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Reconstruct recent multi-population migration history by using identical-by-descent sharing

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Journal of genetics and Genomics 2024年第6期51卷 642-651页

作者： Wenxiao Zhang Kai Yuan Ru Wen Haifang Li Xumin Ni School of Mathematics and Statistics Bejing Jiaotong UniversityBeijing 100044China The Stanley Center for Psychiatric Research Broad Institute of MIT and HarvardCambridgeMA 02142USA Baidu Incorporated Bejing 100085China

Identical-by-descent(IBD)is a fundamental genomic characteristic in population genetics and has been widely used for population history reconstruction.However,limited by the nature of IBD,which could only capture the relationship between two individuals/haplotypes,existing IBD-based history inference is constrained to two populations.In this study,we propose a framework by leveraging IBD sharing in multipopulation and develop a method,MatrixiBD,to reconstruct recent multi-population migration history.Specifically,we employ the structured coalescent theory to precisely model the genealogical process and then estimate the IBD sharing across multiple populations.Within our model,we establish a theoretical connection between migration history and IBD sharing.Our method is rigorously evaluated through simulations,revealing its remarkable accuracy and robustness.Furthermore,we apply MatrixiBD to Central and South Asia in the Human Genome Diversity Project and successfully reconstruct the recent migration history of three closely related populations in South Asia.By taking into account the IBD sharing across multiple populations simultaneously,MatrixlBD enables us to attain clearer and more comprehensive insights into the history of regions characterized by complex migration dynamics,providing a holistic perspective on intricate patterns embedded within the recent population migration history.

关键词： Population genetics IBD sharing Migration history Structured coalescent theory gene flow

Genomic analysis provides insights into the westward expansion of domesticated peaches in China

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Horticultural Plant Journal 2024年第2期10卷 367-375页

作者： Wenqing Li Yong Li Xinwei Wang Guoqing Zhao Gengrui Zhu Ke Cao Weichao Fang Jinlong Wu Kai Ma Changwen Chen Lirong Wang Zhengzhou Fruit Research Institute CAASZhengzhouHennan 450009China Xinjiang Academy of Agricultural Sciences UrumqiXinjiang 830091China Western Research Institute CAASChangjiXinjiang 831100China

Peach, an economically important model plant of the Rosaceae family, has been domesticated and cultivated in China for approximately5 000 years. The Hexi Corridor, an important corridor connecting east-central China and the Tarim Basin, is the starting point of the Silk Road that links China and the Eurasian region. As a globally distributed fruit tree, the spread of peach was accomplished through historical trade routes in the Hexi Corridor and the Tarim Basin. However, knowledge of peach genetic diversity in these regions remains limited. In this study,we examined the relationships and the spread history of domesticated peaches through sequencing and genomic analysis of 161 peach accessions collected from Northwest China, including 43 from the Hexi Corridor and 104 from the Tarim Basin. The results indicate that peach landraces in the Hexi Corridor and the Tarim Basin are derivatives of peaches from the east and south of China (ESC). Notably, the genetic diversity of accessions from both the Hexi Corridor and the Tarim Basin was lower than that of ESC accessions. Reduction of diversity (ROD) and linkage disequilibrium (LD) analyses detected a genetic bottleneck in peaches from these regions. Additionally, these peaches have undergone varying degrees of selection from natural environment. Moreover, genes responsive to biotic and abiotic stresses were under selection, which could be the result of the climate change of Northwest China after the Last Glacial Maximum (LGM). Our findings provide a better understanding of the genetic basis of peach migration in Northwest China. Furthermore, this study expands the available genomic data for peaches and provides critical information for future peach breeding programs.

关键词： Peach Hexi corridor Tarim Basin genetic diversity gene flow

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Speciation with gene flow via cycles of isolation and migration:insights from multiple mangrove taxa

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National Science Review 2019年第2期6卷 275-288页

作者： Ziwen He Xinnian Li Ming Yang Xinfeng Wang Cairong Zhong Norman C.Duke Chung-I Wu Suhua Shi State Key Laboratory of Biocontrol Guangdong Key Lab of Plant Resources Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education InstitutesSchool of Life Sciences Sun Yat-Sen University Department of Ecology and Evolution University of Chicago CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences Hainan Dongzhai Harbor National Nature Reserve Administration Centre for Tropical Water and Aquatic Ecosystem Research James Cook University

Allopatric speciation requiring an unbroken period of geographical isolation has been the standard model of neo-Darwinism. While doubts have been repeatedly raised, strict allopatry without any gene flow remains a plausible mechanism in most cases. To rigorously reject strict allopatry, genomic sequences superimposed on the geological records of a well-delineated geographical barrier are necessary. The Strait of Malacca,narrowly connecting the Pacific and Indian Ocean coasts, serves at different times either as a geographical barrier or a conduit of gene flow for coastal/marine species. We surveyed 1700 plants from 29 populations of 5 common mangrove species by large-scale DNA sequencing and added several whole-genome assemblies. Speciation between the two oceans is driven by cycles of isolation and gene flow due to the fluctuations in sea level leading to the opening/closing of the Strait to ocean currents. Because the time required for speciation in mangroves is longer than the isolation phases, speciation in these mangroves has proceeded through many cycles of mixing-isolation-mixing, or MIM, cycles. The MIM mechanism, by relaxing the condition of no gene flow, can promote speciation in many more geographical features than strict allopatry can. Finally, the MIM mechanism of speciation is also efficient, potentially yielding mn(m > 1) species after n cycles.

关键词： speciation gene flow allopatry geographical isolation mangrove

Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow

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National Science Review 2021年第12期8卷 86-103页

作者： Xiyun Jiao Tomá■ Flouri Ziheng Yang Department of genetics Evolution and EnvironmentUniversity College London Department of Statistics and Data Science Southern University of Science and Technology

Multispecies coalescent(MSC) is the extension of the single-population coalescent model to multiple species. It integrates the phylogenetic process of species divergences and the population genetic process of coalescent, and provides a powerful framework for a number of inference problems using genomic sequence data from multiple species, including estimation of species divergence times and population sizes,estimation of species trees accommodating discordant gene trees, inference of cross-species gene flow and species delimitation. In this review, we introduce the major features of the MSC model, discuss full-likelihood and heuristic methods of species tree estimation and summarize recent methodological advances in inference of cross-species gene flow. We discuss the statistical and computational challenges in the field and research directions where breakthroughs may be likely in the next few years.

关键词： anomaly zone BPP deep coalescence gene flow Markov chain Monte Carlo multispecies coalescent species tree

gene flow from transgenic oilseed rape (Brassica napus L.) to cruciferous weeds under mentor pollen inducement

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Progress in Natural Science:Materials International 2007年第11期17卷 1284-1289页

作者： Zhao Xiangxiang1,2, Luo Yuming1, Lu Weiping2, Qi Cunkou3, Pu Huiming3 and Wang Youping2(1. Biotechnology Key Laboratory of Eco-agriculture in Hongze Lake Region, Jiangsu Province, Huaiyin Normal College, Huai'an 223001, China 2. Jiangsu Provincial Key Laboratory of Crop genetics and Physiology, Yangzhou University, Yangzhou 225009, China 3. Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China) Biotechnology Key Laboratory of Eco-Agriculture in Hongze Lake Region Jiangsu Province Huaiyin Normal College Huai'an 223001 China Jiangsu Provincial Key Laboratory of Crop genetics and Physiology Yangzhou University Yangzhou 225009 China Institute of Industrial Crops Jiangsu Academy of Agricultural Sciences Nanjing 210014 China

The alien gene flow between genetically modified glyphosate-resistant rapeseed variety Q3 (Brassica napus L.) and four cruciferous weeds was studied under mentor pollen inducement. The results showed that when Thlaspi arvense L., Capsella bursa-pastoris (L.) Medic, Cardamine hirsuta L. and Rorippa palustris (L.) Besser were pollinated with mentor pollen, the mixed Q3 and the weed, pollen grains aggregated largely and germinated quickly, and the numbers of pollen tubes penetrating into the style and the ovary were greatly increased as compared with corresponding self-pollination groups. Twenty four to forty eight hours after pollination, several pollen tubes were observed to penetrate into the ovule via micropyle in each mentor combination. However, when the mentor progenies were analyzed by PCR, all of them showed negative for the Q3 herbicide-resistant gene. Collectively, these results indicated that crossing between T. arvense, C. bursa-pastoris, C. hirsuta, R. palustris (as female) and Q3 (as male) was highly incompatible and the herbicide-resistant gene could not flow from Q3 to these four weeds.

关键词： herbicide-resistant rapeseed cruciferous weeds mentor pollination aniline blue fluorescence gene flow

Genome-wide analysis reveals signatures of complex introgressive gene flow in macaques(genus Macaca)

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Zoological Research 2021年第4期42卷 433-449页

作者： Yang Song Cong Jiang Kun-Hua Li Jing Li Hong Qiu Megan Price Zhen-Xin Fan Jing Li Key Laboratory of Bio-resources and Eco-environment of Ministry of Education College of Life SciencesSichuan UniversityChengduSichuan 610064China Institute of Animal genetics and Breeding College of Animal Science and TechnologySichuan Agricultural UniversityChengduSichuan 611130China Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife College of Life SciencesSichuan UniversityChengduSichuan 610064China

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.

关键词： Macaca Whole genome Introgression gene flow Demographic history

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genetic boundary and gene flow between 2 parapatric subspecies of brown rats

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Current Zoology 2020年第6期66卷 677-688页

作者： Lei ZHAO Jian-Xu Zhang Yao-Hua Zhang State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture Institute of ZoologyChinese Academy of SciencesBeichen West Road 1-5Chaoyang DistrictBeijing 100101China CAS Center for Excellence in Biotic Interactions University of Chinese Academy of SciencesBeijing100049China

Two parapatric Rattus norvegicus subspecies,R.n.humiliatus(RNH)and R.n.caraco(RNC),are classified accordi ng to morphological diverge nee and are mainly distributed in North and Northeast China.Here,we aimed to explore the population genetic structure,genetic boundary,and gene flow in these rats using 16 microsatellite loci.Structure analysis and principal component an alysis revealed 3 ancestral clusters.We found that the in termediate cluster exhibited higher genetic diversity and a lower in breeding coefficie nt tha n the other 2 clusters.The genetic differentiation between the 3 clusters was significant but weak,with a higher FST value being observed betwee n the clusters on both sides.The subspecies bou ndary inf erred from microsatellite markers may indicate the existence of an admixture or hybridization area covering Liaoning,Inner Mongolia,and Jilin Provinces,rather than corresponding to the administrative provincial boundaries between Liaoning and Jilin.The RNH and RNC subspecies presented moderate gene exchange and an asymmetric bidirectional gene flow pattern,with higher gene flow from the RNH subspecies to the RNC subspecies,constraining speciation.Such genetic characteristics might be explained by biological processes such as dispersal ability,mate choice,and dynamic lineage boundaries.

关键词： genetic boundary gene flow population genetic structure Rattus norvegicus

The antibiotic resistome： gene flow in environments, animals and human beings

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Frontiers of Medicine 2017年第2期11卷 161-168页

作者： Yongfei Hu George F. Gao Baoli Zhu CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China Beijing Key Laboratory of Microbial Drug Resistance and Resistome Beijing 100101 China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases The First Affiliated Hospital Zhejiang University Hangzhou 310006 China Research Network of lmmunity and Health (RNIH) Beijing Institutes of Life Science Chinese Academy of Sciences Beijing 100101 China Office of Director-general Chinese Center for Disease Control and Prevention (China CDC) Beijing 102206 China

The antibiotic resistance is natural in bacteria and predates the human use of antibiotics. Numerous antibiotic resistance genes （ARGs） have been discovered to confer resistance to a wide range of antibiotics. The ARGs in natural environments are highly integrated and tightly regulated in specific bacterial metabolic networks. However, the antibiotic selection pressure conferred by the use of antibiotics in both human medicine and agriculture practice leads to a significant increase of antibiotic resistance and a steady accumulation of ARGs in bacteria. In this review, we summarized, with an emphasis on an ecological point of view, the important research progress regarding the collective ARGs （antibiotic resistome） in bacterial communities of natural environments, human and animals, i.e., in the one health settings. We propose that the resistance gene flow in nature is ＂from the natural environments＂ and ＂to the natural environments＂; human and animals, as intermediate recipients and disseminators, contribute greatly to such a resistance gene ＂circulation.＂

关键词： antibiotic resistance resistome microbiome gene flow

Migration and population genetics of the grain aphid Macrosiphum miscanti (Takahashi) in relation to the geographic distance and gene flow

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Progress in Natural Science:Materials International 2005年第11期15卷 1000-1004页

作者： GUO Wei, SHEN Zuorui, LI Zhihong and GAO Lingwang (College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China) College of Agronomy and Biotechnology China Agricultural University Beijing 100094 China

The population genetics of the grain aphid Macrosiphum miscanti (Takahashi) is analyzed by microsatellite markers. Samples collected from 15 locations in China have been examined at 5 polymorphic microsatellite loci. Overall, genetic diversity displays a relation between the migration and gene flow in the grain aphid; a free and frequent gene flow is found in the eastern populations, and gene isolation occurs in the two western populations, especially Datong population and Guiyang population. The natural barriers may present an insurmountable obstacle preventing gene flow and aphid migration. However, a spatial genetic differentiation between populations is correlated with their geographical separation, indicating the geographic differentiation may play an important role in shaping the genetic structure of M. miscanti populations. In addition, most populations of grain aphids are out of Hardy-Weinberg equilibrium and there is het-erozygote deficit. Based on F statistics, the average genetic differentiation among different geographical populations is relatively low. It seems that the long distance migration of the grain aphid may enhance gene flow and decrease genetic differentiation among different populations .

关键词： Macrosiphum miscanti microsatellite gene flow migration.