DOI: 10.5061/dryad.z612jm6r1
title: Distinct evolutionary signatures underlie body shape diversity across deep-sea habitats

description: The deep sea is known for extreme biological conditions such as high
 pressure, little to no solar light, and cold temperatures. Despite these
 challenges, deep-sea fishes have been shown to have higher body shape
 diversity than shallow-sea relatives. An open question is whether
 different habitats within the deep sea differentially contribute to this
 surprising phenotypic diversity. Here, we explore the joint effects of two
 major environmental dimensions in marine ecosystems, the benthic-pelagic
 axis and ocean depth, on phenotypic diversification in teleost fishes.
 Using measurements of body shape across nearly 3,000 species, we found
 that increasing ocean depth generally shifted axes of phenotypic evolution
 and promoted diversification for benthic, demersal, and pelagic fishes
 alike. However, body shape diversity and rates of body shape evolution did
 not scale evenly across these habitat divisions. For benthic fishes, the
 rate increased more strongly than diversity with ocean depth, while the
 reverse was true for pelagic fishes. Analyses of historical transition
 rates showed that routes to colonizing deep-pelagic habitats have been
 more variable than those for colonizing deep-benthic habitats, suggesting
 that independent invasions from different sources may help explain the
 diversity of deep-pelagic fishes without invoking high evolutionary rates.
 Relaxed selection on body shape may also explain this diversity, as
 suggested by the extreme range of forms found in the deep pelagic,
 coinciding with an elongation axis shared by all deep-sea fishes. Overall,
 our results reveal a mosaic of pathways through which body plan diversity
 has accumulated across a large vertebrate radiation, underscoring the
 importance of considering finer-scale habitat variation in broad-scale
 evolutionary studies.
description: # Distinct evolutionary signatures underlie body shape diversity across
 deep-sea habitats Dryad DOI: https://doi.org/10.5061/dryad.z612jm6r1 Main
 file: dryad_package_Oct_14_2025.zip Dryad package prepared by Elizabeth
 Santos (neé Miller) on October 14, 2025 Contact with questions:
 [lizmiller2633@gmail.com](mailto:lizmiller2633@gmail.com) R scripts are
 designed to work with the R project "comp_methods.Rproj." Open
 this file first! This R project keeps all folders within a common
 directory so the scripts can all "talk" to each other ##
 Description of files: #### Folder "data" contains input files
 needed to run all analyses **"pruned_rab.tre"** is a
 newick-formatted time-calibrated phylogenetic tree originally published by
 Rabosky et al. 2018, with taxa pruned to match sampling of marine species
 with body shape data (see Table S2).
 **"size_corrected_morph_withcombined_hab_cats.csv"** contains
 body shape variables and habitat data that are input into all analyses. *
 column B "tip_name" matches the tip label in the Rabosky et al.
 phylogeny ("pruned_rab.tre") * Columns C–J contain eight body
 shape variables published by Price et al. 2022 (for methods of collection
 see Price et al. 2019). These variables have been size-adjusted using
 log-shape ratios (see Methods section) * Column K
 "final_combined_habitat" merges the depth classification with
 the water-column-use classification (see below) with an underscore in the
 middle. There are nine categories in total after merging. (referred to as
 "nine-state scheme" throughout our manuscript) * Column L
 "depth_cat" contains the categorical depth classifications for
 each marine species published by Martinez et al. 2021, with no
 modifications * column M "water_col" contains the categorical
 water-column-use classifications for each marine species published by
 Friedman et al. 2020, with no modifications * Column N
 "merged_benthic_dem_cat" is a reclassification of column K after
 subsuming the "benthic" category into the "demersal"
 category (here called simply 'demersal'). This is referred to as
 the 'six-state scheme' throughout our manuscript. #### Folder
 "morphospace": **"plot morphospaces.R"** is an R
 script that reproduces morphospace panels shown in Fig. 1 and Fig. S1 The
 folders "density_panels" and
 "density_panels_merged_demersal" are empty folders meant to
 corral outputs exported by this R script #### Folder
 "phyloMANOVA": **"phyloMANOVA.R"** is an R script that
 reproduces phylogenetic MANOVA analyses and exports results to this folder
 (see Tables S7, S8) #### Folder "simmap":
 **"simmap.R"** is an R script that reproduces SIMMAP analyses
 and exports results to this folder #### Folder "hypervolumes":
 **"hypervolumes.R"** is an R script that calculates observed
 hypervolume size and pairwise comparisons of hypervolume overlap among
 habitats (e.g., Fig. 3, Fig. S8, and red bars of Figs. S6 and S7) The same
 script calculates distributions of permuted hypervolumes for comparison
 with the observed values (see Table S13 and Figs. S6–S7) This script is
 modified from those published by Corn et al. 2022 (link to Zenodo
 repository within script) #### Folder
 "geomorph_rates_disparity_comparison": **"geomorph
 disparity and rates.R"** calculates phenotypic disparity and
 evolutionary rates by habitat (see Fig. 3, Tables S9–12, Fig. S8) ####
 Folder "pairwise_angles": The scripts
 **"functions.R"** and **"run.R"** (written by Sarah
 Friedman) are meant to work together to replicate the analyses comparing
 angles of primary axes of morphological variation (see Fig. 2, Figs. S3
 and S4, Table S5 and S6) The "functions.R" script contains
 custom functions setting up the analyses, and is read by the
 "run.R" script to control running the analyses
 "output" folder is empty and meant to corral outputs associated
 with these scripts only Scripts are modified from those used in Friedman
 et al. 2022 Syst. Biol. ##### Relevant references below: Corn, K. A., S.
 T. Friedman, E. D. Burress, C. M. Martinez, O. Larouche, S. A. Price, and
 P. C. Wainwright. 2022. The rise of biting during the Cenozoic fueled reef
 fish body shape diversification. Proc. Natl. Acad. Sci. U.S.A.
 119:e2119828119. Friedman, S. T., S. A. Price, K. A. Corn, O. Larouche, C.
 M. Martinez, and P. C. Wainwright. 2020. Body shape diversification along
 the benthic–pelagic axis in marine fishes. Proceedings of the Royal
 Society B: Biological Sciences 287:20201053. Friedman, S. T., M. L.
 Collyer, S. A. Price, and P. C. Wainwright. 2022. Divergent Processes
 Drive Parallel Evolution in Marine and Freshwater Fishes. Systematic
 Biology 71:1319–1330. Martinez, C. M., S. T. Friedman, K. A. Corn, O.
 Larouche, S. A. Price, and P. C. Wainwright. 2021. The deep sea is a hot
 spot of fish body shape evolution. Ecology Letters 24:1788–1799. Price, S.
 A., S. T. Friedman, K. A. Corn, C. M. Martinez, O. Larouche, and P. C.
 Wainwright. 2019. Building a Body Shape Morphospace of Teleostean Fishes.
 Integrative and Comparative Biology 59:716–730. Price, S. A., S. T.
 Friedman, K. A. Corn, O. Larouche, K. Brockelsby, A. J. Lee, M. Nagaraj,
 N. G. Bertrand, M. Danao, M. C. Coyne, J. R. Estrada, R. Friedman, E.
 Hoeft, M. Iwan, D. Gross, J. H. Kao, B. Landry, M. J. Linares, C. McGlinn,
 J. A. Nguyen, A. G. Proffitt, S. Rodriguez, M. R. Rupp, E. Y. Shen, V.
 Susman, A. J. Tovar, L. L. J. Vary, K. L. Zapfe, and P. C. Wainwright.
 2022. FishShapes v1: Functionally relevant measurements of teleost shape
 and size on three dimensions. Ecology 103:e3829. Rabosky, D. L., J. Chang,
 P. O. Title, P. F. Cowman, L. Sallan, M. Friedman, K. Kaschner, C.
 Garilao, T. J. Near, M. Coll, and M. E. Alfaro. 2018. An inverse
 latitudinal gradient in speciation rate for marine fishes. Nature
 559:392–395.