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Dynamic evolution of transposable elements,demographic history,and gene content of paleognathous birds 被引量:1
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作者 Zong-Ji Wang Guang-Ji Chen +1 位作者 Guo-Jie Zhang Qi Zhou 《Zoological Research》 SCIE CAS CSCD 2021年第1期51-61,共11页
Palaeognathae includes ratite and tinamou species that are important for understanding early avian evolution.Here,we analyzed the whole-genome sequences of 15 paleognathous species to infer their demographic histories... Palaeognathae includes ratite and tinamou species that are important for understanding early avian evolution.Here,we analyzed the whole-genome sequences of 15 paleognathous species to infer their demographic histories,which are presently unknown.We found that most species showed a reduction of population size since the beginning of the last glacial period,except for those species distributed in Australasia and in the far south of South America.Different degrees of contraction and expansion of transposable elements(TE)have shaped the paleognathous genome architecture,with a higher transposon removal rate in tinamous than in ratites.One repeat family,AviRTE,likely underwent horizontal transfer from tropical parasites to the ancestor of little and undulated tinamous about 30 million years ago.Our analysis of gene families identified rapid turnover of immune and reproductionrelated genes but found no evidence of gene family changes underlying the convergent evolution of flightlessness among ratites.We also found that mitochondrial genes have experienced a faster evolutionary rate in tinamous than in ratites,with the former also showing more degenerated W chromosomes.This result can be explained by the Hill-Robertson interference affecting genetically linked W chromosomes and mitochondria.Overall,we reconstructed the evolutionary history of the Palaeognathae populations,genes,and TEs.Our findings of co-evolution between mitochondria and W chromosomes highlight the key difference in genome evolution between species with ZW sex chromosomes and those with XY sex chromosomes. 展开更多
关键词 Paleognaths demographic history Transposable elements Gene families MITOCHONDRIA
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Large-scale genome-wide SNP analysis reveals the rugged(and ragged)landscape of global ancestry,phylogeny,and demographic history in chicken breeds
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作者 Natalia V.DEMENTIEVA Yuri S.SHCHERBAKOV +11 位作者 Olga I.STANISHEVSKAYA Anatoly B.VAKHRAMEEV Tatiana A.LARKINA Artem P.DYSIN Olga A.NIKOLAEVA Anna E.RYABOVA Anastasiia I.AZOVTSEVA Olga V.MITROFANOVA Grigoriy K.PEGLIVANYAN Natalia R.REINBACH Darren K.GRIFFIN Michael N.ROMANOV 《Journal of Zhejiang University-Science B(Biomedicine & Biotechnology)》 SCIE CAS CSCD 2024年第4期324-340,共17页
The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse origin.This study was a large-scale genome-wide analysis of the landscape of the complex molecula... The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse origin.This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture,genetic variability,and detailed structure among 49 populations.These populations represent a significant sample of the world's chicken breeds from Europe(Russia,Czech Republic,France,Spain,UK,etc.),Asia(China),North America(USA),and Oceania(Australia).Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism(SNP)chip,a bioinformatic analysis was carried out.This included the calculation of heterozygosity/homozygosity statistics,inbreeding coefficients,and effective population size.It also included assessment of linkage disequilibrium and construction of phylogenetic trees.Using multidimensional scaling,principal component analysis,and ADMIXTURE-assisted global ancestry analysis,we explored the genetic structure of populations and subpopulations in each breed.An overall 49-population phylogeny analysis was also performed,and a refined evolutionary model of chicken breed formation was proposed,which included egg,meat,dual-purpose types,and ambiguous breeds.Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding.In general,whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry. 展开更多
关键词 Chicken genome diversity Single nucleotide polymorphism(SNP)analysis Gene pool Global ancestry PHYLOGENY demographic history
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Genetic structure and recent population demographic history of Taihangshan macaque(Macaca mulatta tcheliensis),North China 被引量:2
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作者 Yanyan ZHOU Jundong TIAN Jiqi LU 《Integrative Zoology》 SCIE CSCD 2023年第3期530-542,共13页
Massive actions have been and are being taken into protecting the world’s primates from extinction,while the study of the properties of genetic diversity,demographic history,and ecological relationships will benefit t... Massive actions have been and are being taken into protecting the world’s primates from extinction,while the study of the properties of genetic diversity,demographic history,and ecological relationships will benefit the understand-ing of the long-term survival of a species.The Taihangshan macaque(Macaca mulatta tcheliensis),a subspecies of rhesus macaque(Macaca mulatta),is endemic to China and currently restricted to southern Mt.Taihangshan area.Herein,we evaluated the genetic diversity,population structure,and demographic history of this subspecies using mitochondrial(Cytb and high variable region I:HVR I)and nuclear markers(microsatellite loci)of 131 in-dividuals collected from 9 localities covering the distribution range of this subspecies.Both phylogenetic analyses and genetic assignment revealed that the wild populations of Taihangshan macaques could be divided into 2 major highly divergent clades,THS-east and THS-west.Low genetic diversity(π:0.00266±0.00016)but high haplotype diversity(Hd:0.80352±0.015)were detected in the Taihangshan macaques,particularly in THS-east.Analyses of demographic history suggested that the Taihangshan macaques experiencedfirst a stable historical population size from Holocene to early 19th century but a subtle decline and then slight growth in the recent 200 years.We suggest that bridging the neighbor populations(i.e.setting corridors)would facilitate the male-mediated geneflow and subsequently increase the genetic diversity of the Taihangshan macaque populations. 展开更多
关键词 CONSERVATION demographic history genetic diversity genetic structure Taihangshan macaque(Macaca mulatta tcheliensis)
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Senome-scale analysis of demographic history and adaptive selection 被引量:1
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作者 Qi Wu Pingping Zheng Yibu Hu Fuwen Wei 《Protein & Cell》 SCIE CAS CSCD 2014年第2期99-112,共14页
One of the main topics in population genetics is identi- fication of adaptive selection among populations. For this purpose, population history should be correctly inferred to evaluate the effect of random drift and e... One of the main topics in population genetics is identi- fication of adaptive selection among populations. For this purpose, population history should be correctly inferred to evaluate the effect of random drift and exclude it in selection identification. With the rapid progress in genomics in the past decade, vast genome- scale variations are available for population genetic analysis, which however requires more sophisticated models to infer species' demographic history and robust methods to detect local adaptation. Here we aim to review what have been achieved in the fields of demographic modeling and selection detection. We summarize their rationales, implementations, and some classical applications. We also propose that some widely-used methods can be improved in both theoreti- cal and practical aspects in near future. 展开更多
关键词 GENOMICS demographic history Iocaadaptation natural selection
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Whole-genome resequencing of the wheat A subgenome progenitor Triticum urartu provides insights into its demographic history and geographic adaptation 被引量:1
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作者 Xin Wang Yafei Hu +13 位作者 Weiming He Kang Yu Chi Zhang Yiwen Li Wenlong Yang Jiazhu Sun Xin Li Fengya Zheng Shengjun Zhou Lingrang Kong Hongqing Ling Shancen Zhao Dongcheng Liu Aimin Zhang 《Plant Communications》 SCIE 2022年第5期153-170,共18页
Triticum urartu is the progenitor of the A subgenome in tetraploid and hexaploid wheat.Uncovering the landscape of genetic variations in T.urartu will help us understand the evolutionary and polyploid characteristics ... Triticum urartu is the progenitor of the A subgenome in tetraploid and hexaploid wheat.Uncovering the landscape of genetic variations in T.urartu will help us understand the evolutionary and polyploid characteristics of wheat.Here,we investigated the population genomics of T.urartu by genome-wide sequencing of 59 representative accessions collected around the world.A total of 42.2 million highquality single-nucleotide polymorphisms and 3 million insertions and deletions were obtained by mapping reads to the reference genome.The ancient T.urartu population experienced a significant reduction in effective population size(Ne)from3000000 to140000 and subsequently split into eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations during the Younger Dryas period.A map of allelic drift paths displayed splits and mixtures between different geographic groups,and a strong genetic drift towards hexaploid wheat was also observed,indicating that the direct donor of the A subgenome originated from northwestern Syria.Genetic changes were revealed between the eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations in genes orthologous to those regulating plant development and stress responses.A genome-wide association study identified two single-nucleotide polymorphisms in the exonic regions of the SEMI-DWARF 37 ortholog that corresponded to the different T.urartu ecotype groups.Our study provides novel insights into the origin and genetic legacy of the A subgenome in polyploid wheat and contributes a gene repertoire for genomicsenabled improvements in wheat breeding. 展开更多
关键词 Triticum urartu whole-genome resequencing demographic history geographic adaptation selective sweep GWAS
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Wind-dispersed seeds blur phylogeographic breaks:The complex evolutionary history of Populus lasiocarpa around the Sichuan Basin 被引量:2
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作者 Xue Li Markus Ruhsam +5 位作者 Yi Wang Hong-Ying Zhang Xiao-Yan Fan Lei Zhang Jing Wang Kang-Shan Mao 《Plant Diversity》 SCIE CAS CSCD 2023年第2期156-168,共13页
The strength of phylogeographic breaks can vary among species in the same area despite being subject to the same geological and climate history due to differences in biological traits.Several important phylogeographic... The strength of phylogeographic breaks can vary among species in the same area despite being subject to the same geological and climate history due to differences in biological traits.Several important phylogeographic breaks exist around the Sichuan Basin in Southwest China but few studies have focused on wind-dispersed plants.Here,we investigated the phylogeographic patterns and the evolutionary history of Populus lasiocarpa,a wind-pollinated and wind-dispersed tree species with a circum-Sichuan Basin distribution in southwest China.We sequenced and analyzed three plastid DNA fragments(ptDNA) and eight nuclear microsatellites(nSSRs) of 265 individuals of P.lasiocarpa from 21 populations spanning the entire distribution range.Distribution patterns based on nSSR data revealed that there are three genetic groups in P.lasiocarpa.This is consistent with the three phylogeographic breaks(Sichuan Basin,the Kaiyong Line and the 105°E line),where the Sichuan basin acts as the main barrier to gene flow between western and eastern groups.However,the distribution pattern based on ptDNA haplotypes poorly matched the phylogeographic breaks,and wind-dispersed seeds may be one of the main contributing factors.Species distribution modelling suggested a larger potential distribution in the last glacial maximum with a severe bottleneck during the last interglacial.A DIYABC model also suggested a population contraction and expansion for both western and eastern lineages.These results indicate that biological traits are likely to affect the evolutionary history of plants,and that nuclear molecular markers,which experience higher levels of gene flow,might be better indicators of phylogeographic breaks. 展开更多
关键词 PHYLOGEOGRAPHY Sichuan basin Populus lasiocarpa Kaiyong line demographic history
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Insights into genetic variation and demographic history of sharpnose rays:examinations of three species of Telatrygon(Elasmobranchii,Dasyatidae)from the Indo-West Pacific
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作者 Jiwei QI Fanglei SHI +6 位作者 Baowei ZHANG Xiao CHEN Jie XING Keisuke FURUMITSU Joel B.CORUSH Atsuko YAMAGUCHI Jie ZHANG 《Integrative Zoology》 SCIE CSCD 2022年第6期1063-1077,共15页
Coastal and demersal chondrichthyans(sharks,rays,and skates)are expected to exhibit high levels of genetic differentiation in areas of complex geomorphology.Population genetic studies investigating the extent to which... Coastal and demersal chondrichthyans(sharks,rays,and skates)are expected to exhibit high levels of genetic differentiation in areas of complex geomorphology.Population genetic studies investigating the extent to which demographic history shapes the genetic structure of thesefishes are rare.Here,we combined mitochondrial DNA(Cytb and ND2)and 8 nuclear microsatellite loci from 244 individuals to examine the population genetic structure and demographic history of the 3 Indo-West Pacific species of sharpnose rays(Telatrygon zugei,Telatrygon biasa,and Trygon crozieri).High levels of genetic variation both within and between species were identified.Phylogenetic analysis partitioned haplotypes into 2 lineages supporting divergence of T.zugei from T.crozieri and T.biasa during the Pleistocene.Furthermore,microsatellite-based clustering analyses identified 4 genetic groups(i.e.T.zugei from Japan,T.zugei from coastal China,T.biasa from Gulf of Thailand,and T.crozieri from the Andaman Sea).Measurements of genetic differentiation also support these 4 groups.Additionally,Pleistocene demographic expansions were examined in all genetic groups.The climate oscillations and current hydrologic cycles in the Indo-West Pacific appear to coincide with the hypothesis regarding speciation and the observed demographic history trends of the sharpnose rays.Considering the species group has,until recently,been thought to be one species,these results are critical for defining management units and guiding conservation efforts to preserve stingray biodiversity. 展开更多
关键词 conservation biodiversity of stingray demographic history genetic variation Indo-West Pacific Telatrygon
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Genetic diversity,population structure and demographic history of Dugesia japonica in Taihang Mountains
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作者 Hecai Zhang Tiange Hu +2 位作者 Changying Shi Guangwen Chen Dezeng Liu 《Zoological Systematics》 CSCD 2021年第2期153-162,共10页
The freshwater planarian Dugesia japonica has become a model organism in regeneration biology and toxicology due to its powerful regeneration capability and highly chemical sensitivity.Nonetheless,little is known abou... The freshwater planarian Dugesia japonica has become a model organism in regeneration biology and toxicology due to its powerful regeneration capability and highly chemical sensitivity.Nonetheless,little is known about its evolutionary history and demographics.Taihang Mountains is the natural boundary between the Loess Plateau and the North China Plain,and is considered as one of the important priority areas for biodiversity conservation in China.In order to figure out the genetic diversity,population structure and demographic history of D.japonica in Taihang Mountains,a study based on the mitochondrial COI from 116 individuals sampled across 20 populations has been conducted.The results showed that the 116 COI sequences yielded 32 haplotypes,including 8 shared haplotypes and 24 private ones.The overall haplotype diversity(Hd)and nucleotide diversity(π)were 0.920 and 0.083,respectively.Even though the AMOVA results suggested that the genetic variation among populations was significant(FST=0.480,P<0.01),the phylogeny and haplotype network analysis based on 32 haplotypes revealed no obvious phylogeographic pattern.Furthermore,the significantly positive values of neutrality test(Tajima’s D=2.596,P<0.05;Fu’s Fs=2.769,P<0.01)together with the multimodal arrangement of mismatch distribution indicated that D.japonica in Taihang Mountains would have been undergoing population decline.We hope these findings will arouse conservation and management strategy regarding freshwater planarians and contribute to the biodiversity in the long run. 展开更多
关键词 Dugesia japonica Taihang Mountains genetic diversity population structure demographic history
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Conservation genomic investigation of an endangered conifer,Thuja sutchuenensis,reveals low genetic diversity but also low genetic load 被引量:1
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作者 Tongzhou Tao Richard IMilne +4 位作者 Jialiang Li Heng Yang Shiyang Wang Sihan Chen Kangshan Mao 《Plant Diversity》 SCIE CAS CSCD 2024年第1期78-90,共13页
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
关键词 Sichuan Arborvitae Genetic load Deleterious mutations demographic history Conservation genomics
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Genomic divergence and mutation load in the Begonia masoniana complex from limestone karsts
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作者 Yiqing Chen Lina Dong +2 位作者 Huiqin Yi Catherine Kidner Ming Kang 《Plant Diversity》 SCIE CAS CSCD 2024年第5期575-584,共10页
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
关键词 Conservation genomics Karst landscape demographic history INBREEDING Isolated populations Mutation load
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Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis
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作者 Zhen Yang Lisong Liang +3 位作者 Weibo Xiang Lujun Wang Qinghua Ma Zhaoshan Wang 《Plant Diversity》 SCIE CAS CSCD 2024年第3期294-308,共15页
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
关键词 Conservation genomics demographic history INBREEDING Genetic load Runs of homozygosity Local adaptation
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Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses
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作者 Xing Guo Xin-Xin He +5 位作者 Hong Chen Zhi-Cheng Wang Hui-Fang Li Jiang-Xian Wang Ming-Shan Wang Run-Shen Jiang 《Zoological Research》 SCIE CAS CSCD 2021年第1期43-50,共8页
Although domestic ducks have been important poultry species throughout human history,their origin remains enigmatic,with mallards and/or Chinese spot-billed ducks being proposed as the direct wild ancestor(s)of domest... Although domestic ducks have been important poultry species throughout human history,their origin remains enigmatic,with mallards and/or Chinese spot-billed ducks being proposed as the direct wild ancestor(s)of domestic ducks.Here,we analyzed 118 whole genomes from mallard,Chinese spotbilled,and domestic ducks to reconstruct their evolutionary history.We found pervasive introgression patterns among these duck populations.Furthermore,we showed that domestic ducks separated from mallard and Chinese spotbilled ducks nearly 38 thousand years ago(kya)and 54 kya,respectively,which is considerably outside the time period of presumed duck domestication.Thus,our results suggest that domestic ducks may have originated from another wild duck population that is currently undefined or unsampled,rather than from present-day mallard and/or Chinese spot-billed ducks,as previously thought.Overall,this study provides new insight into the complex evolution of ducks. 展开更多
关键词 DUCK Population structure demographic histories DOMESTICATION
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Population genetic variation and historical dynamics of the natural enemy insect Propylea japonica(Coleoptera: Coccinellidae) in China
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作者 WANG Meng-qi ZHAGN Hong-rui +4 位作者 XI Yu-qiang WANG Gao-ping ZHAO Man ZHANG Li-juan GUO Xian-ru 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2023年第8期2456-2469,共14页
Propylea japonica(Coleoptera:Coccinellidae)is a natural enemy insect with a wide range of predation in Chinese mainland and is commonly used in pest management.However,its genetic pattern(i.e.,genetic variation,geneti... Propylea japonica(Coleoptera:Coccinellidae)is a natural enemy insect with a wide range of predation in Chinese mainland and is commonly used in pest management.However,its genetic pattern(i.e.,genetic variation,genetic structure,and historical population dynamics)is still unclear,impeding the development of biological control of insect pests.Population genetic research has the potential to optimize strategies at different stages of the biological control processes.This study used 23 nuclear microsatellite sites and mitochondrial COI genes to investigate the population genetics of Propylea japonica based on 462 specimens collected from 30 sampling sites in China.The microsatellite dataset showed a moderate level of genetic diversity,but the mitochondrial genes showed a high level of genetic diversity.Populations from the Yellow River basin were more genetically diverse than those in the Yangtze River basin.Propylea japonica has not yet formed a significant genealogical structure in China,but there was a population structure signal to some extent,which may be caused by frequent gene flow between populations.The species has experienced population expansion after a bottleneck,potentially thanks to the tri-trophic plant–insect–natural enemy relationship.Knowledge of population genetics is of importance in using predators to control pests.Our study complements existing knowledge of an important natural predator in agroecosystems through estimating its genetic diversity and population differentiation and speculating about historical dynamics. 展开更多
关键词 demographic history genetic differentiation genetic diversity population expansion MICROSATELLITE mitochondrial Col
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Evolutionary history and biological adaptation of Han Chinese people on the Mongolian Plateau 被引量:1
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作者 Xiangping Li Mengge Wang +20 位作者 Haoran Su Shuhan Duan Yuntao Sun Hongyu Chen Zhiyong Wang Qiuxia Sun Qingxin Yang Jing Chen Ting Yang Yuguo Huang Jie Zhong Xiucheng Jiang Jinyue Ma Shijia Chen Yunhui Liu Lintao Luo Xinyu Lin Shengjie Nie Chao Liu Liping Hu Guanglin He 《hLife》 2024年第6期296-313,共18页
Complex demographic processes and natural selection pressures are critical to resolving patterns of the molecular genetic basis of adaptive traits or complex diseases.Recent ancient genome data allow us to trace how k... Complex demographic processes and natural selection pressures are critical to resolving patterns of the molecular genetic basis of adaptive traits or complex diseases.Recent ancient genome data allow us to trace how key traits evolved in different human populations over time,connecting ancient population history with disease susceptibility in western Eurasians.To fill this gap in eastern Eurasians and provide deep insights into the evolutionary history of the populationspecific genetic basis of complex biological traits,we explored the evolutionary basis of adaptive traits in one integrative modern and ancient genomic database,including 225 out of 5583 genomes first reported here.We comprehensively characterized the demographic history and biological adaptation of Han Chinese individuals on the Mongolian Plateau based on the allele frequency spectrum and haplotype-resolved fragments.We found strong genetic homogeneity among geographically different Han populations from Inner Mongolia(IMH).We reconstructed their admixture models and demographic events,revealing that IMH had a close genetic relationship with ancient millet farmers and obtained additional gene flow from Altaic-speaking populations.The enrichment of selected candidate genes suggested that essential metabolism-related genes promoted the rapid adaptation of eastern Eurasians to ancient environmental shifts and dietary changes during agricultural innovations.Evolutionary trajectory reconstruction of metabolism-related genes of methylenetetrahydrofolate reductase(MTHFR)and fatty acid desaturase 1(FADS1)suggested that ancient dietary shifts during the Neolithic transition period promoted the differentiated metabolic rate of folate and fatty acid.We revealed the polygenicity of biological adaptation traits and the pleiotropy of adaptive genes,indicating that complex recent polygenic adaptations,genetic interactions,and genotype–phenotype correlations have contributed to the genetic architecture of complex traits in eastern Eurasians. 展开更多
关键词 demographic history biological adaptation polygenicity and pleiotropy metabolic fitness
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First genetic assessment of brackish water polychaete Tylorrhynchus heterochaetus: mitochondrial CO/sequences reveal strong genetic differentiation and population expansion in samples collected from southeast China and north Vietnam 被引量:5
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作者 Xing-Han Chen Sen Yang +5 位作者 Wei Yang Yuan-Yuan Si Rui-Wen Xu Bin Fan Le Wang Zi-Ning Meng 《Zoological Research》 SCIE CAS CSCD 2020年第1期61-69,共9页
Tylorrhynchus heterochaetus is a widespread benthic polychaete worm found in coastal brackish waters of the west Pacific.It has high ecological and economic value as a biomarker of water quality and as a high-quality ... Tylorrhynchus heterochaetus is a widespread benthic polychaete worm found in coastal brackish waters of the west Pacific.It has high ecological and economic value as a biomarker of water quality and as a high-quality feed in aquaculture and fisheries and is considered a delicacy in some areas of Asia.However,it has experienced a marked reduction in recent years due to overexploitation as well as changes in the environment and climate.Here,to comprehensively understand its genetic background and thus provide insights for better conservation and utilization of this species,we assessed the genetic variability and demographic history of T.heterochaetus individuals sampled from eight locations along the coasts of southeast China and north Vietnam based on mitochondrial cytochrome c oxidase I(COI)sequences.We observed high haplotype diversity(Hd),with an average of 0.926,but relatively low nucleotide diversity(π),with a mean of 0.032 across all samples.A total of 94 polymorphic sites and 85 haplotypes were identified among 320 individuals.The pairwise genetic distances among haplotypes ranged from 0.001 to 0.067,with the high intraspecific divergence possibly reflecting geographic isolation and gene pool fragmentation.Significant genetic structures were revealed among the studied locations;specifically,the eight locations could be treated as six genetically different populations based on pairwiseΦST results(0.026–0.951,P<0.01).A significant pattern of isolation-by-distance was detected between the genetic and geographic distances(r=0.873,P=0.001).Three geographic lineages were defined based on phylogenetic tree and network analyses of COI haplotypes.AMOVA results indicated that genetic variations mainly occurred among the three lineages(89.96%).Tests of neutrality and mismatch distribution suggested that T.heterochaetus underwent recent population expansion.These results provide the first report on the genetic status of T.heterochaetus and will be valuable for the management of genetic resources and better understanding of the ecology and evolution in this species. 展开更多
关键词 Tylorrhynchus heterochaetus Mitochondrial DNA Genetic diversity Population structure demographic history
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Genome-wide analysis reveals signatures of complex introgressive gene flow in macaques(genus Macaca) 被引量:1
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作者 Yang Song Cong Jiang +5 位作者 Kun-Hua Li Jing Li Hong Qiu Megan Price Zhen-Xin Fan Jing Li 《Zoological Research》 SCIE CAS CSCD 2021年第4期433-449,共17页
The genus Macaca serves as an ideal research model for speciation and introgressive gene flow due to its short period of diversification(about five million years ago)and rapid radiation of constituent species.To under... The genus Macaca serves as an ideal research model for speciation and introgressive gene flow due to its short period of diversification(about five million years ago)and rapid radiation of constituent species.To understand evolutionary gene flow in macaques,we sequenced four whole genomes(two M.arctoides and two M.thibetana)and combined them with publicly available macaque genome data for genome-wide analyses.We analyzed 14 individuals from nine Macaca species covering all Asian macaque species groups and detected extensive gene flow signals,with the strongest signals between the fascicularis and silenus species groups.Notably,we detected bidirectional gene flow between M.fascicularis and M.nemestrina.The estimated proportion of the genome inherited via gene flow between the two species was 6.19%.However,the introgression signals found among studied island species,such as Sulawesi macaques and M.fuscata,and other species were largely attributed to the genomic similarity of closely related species or ancestral introgression.Furthermore,gene flow signals varied in individuals of the same species(M.arctoides,M.fascicularis,M.mulatta,M.nemestrina and M.thibetana),suggesting very recent gene flow after the populations split.Pairwise sequentially Markovian coalescence(PSMC)analysis showed all macaques experienced a bottleneck five million years ago,after which different species exhibited different fluctuations in demographic history trajectories,implying they have experienced complicated environmental variation and climate change.These results should help improve our understanding of the complicated evolutionary history of macaques,particularly introgressive gene flow. 展开更多
关键词 MACACA Whole genome INTROGRESSION Gene flow demographic history
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Comparative population genomics reveals glacial cycles to drive diversifications in tropical montane birds(Aves,Timaliidae)
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作者 Per G.P.Ericson Martin Irestedt 《Avian Research》 SCIE CSCD 2022年第4期399-406,共8页
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
关键词 AVES Timaliidae Babblers demographic history Fragmented distributions Pleistocene glacial cycles Population genomics Tropical mountain forests
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Conservation genomics of the critically endangered Chinese pangolin
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作者 Shichao Wei Huizhong Fan +7 位作者 Wenliang Zhou Guangping Huang Yan Hua Shibao Wu Xiao Wei Yiting Chen Xinyue Tan Fuwen Wei 《Science China(Life Sciences)》 SCIE CAS CSCD 2024年第10期2051-2061,共11页
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
关键词 Manis pentadactyla conservation genomics demographic history human activities conservation strategies
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Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern Tibetan Plateau
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作者 Jing-Fang Guo Wei Zhao +2 位作者 Bea Andersson Jian-Feng Mao Xiao-Ru Wang 《Plant Communications》 SCIE CSCD 2023年第4期240-254,共15页
Most species have clearly defined distribution ranges and ecological niches.The genetic and ecological causes of species differentiation and the mechanisms that maintain species boundaries between newly evolved taxa a... Most species have clearly defined distribution ranges and ecological niches.The genetic and ecological causes of species differentiation and the mechanisms that maintain species boundaries between newly evolved taxa and their progenitors are,however,less clearly defined.This study investigated the genetic structure and clines in Pinus densata,a pine of hybrid origin on the southeastern Tibetan Plateau,to gain an understanding of the contemporary dynamics of species barriers.We analyzed genetic diversity in a range-wide collection of P.densata and representative populations of its progenitors,Pinus tabuliformis and Pinus yunnanensis,using exome capture sequencing.We detected four distinct genetic groups within P.densata that reflect its migration history and major gene-flow barriers across the landscape.The demographies of these genetic groups in the Pleistocene were associated with regional glaciation histories.Interestingly,population sizes rebounded rapidly during interglacial periods,suggesting persistence and resilience of the species during the Quaternary ice age.In the contact zone between P.densata and P.yunnanensis,3.36%of the analyzed loci(57849)showed exceptional patterns of introgression,suggesting their potential roles in either adaptive introgression or reproductive isolation.These outliers showed strong clines along critical climate gradients and enrichment in a number of biological processes relevant to high-altitude adaptation.This indicates that ecological selection played an important role in generating genomic heterogeneity and a genetic barrier across a zone of species transition.Our study highlights the forces that operate to maintain species boundaries and promote speciation in the Qinghai-Tibetan Plateau and other mountain systems. 展开更多
关键词 ecological selection demographic history genomic cline introgression outliers reproductive isolation species boundary
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An instantaneous coalescent method insensitive to population structure 被引量:1
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作者 Zeqi Yao Kehui Liu +1 位作者 Shanjun Deng Xionglei He 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2021年第3期219-224,共6页
Conventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic.However,most populations are structured.This complicates the prevailing coalesce... Conventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic.However,most populations are structured.This complicates the prevailing coalescent analyses and sometimes leads to inaccurate estimates.To develop a coalescent method unhampered by population structure,we perform two analyses.First,we demonstrate that the coalescent probability of two randomly sampled alleles from the immediate preceding generation(one generation back)is independent of population structure.Second,motivated by this finding,we propose a new coalescent method:i-coalescent analysis.The i-coalescent analysis computes the instantaneous coalescent rate by using a phylogenetic tree of sampled alleles.Using simulated data,we broadly demonstrate the capability of i-coalescent analysis to accurately reconstruct population size dynamics of highly structured populations,although we find this method often requires larger sample sizes for structured populations than for panmictic populations.Overall,our results indicate i-coalescent analysis to be a useful tool,especially for the inference of population histories with intractable structure such as the developmental history of cell populations in the organs of complex organisms. 展开更多
关键词 COALESCENT Population structure demographic history Population size Phylogenetic tree
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