Estimation of divergence time for cytb gene.
Divergence times between Aporodon clades were inferred in BEAST2 (Bouckaert et al. 2014). We obtained a time-calibrated phylogeny using a Birth-Death model tree prior and an uncorrelated relaxed lognormal clock. Substitution rate and calibration nodes were established in the same way as in Martínez-Borrego et al. (2022a). MCMC analyses were executed with two runs of 10 million generations each, sampling once every 1000 generations. The BEAST log file was examined in Tracer (Rambaut et al. 2018) to assess the convergence of the independent runs, as well as the effective sample size (ESS≥200). A Maxime clade credibility tree was obtained in TreeAnotator after discarding the trees prior to the stationary phase as burn-in.
Geometric morphometrics of the R. mexicanus species complex