DOI: 10.5061/dryad.9kd51c5mw
title: Datasets used for Western Mediterranean Dugesia phylotranscriptomic analyses

description: The Mediterranean is one of the most biodiverse areas of the Paleartic
 region. Here, basing on large data sets of single copy orthologs obtained
 from transcriptomic data, we investigated the evolutionary history of the
 genus Dugesia in the Western Mediterranean area. The
 results corroborated that the complex paleogeological history of the
 region was an important driver of diversification for the genus,
 speciating as microplates and islands were forming. These processes led to
 the differentiation of three main biogeographic clades:
 Iberia-Apennines-Alps, Corsica-Sardinia, and Iberia-Africa. The internal
 relationships of these major clades were analysed with several
 representative samples per species. The use of large data sets regarding
 the number of loci and samples, as well as
 state-of-the-art phylogenomic inference methods allowed us to answer
 different unresolved questions about the evolution of particular groups,
 such as the diversification path of D. subtentaculata in
 the Iberian Peninsula and its colonization of Africa. Additionally, our
 results support the differentiation of D. benazzii in two
 lineages which could represent two species. Finally, we analysed here for
 the first time a comprehensive number of samples from several asexual
 Iberian populations whose assignment at the species level has been an
 enigma through the years. The phylogenies obtained with different
 inference methods showed a branching topology of asexual individuals at
 the base of sexual clades. We hypothesize that this unexpected topology is
 related to long-term asexuality. This work represents the first
 phylotranscriptomic analysis of Tricladida, laying the first stone of the
 genomic era in phylogenetic studies on this taxonomic group.
description: This data has been obtained
 from intermediate steps described in the Phylotranscriptomic workflow
 available at https://github.com/lisy87/dugesia-transcriptome that includes all necessary scripts and commands to perform every step. After filtering, 82 samples of <em>Dugesia </em>species (Platyhelminthes: Tricaldida: Dugesiidae) from the Western Mediterranean region were analyzed.
description: Data Description: This data has been obtained
 from intermediate steps described in the Phylotranscriptomic workflow
 available at https://github.com/lisy87/dugesia-transcriptome. After
 filtering, 82 samples of Dugesia species (Platyhelminthes: Tricaldida:
 Dugesiidae) from Western Mediterranean region were analyzed. All files are
 in fasta format. Groups of files: 1)
 *_longiso_pep.fasta Protein sequence of longest
 isorforms These files contain the longest isorfoms
 obtained from Transdecoder output (*.pep), which were the input files in
 the orthologs searches with Orthofinder. One file by sample is
 available.   2)
 OG*_SC_**_prot.fasta     
 OG*_SC_**_nuc.fasta.  Single Copy orthogroups
 (SC): These files contain the nucleotide (*_nuc.fasta)
 and protein (*_prot.fasta) sequences of every SC (OG*). Every file
 contains one representative sequence by sample.  **:
 “all”, “subte”, and “etru-ligu” are the three orthologs searches
 performed. For them were obtained: 717 SC (all), 4175 SC (subte), and 1984
 SC (etru-ligu).   3) 
 Align_Dataset_*.fasta Final alignments of nucleotide
 sequences. One alignment by dataset: Dataset 1: All
 samples retained after filtering (82 samples, “all” orthogroups search,
 717 SC) Dataset 2: Reduced Dataset 1 (29 samples, “all”
 orthogroups search, 717 SC)  Dataset 3: Reduced Dataset
 1 (13 samples, “all” orthogroups search, 717 SC)
 Dataset 4: Subtentaculata group (23 samples, “subte” orthogroups
 search, 4175 SC) Dataset 5: Etrusca-liguriensis group
 (36 samples, “etru-ligu” orthogroups search, 1984 SC)
 Dataset 6: Dataset 5 without samples from Berga (31 samples,
 “etru-ligu” orthogroups search, 1984 SC)