Background: Cherleria (Caryophyllaceae) is a circumboreal genus that also occurs in the high mountains of the northern hemisphere. In this study, we focus on a clade that diversified in the European High Mountains, which was identified using nuclear ribosomal (nrDNA) sequence data in a previous study. With the nrDNA data, all but one species was monophyletic, with little sequence variation within most species. Here, we use genotyping by sequencing (GBS) data to determine whether the nrDNA data showed the full picture of the evolution in the genomes of these species.

Results: The overall relationships found with the GBS data were congruent with those from the nrDNA study. Most of the species were still monophyletic and many of the same subclades were recovered, including a clade of three narrow endemic species from Greece and a clade of largely calcifuge species. The GBS data provided additional resolution within the two species with the best sampling, C. langii and C. laricifolia, with structure that was congruent with geography. In addition, the GBS data showed significant hybridization between several species, including species whose ranges did not currently overlap.

Conclusions: The hybridization led us to hypothesize that lineages came in contact on the Balkan Peninsula after they diverged, even when those lineages are no longer present on the Balkan Peninsula. Hybridization may also have helped lineages expand their niches to colonize new substrates and different areas. Not only do genome-wide data provide increased phylogenetic resolution of difficult nodes, they also give evidence for a more complex evolutionary history than what can be depicted by a simple, branching phylogeny.

Most of the data are Genotyping by Sequencing data, gathered following the protocol of Elshire et al. (2011), modified following Dillenberger and Kadereit (2017).  The BamHI restriction enzyme was used to digest the DNA and gel extraction was used for size selection.  The data were analyzed using a modification of the RTD pipeline of Peterson et al. (2012), as described in Dillenberger and Kadereit (2017).  The scripts for the modification are on GitHub (https://github.com/abigail-Moore/GBS-analysis/).  Datasets, scripts, and results files involving these data are labeled GBS.

Some of the data are nuclear ribosomal DNA sequence data from the internal transcribed spacer (ITS) and external transcribed spacer (ETS) regions.  Datasets and results files involving these data are labeled nrDNA.

Some of the data are locality data.  The localities are a mixture of those the authors personally visited and those found on georeferenced herbarium specimens.  The identification of nearly all herbarium specimens (including all of them that came from regions where multiple species co-occurred) was verified before including them.

Details on the individual files are given in the ReadMe (README.txt).

Details on the sampling localities, voucher information, and GenBank and NCBI SRA numbers for each individual are given in the voucher table (Voucher_Table.txt).