Limited effects of among-lineage rate variation on the phylogenetic performance of molecular markers

Variation in substitution rates among evolutionary lineages (among-lineage rate variation or ALRV) has been reported to negatively affect the estimation of phylogenies. When the substitution processes underlying ALRV are modeled inadequately, non-sister taxa with similar substitution rates are estimated incorrectly as sister species due to long-branch attraction. Recent advances in modeling site-specific rate variation (heterotachy) have reduced the impacts of ALRV on phylogeny estimation in several empirical and simulated datasets. However, the addition of parameters to the substitution model reduces power to estimate each parameter correctly, which can also lead to incorrect phylogeny estimation. A potential solution to this problem is to identify the levels of ALRV that negatively impact phylogeny estimation such that molecular markers with non-deleterious levels of ALRV can be identified. To this end, we used analyses of empirical and simulated gene datasets to evaluate whether levels of ALRV identified in a mitochondrial genomic dataset for salamanders negatively impacted phylogeny estimation. We simulated data with and without ALRV, holding all other evolutionary parameters constant, and compared the phylogenetic performance of both simulated and empirical datasets. Overall, we found limited, positive effects of ALRV on phylogeny estimation in this dataset, the majority of which resulted from an increase in substitution rate on short branches. We conclude that ALRV does not always negatively impact phylogeny estimation. Therefore, ALRV can likely be disregarded as a criterion for marker selection in comparable phylogenetic studies.