Concordance and discordance in the phylogenomics of the wrasses and parrotfishes (Teleostei: Labridae)
Data files
Sep 29, 2022 version files 220.52 MB
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Appendix2_Alignments_Trees.zip
160.62 MB
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Appendix3_BEASTFiles.zip
2.09 MB
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Appendix4_GeneTrees.zip
21.49 MB
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Appendix5_Introgression.zip
36.31 MB
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README.md
1.08 KB
Jan 29, 2025 version files 220.52 MB
-
Appendix2_Alignments_Trees.zip
160.62 MB
-
Appendix3_BEASTFiles.zip
2.09 MB
-
Appendix4_GeneTrees.zip
21.49 MB
-
Appendix5_Introgression.zip
36.31 MB
-
README.md
1.35 KB
Abstract
Phylogenomic analysis of large genome-wide sequence data sets can resolve phylogenetic tree topologies for large species groups, help test the accuracy of and improve resolution for earlier multilocus studies, and reveal the level of agreement or concordance within partitions of the genome for various tree topologies. Here we used a target-capture approach to sequence more than 1,000 single-copy exons for more than 200 labrid fishes together with more than 100 outgroup taxa to generate a new data-rich phylogeny for the family Labridae. Our time-calibrated phylogenetic analysis of exon-capture data pushes the root node age of the family Labridae back into the Cretaceous to about 79 Ma years ago. The monotypic Centrogenys vaigiensis, and the order Uranoscopiformes (stargazers) are identified as the sister lineages of Labridae. The phylogenetic relationships among major labrid subfamilies and within these clades was largely congruent with prior analyses of select mitochondrial and nuclear datasets. However, the position of the tribe Cirrhilabrini (fairy and flame wrasses) showed discordance, resolving either as the sister to a crown julidine clade or alternatively sister to a group formed by the labrines, cheilines and scarines. Exploration of this pattern using multiple approaches leads to slightly higher support for this latter hypothesis, highlighting the importance of genome-level data sets for resolving short internodes at key phylogenetic positions in large, economically important groups of coral reef fishes.
Phylogenetic trees and matrices from: Concordance and Discordance in the Phylogenomics of Wrasses and Parrotfishes (Teleostei: Labridae).
Description of the Data and file structure
Supplemental Tables and Figures (Zenodo)
Supplemental Tables S1-S2: SupplementaryTables_S1-S2.docx
Table S1: Voucher Information
Table S2: Genome & transcriptome accession numbers
Supplemental Figures S1-S28: SupplementalFigures_S1-S28.pdf
Appendices
Appendix1_FossilCalibrations.docx (Zenodo)
- Contains all references and justifications for fossil placements. See also Fig. S1.
- Labridae_Hedman2010.R: R code for determining soft upper bounds of fossil calibrations. (Zenodo)
Appendix2_Alignments&Trees.zip
- Contains all concatenated alignments, ML and ASTRAL trees, and concordance factors.
Appendix3_BEASTFiles.zip
- Contains all .xml files and MCC trees from the four BEAST runs.
Appendix4_GeneTrees.zip
- Contains gene alignments, partitioned models, and trees for all loci, used as input for ASTRAL.
Appendix5_Introgression.zip
- Contains all resampled trees and observed concordance factors. R code for calculating Delta is hosted on Zenodo.
Change Log
Jan 2025: Added Labridae_Hedman2010.R which was previously missing
See ReadMe.docx for an explanation of Supplemental Tables, Figures, and Appendices.