Bayesian Divergence Time Estimation and Evolutionary Rate Analysis of Potamidae Crabs

Beast v1.8.4 (Drummond et al., 2012 ) was used to estimate the divergence time with Bayesian analysis method. A beast XML file was generated by BEAUTi v1.8.3 using an uncorrelated lognormal‐distribution relaxed‐clock model and a Yule speciation process as the tree prior. Two fossil constraints were used in this study: the Palaemonoidea (including E. carinicauda and M. lanchesteri) and the Alpheoidea (including A. distinguendus) diverged in Early Cretaceous (Albian) (99.6–112 Mya), the Astacidea species (including C. destructor, H. americanus, and P. clarkii) divergence occurred in Middle Triassic (Upper Ladinian) (227–234 Mya) (Porter et al., 2005 (link); Yang et al., 2012 (link)). These time estimates were assessed under the GTR + I + G model. The divergence times were sampled once every 1000 generations from 100 million Markov Chain Monte Carlo (MCMC) iterations after a burn‐in of the initial 50% cycles. Then the sampled trees were annotated by the TreeAnnotator v1.6.1 (BEAST software) and the visualization was conducted by Figtree v1.3.1. Finally, the Bayesian statistical significance of all parameters were evaluated by the ESSs values (ESS > 200) in TRACER v1.5 (Rambaut & Drummond, 2007 ).
To estimate the rate of evolution of these Potamidae species, EasyCodeML v 1.0 (Gao et al., 2019 (link)) procedure was used to estimate the ratio of nonsynonymous (dN) to synonymous (dS) substitution rates (ω = dN/dS) with a free‐ratio model (model = 1) based on the 13 concatenated PCGs of 34 Potamidae crabs.