Recent origin of a range-restricted species with subsequent introgression in its widespread congener in the Phyteuma spicatum group (Campanulaceae)

Understanding the causes of restricted geographic distributions is of major interest to evolutionary and conservation biologists. Inferring historical factors has often relied on ad hoc interpretations of genetic data, and hypothesis testing within a statistical framework under different demographic scenarios remains underutilized. Using coalescent modeling on RAD-sequencing data we (i) test hypotheses about the origin of Phyteuma gallicum (Campanulaceae), a range-restricted endemic of central France sympatric with its widespread congener P. spicatum, and (ii) date its origin, irrespective of its mode of origin, to test the hypothesis that the restricted range is due to a recent time of origin. The best-supported model of origin is one of a dichotomous split of P. gallicum, confirmed as a distinct species, and the Central European P. nigrum with subsequent gene flow between P. gallicum and P. spicatum. The split of Ph. gallicum and P. nigrum is estimated at 45–55,000 years ago. Coalesce..., Leaf material along with voucher specimens from several sampling sites for each study taxon were sampled in the field and stored in silica-gel. DNA was extracted using the Invisorb Spin Plant Mini Kit (Invitec Molecular, Berlin, Germany) following the manufacturer’s protocol with one modification. The genomic extracts were cleaned with NucleoSpin gDNA Clean‑up. RAD libraries were prepared using a custom protocol.
The reads were demultiplexed and quality filtered using BamIndexDecoder from illumina2bam 1.03 and process_radtags from Stacks2 2.41. assembly was done using denovo_map.pl script from Stacks2. We retained polymorphic RADtags with a maximum of 60% missing data across individuals and a maximum of ten SNPs per locus using a combination of populations from Stacks2 and a custom script. Additionally, we retained only loci identified as belonging to a spermatophyte by blasting the RADtags against the BLAST databases.
We further mapped the raw reads of all individuals against an artifi..., , # Recent origin of a range-restricted species with subsequent introgression in its widespread congener in the *Phyteuma spicatum* group (Campanulaceae)

[https://doi.org/10.5061/dryad.8gtht76x2 ](https://doi.org/10.5061/dryad.8gtht76x2)10.5061/dryad.8gtht76x2

This dataset contains the files used to reconstruct the phylogenetic structure between *P. gallicum* and its closest relatives *P. nigrum*, *P. spicatum,* and *P. pyrenaicum,* and any potentially reticulate relations between them using *Splitstree*, PCA (Principal Components Analysis), and *sNMF* and the data files used to test the best coalescent model and the divergence time using *Fastsimcoal2*.

## Description of the data and file structure

The files for each step are placed in separate folders numerated by their order. For example, 01_artifical_reference_mapping_snp_calling contains the files of the first step.

### 1. Artificial reference, mapping, and SNP calling

First, the optimal parameters for de novo assembly are tes...