DOI: 10.5061/dryad.jh9w0vt7s
title: Using demographic model selection to untangle allopatric divergence and diversification mechanisms in the Rheum palmatum complex in the Eastern Asiatic Region

description: Allopatric divergence is often initiated by geological uplift and
 restriction to sky-islands, climate oscillations, or river capture.
 However, it can be difficult to establish which mechanism was the most
 likely to generate the current phylogeographic structure of a species.
 Recently, genomic data in conjunction with a model testing framework have
 been applied to address this issue in animals. To test whether such an
 approach is also likely to be successful in plants we used population
 genomic data of the Rheum palmatum complex from the Eastern Asiatic
 Region, in conjunction with biogeographical reconstruction and demographic
 model selection to identify the potential mechanism(s) which have led to
 the current level of divergence. Our results indicate that the R. palmatum
 complex originated in the central Hengduan Mts. and possibly in regions
 further to the east, and then dispersed westward and eastward resulting in
 genetically distinct lineages. Populations are likely to have diverged in
 refugia during climate oscillations followed by subsequent expansion and
 secondary contact. However, model simulations within the western lineage
 of the R. palmatum complex cannot reject a restriction to sky-islands as a
 possible mechanism of diversification due to the genetically ambiguous
 position of one population. This highlights that genetically mixed
 populations might introduce ambiguity regarding the best diversification
 model in some cases. Although it might be possible to resolve this
 ambiguity using other data, sometimes this could prove to be difficult in
 complex biogeographic areas.
description: The input files and R scripts which are used for model-testing
 framework (dadi), Bayesian clustering and biogeographical reconstruction
 based on genomic data (i.e., SLAF-seq data).
description: <b>BioGeoBEARS Data files</b> We
 include the input files and R script which used for the analyses of
 ancient distribution reconstruction. <b>dadi Data
 files</b> We include a script for each of our
 2D-JSFS and 3D-JSFS analyses. <b>DAPC Data
 files</b> We include the input file and R script
 which used for DAPC analyses.
 <b>EEMS</b> 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 a R script for plotting.
 <b>singleRandomSNP_haplotype Data files</b>
 We include Python script, input file and result file for
 generating the FIRST SNP site within a locus if the locus has more than
 one SNP site. <b>SNAPP</b>
 We include the xml input file for the SNAPP BEAST analysis, along
 with the combined maximum clade credibility tree.
 <b>Stacks results</b> We include
 two files (i.e., DH_0805_p35_r075.batch_1.vcf and
 DH_0805_p35_r075.haplotypes.tsv) after using the workflow of Stacks
 v1.48. Stacks.rar
 <b>Structure</b> We include the
 input file for the Structure program.