Data from: Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians.

University of Groningen research database (University of Groningen / Centre for Information Technology)

Abstract

This repository contains genetic sequences obtained from Hybrid-Enrichment and RAD sequencing protocols of the amphibian genera Discoglossus, Lissotriton, Rana and Triturus, as well as phylogenetic trees inferred from the RADseq data. This data was generated for the manuscript "Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians.", in which we tested the influence of the clustering threshold used to assemble RADseq data on downstream phylogenetic inferences. Details on the data generation and analyses can be found in the manuscript and related supplementary materials. The repository is organised as follow: -> Hybrid-Enrichment: alignments of the Hybrid-Enrichment markers in phylip/fasta format (with one subdirectory for each of the four datasets assembled: Discoglossus, Lissotriton, Rana, Triturus) --> RADseq: Assemblies and phylogenetic trees obtained from a RADseq protocol --> Assemblies: RADseq assemblies (complete loci sequences and SNP matrices, spreadsheets with assembly metrics). Divided into "iCT" (assemblies produced with 23 different intra-sample Clustering Threshold [iCT] and a fixed between-samples Clustering Threshold [bCT]) and "bCT" (assemblies produced with a fixed iCT and 23 different bCT). Both iCT and bCT are further divided in four sub-directories corresponding to the four datasets: Discoglossus, Lissotriton, Rana, Triturus) --> Trees: Phylogenetic trees inferred from the aforementionned assemblies. Divided into "iCT" (RAxML concatenation trees inferred from the assemblies with different iCTs) and "bCT" (RAxML concatenation trees and Tetrad species trees inferred from the assemblies with different bCTs).

Authors 17

1. Loïs Rancilhac

   Uppsala University

   Affiliation as printed

   Uppsala University

2. Florent Sylvestre

   Université Laval

   Affiliation as printed

   Université Laval

3. Carl R. Hutter

   Louisiana State University

   Affiliation as printed

   Louisiana State University

4. Jan W. Arntzen Aachen Naturalis Biodiversity Center

   Naturalis Biodiversity Center

   Affiliation as printed

   Naturalis Biodiversity Center

5. Wiesław Babik

   Jagiellonian University

   Affiliation as printed

   Jagiellonian University

6. Pierre‐André Crochet

   Centre d'Écologie Fonctionnelle et Évolutive

   Affiliation as printed

   Centre d'Écologie Fonctionnelle et Évolutive

7. Grégory Deso
   Affiliation as printed

   Association Herpétologique de Provence Alpes Méditerranée

8. Rémi Duguet
   Affiliation as printed

   Alcedo Faune et Flore

9. Pedro Galán

   Universidade da Coruña

   Affiliation as printed

   Universidade da Coruña

10. Maciej Pabijan

    Jagiellonian University

    Affiliation as printed

    Jagiellonian University

11. Mathieu Policain
12. Pauline Priol
    Affiliation as printed

    Statipop-Scientific consulting

13. Joana Sabino‐Pinto

    University of Groningen

    Affiliation as printed

    University of Groningen

14. Maria Capstick

    University of Glasgow

    Affiliation as printed

    University of Glasgow

15. Kathryn R. Elmer

    University of Glasgow

    Affiliation as printed

    University of Glasgow

16. Christophe Dufresnes

    Nanjing Forestry University

    Affiliation as printed

    Nanjing Forestry University

17. Miguel Vences

    Technische Universität Braunschweig

    Affiliation as printed

    Technische Universität Braunschweig