and higher inbreeding in O.esquirolii,despite its overall reduced mutational burden.Notably,O.esquirolii exhibits an elevated proportion of strongly deleterious mutations relative to O.maximowiczii,suggesting that limited opportunities for purging have allowed these variants to accumulate.These contrasting genomic profileslikely reflectdivergent demographic histories,with O.esquirolii having experienced severe bottlenecks and protracted population decline.Collectively,our findingshighlight the critically endangered status of O.esquirolii,characterized by diminished genetic diversity,pronounced inbreeding,and reduced ability to eliminate deleterious alleles.This study provides valuable genomic resources for the Gesneriaceae family and underscores the urgent need for targeted conservation measures,including habitat protection and ex situ preservation efforts,to mitigate the extinction risk facing O.esquirolii and potentially other threatened congeners.
基金the Faculty of Natural Sciences of the NorthWest University for contributing to funding and Thermo Fisher South Africa for providing additional technical resources to this studypartially funded by the South African National Research Foundation+4 种基金Medical Research CouncilROCHE DiagnosticsNorth-West University,South Africaas well as the Metabolic Syndrome Institute,Francefunding support from the Royal Society and the National Research Foundation of South Africa, for the academic meeting at which the project was mapped out
文摘Mitochondrial DNA（mt DNA） variation has been implicated in many common complex diseases, but inconsistent and contradicting results are common. Here we introduce a novel mutational load hypothesis, which also considers the collective effect of mainly rare variants, utilising the Mut Pred Program.We apply this new methodology to investigate the possible role of mt DNA in two cardiovascular disease（CVD） phenotypes（hypertension and hyperglycaemia）, within a two-population cohort（n = 363; mean age 45 ± 9 yrs）. Very few studies have looked at African mt DNA variation in the context of complex disease, and none using complete sequence data in a well-phenotyped cohort. As such, our study will also extend our knowledge of African mt DNA variation, with complete sequences of Southern Africans being especially under-represented. The cohort showed prevalence rates for hypertension（58.6%） and prediabetes（44.8%）. We could not identify a statistically significant role for mt DNA variation in association with hypertension or hyperglycaemia in our cohort. However, we are of the opinion that the method described will find wide application in the field, being especially useful for cohorts from multiple locations or with a variety of mt DNA lineages, where the traditional haplogroup association method has been particularly likely to generate spurious results in the context of association with common complex disease.
基金funded by the National Natural Science Foundation of China(Grant No.31872244 to Z.Z.)Priority Academic Program Development of Jiangsu Higher Education Institutions,Beijing Zoo Management Office(No.zx2019016 to J.Z.)the Biodiversity Survey,Monitoring and Assessment Project(2019-2023)of the Ministry of Ecology and Environment,China(No.2019HB2096001006 to Z.Z.)。
文摘Evaluating the genetic status of threatened species is an essential task in conservation genetics.However,the genetic status of threatened species has been mostly evaluated through techniques that fail to estimate genetic diversity at the whole genomic level.Next generation sequencing can meet this demand,but high quality samples such as blood or muscle tissues are required.However,it is difficult to collect such samples from threatened species because sampling work may impact their health.Therefore,it is essential to design a workflow to evaluate the whole genomic status of threatened species using non-destructive sampling.Even though non-destructive sampling has been used in traditional barcoding technique,the barcoding technique cannot evaluate the whole genomic status.Brown Eared Pheasant(Crossoptilon mantchuricum)is an endangered species,with captive populations maintained in Taiyuan Zoo,China,and Europe.However,the genetic diversity,inbreeding pattern,and mutation load of these two populations are unclear.To uncover the genetic status of these two captive populations,we applied 2b-RAD technology to evaluate the genomic status of these populations using feathers as samples.The feathers could be collected by non-destructive sampling.The results indicate that the Taiyuan Zoo population has a lower genetic diversity and higher inbreeding coefficient than the European population.The Taiyuan Zoo population has lethal mutations when homozygous.The current project uses a non-destructive sampling technique to evaluate the whole genomic status of the two captive populations,providing a paradigm for conservation genetics,which will facilitate the development of conservation biology.
文摘According to current theoretical predictions, any deleterious mutations that reduce nonsexual fitness may have a negative influence on mating success. This means that sexual selection may remove deleterious mutations from the populations. Males of good genetic quality should be more successful in mating, compared to the males of lower genetic quality. As mating success is a condition dependent trait, large fractions of the genome may be a target of sexual selection and many behavioral traits are likely to be condition dependent. We manipulated the genetic quality of Drosophila subobscura males by inducing mutations with ionizing radiation and observed the effects of the obtained heterozygous mutations on male mating behavior： courtship occurrence, courtship latency, mating occurrence, latency to mating and duration of mating. We found possible effects of mutations. Females mated more frequently with male progeny of nonirradiated males and that these males courted females faster compared to the male progeny of irradiated males. Our findings indicate a possible important role of sexual selection in purging deleterious mutations.
