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

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.