多群体的隔离与迁移模型。
Isolation with migration models for more than two populations.
机构信息
Department of Genetics, Rutgers University, USA.
出版信息
Mol Biol Evol. 2010 Apr;27(4):905-20. doi: 10.1093/molbev/msp296. Epub 2009 Dec 2.
Abstract
A method for studying the divergence of multiple closely related populations is described and assessed. The approach of Hey and Nielsen (2007, Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci USA. 104:2785-2790) for fitting an isolation-with-migration model was extended to the case of multiple populations with a known phylogeny. Analysis of simulated data sets reveals the kinds of history that are accessible with a multipopulation analysis. Necessarily, processes associated with older time periods in a phylogeny are more difficult to estimate; and histories with high levels of gene flow are particularly difficult with more than two populations. However, for histories with modest levels of gene flow, or for very large data sets, it is possible to study large complex divergence problems that involve multiple closely related populations or species.
摘要
描述并评估了一种研究多个密切相关群体分歧的方法。Hey 和 Nielsen（2007 年，《在费尔森斯坦方程中整合以改进群体遗传学中的马尔可夫链蒙特卡罗方法》，美国国家科学院院刊。104:2785-2790）用于拟合隔离与迁移模型的方法被扩展到具有已知系统发育的多个群体的情况。对模拟数据集的分析揭示了多群体分析可获得的历史类型。必然地，与系统发育中较旧时期相关的过程更难以估计；并且具有高水平基因流动的历史在超过两个群体时特别困难。然而，对于具有适度基因流动的历史或非常大的数据集，有可能研究涉及多个密切相关的群体或物种的大型复杂分歧问题。
相似文献
1
Isolation with migration models for more than two populations.多群体的隔离与迁移模型。
Mol Biol Evol. 2010 Apr;27(4):905-20. doi: 10.1093/molbev/msp296. Epub 2009 Dec 2.
2
Phylogeny Estimation by Integration over Isolation with Migration Models.基于隔离迁徙模型的系统发育估计。
Mol Biol Evol. 2018 Nov 1;35(11):2805-2818. doi: 10.1093/molbev/msy162.
3
Distinguishing migration from isolation: a Markov chain Monte Carlo approach.区分迁移与隔离：一种马尔可夫链蒙特卡罗方法。
Genetics. 2001 Jun;158(2):885-96. doi: 10.1093/genetics/158.2.885.
4
Joint inference of population assignment and demographic history.群体归属和人口历史的联合推断。
Genetics. 2011 Oct;189(2):561-77. doi: 10.1534/genetics.111.129205. Epub 2011 Jul 20.
5
Composite likelihood estimation of demographic parameters.人口统计学参数的复合似然估计
BMC Genet. 2009 Nov 12;10:72. doi: 10.1186/1471-2156-10-72.
6
Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods.古代DNA中替代率估计值升高：贝叶斯方法的模型违背与偏差
Mol Ecol. 2009 Nov;18(21):4390-7. doi: 10.1111/j.1365-294X.2009.04333.x. Epub 2009 Sep 7.
7
Population divergence time estimation using individual lineage label switching.利用个体谱系标记交换进行种群分歧时间估计。
G3 (Bethesda). 2022 Apr 4;12(4). doi: 10.1093/g3journal/jkac040.
8
Comparison of Bayesian and maximum-likelihood inference of population genetic parameters.群体遗传参数的贝叶斯推断与最大似然推断比较
Bioinformatics. 2006 Feb 1;22(3):341-5. doi: 10.1093/bioinformatics/bti803. Epub 2005 Nov 29.
9
mstree: A Multispecies Coalescent Approach for Estimating Ancestral Population Size and Divergence Time during Speciation with Gene Flow.多物种合并方法在有基因流的物种形成中估计祖先种群大小和分化时间
Genome Biol Evol. 2020 May 1;12(5):715-719. doi: 10.1093/gbe/evaa087.
10
A new approach to estimate parameters of speciation models with application to apes.一种估计物种形成模型参数的新方法及其在猿类中的应用。
Genome Res. 2007 Oct;17(10):1505-19. doi: 10.1101/gr.6409707. Epub 2007 Aug 21.
引用本文的文献
1
Connectivity differs by orders of magnitude among co-distributed corals, affecting spatial scales of eco-evolutionary processes.在共同分布的珊瑚中，连通性在数量级上存在差异，影响着生态进化过程的空间尺度。
Sci Adv. 2025 Jul 4;11(27):eadt2066. doi: 10.1126/sciadv.adt2066. Epub 2025 Jul 2.
2
Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified.当模式、方向和谱系指定错误时，从基因组数据推断物种间的基因流动
Mol Biol Evol. 2025 Jun 4;42(6). doi: 10.1093/molbev/msaf121.
3
The Divergence History of Two Japanese Taxa (Taxaceae): Implications for Species Diversification in the Japanese Archipelago.两种日本红豆杉科植物的分化历史：对日本列岛物种多样化的启示
Plants (Basel). 2025 May 20;14(10):1537. doi: 10.3390/plants14101537.
4
Deep genetic divergences and few morphological changes support the cryptic speciation in Larimus breviceps (Sciaenidae, Acanthuriformes) from the western South Atlantic.深度遗传分化和极少的形态变化支持了来自南大西洋西部的短头拟牙䱛（拟牙䱛科，刺尾鱼目）的隐存物种形成。
Sci Rep. 2024 Dec 28;14(1):31541. doi: 10.1038/s41598-024-83196-8.
5
Phylogeographical patterns match the floristic subdivisions: the diversification history of a widespread herb in subtropical China.系统发育地理学模式与植物区系划分相匹配：中国亚热带一种广布草本植物的多样化历史。
Ann Bot. 2024 Dec 31;134(7):1263-1276. doi: 10.1093/aob/mcae157.
6
Hierarchical Heuristic Species Delimitation Under the Multispecies Coalescent Model with Migration.具有迁移的多物种溯祖模型下的分层启发式物种界定
Syst Biol. 2024 Nov 29;73(6):1015-1037. doi: 10.1093/sysbio/syae050.
7
Coastal dunes as drivers of genetic differentiation in the honeypot ant Myrmecocystus baja (Formicidae: Formicinae).沿海沙丘是蜜罐蚁 Myrmecocystus baja（蚁科：蚁亚科）遗传分化的驱动因素。
Naturwissenschaften. 2024 Jul 15;111(4):39. doi: 10.1007/s00114-024-01925-5.
8
A leading-edge scenario in the phylogeography and evolutionary history of East Asian insular in Taiwan and the Philippines.台湾和菲律宾东亚岛屿生物地理学和进化史中的前沿情景。
Front Genet. 2024 May 2;15:1372309. doi: 10.3389/fgene.2024.1372309. eCollection 2024.
9
Genetic diversities in wild and cultivated populations of the two closely-related medical plants species, Tripterygium Wilfordii and T. Hypoglaucum (Celastraceae).两种密切相关的药用植物物种（卫矛科雷公藤属和雷公藤属）的野生和栽培种群的遗传多样性。
BMC Plant Biol. 2024 Mar 16;24(1):195. doi: 10.1186/s12870-024-04826-x.
10
Forty Years of Inferential Methods in the Journals of the Society for Molecular Biology and Evolution.《分子生物学与进化学会期刊》中的推理方法四十年。
Mol Biol Evol. 2024 Jan 3;41(1). doi: 10.1093/molbev/msad264.
本文引用的文献
1
LABORATORY EXPERIMENTS ON SPECIATION: WHAT HAVE WE LEARNED IN 40 YEARS?物种形成的实验室实验：40 年来我们学到了什么？
Evolution. 1993 Dec;47(6):1637-1653. doi: 10.1111/j.1558-5646.1993.tb01257.x.
2
SKEPTICISM TOWARDS SANTA ROSALIA, OR WHY ARE THERE SO FEW KINDS OF ANIMALS?对圣罗莎莉亚的质疑，或者说为何动物种类如此之少？
Evolution. 1981 Jan;35(1):124-138. doi: 10.1111/j.1558-5646.1981.tb04864.x.
3
Learning about modes of speciation by computational approaches.通过计算方法了解物种形成模式。
Evolution. 2009 Oct;63(10):2547-62. doi: 10.1111/j.1558-5646.2009.00662.x. Epub 2009 Feb 18.
4
Non-equilibrium estimates of gene flow inferred from nuclear genealogies suggest that Iberian and North African wall lizards (Podarcis spp.) are an assemblage of incipient species.从核基因谱系推断出的基因流非平衡估计表明，伊比利亚和北非壁蜥（Podarcis属）是一组初始物种。
BMC Evol Biol. 2008 Feb 26;8:63. doi: 10.1186/1471-2148-8-63.
5
A new approach to estimate parameters of speciation models with application to apes.一种估计物种形成模型参数的新方法及其在猿类中的应用。
Genome Res. 2007 Oct;17(10):1505-19. doi: 10.1101/gr.6409707. Epub 2007 Aug 21.
6
Evolution of population structure in a highly social top predator, the killer whale.高度社会化顶级捕食者虎鲸的种群结构演变
Mol Biol Evol. 2007 Jun;24(6):1407-15. doi: 10.1093/molbev/msm063. Epub 2007 Mar 30.
7
Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics.整合到费尔森斯坦方程中以改进群体遗传学中的马尔可夫链蒙特卡罗方法。
Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2785-90. doi: 10.1073/pnas.0611164104. Epub 2007 Feb 14.
8
Studies on Hybrid Sterility. II. Localization of Sterility Factors in Drosophila Pseudoobscura Hybrids.杂种不育性研究。二、果蝇拟暗果蝇杂种不育因子的定位。
Genetics. 1936 Mar;21(2):113-35. doi: 10.1093/genetics/21.2.113.
9
Recent advances in assessing gene flow between diverging populations and species.评估分化种群和物种间基因流动的最新进展。
Curr Opin Genet Dev. 2006 Dec;16(6):592-6. doi: 10.1016/j.gde.2006.10.005. Epub 2006 Oct 19.
10
Inferring phylogeny despite incomplete lineage sorting.尽管存在不完全谱系分选仍能推断系统发育。
Syst Biol. 2006 Feb;55(1):21-30. doi: 10.1080/10635150500354928.
Zotero 插件