Predictability and parallelism in the contemporary evolution of hybrid genomes.
Predictability and parallelism in the contemporary evolution of hybrid genomes.
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DOI：
10.1371/journal.pgen.1009914
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发表时间：
2022-01
期刊：
影响因子：
4.5
通讯作者：
Schumer M
中科院分区：
文献类型：
--
作者：
Langdon QK;Powell DL;Kim B;Banerjee SM;Payne C;Dodge TO;Moran B;Fascinetto-Zago P;Schumer M
物种间的杂交在整个生命之树上非常普遍。因此，包括人类在内的许多物种，其基因组的某些区域都来自于杂交。尽管认识到这一过程是普遍存在的，但我们对杂交后基因组如何稳定知之甚少，以及驱动这种稳定的机制是否倾向于跨物种共享。在这里，我们剖析了剑尾鱼（Xiphophorus birchmanni × X. cortezi）和剑尾鱼（X. birchmanni × X. malinche）两种物种间复制杂交事件中本地祖先变异的驱动因素。我们意外地发现，在两种类型的杂交种群中，本地祖先的可重复性很高。这种可重复性部分归因于这样一个事实，即重组景观和功能重要元素的位置在驱动两种类型杂交群体的本地祖先变异方面发挥了主要作用。除了这些广泛的模式之外，我们还确定了基因组的数十个区域，其中次要亲本祖先在物种对中异常低或高。对这些区域的分析表明，在物种对之间的选择中存在共同的位点，在某些情况下，存在共同的选择机制。我们发现其中一个这样的区域是一个以前未知的杂交不亲和性，它在X. birchmanni × X. cortezi和X. birchmanni × X. malinche杂交群体中共享。我们现在知道，杂交，或不同物种个体之间产生后代，在许多植物、动物和真菌群体中经常发生。因此，许多当代物种的基因组包含来自这些杂交事件的物质。与此同时，杂交可能对生物体的生存和繁殖能力产生负面影响。一个主要的问题是，是否有共同的原则来决定基因组的哪些部分可以在物种之间移动，哪些不能。在这里，我们比较了几个独立形成的杂交种群的基因组，这些杂交种群分别是birchmanni和X. cortezi以及X. birchmanni和X. malinche，以开始解决这个问题。我们发现，在杂交种群中，重组率特别低或基因密度特别高的基因组区域更有可能来自为杂交贡献了大部分基因组的亲本物种。此外，我们确定了在两种类型的杂交群体中负相互作用的基因组区域。总之，我们的结果表明，不同物种对之间杂交的基因组结果在一定程度上是可预测的。
Hybridization between species is widespread across the tree of life. As a result, many species, including our own, harbor regions of their genome derived from hybridization. Despite the recognition that this process is widespread, we understand little about how the genome stabilizes following hybridization, and whether the mechanisms driving this stabilization tend to be shared across species. Here, we dissect the drivers of variation in local ancestry across the genome in replicated hybridization events between two species pairs of swordtail fish: Xiphophorus birchmanni × X. cortezi and X. birchmanni × X. malinche. We find unexpectedly high levels of repeatability in local ancestry across the two types of hybrid populations. This repeatability is attributable in part to the fact that the recombination landscape and locations of functionally important elements play a major role in driving variation in local ancestry in both types of hybrid populations. Beyond these broad scale patterns, we identify dozens of regions of the genome where minor parent ancestry is unusually low or high across species pairs. Analysis of these regions points to shared sites under selection across species pairs, and in some cases, shared mechanisms of selection. We show that one such region is a previously unknown hybrid incompatibility that is shared across X. birchmanni × X. cortezi and X. birchmanni × X. malinche hybrid populations. We now know that hybridization, or the production of offspring between individuals of different species, happens frequently across many plant, animal, and fungi groups. As a result, the genomes of many contemporary species contain material derived from these hybridization events. At the same time, hybridization can have negative consequences on an organism’s ability to survive and reproduce. One major question is whether there are shared principles that determine which parts of the genome can move between species and which cannot. Here, we compare the genomes of several independently formed hybrid populations between the fish species pairs of Xiphophorus birchmanni and X. cortezi as well as X. birchmanni and X. malinche to begin to address this question. We find that across hybrid populations, regions of the genome with especially low recombination rates or especially high gene density are more likely to be derived from the parent species that contributed the majority of the genome to hybrids. Moreover, we identify regions of the genome that negatively interact in both types of hybrid population. Together our results demonstrate that genomic outcomes of hybridization between distinct species pairs are in part predictable.
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影响因子：
4.9
作者：
Culumber, Z. W.;Fisher, H. S.;Rosenthal, G. G.
通讯作者：
Rosenthal, G. G.
影响因子：
5.8
作者：
Hickey, Glenn;Paten, Benedict;Haussler, David
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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：
64.8
作者：
Zoonomia Consortium
通讯作者：
Zoonomia Consortium
影响因子：
4.5
作者：
Kim BY;Huber CD;Lohmueller KE
通讯作者：
Lohmueller KE