Assessing the sensitivity of divergence time estimates to locus-sampling, calibration points, and model priors in a RAD-seq phylogeny of Carex section Schoenoxiphium

In this study, we investigate the sensitivity of Bayesian relaxed clock estimates of divergence times to alternative analytical decisions on an empirical RAD-seq phylogenetic matrix. We explored the relative contribution of secondary calibration strategies (a single constraint in the root vs multiple constraints, including the root), amount of missing data (both nucleotide removals and deletion of individuals), and the data partition analyzed (i.e., which RAD-seq loci were subsampled for Bayesian MCMC) to overall variance in divergence times inferred using BEAST MCMC analyses of a well-characterized sedge clade, Carex section Schoenoxiphium (Cyperaceae).