DOI: 10.5061/dryad.8931zcs04
title: Compounding heterochrony shapes the salamander visual system across adaptive zones

description: Transitioning between disparate environments presents new physical
 challenges, and metamorphosis can provide solutions. The life cycles of
 most amphibians involve an aquatic-to-terrestrial transition and
 concomitant metamorphosis, but shifts in developmental timing
 (heterochrony) have also produced a wide variety of aquatic-only and
 terrestrial-only forms. Thyroid hormone signaling governs the timing of
 tissue transformation and may be a key mechanism behind the relationship
 between development and diversification of some metamorphic
 traits.  Here, we show that life-cycle mode and cave-adaptation
 (troglomorphy) through heterochrony primarily explain variation in
 salamander eyes and retina. Across levels of organization (organ/tissue),
 heterochrony led to serial reductions in the visual system of larval-form
 paedomorphs that lost metamorphosis. This pattern is compounded in
 larval-form paedomorphic lineages that subsequently transitioned to
 subterranean environments and evolved troglomorphic traits. Following
 Haller’s Rule, visual system investment declines across ontogeny but at a
 faster rate in paedomorphs and even faster (for eye size) in troglomorphs.
 Thyroid hormone typically increases eye size during metamorphosis,
 however, we show responsiveness is reduced in paedomorphs and lost or
 reversed in troglomorphs. Salamander visual system variation is an example
 of how alterations to hormone-mediated transformation can shift
 developmental trajectories and compound phenotypic modifications as
 species move into more specialized environments.
description: This database includes two files with data and one file with
 trees. Life cycle and habitat/ecological data were compiled from the
 literature and personal observations. Morphometric data are primarily
 external measurements. Retinal cell count data were from histological
 slides and published images. Names and codes for each variable are
 described in the README file. Posterior distribution of 1000 trees of 559
 taxa was reconstructed in BEAST. See the associated manuscript and
 electronic supplemental document for additional methodological details,
 alternative regime models, and specimen numbers.
description: # Compounding heterochrony shapes the salamander visual system across
 adaptive zones https://doi.org/10.5061/dryad.8931zcs04 This database
 includes: * one file with 1000 phylogenetic trees (chronograms). Life
 cycle and habitat/ecological data were compiled from the literature.
 Morphometric data are primarily external measurements. Retinal cell count
 data were from histological slides and published images. Posterior
 distribution of 1000 trees with 559 taxa was reconstructed in BEAST. * two
 data files containing the values used in phylogenetic comparative analyses
 * three files with base commands for BayesTraits, OUwie, PGLS, and Phylolm
 *See Manuscript and Electronic Supplemental Material for methodological
 details, alternative regime models, and specimen numbers. ### **TREES
 FILE: “1000_Chronograms_559_Salamander_lineages.tre”** A file with 1000
 post-burnin Bayesian Chronograms of 559 salamander lineages. Names match
 those listed in the data files. ### DATA FILE:
 “Eye_Retina_dataset_18Aug2025.csv”** Species: Lists 156 species (lineages)
 included in one or more of the analyses. LifeCycle is coded as three
 states: pd = obligate paedomorphic, bi = biphasic, dd = direct development
 Eco_LJ is the habitat/ecology of the larval/juvenile stage in 4
 categories: aquatic (lo = lotic or le = lentic) and terrestrial (gd =
 ground-dwelling or cb = climbing) Eco_A is the habitat/ecology of the
 adult stage in 4 categories: aquatic (lo = lotic or le = lentic) and
 terrestrial (gd = ground-dwelling or cb = climbing) Eco_SfTg is surface or
 “obligate” cave-dwelling as 2 categories:  sf = surface-dwelling or tg =
 troglomorphic (“obligate” cave-dwelling, but we acknowledge local
 exceptions). EWHL_Stg40 is the relative eye width at Harrison Embryonic
 stage 40. Eye width is scaled to head length. EWHW_H is the relative eye
 width at hatching regardless of embryonic staging. Eye width is scaled to
 head width. EWHW_LJ is the relative eye width at the larval/juvenile
 stage. Eye width is scaled to head width. EWHW_A is the relative eye width
 at the adult stage. Eye width is scaled to head width. RGC_dep_LJ is the
 depth of the RGC (Retinal Ganglion Cell) layer based on cell counts for
 the larval/juvenile stage. INL_dep_LJ is the depth of the INL (Inner
 Nuclear Layer) based on cell counts for the larval/juvenile stage.
 ONL_dep_LJ is the depth of the ONL (Outer Nuclear Layer) based on cell
 counts for the larval/juvenile stage. Total_dep_LJ is the total cell depth
 (RGC + INL + ONL) based on cell counts for the larval/juvenile stage.
 GC_dep_A is the depth of the RGC (Retinal Ganglion Cell) layer based on
 cell counts for the adult stage. INL_dep_A is the depth of the INL (Inner
 Nuclear Layer) based on cell counts for the adult stage. ONL_dep_A is the
 depth of the ONL (Outer Nuclear Layer) based on cell counts for the adult
 stage. Total_dep_A is the total cell depth (RGC + INL + ONL) based on cell
 counts for the adult stage. RGC_CompSectHW_LJ is the RGC count of a
 complete section for the larval/juvenile stage, scaled to head width.
 INL_CmpSectHW_LJ is the INL cell count of a complete section for the
 larval/juvenile stage, scaled to head width. ONL_CompSectHW_LJ is the ONL
 cell count of a complete section for the larval/juvenile stage, scaled to
 head width. Total_CompSectHW_LJ is the total (RCG + INL + ONL) cell count
 of a complete section for the larval/juvenile stage, scaled to head width.
 RGC_CompSectHW_A is the RGC count of a complete section for the adult
 stage, scaled to head width. INL_CmpSectHW_A is the INL cell count of a
 complete section for the adult stage, scaled to head width.
 ONL_CompSectHW_A is the ONL cell count of a complete section for the adult
 stage, scaled to head width. Total_CompSectHW_A is the total (RCG + INL +
 ONL) cell count of a complete section for the adult stage, scaled to head
 width. Cell_Sz is the cell size based on two 2D INL cell measurements
 Gnm_Sz is the genome size based on c-values from the literature
 GillL_Chng_TH is the measured percent change in gill length with 5 nM TH
 treatment for 21 days EW_Chng_TH is the measured percent change in eye
 width with 5 nM TH treatment for 21 days " - " Indicates no data
 ### **DATA FILE: “Discrete_Photoreceptor_dataset_18Aug2025.txt” (tab
 delimited)** Species: Lists 559 species (lineages) included in one or more
 of the multistate and discrete analyses. LifeCycle is coded as three
 states: pd = obligate paedomorphic, bi = biphasic, dd = direct development
 Eco_SfTg is surface or “obligate” cave-dwelling as 2 categories:  1 =
 surface-dwelling or 0 = troglomorphic (“obligate” cave-dwelling, but we
 acknowledge local exceptions). PHOTO_LJ is whether the photoreceptor
 segment is present 1 or absent 0 for Larvae/Juveniles PHOTO_A is whether
 the photoreceptor segment is present 1 or absent 0 for Adults Data is only
 included when observed. Otherwise, we used " - ", which is a
 missing data symbol for BayesTraits. " - " Indicates no data ###
 **ANALYSIS FILE: “BAYESTRAITS_COMMANDS_12April2025.rtf” - Run in Mac
 Terminal BayesTraits v4.1.1 was used to reconstruct ancestral life cycle
 modes (pd, bi, dd) and ecology (sf, tg) using an exponential prior set to
 0.0005. It was also used to test for associations (Dependencies) between
 binary traits. Specifically, we tested whether troglomorphy is dependent
 on paedomorphosis and the loss of the photoreceptive segment (PHOTO) in
 larvae/juveniles and adults. ### **ANALYSIS FILE:
 “OUwie_COMMANDS_6Aug2025.R” - Run in R OUwie v 2.10 was used to compare
 the fit of various life cycle and ecological models to continuous
 variables (relative eye size and various retinal cell depth measurements).
 This approach allows for testing hypotheses of evolutionary shifts in the
 optimum (θ) and rate of evolution (σ2) of a continuous trait in response
 to different categorical selective regimes, such as life cycle mode
 (paedomorphic, biphasic, direct development) and/or habitat (obligate
 cave, aquatic, terrestrial). Models are defined in the Electronic
 Supplemental Materials document. ### **ANALYSIS FILE:
 “PGLS_and__Phylolm_COMMANDS_12April2025” - Run in R We used Phylogenetic
 Generalized Least Squares (PGLS) implemented in the R package caper to
 determine whether genome size (c-value) is correlated with retinal cell
 size (based on 2D measurements of INL soma), which could impact retinal
 cell parameters. Also included in the file are base codes for Phylogenetic
 Linear Regressions, which we used to test for differences in life cycle
 mode or habitat/ecology on retinal variables (RGC and INL depth) while
 accounting for covariates, genome size, or cell size.