DOI: 10.5061/dryad.0zpc8674w
title: Fejervarya mtDNA phylogenetics files

description: 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.
description: 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).
description: # 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
 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). --- # Description of the
 data and file structure These are the individual names and descriptions of
 the files in this DRYAD repository. All files (.fas, .log, .phy, .tre,
 .trees, .xml) can be viewed in a standard text editor. 1.
 iskandari_IQTree.phy A phyllip alignment of 16S and COI for frogs
 belonging to the Fejervarya iskandari species complex. It contains 90
 sequences (including outgroups) and the total sequence length is 1552 base
 pairs. 2. iskandari IQTree results.txt The results from Maximum Likelihood
 analysis of the iskandari_IQTree.phy file with IQTree software. 3.
 cancrivora+verruculosa_IQTree.phy A phyllip alignment of 16S and COI for
 frogs belonging to the Fejervarya cancrivora and verruculosa species
 complexes. It contains 428 sequences (including outgroups) and the total
 sequence length is 1590 base pairs. 4. cancrivora_verruculosa_IQTree
 results.txt The results from Maximum Likelihood analysis of the
 cancrivora+verruculosa_IQTree.phy file with IQTree software. 5.
 iskandari_beast.fas 15 of the 16S + COI sequences from the
 iskandari_IQTree.phy file listed above chosen to estimate major lineage
 divergence events in BEAST. 6. iskandari_beast.xml The parameter file used
 to run divergence dating analyses on the iskandari_beast.fas alignment in
 BEAST2. 7. iskandari_beast run1.log BEAST run log file for the first run
 on the iskandari dataset. This file can be read with the software TRACER,
 or combined with the second run log file with the software LogCombiner. 8.
 iskandari_beast run1.trees Saved tree files from the first run on the
 iskandari dataset. This file can be summarized with the software
 TreeAnnotator, or combined with the second run tree file with the software
 LogCombiner. 9. iskandari_beast run2.log BEAST run log file for the second
 run on the iskandari dataset. This file can be read with the software
 TRACER, or combined with the first run log file with the software
 LogCombiner. 10. iskandari_beast run2.trees Saved tree files from the
 second run on the iskandari dataset. This file can be summarized with the
 software TreeAnnotator, or combined with the first run tree file with the
 software LogCombiner. 11. iskandari_combined.trees The combined trees from
 runs 1 and 2 of the iskandari dataset after the removal of the first 25%
 of trees from each run as burn in. The tree files were combined with the
 software LogCombiner, and can be summarized with the software
 TreeAnnotator. 12. iskandari_combined.tre The maximum clade credibility
 tree produced from summarizing the iskandari_combined.trees file with the
 software TreeAnnotator. This phylogenetic tree can be viewed with the
 software FigTree. 13. verruculosa_beast.fas 25 of the 16S + COI sequences
 from the verruculosa_IQTree.phy file listed above chosen to estimate major
 lineage divergence events in BEAST. 14. verruculosa_beast.xml The
 parameter file used to run divergence dating analyses on the
 verruculosa_beast.fas alignment in BEAST2. 15. verruculosa_beast run1.log
 BEAST run log file for the first run on the verruculosa dataset. This file
 can be read with the software TRACER, or combined with the second run log
 file with the software LogCombiner. 16. verruculosa_beast run1.trees Saved
 tree files from the first run on the verruculosa dataset. This file can be
 summarized with the software TreeAnnotator, or combined with the second
 run tree file with the software LogCombiner. 17. verruculosa_beast
 run2.log BEAST run log file for the second run on the verruculosa dataset.
 This file can be read with the software TRACER, or combined with the first
 run log file with the software LogCombiner. 18. verruculosa_beast
 run2.trees Saved tree files from the second run on the verruculosa
 dataset. This file can be summarized with the software TreeAnnotator, or
 combined with the first run tree file with the software LogCombiner. 19.
 verruculosa_combined.trees The combined trees from runs 1 and 2 of the
 verruculosa dataset after the removal of the first 25% of trees from each
 run as burn in. The tree files were combined with the software
 LogCombiner, and can be summarized with the software TreeAnnotator. 20.
 verruculosa_combined.tre The maximum clade credibility tree produced from
 summarizing the verruculosa_combined.trees file with the software
 TreeAnnotator. This phylogenetic tree can be viewed with the software
 FigTree. --- # Sharing/Access information All sequences greater than 200
 base pairs in length are deposited in GenBank. Accession numbers are found
 in the supplemental materials of: Tanoyo AN, Reilly SB, Doughty P, Arida
 E, Iskandar DT, McGuire JA (In Press) Systematics and biogeography of
 Lesser Sunda paddy frogs (Dicroglossidae: Fejervarya): a long-awaited
 revision. Records of the Western Australian Museum.