Fejervarya mtDNA phylogenetics files

These sequence data were collected from cycle sequenced PCR products of the 16S ribosomal RNA gene and COI gene, both part of the mitochondrial genome. They were sequenced on an ABI 3730 sequencer. Forward and reverse read of the PCR prodects were combined in GENEIOUS and aligned with Clustal Omega. The alignment was analyzed in IQTree with automatic model selection according to Bayesian information criterion (BIC) scores and nodal support determined with 1000 ultrafast bootstrap replicates and 1000 replicates of the single branch test. Lineage divergence times were estimated using the Bayesian phylogenetic software BEAST2 v2.7We chose a subset of samples representing the major mitochondrial lineages identified by the ML analysis and chose samples with both genes sequenced when available. The program was run under the GTR+G model of sequence evolution, which was the highest supported model from IQTree implemented in beast2. Because we are examining intrageneric divergence, we used a strict molecular clock model assuming a rate of 1.3% lineage divergence per million years (estimated for the 16S gene in a group of ranid frogs). Two separate analyses were run for 50 million generations, sampled every 5000 generations. After completion the log files were viewed in TRACER v1.7 to confirm that parameters had converged by checking that the effective sample size (ESS) values for each parameter were greater than 200, and also to confirm that both runs converged on the same posterior distribution. After discarding 25% of the samples as burn-in from each of the two runs, the remaining 15,000 trees were combined to generate a maximum clade credibility tree for which the branch lengths represent time, specifically millions of years ago (Ma).