Supplementary data from: Marine origins and freshwater radiations of the otophysan fishes

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.
, , , # Supplementary data from: Marine origins and freshwater radiations of the otophysan fishes

Dataset DOI: [10.5061/dryad.280gb5mzc](https://doi.org/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 ...,