Data from: Evaluating mechanisms of diversification in a Guineo-Congolian tropical forest frog using demographic model selection

Portik DM, Leaché AD, Rivera D, Barej MF, Burger M, Hirschfeld M, Rödel M, Blackburn DC, Fujita MK

Date Published: July 19, 2017

DOI: http://dx.doi.org/10.5061/dryad.7p7n2

 

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Title ddRADSeq Data Files
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Description We include the output haplotypes.tsv file resulting from the populations module of Stacks, our custom filtered haplotypes files, and the resulting input files generated for various programs from the filtered haplotypes file. The filtering and input files were generated as part of the pipeline developed for processing ddRADseq data, available at https://github.com/dportik/Stacks_pipeline.
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Title Arlequin Data Files and Results
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Description We include all input files for the mtDNA and SNPs data sets to perform various partitioning schemes of AMOVA. The commands for running Arlecore are included, along with a results folder for each input file.
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Title BEAST data files
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Description We include the xml input file for the mtDNA BEAST analysis, along with resulting log file and maximum clade credibility tree.
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Title EEMS
Downloaded 4 times
Description We include several folders of data files required to run the estimating effective migration surfaces program. This includes the conversion of the plink file to bed format, the output of the bed2diffs module (to create dissimilarity matrix), and finally the actual input files for running EEMS. We include the results of the analysis along with an R script for plotting.
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Title Structure
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Description We include three folders of data, representing analyses of particular populations sets (all, Northern, Southern). The input files, parameter files, and results from StructureHarvester are included in each directory.
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Title dadi Data files
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Description We include a directory for each of our 2D-JSFS analyses. Within each directory is the SNPs format input file, the optimized model results, and the plot for each model tested. This work resulted from the pipeline available at https://github.com/dportik/dadi_pipeline.
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Title SNAPP
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Description We include the xml input file for two runs of the SNAPP BEAST analysis, along with resulting log and tree files and combined maximum clade credibility tree.
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Title Admixture Data Files and Results
Downloaded 2 times
Description We include two folders of data, representing analyses of particular populations sets (Northern, Southern), and an R script for generating plots from cross-validation error values. The input files were analyzed using the admixture pipeline available at: https://github.com/dportik/Phylo_Wrapper_Scripts/tree/master/Admixture
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When using this data, please cite the original publication:

Portik DM, Leaché AD, Rivera D, Barej MF, Burger M, Hirschfeld M, Rödel M, Blackburn DC, Fujita MK (2017) Evaluating mechanisms of diversification in a Guineo-Congolian tropical forest frog using demographic model selection. Molecular Ecology, online in advance of print. http://dx.doi.org/10.1111/mec.14266

Additionally, please cite the Dryad data package:

Portik DM, Leaché AD, Rivera D, Barej MF, Burger M, Hirschfeld M, Rödel M, Blackburn DC, Fujita MK (2017) Data from: Evaluating mechanisms of diversification in a Guineo-Congolian tropical forest frog using demographic model selection. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.7p7n2
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