DOI: 10.5061/dryad.bvq83bknf
title: Loss of a morph is associated with asymmetric character release in a radiation of woodland salamanders

description: Color polymorphism, the occurrence of multiple discrete color morphs with
 co-adapted sets of traits within the same population, may provide the raw
 materials for rapid species formation. It has been hypothesized that
 fixation of a single morph can result in character release, whereby the
 monomorphic form evolves without the constraint of accommodating multiple
 adaptive peaks. However, rates of evolution between populations fixed for
 different morphs likely depend on the specific adaptive zones occupied by
 each morph. We studied the evolution of dorsal color polymorphism (striped
 and unstriped morphs) in woodland salamanders (Plethodon), a North
 American radiation in which the polymorphism can be found in even the most
 distantly related species (~44 Ma divergence). We estimated a phylogenomic
 tree of Plethodon, representing all extant taxa and including multiple
 samples across the range of most species. Morphometric data suggest that
 between-species variation exists predominantly along an axis of relative
 body elongation, corresponding to a terrestrial–fossorial continuum.
 Polymorphic species occupy an intermediate phenotypic space between the
 evolutionary optima of striped and unstriped species. Faster rates of body
 shape evolution were observed in only small-bodied unstriped species,
 suggesting that body elongation, which is co-adapted with the unstriped
 morph, could be constrained by the polymorphism. Striped species, but also
 large-bodied species of eastern Plethodon that lack a dorsal stripe, had
 slower rates of phenotypic evolution. Our results demonstrate that rates
 of phenotypic evolution and speciation following character release can be
 asymmetric and idiosyncratic depending on the alternative adaptations of
 each morph.
description: # Loss of a morph is associated with asymmetric character release in a
 radiation of woodland salamanders Dataset DOI:
 [10.5061/dryad.bvq83bknf](10.5061/dryad.bvq83bknf) ## Description of the
 data and file structure Supplementary Appendix and tables as well as
 phylogenomic trees and morphological data used for analyses of woodland
 salamanders (genus: *Plethodon*). README.txt files below are also included
 within subfolders which explain data files and their contents. Discrete
 character states throughout files refer to whether species were scored as
 unstriped ("U"), striped ("S"), polymorphic
 ("S+U"), or other ("other") under a given
 classification scheme, which account for uncertainty in assignment and are
 detailed in the publication. Eight schemes used these four color morph
 states ("Discrete4a" through "Discrete4h"), whereas
 alternative schemes considered only three states ("Discrete3a"
 through "Discrete3d") or two states ("Discrete2a"
 through "Discrete2c"). ### Supplementary Appendix (on Zenodo)
 #### 'Plethodon_polymorphism_Evolution_SI_Appendix.pdf'
 Supplementary materials & methods and results ### Supplementary Tables
 ("./Supplementary_Tables.zip/") ####
 'Table_S1_sample_info.xlsx' Table S1. Sample information,
 including BioSample accession numbers. Some species names in the Sequence
 Name and Old Species Name columns reflect names prior to taxonomic
 revision, and updates are reflected in the New Species Name column (bold).
 The phylogroup column designates phylogroup membership within species
 recognized for this study, based on previous phylogeographic studies or on
 our preliminary phylogenetic analyses. Proportion missing data indicates
 sample-level missing data in the concatenated matrix of DNA sequences, and
 the MCMCTree column marks which samples were maintained as representatives
 for divergence dating of species or phylogroups in MCMCTree. Collection
 abbreviations: UF = Univeristy of Florida; MVZ = Museum of Vertebrate
 Zoology; UMMZ = University of Michigan Museum of Zoology; MSB = Museum of
 Southwestern Biology. #### 'Table_S2_per_locus_statistics.xlsx'
 Table S2. Summary statistics for anchored hybrid enrichment data. Number
 of taxa includes the number of samples with any data available (i.e. did
 not have completely missing data). ####
 'Table_S3_raw_morphology.xlsx' Table S3. Raw morphological data
 and eight discrete color morph classifications. Costal groove counts (CG)
 were obtained for Fisher-Reid and Wiens (2015) except where noted in the
 text. Sample size (N) reflects the numbers used for all remaining
 morphometric variables (measured in millimeters), which represent weighted
 averages from means and sample sizes reported in Baken and Adams (2019) or
 Adams et al. (2009) except where noted in the text. SVL = snout-vent
 length; S.E = snout-eye length; HL = head length; BW = body width; FLL =
 forelimb length; HLL = hindlimb length; TL = tail length. Values with
 "NA" were phylogenetically imputed after continuous measurements
 were standardized by SVL and log-transformed. ####
 'Table_S4_discrete_character_model_selection.xlsx' Table S4a.
 Model selection tables for 12 discrete character evolution models across
 eight color classification schemes (4a-h). Model names are consistent with
 Supplementary Figure S3 in the SI Appendix. ####
 'Table_S5_Plethodon_phylosignal.xlsx' Table S5. Phylogenetic
 signal and associated p-values using Pagel's lambda and
 Blomberg's K. All variables except costal groove count (CG) were
 divided by snout-vent length and log-transformed to correct for body size.
 S.E = snout-eye length; HL = head length; BW = body width; FLL = forelimb
 length; HLL = hindlimb length. ####
 'Table_S6_pPCA_loadings.xlsx' Table S6. Phylogenetic PCA
 loadings for six morphometric traits. All traits except CG were
 body-size-corrected (divided by snout-vent length and log-transformed).
 #### 'Table_S7_OUwie_3cat_2cat.xlsx' Table S7. Rates of
 phenotypic evolution and lineage diversification rates across color morph
 states using three or two color morph categories. Phenotypic optima (θ)
 and rates (σ2) were estimated using OUwie for the first axis of
 phylogenetic PCA, representing mean values and standard errors (SE) for
 100 stochastic character maps repeated across eight color classification
 schemes. For the 3 Morph Categories optima, four simulations yielding
 extreme outlier optima (&gt;100) were omitted prior to calculating means
 and errors. Lineage diversification rates, or tip rates, were estimated
 using the DR statistic (λDR). Mean λDR is the mean value for species
 across all eight classification schemes, while the mean range provides the
 lowest and highest mean values across schemes. The min λDR and max λDR
 represent the minimum and maximum tip rates, respectively, observed across
 species within each color morph state for any scheme. ### Plethodon
 phylogenomic trees ("./Trees.zip/") #### IQ-Tree and wASTRAL
 ##### 'plethodon-cat.treefile' Concatenated IQ-Tree analysis of
 all 198 samples ##### 'wASTRAL-plethodon.tree' Species tree from
 wASTRAL with samples assigned to species, phylogroups, or
 polyphyletic/paraphyletic units #### Ultrametric trees #####
 'Plethodon-MCMCtree-10Ma.tre' Time-calibrated MCMCtree
 "Figtree" output tree. Includes 95% HPD. *Branch lengths are in
 units of 10 Ma! Since this file is not readily usable for in most programs
 for comparative analyses, additional files were prepared below. #####
 'plethodon-unpruned.tree' Time-calibrated topology taken from
 'Plethodon_MCMCtree_10Ma.tre', but with branch units converted
 to 1 Ma (no HPD included). Can be easily imported into R or other software
 for comparative analyses. ##### 'plethodon-pruned.tree' Same
 tree as 'plethodon-unpruned.tree', but intraspecific groups
 (e.g. phylogroups or polyphyletic samples) were pruned so that each named
 species is represented by a single tip. ### Morphological data
 ("./Morphology.zip/") #####
 'Plethodon_morphology_R_Processed.csv' Includes morphological
 data used for comparative analyses. Note that measurements represent
 averages at the species level from other publications (see manuscript for
 details), including a weighted average across studies based on sample
 sizes provided in those publications. **Columns** CG = costal groove count
 N = sample size SVL = snout-vent length (mm) S.E = snout-eye length (mm)
 HL = head length (mm) BW = body width (mm) FLL = forelimb length (mm) HLL
 = hindlimb length (mm) TL = tail length (mm; not used in this study)
 Discrete2a Discrete2b Discrete2c = 2-state morph classifications (see text
 for description) Discrete3a Discrete3b Discrete3c Discrete3d = 3-state
 morph classifications (see text for description) Discrete4a Discrete4b
 Discrete4c Discrete4d Discrete4e Discrete4f Discrete4g Discrete4h =
 4-state morph classifications (see text for description) S.E.sc =
 snout-eye length (divided by SVL and log transformed) HL.sc = head length
 (divided by SVL and log transformed) BW.sc = body width (divided by SVL
 and log transformed) FLL.sc = forelimb length (divided by SVL and log
 transformed) HLL.sc = hindlimb length (divided by SVL and log transformed)