Tonini João, Moore Andrew, Stern David, Shcheglovitova Maryia, Ortí Guillermo
Department of Biological Sciences, The George Washington Univerisity, Washington, District of Columbia, USA.
Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA.
PLoS Curr. 2015 Mar 9;7:ecurrents.tol.34260cc27551a527b124ec5f6334b6be. doi: 10.1371/currents.tol.34260cc27551a527b124ec5f6334b6be.
Phylogeneticists have long understood that several biological processes can cause a gene tree to disagree with its species tree. In recent years, molecular phylogeneticists have increasingly foregone traditional supermatrix approaches in favor of species tree methods that account for one such source of error, incomplete lineage sorting (ILS). While gene tree-species tree discordance no doubt poses a significant challenge to phylogenetic inference with molecular data, researchers have only recently begun to systematically evaluate the relative accuracy of traditional and ILS-sensitive methods. Here, we report on simulations demonstrating that concatenation can perform as well or better than methods that attempt to account for sources of error introduced by ILS. Based on these and similar results from other researchers, we argue that concatenation remains a useful component of the phylogeneticist's toolbox and highlight that phylogeneticists should continue to make explicit comparisons of results produced by contemporaneous and classical methods.
系统发育学家早就明白，有几种生物学过程会导致基因树与其物种树不一致。近年来，分子系统发育学家越来越多地放弃传统的超级矩阵方法，转而采用物种树方法，这种方法考虑了一种错误来源，即不完全谱系分选（ILS）。虽然基因树与物种树的不一致无疑给利用分子数据进行系统发育推断带来了重大挑战，但研究人员直到最近才开始系统地评估传统方法和对ILS敏感方法的相对准确性。在此，我们报告模拟结果，表明串联法的表现可以与试图考虑ILS引入的错误来源的方法一样好，甚至更好。基于这些以及其他研究人员的类似结果，我们认为串联法仍然是系统发育学家工具箱中的一个有用工具，并强调系统发育学家应该继续对当代方法和经典方法产生的结果进行明确比较。
