DOI: 10.5061/dryad.280gb5mzc
title: Supplementary data from: Marine origins and freshwater radiations of the otophysan fishes

description: 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.
description: # 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 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](https://doi.org/10.5061/dryad.n9g60)