Discipline of Mathematics, School of Physical Sciences, University of Tasmania, Hobart, Australia
Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
Genome Biol Evol. 2016 May 9;8(5):1299-315. doi: 10.1093/gbe/evw065.
We introduce a gene tree simulator that is designed for use in conjunction with approximate Bayesian computation approaches. We show that it can be used to determine the relative importance of hybrid speciation and introgression compared with incomplete lineage sorting (ILS) in producing patterns of incongruence across gene trees. Important features of the new simulator are (1) a choice of models to capture the decreasing probability of successful hybrid species formation or introgression as a function of genetic distance between potential parent species; (2) the ability for hybrid speciation to result in asymmetrical contributions of genetic material from each parent species; (3) the ability to vary the rates of hybrid speciation, introgression, and divergence speciation in different epochs; and (4) incorporation of the coalescent, so that patterns of incongruence due to ILS can be compared with those due to hybrid evolution. Given a set of gene trees generated by the simulator, we calculate a set of statistics, each measuring in a different way the discordance between the gene trees. We show that these statistics can be used to differentiate whether the gene tree discordance was largely due to hybridization, or only due to lineage sorting.
我们介绍了一个基因树模拟器，该模拟器专为与近似贝叶斯计算方法结合使用而设计。我们表明，它可用于确定杂种形成和基因渗入相对于不完全谱系分选（ILS）在产生跨基因树不一致模式方面的相对重要性。新模拟器的重要功能包括：（1）选择模型来捕获随着潜在亲本物种之间遗传距离的增加，成功杂种形成或基因渗入的可能性降低的情况；（2）杂种形成能够导致来自每个亲本物种的遗传物质的不对称贡献；（3）在不同时期改变杂种形成、基因渗入和分歧进化的速率的能力；（4）合并聚簇，以便将由于 ILS 引起的不一致模式与由于杂种进化引起的不一致模式进行比较。给定一组由模拟器生成的基因树，我们计算一组统计量，每个统计量以不同的方式测量基因树之间的不协调性。我们表明，这些统计量可用于区分基因树不协调性主要是由于杂交还是仅由于谱系分选造成的。
