{"title":"IM 模型下的家谱不对称和基因流动的双染色体检验。","authors":"Alexander Mackintosh, Derek Setter","doi":"10.1093/genetics/iyae157","DOIUrl":null,"url":null,"abstract":"<p><p>Methods for detecting gene flow between populations often rely on asymmetry in the average length of particular genealogical branches, with the ABBA-BABA test being a well known example. Currently, asymmetry-based methods cannot be applied to a pair of populations and such analyses are instead performed using model-based methods. Here we investigate genealogical asymmetry under a two-population Isolation with Migration model. We focus on genealogies where the first coalescence event is between lineages sampled from different populations, as the external branches of these genealogies have equal expected length as long as there is no post-divergence gene flow. We show that unidirectional gene flow breaks this symmetry and results in the recipient population having longer external branches. We derive expectations for the probability of this genealogical asymmetry and propose a simple statistic (Am) to detect it from genome sequence data. Am provides a two-taxon test for gene flow that only requires a single unphased diploid genome from each population, with no outgroup information. We use analytic expectations and simulations to explore how recombination, unequal effective population sizes, bidirectional gene flow and background selection influence Am and find that the statistic provides unambiguous evidence for gene flow under a continent-island history. We estimate Am for genome sequence data from Heliconius butterflies and Odocoileus deer, generating results consistent with previous model-based analyses. Our work highlights a signal of gene flow overlooked to date and provides a method that complements existing approaches for investigating the demographic history of recently diverged populations.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":3.3000,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631468/pdf/","citationCount":"0","resultStr":"{\"title\":\"Genealogical asymmetry under the IM model and a two-taxon test for gene flow.\",\"authors\":\"Alexander Mackintosh, Derek Setter\",\"doi\":\"10.1093/genetics/iyae157\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Methods for detecting gene flow between populations often rely on asymmetry in the average length of particular genealogical branches, with the ABBA-BABA test being a well known example. 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We use analytic expectations and simulations to explore how recombination, unequal effective population sizes, bidirectional gene flow and background selection influence Am and find that the statistic provides unambiguous evidence for gene flow under a continent-island history. We estimate Am for genome sequence data from Heliconius butterflies and Odocoileus deer, generating results consistent with previous model-based analyses. 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引用次数: 0
摘要
检测种群间基因流动的方法通常依赖于特定谱系分支平均长度的不对称性,ABBA-BABA 检验就是一个众所周知的例子。目前,基于非对称性的方法无法应用于一对种群,此类分析只能使用基于模型的方法。在这里,我们研究了双种群隔离与迁移模型下的系谱不对称性。我们将重点放在从不同种群采样的世系之间发生第一次聚合事件的系谱上,因为只要没有分化后的基因流动,这些系谱的外部分支具有相同的预期长度。我们的研究表明,单向基因流动会打破这种对称性,导致接受种群具有更长的外部分支。我们推导出了这种系谱不对称概率的期望值,并提出了一个简单的统计量(Am)来从基因组序列数据中检测这种不对称。Am 提供了一种基因流的双群检验方法,它只需要每个种群的一个未分期的二倍体基因组,不需要外群信息。我们利用分析期望和模拟来探讨重组、有效种群大小不等、双向基因流动和背景选择如何影响 Am,并发现该统计量为大陆-岛屿历史下的基因流动提供了明确的证据。我们对 Heliconius 蝴蝶和 Odocoileus 鹿的基因组序列数据进行了 Am 估算,结果与之前基于模型的分析一致。我们的工作强调了迄今为止被忽视的基因流信号,并提供了一种方法来补充现有的调查新近分化种群人口历史的方法。
Genealogical asymmetry under the IM model and a two-taxon test for gene flow.
Methods for detecting gene flow between populations often rely on asymmetry in the average length of particular genealogical branches, with the ABBA-BABA test being a well known example. Currently, asymmetry-based methods cannot be applied to a pair of populations and such analyses are instead performed using model-based methods. Here we investigate genealogical asymmetry under a two-population Isolation with Migration model. We focus on genealogies where the first coalescence event is between lineages sampled from different populations, as the external branches of these genealogies have equal expected length as long as there is no post-divergence gene flow. We show that unidirectional gene flow breaks this symmetry and results in the recipient population having longer external branches. We derive expectations for the probability of this genealogical asymmetry and propose a simple statistic (Am) to detect it from genome sequence data. Am provides a two-taxon test for gene flow that only requires a single unphased diploid genome from each population, with no outgroup information. We use analytic expectations and simulations to explore how recombination, unequal effective population sizes, bidirectional gene flow and background selection influence Am and find that the statistic provides unambiguous evidence for gene flow under a continent-island history. We estimate Am for genome sequence data from Heliconius butterflies and Odocoileus deer, generating results consistent with previous model-based analyses. Our work highlights a signal of gene flow overlooked to date and provides a method that complements existing approaches for investigating the demographic history of recently diverged populations.
期刊介绍:
GENETICS is published by the Genetics Society of America, a scholarly society that seeks to deepen our understanding of the living world by advancing our understanding of genetics. Since 1916, GENETICS has published high-quality, original research presenting novel findings bearing on genetics and genomics. The journal publishes empirical studies of organisms ranging from microbes to humans, as well as theoretical work.
While it has an illustrious history, GENETICS has changed along with the communities it serves: it is not your mentor''s journal.
The editors make decisions quickly – in around 30 days – without sacrificing the excellence and scholarship for which the journal has long been known. GENETICS is a peer reviewed, peer-edited journal, with an international reach and increasing visibility and impact. All editorial decisions are made through collaboration of at least two editors who are practicing scientists.
GENETICS is constantly innovating: expanded types of content include Reviews, Commentary (current issues of interest to geneticists), Perspectives (historical), Primers (to introduce primary literature into the classroom), Toolbox Reviews, plus YeastBook, FlyBook, and WormBook (coming spring 2016). For particularly time-sensitive results, we publish Communications. As part of our mission to serve our communities, we''ve published thematic collections, including Genomic Selection, Multiparental Populations, Mouse Collaborative Cross, and the Genetics of Sex.