Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis.
Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis.
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DOI：
10.1111/mec.13544
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发表时间：
2016-06
影响因子：
4.9
通讯作者：
Nakhleh L
中科院分区：
文献类型：
--
作者：
Wen D;Yu Y;Hahn MW;Nakhleh L
杂交和随后的渐渗的作用已在越来越多的物种中得到证实。最近，方丹（Fontaine）等人（Science，347，2015，1258524）对冈比亚按蚊种复合体的六个成员进行了染色体组分析。他们的分析揭示了一个网状的进化历史，并指出了所有四个常染色体臂上的广泛基因渗入。该研究进一步强调了复杂的进化信号，即不完全谱系分选（ILS）和基因渗入的共同发生可能会在基因组分析中产生。虽然在研究中使用了基于树的方法，但系统发育网络提供了一个更自然的模型来捕捉网状进化历史。在这项工作中，我们重新分析了按蚊的数据，使用最近设计的框架，结合了多物种结合与系统发育网络。这个框架使我们能够同时捕获ILS和基因渗入，并形成了推断网状进化历史的统计方法的基础。新的分析揭示了一个具有多个杂交事件的系统发育网络，其中一些与原始研究中报道的不同。为了阐明整个基因组的基因渗入的程度和模式，我们设计了一种新的方法，量化每个基因组区域在系统发育网络中使用的网状分支。将该方法应用于蚊子数据集，揭示了所有染色体的进化历史。这项研究强调了“网络思维”的实用性和它可以发现的新见解，特别是在具有广泛基因树不一致性的大型数据集的基因组分析中。
The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of ‘network thinking’ and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence.
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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.
影响因子：
6.5
作者：
DeGiorgio, Michael;Degnan, James H.
通讯作者：
Degnan, James H.
DOI：
10.1093/bioinformatics/btq202
发表时间：
2010-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
van Iersel L;Kelk S;Rupp R;Huson D
通讯作者：
Huson D
影响因子：
64.8
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