Supplementary data from: Marine origins and freshwater radiations of the otophysan fishes
Data files
Oct 02, 2025 version files 30.27 KB
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Data_matrix_S1_R1_Morphological_characters_data_matrix_sim.nex
1.83 KB
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Data_matrix_S2_Revised_Morphological_characters_data_matrix_final_sim.nex
1.92 KB
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Data_S3_PP_R1_taxa.tsv
1.12 KB
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Data_S4_PP_R1_n6_range.nex
1.82 KB
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Data_S5_PP_R1_habitat.nex
1.61 KB
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Data_S6_PP_R1_habitat_binary.nex
1.61 KB
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README.md
4.20 KB
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Script_S1_PP_FBD_R1.Rev
1.34 KB
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Script_S2_model_FBDP.Rev
4.04 KB
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Script_S3_model_Morph.Rev
562 B
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Script_S4_model_GTRG.Rev
806 B
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Script_S5_model_UExp.Rev
908 B
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Script_S6_run_simple.Rev
2.92 KB
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Script_S7_make_anc_state.Rev
1.61 KB
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Script_S8_mcmc_ase_freeK.Rev
1.98 KB
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Script_S9_mcmc_ase_freeK_binary.Rev
1.99 KB
Abstract
Otophysans, known for their enhanced hearing enabled by the complex Weberian apparatus, comprise two-thirds of extant freshwater fish species. Previously, they were thought to have originated in freshwater before the breakup of Pangea, implying a nearly 80-million-year gap between the origin and the oldest known fossil. However, the discovery of a Late Cretaceous freshwater otophysan challenges this view. Integrating fossil, morphological, and genomic data, we estimate a younger crown group origin of ~154 million years ago. Notably, ancestral range and habitat reconstructions indicate marine origins for the otophysan crown groups, with at least two transitions to freshwater. Functional simulations of the Weberian ossicles of this fossil suggest that the distinctive hearing capabilities of otophysans evolved in conjunction with the fusion of hearing ossicle parts and freshwater adaptations.
Dataset DOI: 10.5061/dryad.280gb5mzc
Description of the data and file structure
Files Data_matrix_S1, Data_matrix_S2, and Data_S3 were used for the phylogenetic analyses.
- For maximum-parsimony analyses, use either Data_matrix_S1 or Data_matrix_S2.
- For combined-evidence analyses, use either Data_matrix_S1 or Data_matrix_S2 together with the genomic dataset from Chakrabarty et al. (2017; full citation below) and Data_S3.
Files Data_S4 was used for ancenstral geographic range estimation.
Files Data_S5 was used for ancestral habitate state estimation using independent rates model with multiple states.
Files Data_S6 was used for ancestral habitate state estimation using independent rates model with binary states.
Files and variables
File: Data_matrix_S1_R1_Morphological_characters_data_matrix_sim.nex
Description: morphological dataset of the original analysis.
File: Data_matrix_S2_Revised_Morphological_characters_data_matrix_final_sim.nex
Description: morphological dataset of the revised/additional analysis. Re-run the analysis only need either of this matrix or the S1, then combine with the genomic dataset as linked in the data page.
File: Data_S3_PP_R1_taxa.tsv
Description: a compiled list of taxon for the combined phylogenetic analysis.
Variables
- taxon: species appeared in morphological and molecular dataset
- min_age: minimum age (millions of years) of fossils as reported, or 0 for extant species.
- max_age: maximum age of fossils as reported, or 0 for extant species.
File: Data_S4_PP_R1_n6_range.nex
Description: coded geographical range of terminal taxa
File: Data_S5_PP_R1_habitat.nex
Description: coded habitat type of terminal taxa, multiple states
File: Data_S6_PP_R1_habitat_binary.nex
Description: coded habitat type of terminal taxa, binary states
Code/software
All of the following scripts were used with RevBayes v1.2.1: Script_S1–S5 for combined-evidence phylogenetic analyses; Script_S6–S7 to estimate ancestral ranges under the DEC model; and Script_S8–S9 to infer ancestral habitat states (multistate and binary, respectively).
File: Script_S1_PP_FBD_R1.Rev
Description: the master Rev file that loads the data, the separate model files and specifies the monitors and MCMC sampler.
File: Script_S2_model_FBDP.Rev
Description: specifies the model parameters and moves required for the fossilized birth-death range process prior on the tree topology, divergence times, fossil occurrence ranges, and diversification dynamics
File: Script_S3_model_Morph.Rev
Description: specifies the model describing discrete morphological character change (multi-states characters) under a morphological clock.
File: Script_S4_model_GTRG.Rev
Description: specifies the parameters and moves for the general time-reversible model of sequence evolution with gamma-distributed rates across sites (GTR+Γ).
File: Script_S5_model_UExp.Rev
Description: specifies the components of the uncorrelated exponential model of lineage-specific substitution rate variation.
File: Script_S6_run_simple.Rev
Description: Estimating ancestral ranges using DEC model and MCMC simulation and produce traces
File: Script_S7_make_anc_state.Rev
Description: compute and save the ancestral state tree
File: Script_S8_mcmc_ase_freeK.Rev
Description: estemate ancentral states using independent rates model freeK with multiple states
File: Script_S9_mcmc_ase_freeK_binary.Rev
Description: estemate ancentral states using independent rates model freeK with binary states
Access information
Genomic Data was derived from the following sources:
- Chakrabarty, Prosanta; Faircloth, Brant C.; Alda, Fernando et al. (2017). Data from: Phylogenomic systematics of Ostariophysan fishes: ultraconserved elements support the surprising non-monophyly of Characiformes [Dataset]. Dryad. https://doi.org/10.5061/dryad.n9g60