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.

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).

BioGeoBEARS Data files

We include the input files and R script which used for the analyses of ancient distribution reconstruction.

dadi Data files

We include a script for each of our 2D-JSFS and 3D-JSFS analyses.

DAPC Data files

We include the input file and R script which used for DAPC analyses.

EEMS

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.

singleRandomSNP_haplotype Data files

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.

SNAPP

We include the xml input file for the SNAPP BEAST analysis, along with the combined maximum clade credibility tree.

Stacks results

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

Structure

We include the input file for the Structure program.