DOI: 10.5061/dryad.6q573n678
title: Phylogenomics of African <em>Labeo</em> (Cypriniformes: Cyprinidae) emphasizing central African species

description: Here we present the first large-scale phylogenomic analysis of the genus
 Labeo using 2,187 ultraconserved elements (UCEs) from 85 taxa, including
 56 recognized species, 27 cryptic (candidate) species, and outgroups from
 the Asian Labeonini. Concatenated and coalescence-based phylogenetic
 analyses both strongly support the monophyly of African Labeo and recover
 three main clades (designated here as subgenera) comprising at least nine
 species groups.
description: Libraries for the entire dataset were sent to and prepared by
 RAPiD Genomics (https://healthcare.rapid-genomics.com/services/) using the
 set of 6,737 baits developed by Faircloth et al. (2020) to target 2,708
 UCE loci. Sequencing of the captured UCEs also was performed by RAPiD
 Genomics on an Illumina Hiseq 2500 platform.
description: # Phylogenomics of African *Labeo* (Cypriniformes: Cyprinidae) emphasizing
 central African species
 [https://doi.org/10.5061/dryad.6q573n678](https://doi.org/10.5061/dryad.6q573n678) ## Description of the data and file structure ### Files and variables #### File: Supplementary_Materials_R2 **Description:** We submitted a compressed folder (Supplementary_materials_R2.zip) containing the following folders and files: * Appendix 1: contains tree files and trip identification * 99_specimens: list of six alternative Maximum likelihood (ML) and Astrall tree files (.tre) based on the dataset with 99 tips and different percentage of matrix completeness (75, 85, and 90 %) * Astral_tree_75percent_50collapse.tre * Astral_tree_85percent_50collapse.tre * Astral_tree_90percent_50collapse.tre * ML_tree_75percent.tre * ML_tree_85percent.tre * ML_tree_90percent.tre * 184_specimens: list of two ML alternative tree files (.tre) based on based on the dataset with 184 tips and a sheadsheet (.xlsx) with tips identification. * ML_tree_75percent.tre * ML_tree_90percent.tre * Tips_identifacation.xlsx * Appendix 2: UCE alignments files and R scripts used to run phylogenetic analyses using both concatenated (ML) and coalescent-based approaches: * Coalescent_R_Script.R * ML_R_Script.R * 184_specimens: dataset with 184 specimens * best_models_scheme_75_ML.nex * best_models_scheme_90_ML.nex * uces_alignment_fasta_files_75_percent_matrix: list of 1,589 UCE alignments in the 75 % complete matrix * uce-0.nexus.fasta * uce-3.nexus.fasta * uce-5.nexus.fasta * uce-6.nexus.fasta * uce-9.nexus.fasta * uce-14.nexus.fasta * uce-15.nexus.fasta * 
 
 etc * uces_alignment_fasta_files_90_percent_matrix: list of 185 UCE
 alignments in the 90 % complete matrix * uce-3.nexus.fasta *
 uce-14.nexus.fasta * uce-15.nexus.fasta * uce-40.nexus.fasta *
 uce-41.nexus.fasta * uce-43.nexus.fasta * uce-46.nexus.fasta * 
 
 etc * 99_specimens: dataset with 99 specimens *
 best_models_scheme_70_coalescent.txt * best_models_scheme_70_ML.nex *
 best_models_scheme_75_coalescent.txt * best_models_scheme_75_ML.nex *
 best_models_scheme_85_coalescent.txt * best_models_scheme_85_ML.nex *
 best_models_scheme_90_coalescent.txt * best_models_scheme_90_ML.nex *
 uces_alignment_fasta_files_70_percent_matrix: list of 2 187 UCE alignments
 in the 70 % complete matrix * uce-0.nexus.fasta * uce-2.nexus.fasta *
 uce-3.nexus.fasta * uce-5.nexus.fasta * uce-6.nexus.fasta *
 uce-9.nexus.fasta * uce-10.nexus.fasta * 
 
 etc * uces_alignment_fasta_files_75_percent_matrix: list of 2 090 UCE
 alignments in the 75 % complete matrix * uce-0.nexus.fasta *
 uce-3.nexus.fasta * uce-5.nexus.fasta * uce-6.nexus.fasta *
 uce-9.nexus.fasta * etc *
 uces_alignment_fasta_files_85_percent_matrix: list of 1 441 UCE
 alignments in the 85 % complete matrix * uce-0.nexus.fasta *
 uce-3.nexus.fasta * uce-5.nexus.fasta * uce-14.nexus.fasta *
 uce-15.nexus.fasta * etc *
 uces_alignment_fasta_files_90_percent_matrix: list of 739 UCE
 alignments in the 90 % complete matrix * uce-3.nexus.fasta *
 uce-14.nexus.fasta * uce-15.nexus.fasta * uce-21.nexus.fasta *
 uce-28.nexus.fasta * etc * Appendix 3: contains files used in ancestral
 range reconstruction. Included geographic ranges are: **A**: Asia, **AH**:
 Abyssinian Highlands, **C**: Congo, **EC**: East Coast, **LG**: Lower
 Guinea, **NS**: Nilo-Sudan, **Q**: Quanza, **S**: Southern, **UG**: Upper
 Guinea, **Z**: Zambezi. * BioGeo_distribution.txt: geographic distribution
 matrix [including each tip (taxon) in the time calibrated phylogenetic
 tree]. * dispersal_multipliers_M0.txt: dispersal scheme model M0 *
 dispersal_multipliers_M1.txt: dispersal scheme model M1 *
 Labeo_time_cal_tree.tre: time-calibrated phylogenetic tree * Appendix
 4: contains morphometric data used for PCA  * TableS3.csv: contribution of
 different morphometric characters in the total inertia of PC1 through PC5
 * TableS4.xlsx: morphometric data based on 17 characters, 60 species, and
 419 specimens of Labeo. * Appendix 5: contains files used for ancestral
 state reconstruction for the Urohyal *
 Labeo_time_cal_tree.tre: time-calibrated phylogenetic tree * Urohyal.txt:
 Urohyal character states matrix [including each tip (taxon) in the
 time-calibrated phylogenetic tree]. * Table S1.xlsx: Liste of all genetic
 samples (tissues) compiled for this study. * Table S2_R2.xlsx: List of all
 currently described and potentially undescribed African Labeo species
 placed in their respective clade and species groups. ## Code/software
 Figtree (a graphical viewer of phylogenetic trees) can be used to
 visualize phylogenetic trees. The rest of the data can be visualized by
 using any text editors (including Notepad++, BBedit, ...) and and excel. R
 scripts can be run using R (R Core Team 2013). ## Access information Other
 publicly accessible locations of the data: * NA Data was derived from the
 following sources: * NA