Data from: Robustness of divergence time estimation despite gene tree error: A case study of fireflies (Coleoptera: Lampyridae)

Genomic data has become ubiquitous in phylogenomic studies, including
divergence time estimation, but provides new challenges. These challenges
include, amongst others, biological gene tree discordance, methodological
gene tree estimation error, and computational limitations on performing
full Bayesian inference under complex models. In this study, we use a
recently published firefly (Coleoptera: Lampyridae) anchored hybrid
enrichment dataset (AHE; 436 loci for 88 Lampyridae species and 10
outgroup species) as a case study to explore gene tree estimation error
and the robustness of divergence time estimation. First, we explored the
amount of model violation using posterior predictive simulations. We
specifically focused on missing data (either uniformly distributed or
systematically) and the distribution of highly variable and conserved
sites (either uniformly distributed or clustered). Our assessment of model
adequacy showed that standard phylogenetic substitution models are not
adequate for any of the 436 AHE loci which is likely to bias phylogenetic
inferences. We tested if the model violations resulted indeed in gene tree
estimation error by comparing the observed gene tree discordance to
simulated gene tree discordance under the multispecies coalescent model.
Thus, we show that the inferred gene tree discordance is not only due to
biological mechanisms but primarily due to inference errors. Lastly, we
explored if divergence time estimation is robust despite the observed gene
tree estimation error. We selected four subsets of the full AHE dataset,
concatenated each subset, and performed a Bayesian relaxed clock
divergence estimation in RevBayes. The estimated divergence times
overlapped for all nodes that are shared between the topologies. Thus,
divergence time estimation is robust using any well-selected data subset
as long as the topology inference is robust.