DOI: 10.5061/dryad.7p7n2
title: Data from: Evaluating mechanisms of diversification in a Guineo-Congolian tropical forest frog using demographic model selection

description: The accumulation of biodiversity in tropical forests can occur through
 multiple allopatric and parapatric models of diversification, including
 forest refugia, riverine barriers and ecological gradients. Considerable
 debate surrounds the major diversification process, particularly in the
 West African Lower Guinea forests, which contain a complex geographic
 arrangement of topographic features and historical refugia. We used
 genomic data to investigate alternative mechanisms of diversification in
 the Gaboon forest frog, Scotobleps gabonicus, by first identifying
 population structure and then performing demographic model selection and
 spatially explicit analyses. We found that a majority of population
 divergences are best explained by allopatric models consistent with the
 forest refugia hypothesis and involve divergence in isolation with
 subsequent expansion and gene flow. These population divergences occurred
 simultaneously and conform to predictions based on climatically stable
 regions inferred through ecological niche modelling. Although forest
 refugia played a prominent role in the intraspecific diversification of S.
 gabonicus, we also find evidence for potential interactions between
 landscape features and historical refugia, including major rivers and
 elevational barriers such as the Cameroonian Volcanic Line. We outline the
 advantages of using genomewide variation in a model-testing framework to
 distinguish between alternative allopatric hypotheses, and the pitfalls of
 limited geographic and molecular sampling. Although phylogeographic
 patterns are often species-specific and related to life-history traits,
 additional comparative studies incorporating genomic data are necessary
 for separating shared historical processes from idiosyncratic responses to
 environmental, climatic and geological influences on diversification.
description: ddRADSeq Data
 FilesWe 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.ddRADSeq.zipArlequin Data Files and ResultsWe 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.Arlequin.zipBEAST data filesWe include the xml input file for the mtDNA BEAST analysis, along with resulting log file and maximum clade credibility tree.BEAST.zipEEMSWe 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.StructureWe 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.dadi Data filesWe 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.dadi.zipSNAPPWe 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.Admixture Data Files and ResultsWe 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/AdmixtureAdmixture.zip