Bayes_phylogram_Ligia_oceanica_CO1

Bayesian tree by MrBayes 3.2.1 (Ronquist et al., 2012) for the 61 CO1 haplotypes of Ligia oceanica. The most appropriate model was determined beforehand using the Bayesian information criterion (BIC) as implemented in jModeltest 2.1.1 (Darriba et al., 2012), indicating TPM1uf+I+G to be the optimal nucleotide substitution model with the following parameters: nucleotide frequencies A: 0.27, C: 0.19, G: 0.17, T: 0.37; substitution rates RAC: 1, RAG: 13.33, RAT: 4.63, RCG: 4.63, RCT: 13.33, RGT: 1; gamma distribution shape = 0.48; and proportion of invariable sites = 0.38. The Bayesian analysis employed 10,000,000 Markov chain Monte Carlo (MCMC) generations in two parallel runs, each with three cold chains and one hot chain. Trees were sampled every 500th generation, with the number of burn-in generations being determined using the likelihood scores over all generations in Tracer 1.5 (Rambaut & Drummond, 2007). The determination of the split frequencies in both independent runs (< 0.01) with 2 x 20,001 tree samples showed good convergence after 5,000 sampled trees (split frequency < 0.01), which was therefore set as the burn-in.