Fejervarya mtDNA phylogenetics files

The Lesser Sunda Archipelago is one of the world’s most tectonically complex regions and hosts a unique assemblage of amphibian species. Paddy frogs (genus Fejervarya) occur throughout the region, but the distribution of each constituent species remains unclear. We present a set of mtDNA sequence data on the three paddy frog species (or species complexes) in the Lesser Sundas, F. cancrivora, F. iskandari, and F. verruculosa. These data were analyzed with the Maximum Likelihood phylogenetic software IQTree as well as the Bayesian phylogenetic software BEAST2. The DNA alignments, results files, log files, and tree files are deposited here., 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 str..., , # Mitochondrial DNA phylogenetic analyses run files for Lesser Sunda Fejervarya frogs

Written and prepared by Sean B. Reilly, January 2024

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 evol...