Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses

In summary (two-step) coalescent analyses of empirical data, researchers typically apply the bootstrap to quantify branch support for clades inferred on the optimal species tree. We tested whether site-wise bootstrap analyses provide consistently more conservative support than gene-wise bootstrap analyses. We did so using data from three empirical phylogenomic studies and employed four coalescent methods (ASTRAL, MP-EST, NJst, and STAR). We demonstrate that application of site-wise bootstrapping generally resulted in gene-trees with substantial additional conflicts relative to the original data and this approach therefore cannot be relied upon to provide conservative support. Instead the site-wise bootstrap can provide high support for apparently incorrect clades. We provide a script (https://github.com/dbsloan/msc_tree_resampling) that implements gene-wise re-sampling, using either the bootstrap or the jackknife, for use with ASTRAL, MP-EST, NJst, and STAR. We demonstrate that the gene-wise bootstrap outperformed the site-wise bootstrap for the primary focal clades for all four coalescent methods that were applied to all three empirical studies. For summary coalescent analyses we suggest that gene-wise resampling support should be favored over gene + site or site-wise resampling when numerous genes are sampled because site-wise resampling causes substantially greater gene-tree-estimation error.