Coalescent_analyses

The potential effects of independent lineage sorting on our dataset were explored by performing coalescent analyses with ASTRAL-III v. 5.7.7 (Zhang et al., 2018). ASTRAL-III is a java program for estimating a species tree given a set of unrooted gene trees, each inferred from a different part of a genome. This approach aims to explain the genealogical discordances between gene trees and species trees which might be caused by incomplete lineage sorting (Zhang et al., 2018). Gene trees were reconstructed from 2055 UCE loci retained in the 70% dataset, 1235 UCE loci retained by 80% dataset and 88 UCE loci retained by the 90% dataset. We estimated gene trees using the following command in IQ-TREE version 2.1.2 (Minh et al., 2020): iqtree2 -S ALN_DIR --prefix loci -T AUTO.

我们采用ASTRAL-III v. 5.7.7（Zhang等，2018）开展溯祖分析，以此探究独立谱系分选对本数据集的潜在影响。ASTRAL-III是一款基于Java开发的程序，可基于一系列非根基因树推断物种树，其中每棵基因树均由基因组的不同区域推导而来。该方法旨在阐释由不完全谱系分选（incomplete lineage sorting）引发的基因树与物种树之间的系统发育拓扑冲突。本研究的基因树分别基于三类位点集构建：70%数据集保留的2055个超保守元件（Ultraconserved Element, UCE）位点、80%数据集保留的1235个UCE位点，以及90%数据集保留的88个UCE位点。我们使用IQ-TREE v2.1.2（Minh等，2020）执行以下命令以推断基因树：iqtree2 -S ALN_DIR --prefix loci -T AUTO。