Schrago Carlos G, Mello Beatriz, Pereira Anieli G, Furtado Carolina, Seuánez Hector N
Department of Genetics Federal University of Rio de Janeiro Rio de Janeiro RJ Brazil.
Division of Genetics National Cancer Institute Rio de Janeiro Brazil.
Ecol Evol. 2017 Dec 20;8(2):1206-1216. doi: 10.1002/ece3.3736. eCollection 2018 Jan.
Multispecies coalescent (MSC) theory assumes that gene trees inferred from individual loci are independent trials of the MSC process. As genes might be physically close in syntenic associations spanning along chromosome regions, these assumptions might be flawed in evolutionary lineages with substantial karyotypic shuffling. Neotropical primates (NP) represent an ideal case for assessing the performance of MSC methods in such scenarios because chromosome diploid number varies significantly in this lineage. To this end, we investigated the effect of sequence length on the theoretical expectations of MSC model, as well as the results of coalescent-based tree inference methods. This was carried out by comparing NP with hominids, a lineage in which chromosome macrostructure has been stable for at least 15 million years. We found that departure from the MSC model in Neotropical primates decreased with smaller sequence fragments, where sites sharing the same evolutionary history were more frequently found than in longer fragments. This scenario probably resulted from extensive karyotypic rearrangement occurring during the radiation of NP, contrary to the comparatively stable chromosome evolution in hominids.
多物种合并（MSC）理论假设从各个基因座推断出的基因树是MSC过程的独立试验。由于基因在沿染色体区域的同线关联中可能在物理上紧密相邻，在具有大量核型重排的进化谱系中，这些假设可能存在缺陷。新热带灵长类动物（NP）是评估MSC方法在这种情况下性能的理想案例，因为该谱系中的染色体二倍体数差异很大。为此，我们研究了序列长度对MSC模型理论预期的影响，以及基于合并的树推断方法的结果。这是通过将NP与人类进行比较来实现的，在人类谱系中，染色体宏观结构至少在1500万年里一直保持稳定。我们发现，新热带灵长类动物中与MSC模型的偏差随着序列片段变小而减小，与较长片段相比，共享相同进化历史的位点在较小片段中更频繁出现。这种情况可能是由于NP辐射期间发生了广泛的核型重排，这与人类相对稳定的染色体进化形成对比。
