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The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times

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Current Zoology 2015年第5期61卷 874-885页

作者： Konstantinos ANGELIS Mario DOS REIS Department of Genetics Evolution and Environment University College London Gower Street London WC 1E 6BT UK

Although the effects of the coalescent process on sequence divergence and genealogies are well understood, the vir- tual majority of studies that use molecular sequences to estimate times of divergence among species have failed to account for the coalescent process. Here we study the impact of ancestral population size and incomplete lineage sorting on Bayesian estimates of species divergence times under the molecular clock when the inference model ignores the coalescent process. Using a combination of mathematical analysis, computer simulations and analysis of real data, we find that the errors on estimates of times and the molecular rate can be substantial when ancestral populations are large and when there is substantial incomplete lineage sorting. For example, in a simple three-species case, we find that if the most precise fossil calibration is placed on the root of the phylogeny, the age of the internal node is overestimated, while if the most precise calibration is placed on the internal node, then the age of the root is underestimated. In both cases, the molecular rate is overestimated. Using simulations on a phylogeny of nine species, we show that substantial errors in time and rate estimates can be obtained even when dating ancient divergence events. We analyse the hominoid phylogeny and show that estimates of the neutral mutation rate obtained while ignoring the coalescent are too high. Using a coalescent-based technique to obtain geological times of divergence, we obtain estimates of the mutation rate that are within experimental estimates and we also obtain substantially older divergence times within the phylogeny [Current Zoology 61 （5）： 874-885, 2015].

关键词： Ancestral polymorphism incomplete lineage sorting Divergence time estimation Gene tree Species tree

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Widespread incomplete lineage sorting and introgression shaped adaptive radiation in the Gossypium genus

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Plant Communications 2024年第2期5卷 185-197页

作者： Yanchao Xu Yangyang Wei Zhongli Zhou Xiaoyan Cai Scott ABoden Muhammad Jawad Umer Luqman BSafdar Yuling Liu Dingsha Jin Yuqing Hou Yuhong Wang Sarah Brooke Wall Kunbo Wang Shuxun Yu Baohong Zhang Renhai Peng Fang Liu National Key Laboratory of Cotton Bio-breeding and Integrated Utilization Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang 455000China College of Plant Science and Technology Huazhong Agricultural UniversityWuhan 40070China College of Biology and Food Engineering Anyang Institute of TechnologyAnyang 455000China National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572024China School of Agriculture Food and WineUniversity of AdelaideAdelaideSA 5005Australia Sanya Institute Hainan Academy of Agricultural SciencesSanya 572000China Department of Biology East Carolina UniversityGreenvilleNC 27858USA School of Agricultural Sciences Zhengzhou UniversityZhengzhou 450001China

Cotton(Gossypium)stands as a crucial economic crop,serving as the primary source of naturalfiber for the textile ***,the evolutionary mechanisms driving speciation within the Gossypium genus remain *** this investigation,we leveraged 25 Gossypium genomes and introduced four novel assem-blies—***,***,***,and ***(Gklo)—to delve into the speciation history of this ***,we encountered intricate phylogenies potentially stemming from *** complexities are further compounded by incomplete lineage sorting(ILS),a factor likely to have been instrumental in shaping the swift diversification of *** focus subsequently shifted to the rapid radiation episode during a concise period in Gossypium *** a recently diverged lineage comprising ***,Gklo,and ***,we constructed afinely detailed ILS ***,this analysis revealed the non-random distribution of ILS regions across the reference Gklo ***,we identified signs of robust natural selection influencing specific ILS *** variations per-taining to speciation emerged between the closely related sister species Gklo and ***-mately 15.74%of speciation structural variation genes and 12.04%of speciation-associated genes were esti-mated to intersect with ILS *** enrich our understanding of the role of ILS in adaptive radiation,shedding fresh light on the intricate speciation history of the Gossypium genus.

关键词： cotton speciation Gossypium genus incomplete lineage sorting ILS phylogenetic analysis gene tree resolution

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The Metasequoia genome and evolutionary relationships among redwoods

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Plant Communications 2023年第6期4卷 342-355页

作者： Fangfang Fu Chi Song Chengjin Wen Lulu Yang Ying Guo Xiaoming Yang Ziqiang Shu Xiaodong Li Yangfan Feng Bingshuang Liu Mingsheng Sun Yinxiao Zhong Li Chen Yan Niu Jie Chen Guibin Wang Tongming Yin Shilin Chen Liangjiao Xue Fuliang Cao State Key Laboratory of Tree Genetics and Breeding Co-Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjing 210037China Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China Wuhan Benagen Technology Company Limited Wuhan 430000China Wuhan Botanical Garden Chinese Academy of SciencesWuhan 430074China China Academy of Chinese Medical Sciences Institute of Chinese Materia MedicaBeijing 100070China

Redwood trees(Sequoioideae),including Metasequoia glyptostroboides(dawn redwood),Sequoiadendron giganteum(giant sequoia),and Sequoia sempervirens(coast redwood),are threatened and widely recognized iconic tree *** resources for redwood trees could provide clues to their evolutionary ***,we report the 8-Gb reference genome of *** and a comparative analysis with two related *** than 62%of the *** genome is composed of repetitive ***-specific bursts of long terminal repeat retrotransposons may have contributed to genomic differentiation in the three *** chromosomal synteny between *** and *** is extremely high,whereas there has been significant chromosome reorganization in *** analysis of marker genes indicates that *** is an autopolyploid,and more than 48%of the gene trees are incongruent with the species *** of multiple analyses suggest that incomplete lineage sorting(ILS)rather than hybridization explains the inconsistent phylogeny,indicating that genetic variation among redwoods may be due to random retention of polymorphisms in ancestral *** analysis of ortholog groups indicates that gene families of ion channels,tannin biosynthesis enzymes,and transcription factors for meristem maintenance have expanded in *** and ***,which is consistent with their extreme *** a wetland-tolerant species,*** shows a transcriptional response to flooding stress that is conserved with that of analyzed angiosperm *** study offers insights into redwood evolution and adaptation and provides genomic resources to aid in their conservation and management.

关键词： Metasequoia glyptostroboides redwood incomplete lineage sorting polyploidy flooding stress

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Evolutionary relationships of mitogenomes in a recently radiated Old World avian family

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Avian Research 2023年第2期14卷 153-159页

作者： Wenqing Zang Zhiyong Jiang Per G.P.Ericson Gang Song Sergei VDrovetski Takema Saitoh Fumin Lei Yanhua Qu Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijingChina College of Life Sciences University of Chinese Academy of SciencesBeijingChina Department of Bioinformatics and Genetics Swedish Museum of Natural HistoryPO Box 50007SE-10405StockholmSweden Laboratories of Analytical Biology National Museum of Natural HistorySmithsonian InstitutionWashingtonDC 20004USA U.S.Geological Survey Eastern Ecological Science Center at Patuxent Research RefugeLaurelMD 20708USA Yamashina Institute for Ornithology AbikoChibaJapan Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming650223China

Environmentally heterogeneous mountains provide opportunities for rapid diversification and *** family Prunellidae(accentors)is a group of birds comprising primarily mountain specialists that have recently radiated across the Palearctic *** rapid diversification poses challenges to resolving their *** we sequenced the complete mitogenomes and estimated the phylogeny using all 12(including 28 individuals)currently recognized species of *** reconstructed the mitochondrial genome phylogeny using 13 protein-coding genes of 12 species and 2 Eurasian Tree Sparrows(Passer montanus).Phylogenetic relationships were estimated using a suite of analyses:maximum likelihood,maximum parsimony and the coalescent-based *** times were estimated by implementing a Bayesian relaxed clock model in *** on the BEAST time-calibrated tree,we implemented an ancestral area reconstruction using RASP *** phylogenies based on the maximum likelihood,maximum parsimony and SVDquartets approaches support a clade of large-sized accentors(subgenus Laiscopus)to be sister to all other accentors with small size(subgenus Prunella).In addition,the trees also support the sister relationship of *** and ***+*** with 100%bootstrap support,but the relationships among the remaining eight species in the Prunella clade are poorly *** species cluster in different positions in the three phylogenetic trees and the nodes are often poorly *** five nodes separating the seven species diverged simultaneously within less than half million years(i.e.,between 2.71 and 3.15 million years ago),suggesting that the recent radiation is likely responsible for rampant incomplete lineage sorting and gene tree *** area reconstruction indicates a central Palearctic region origin for *** study highlights that whole mitochondrial genome phylogeny can resolve major lineages within Prun

关键词： incomplete lineage sorting Mitochondrial genome Mountain specialists Radiation

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Phylogenomics and the flowering plant tree of life

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Journal of Integrative Plant Biology 2023年第2期65卷 299-323页

作者： Cen Guo Yang Luo Lian-Ming Gao Ting-Shuang Yi Hong-Tao Li Jun-Bo Yang De-Zhu Li Germplasm Bank of Wild Species Kunming Institute of Botanythe Chinese Academy of SciencesKunming 650201China CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botanythe Chinese Academy of SciencesKunming 650201China Lijiang Forest Diversity National Observation and Research Station Kunming Institute of BotanyChinese Academy of SciencesLijiang 674100China Kunming College of Life Science University of Chinese Academy of SciencesKunming 650201China

The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic *** the past decade,a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new *** the meantime,a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is *** review focuses on the utility of genomic data(from organelle genomes,to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations,describes the baseline methodology of experimental and analytical procedures,and summarizes recent progress in flowering plant phylogenomics at the ordinal,familial,tribal,and lower *** also discuss the challenges,such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors,and underlying biological factors,such as whole-genome duplication,hybridization/introgression,and incomplete lineage sorting,together suggesting that a bifurcating tree may not be the best model for the tree of ***,we discuss promising avenues for future plant phylogenomic studies.

关键词： angiosperms hybridization incomplete lineage sorting orthology inference phylogenetic conflicts reduced representation sequencing whole-genome sequencing whole-genome duplication

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Models, methods and tools for ancestry inference and admixture analysis

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Frontiers of Electrical and Electronic Engineering in China 2017年第3期5卷 236-250页

作者： Kai Yuan Ying Zhou Xumin Ni Yuchen Wang Chang Liu Shuhua Xu CAS Key Laboratory of Computational Biology Max Planck Independent Research Group on Population Genomics CAS-MPG Partner Institute for Computational Biology Shanghai Institutes for Biological Sciences CAS Shanghai 200031 China University of Chinese Academy of Sciences Beijing 100049 China Department of Mathematics School of Science Beijing Jiaotong University Beijing 100044 China School of Life Science and Technology ShanghaiTech University Shanghai 201210 China Collaborative Innovation Center of Genetics and Development Shanghai 200438 China

Background： Genetic admixture refers to the process or consequence of interbreeding between two or more previously isolated populations within a species. Compared to many other evolutionary driving forces such as mutations, genetic drift, and natural selection, genetic admixture is a quick mechanism for shaping population genomie diversity. In particular, admixture results in ＂recombination＂ of genetic variants that have been fixed in different populations, which has many evolutionary and medical implications. Results： However, it is challenging to accurately reconstruct population admixture history and to understand of population admixture dynamics. In this review, we provide an overview of models, methods, and tools for ancestry inference and admixture analysis. Conclusions： Many methods and tools used for admixture analysis were originally developed to analyze human data, but these methods can also be directly applied and/or slightly modified to study non-human species as well.

关键词： genetic admixture ancestry population structures demographic history archaic introgression incomplete lineage sorting

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Phylogeography and evolution of three closely related species of Tsuga (hemlock) from subtropical Asia: Further insights into speciation of conifers

Phylogeography and evolution of three closely related specie...

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生态文明建设中的植物学：现在与未来——中国植物学会第十五届会员代表大会暨八十周年学术年会

作者： Yu-Zhi Cun Xiao-Quan Wang State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Dali University

Biogeography and speciation of conifers are of special interest due to the high ecological importance of this group, and evolutionary relationships among closely related species of conifers are difficult to be disentangled because of frequent interspecific gene flow and incomplete lineage sorting. Here, a phylogeographic study was conducted for three closely related species of Tsuga (hemlock) from subtropical mainland Asia, based on sequence analyses of paternal chloroplast and maternal mitochondrial DNA and coalescent simulations. The results indicated that, in the T. chinensis/T. forrestii species pair, the latter originated through peripatric speciation and a genetic break formed between eastern and western populations of the former. Surprisingly, the split between western and eastern T. chinensis was earlier than that

关键词： Phylogeography Peripatric speciation Gene flow incomplete lineage sorting Cryptic speciation Tsuga

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