Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of the erato-sara Group of Heliconius Butterflies.
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of the erato-sara Group of Heliconius Butterflies.
复制标题
DOI：
10.1093/sysbio/syac009
复制
发表时间：
2022-08-10
影响因子：
6.5
通讯作者：
中科院分区：
文献类型：
--
作者：
渐渗杂交在许多物种群体的适应性进化和物种多样化中发挥着关键作用。然而，物种之间频繁的杂交和基因流动使得物种系统发育和关键种群参数的估计具有挑战性。在这里，我们表明，通过考虑分相并使用全似然方法，可以从全基因组序列数据可靠地估计渗入历史和群体参数。我们采用带有和不带有基因流的多物种合并（MSC）模型，利用来自 Heliconius 蝴蝶erato-sara 分支的六个成员的基因组数据来推断物种系统发育和跨物种渗入事件。由于深度合并，这些方法自然地适应了整个基因组谱系历史的随机波动。为了避免基因组组装方法通常产生的单倍体序列中的杂合子定相错误，我们处理和编译非定相二倍体序列比对，并使用分析方法对杂合子相位分辨率的不确定性进行平均。有强有力的证据表明基因组中存在基因渗入，无论是在系统发育深处的远亲物种之间，还是在树的浅层部分的姐妹物种之间。我们获得了关键种群参数的染色体特异性估计，例如基因渗入方向、时间和概率，以及现代和祖先物种的物种分化时间和种群规模。我们确认了 sara 进化枝和 Heliconius telesiphe 祖先种群之间的祖先基因流（Heliconius hecalesia 可能是杂交物种起源），以及姐妹种 Heliconiuserato 和 Heliconius Himera 之间的基因流。祖先物种之间推断的渐渗也解释了该群体系统发育深处的两次染色体倒位的历史。这项研究说明了基于 MSC 的全似然方法如何能够从基因组数据中提取物种分化和基因流的丰富历史信息。 [3秒； bpp;基因流；赫利科尼厄斯；杂种形成；基因渗入；反转；多物种聚结]
Introgressive hybridization plays a key role in adaptive evolution and species diversification in many groups of species. However, frequent hybridization and gene flow between species make estimation of the species phylogeny and key population parameters challenging. Here, we show that by accounting for phasing and using full-likelihood methods, introgression histories and population parameters can be estimated reliably from whole-genome sequence data. We employ the multispecies coalescent (MSC) model with and without gene flow to infer the species phylogeny and cross-species introgression events using genomic data from six members of the erato-sara clade of Heliconius butterflies. The methods naturally accommodate random fluctuations in genealogical history across the genome due to deep coalescence. To avoid heterozygote phasing errors in haploid sequences commonly produced by genome assembly methods, we process and compile unphased diploid sequence alignments and use analytical methods to average over uncertainties in heterozygote phase resolution. There is robust evidence for introgression across the genome, both among distantly related species deep in the phylogeny and between sister species in shallow parts of the tree. We obtain chromosome-specific estimates of key population parameters such as introgression directions, times and probabilities, as well as species divergence times and population sizes for modern and ancestral species. We confirm ancestral gene flow between the sara clade and an ancestral population of Heliconius telesiphe, a likely hybrid speciation origin for Heliconius hecalesia, and gene flow between the sister species Heliconius erato and Heliconius himera. Inferred introgression among ancestral species also explains the history of two chromosomal inversions deep in the phylogeny of the group. This study illustrates how a full-likelihood approach based on the MSC makes it possible to extract rich historical information of species divergence and gene flow from genomic data. [3s; bpp; gene flow; Heliconius; hybrid speciation; introgression; inversion; multispecies coalescent]
登录
查看更多内容
影响因子：
64.8
作者：
Dasmahapatra, Kanchon K.;Walters, James R.;Briscoe, Adriana D.;Davey, John W.;Whibley, Annabel;Nadeau, Nicola J.;Zimin, Aleksey V.;Hughes, Daniel S. T.;Ferguson, Laura C.;Martin, Simon H.;Salazar, Camilo;Lewis, James J.;Adler, Sebastian;Ahn, Seung-Joon;Baker, Dean A.;Baxter, Simon W.;Chamberlain, Nicola L.;Chauhan, Ritika;Counterman, Brian A.;Dalmay, Tamas;Gilbert, Lawrence E.;Gordon, Karl;Heckel, David G.;Hines, Heather M.;Hoff, Katharina J.;Holland, Peter W. H.;Jacquin-Joly, Emmanuelle;Jiggins, Francis M.;Jones, Robert T.;Kapan, Durrell D.;Kersey, Paul;Lamas, Gerardo;Lawson, Daniel;Mapleson, Daniel;Maroja, Luana S.;Martin, Arnaud;Moxon, Simon;Palmer, William J.;Papa, Riccardo;Papanicolaou, Alexie;Pauchet, Yannick;Ray, David A.;Rosser, Neil;Salzberg, Steven L.;Supple, Megan A.;Surridge, Alison;Tenger-Trolander, Ayse;Vogel, Heiko;Wilkinson, Paul A.;Wilson, Derek;Yorke, James A.;Yuan, Furong;Balmuth, Alexi L.;Eland, Cathlene;Gharbi, Karim;Thomson, Marian;Gibbs, Richard A.;Han, Yi;Jayaseelan, Joy C.;Kovar, Christie;Mathew, Tittu;Muzny, Donna M.;Ongeri, Fiona;Pu, Ling-Ling;Qu, Jiaxin;Thornton, Rebecca L.;Worley, Kim C.;Wu, Yuan-Qing;Linares, Mauricio;Blaxter, Mark L.;Ffrench-Constant, Richard H.;Joron, Mathieu;Kronforst, Marcus R.;Mullen, Sean P.;Reed, Robert D.;Scherer, Steven E.;Richards, Stephen;Mallet, James;McMillan, W. Owen;Jiggins, Chris D.
通讯作者：
Jiggins, Chris D.
三个物种的隔离与迁移模型的最大似然实现
影响因子：
6.5
作者：
Dalquen, Daniel A.;Zhu, Tianqi;Yang, Ziheng
通讯作者：
Yang, Ziheng
影响因子：
10.7
作者：
Hey, Jody
通讯作者：
Hey, Jody
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
--
DOI：
10.1126/science.1258524
发表时间：
2015-01-02
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Fontaine MC;Pease JB;Steele A;Waterhouse RM;Neafsey DE;Sharakhov IV;Jiang X;Hall AB;Catteruccia F;Kakani E;Mitchell SN;Wu YC;Smith HA;Love RR;Lawniczak MK;Slotman MA;Emrich SJ;Hahn MW;Besansky NJ
通讯作者：
Besansky NJ