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.