Datasets used for Western Mediterranean Dugesia phylotranscriptomic analyses

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 P..., 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 Dugesia species (Platyhelminthes: Tricaldida: Dugesiidae) from the Western Mediterranean region were analyzed., 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 1...,

地中海是古北界（Palaearctic region）中生物多样性最高的区域之一。本研究基于从转录组数据（transcriptomic data）中获取的单拷贝直系同源基因（single copy orthologs）大型数据集，探究了西地中海区域三角涡虫属（Dugesia）的演化历史。研究结果证实，该区域复杂的古地质历史是该属物种分化的重要驱动因素，物种形成过程伴随微板块与岛屿的形成。上述过程造就了3个主要生物地理支系的分化：伊比利亚-亚平宁-阿尔卑斯支系、科西嘉-撒丁岛支系，以及伊比利亚-非洲支系。本研究针对每个物种选取多个代表性样本，对这些主要支系的内部亲缘关系展开分析。借助基因座与样本数量均可观的大型数据集，以及当前最先进的系统发育组学（phylogenomic）推断方法，我们得以解答此前关于特定类群演化的诸多未决问题，例如伊比利亚半岛中亚热带三角涡虫（D. subtentaculata）的分化路径。本数据集的获取流程参考了公开于https://github.com/lisy87/dugesia-transcriptome的系统发育转录组学工作流中的中间步骤，该工作流包含执行所有分析步骤所需的全部脚本与命令。
经过筛选后，本研究共分析了来自西地中海区域的82份三角涡虫属（Dugesia）物种样本（扁形动物门：三肠目（Tricladida）：三角涡虫科（Dugesiidae））。
数据说明：
本数据集的获取流程参考了公开于https://github.com/lisy87/dugesia-transcriptome的系统发育转录组学工作流。经过筛选后，本研究共分析了来自西地中海区域的82份三角涡虫属（Dugesia）物种样本（扁形动物门：三肠目（Tricladida）：三角涡虫科（Dugesiidae））。所有文件均采用FASTA格式。
文件分组如下：
1) *_longiso_pep.fasta
最长异构体蛋白序列
此类文件包含从Transdecoder输出结果（*.pep）中提取的最长异构体序列，此类序列作为正交同源基因搜索的输入文件供Orthofinder使用。每个样本对应一个独立文件。

2) OG*_SC_**_prot.fasta 与 OG*_SC_**_nuc.fasta
单拷贝正交群（Single Copy orthogroups, SC）：
此类文件包含每个单拷贝正交群（OG*）的核苷酸序列（*_nuc.fasta）与蛋白序列（*_prot.fasta）。每个文件包含对应每个样本的一条代表性序列。
**：本次共开展了3次正交同源基因搜索，分别为"all""subte"与"etru-ligu"，由此分别得到717个单拷贝正交群（all组）、4175个单拷贝正交群（subte组）以及1...