Fejervarya mtDNA phylogenetics files
Data files
Feb 07, 2024 version files 73.14 MB
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cancrivora_verruculosa_IQTree_results.txt
165.31 KB
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cancrivora_verruculosa_IQTree.phy
688.19 KB
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iskandari_beast_run1.log
3.18 MB
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iskandari_beast_run1.trees
6.26 MB
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iskandari_beast_run2.log
3.17 MB
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iskandari_beast_run2.trees
6.26 MB
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iskandari_beast.fas
23.48 KB
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iskandari_beast.xml
35.24 KB
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iskandari_combined.tre
13.44 KB
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iskandari_combined.trees
9.39 MB
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iskandari_IQTree_results.txt
46.56 KB
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iskandari_IQTree.phy
141.39 KB
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README.md
6.77 KB
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varruculosa_beast.xml
54.74 KB
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verruculosa_beast_run1.log
3.36 MB
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verruculosa_beast_run1.trees
10.55 MB
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verruculosa_beast_run2.log
3.36 MB
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verruculosa_beast_run2.trees
10.55 MB
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verruculosa_beast.fas
40.19 KB
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verruculosa_combined.tre
23.02 KB
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verruculosa_combined.trees
15.83 MB
Abstract
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.
README: 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.
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.iskandari IQTree results.txt
The results from Maximum Likelihood analysis of the iskandari_IQTree.phy file with IQTree software.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.cancrivora_verruculosa_IQTree results.txt
The results from Maximum Likelihood analysis of the cancrivora+verruculosa_IQTree.phy file with IQTree software.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.iskandari_beast.xml
The parameter file used to run divergence dating analyses on the iskandari_beast.fas alignment in BEAST2.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.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.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.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.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.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.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.verruculosa_beast.xml
The parameter file used to run divergence dating analyses on the verruculosa_beast.fas alignment in BEAST2.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.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.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.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.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.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.
Methods
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).