3RAD datasets used for phylogenomic, species delimitation, biogeography, and introgression analyses on Dugesia from Corsica and Sardinia

Speciation is a complex process where many evolutionary forces interplay. The Mediterranean is acknowledged as one of the most relevant biodiverse areas in the Palearctic region and researchers have long studied the species inhabiting it to pursue the goals of evolutionary biology. Here, we study a complex of freshwater flatworm species of the genus Dugesia from Corsica and Sardinia using restriction site-associated DNA sequencing (specifically, 3RAD) data to unravel their evolutionary history and tackle the processes driving it. We assess the phylogenetic relationships and population structure within the group and evaluate new species boundaries using multispecies coalescent approaches. Furthermore, we offer insights into the environmental niche model of the group and use said model to guide our sampling efforts and collect and present molecular evidence for the first time of Dugesia leporii specimens, endemic from Sardinia last spotted in 1999. Our results indicate that paleoclimatic ..., , , # Dols-Serrate\_et\_al\_2025\_3RAD\_Dugesia

[https://doi.org/10.5061/dryad.v15dv4274](https://doi.org/10.5061/dryad.v15dv4274)

## Description of the data and file structure

Demultiplexed data and datasets used for phylogenomic, biogeography, and introgression analyses on *Dugesia* species from Corsica and Sardinia.

### Files and variables

#### File: `Dols-Serrate_et_al_MPE_2025.tar.gz`

**Description:** These data were generated using the 3RAD sequencing protocol (details in Supplementary Materials and Methods) and processed with the Stacks v2.52 de novo pipeline (available at: [https://catchenlab.life.illinois.edu/stacks/manual/](https://catchenlab.life.illinois.edu/stacks/manual/)). The dataset includes demultiplexed sequencing data for all 90 samples, representing multiple *Dugesia* species from Corsica and Sardinia.

Files contained within `Dols-Serrate_et_al_MPE_2025.tar.gz` :

1\) `Demultiplexed_data_90sample.tar.gz`

A compressed file containing all **demultiplexed RAD pair-...,