Phylogenomics of African Labeo (Cypriniformes: Cyprinidae) emphasizing central African species

Liyandja, Tobit L. D.1 ; Smith, Brian2 ; Alter, S. Elizabeth3 ; Sidlauskas, Brian4 ; Stiassny, Melanie2

Published Jan 27, 2026 on Dryad. https://doi.org/10.5061/dryad.6q573n678

Data files

Jan 27, 2026 version files 35.12 MB

README.md

5.32 KB
Supplementary_materials_R2.zip

35.12 MB

Abstract

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.

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:

Data was derived from the following sources: