Cenozoic evolutionary history obscures the Mesozoic origins of acanthopterygian fishes
Data files
Oct 28, 2024 version files 18.39 GB
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BEAST.zip
18.37 GB
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COI_Beryciformes.zip
53.58 KB
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gene_trees_mark_1.zip
467.73 KB
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Habitat_states_all.csv
6.66 KB
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IQ_TREE.zip
20.48 MB
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Larva__malesBiSSE.csv
8.48 KB
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README.md
2.31 KB
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Whalefishes_code.R
7.03 KB
Dec 20, 2024 version files 18.39 GB
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BEAST.zip
18.37 GB
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COI_Beryciformes.zip
53.58 KB
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gene_trees_mark_1.zip
467.73 KB
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Habitat_states_all.csv
6.66 KB
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IQ_TREE.zip
20.48 MB
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Larva__malesBiSSE.csv
8.45 KB
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README.md
2.42 KB
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Whalefishes_code.R
7.03 KB
Jan 20, 2025 version files 19.51 GB
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BEAST.zip
18.37 GB
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COI_Beryciformes.zip
53.58 KB
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gene_trees_mark_1.zip
467.73 KB
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Habitat_states_all.csv
6.66 KB
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HISSE.zip
137.86 KB
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IQ_TREE.zip
1.14 GB
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Larva__malesBiSSE.csv
8.45 KB
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README.md
2.93 KB
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Whalefishes_code.R
7.03 KB
Feb 04, 2025 version files 19.51 GB
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Ancestral_Reconstruction_Data.zip
10.31 KB
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BEAST.zip
18.37 GB
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COI_Beryciformes.zip
53.58 KB
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gene_trees_mark_1.zip
467.73 KB
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IQ_TREE.zip
1.14 GB
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README.md
2.57 KB
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Whalefishes_code.R
7.03 KB
Feb 10, 2025 version files 19.51 GB
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Ancestral_Reconstruction_Data.zip
10.31 KB
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BEAST.zip
18.37 GB
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COI_Beryciformes.zip
53.58 KB
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IQ_TREE.zip
1.14 GB
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README.md
2.68 KB
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Whalefishes_code.R
7.03 KB
Abstract
Sister lineage comparisons provide a valuable tool for understanding evolutionary origins of species-rich clades. Percomorpha, comprising over 18,900 species, represents one of the most species-rich vertebrate clades. However, the phylogenetic resolution of its sister lineage remains unclear, obscuring whether contrasts in histories of diversification provide insights into the factors that gave rise to this clade’s diversity. Using 887 ultraconserved element loci and Sanger-sequenced nuclear genes, we resolve the phylogenetic relationships of the three closest relatives of Percomorpha-the roughies, flashlightfishes, porcupinefishes, and fangtooths (Trachichthyiformes), the squirrelfishes and soldierfishes (Holocentridae), and the whalefishes, bigscales, and alfonsinos (Berycoidei)-and the placement of percomorphs among them. Contrary to expectations from the fossil record, we demonstrate that living lineages of Berycoidei, Holocentridae, and Trachichthyiformes all diversified after the Cretaceous-Paleogene mass extinction. Our findings show that multiple clades in Trachichthyiformes and Berycoidei independently colonized deep ocean habitats during the climatically unstable Eocene and Oligocene and shallow-water reefs during the extensive hotspot migration and faunal turnover of the Early Miocene. Due to their complex evolutionary history, the closest relatives of Percomorpha are not ideal for understanding the origins of this exceptionally species-rich clade.
https://doi.org/10.5061/dryad.s7h44j1gz
Description of the data and file structure
All data was either downloaded from Genbank or, in the case of newly-sequenced DNA, was sanger-sequenced from loaned or previously collected specimens.
Files and variables
File: Whalefishes_code.R
Description: R code for all analyses conducted in R in this study
File: Ancestral_Reconstruction_Data.zip
Description: Input data to R for life history trait ancestral state reconstructions
Files
- Habitat_phytools.csv: habitat states for phytools with references
- Habitat_states: habitat states for phytools direct input
- Reef_association: reef association states for phytools
- Larval_morphology_and_sexual_dimorphism: presence/absence of the megalomycterid male stage and larval morphologies for phytools
File: COI_Beryciformes.zip
Description: Sequence data and IQ-TREE output from the analysis of COI data from Berycoidea on Genbank
File: gene_trees_mark_1.zip
Description: Sequence data and IQ-TREE output from the analysis of Sanger-sequenced nuclear gene data (newly generated + Genbank); Genbank sequences are annotated with their NCBI accession numbers
File: IQ_TREE.zip
Description: IQTREE and ASTRAL outputs from the analysis of the UCE data from available contigs + UCEs extracted from available whole genome sequences on Genbank.
File: BEAST.zip
Description: Input and output for BEAST time calibration analyses.
Code/software
R/RStudio: for analyzing the csv files
IQ-TREE: all maximum likelihood analyses were conducted in IQ-TREE
BEAST: Bayesian time-calibration analysis was conducted in BEAST
Access information
Other publicly accessible locations of the data:
- NCBI Genbank
Data was derived from the following sources:
- NCBI Genbank
Change log
- Dec 2024: some formatting was modified in accordance with our revisions, including reorganization
- Jan 2025: added HiSSE output directory and IQTREE output directory with re-run analyses based on revised UCE set
- Feb 2025: removed diversification output directories (HiSSE) and input; these analyses were removed upon peer-review given that they are not relevant to the push of the paper and do not show any clear result; they are included in earlier versions for reference; reorganized files into Ancestral_Reconstruction_Data.zip and updated README.
- Feb 10 2025: removed gene-trees-mark1.zip, new sequences are uploaded to genbank and in Table 1 of the article.