DOI: 10.5061/dryad.cz8w9gjcx
title: Data from: The macroevolutionary dynamics of pharyngognathy in fishes fail to support the key innovation hypothesis

description: Key innovations, traits that provide species access to novel niches, are
 thought to be a major generator of biodiversity. One commonly cited
 example of key innovation is pharyngognathy, a set of modifications to the
 pharyngeal jaws found in some highly species-rich fish clades such as
 cichlids and wrasses. Here, using comparative phylogenomics and
 phylogenetic comparative methods, we investigate the genomic basis of
 pharyngognathy and the impact of this innovation on diversification. Whole
 genomes resolve the relationships of fish clades with this innovation and
 their close relatives, but high levels of topological discordance suggest
 the innovation may have evolved fewer times than previously thought.
 Closer examination of the topology of noncoding elements accelerated in
 clades with the pharyngognathy innovation reveals hidden patterns of
 shared ancestry across putatively independent transitions to
 pharyngognathy. When our updated phylogenomic relationships are used
 alongside large-scale phylogenetic and ecological datasets, we find no
 evidence pharyngognathy consistently modifies the macroevolutionary
 landscape of trophic ecology nor does it increase diversification. Our
 results highlight the necessity of incorporating genomic information in
 studies of key innovation.
description: # DATA DRYAD REPOSITORY README Citation: Borstein SR, Hammer MP,
 O'Meara BC, and McGee MD. 2024. The macroevolutionary dynamics of
 pharyngognathy in fishes fail to support the key innovation hypothesis.
 *Nature Communications* 15:10325. 10.1038/s41467-024-53141-4 ##
 Description of the data and file structure ### Directories ####
 DietAnalysis: Data, results, and scripts related to phylogenetic
 comparative analysis of trophic levels ##### Files * BBMV_Data.RData:
 Phylogeny and formatted data used in BBMV analysis. Used in BBMV_MCM.R and
 BBMV_Scripts.R * BBMV_MCMC.R: Script to perorm MCMC BBMV analyses *
 BBMV_Scripts.R: Script to run BM, OU, and BBMV model comparisons. *
 BBMV_Scripts.RData: Output for models in BBMV_Scripts.R *
 BBMV_Summary_Scripts.R: Scripts to calculate 95% CI for BBMV parameter
 estimates and make figures of macroevolutionary landscapes. *
 nonpharyngognath_TL.BBMV.Dat: R data object for BBMV MCMC analysis for
 non-pharyngognathous fishes. *
 pharyngognath_PJA.TL.LOO_Cichlidae.BBMV.Dat: R data object for BBMV MCMC
 analysis for pharyngognathous fishes excluding the family Cichlidae. *
 pharyngognath_PJA.TL.LOO_Embiotocidae.BBMV.Dat: R data object for BBMV
 MCMC analysis for pharyngognathous fishes excluding the family
 Embiotocidae. * pharyngognath_PJA.TL.LOO_Exocoetidae.BBMV.Dat: R data
 object for BBMV MCMC analysis for pharyngognathous fishes excluding the
 family Exocoetidae. * pharyngognath_PJA.TL.LOO_Labridae.BBMV.Dat: R data
 object for BBMV MCMC analysis for pharyngognathous fishes excluding the
 family Labridae. * pharyngognath_PJA.TL.LOO_MalawiVic.BBMV.Dat: R data
 object for BBMV MCMC analysis for pharyngognathous fishes excluding Malawi
 and Victorian Cichlids. * pharyngognath_PJA.TL.LOO_Pomacentridae.BBMV.Dat:
 R data object for BBMV MCMC analysis for pharyngognathous fishes excluding
 the family Labridae. * pharyngognath_TL.BBMV.Dat: R data object for BBMV
 MCMC analysis for pharyngognathous fishes. * PJA_Diet_Analyses.R: Scripts
 for formatting data for BBMV and performing tests of BM, OU, and EV models
 of evolution for trophic level in mvMorph. * PJA_Diet_Analyses.RData: R
 data object of results from mvMorph tests of evolutionary models for
 trophic level evolution. * PJA_Tree.tree: Time-calibrated phylogeny used
 in scripts for analyses of trophic level evolution. *
 TrophicLevel_Data.csv: Trophic levels for species from individual studies
 used in analyses. * Species: Scientific name of species * TrophicLevel:
 Calculated trophic level obtained from dietr * n: number of individuals
 used for gut content analysis * PredState: lifehistory stage of the
 specimens used in gut content analysis. Either adults or a mix of juvenile
 and adults (juv./adults). * FullCitation: Full citation for source of the
 data. * TrophicLevel_Data_Species_Averages.csv: Average trophic levels for
 species used in analyses. * Species: Scientific name of species *
 TrophicLevel: Mean trophic level across studies * SE: Standard error
 around the mean trophic level calculation. When species have only as
 single observation, this value was set to the global standard error for
 the dataset. * nObs: The number of dietary records used to calculate the
 mean trophic level per species. #### Diversification: Data, results, and
 scripts related to lineage dieversification analyses ##### Files *
 fissPJA.R: Scripts used to perform FiSSE diversification analyses. *
 FisseResults.RData: R data object containing results of analyses performed
 in fissePJA.R. * HiSSE_Models.zip: R saves of HiSSE models. model numbers
 correspond to those named in HiSSE_Scripts.R * HiSSE_Scripts.R: Scripts to
 run and process HiSSE models. * Oval_HiSSE_Scripts.R: Scripts to run and
 process HiSSE models for the clade Ovalentaria. *
 Ovalentaria_HiSSE_Models.zip: R saves of HiSSE models for Ovalentaria.
 model numbers correspond to those named in Oval_HiSSE_Scripts.R *
 PJA_Presence.csv: Binary presence (1) or absence (0) for each species in
 the phylogeny PJA_Tree.tree used for analyses of lineage diversification.
 * taxon: Species name * state: Binary presence (1) or absence (0) of
 pharyngognathy for each species in the phylogeny PJA_Tree.tree used for
 analyses of lineage diversification. * PJA_Tree.tree: Time-calibrated
 phylogeny used in scripts for analyses of lineage diversification. ####
 Genomic_PhylogenomicAnalyses: Scripts and data used in genomic assembly
 and analysis of hemiplasy ##### Files * Alfaro2018Tree_Rooted.tre: ASTRAL
 derived coalescent tree from Alfaro et. al. (2018) Nat. Ecol. Evol.
 2:688-696. in Newick format used in hemiplasy risk factor analysis (Fig. 4
 & Fig. S5). * AlfaroTips.csv: CSV file with columns for the
 tip/species, family, and pharyngognath status used to subset the
 Alfaro2018Tree_Rooted.tre for hemiplasy risk factor analysis (Fig. 4 &
 Fig. S5). * Species: Species name * Family: Family assignment * PJ: Binary
 presence (1) or absence (0) of pharyngognathy for each species in the
 phylogeny. * astral_eytan3b_rooted.tre: ASTRAL derived coalescent tree
 from Anchored Hybrid Enrichment sequence data in Eytan et. al. (2015) BMC
 Evol Biol 15:113 in Newick format used in hemiplasy risk factor analysis
 (Fig. 4 & Fig. S3). * ASTRAL_Phararyngognath_32Tip_rooted.tre: ASTRAL
 derived coalescent tree from whole genomes of 32 species in Newick format
 used in hemiplasy risk factor analysis (Fig. 1A-B). *
 ASTRAL_Phararyngognath_64Tip__Rooted.tre: ASTRAL derived coalescent tree
 from whole genomes of 64 species in Newick format used in hemiplasy risk
 factor analysis (Fig. S2). * astral_thin100k_rooted.tree: ASTRAL derived
 coalescent tree derived loci of at least 300 base pairs in length in our
 32 taxa in which we randomly removed loci within 100kb or less of each
 other. Supplied in Newick format used in hemiplasy risk factor analysis
 (Fig. S7). * Fig2SIMMAP.Rmd: R Markdown file with code to generate simmaps
 and perform BRMS regression shown in Figure 2. * Fig2SIMMAP.Robj: R object
 containing data used in scripts in Fig2SIMMAP.Rmd. *
 full_coalescent_tree_calculated_from_sCF_Rooted.tre: Coalescent tree in
 Newick format derived from IQ-Tree2 site-concordance factors used in
 hemiplasy risk factor analysis (Fig. 1C). *
 Ghezelayagh2022_Tree_Rooted.tre: ASTRAL derived coalescent tree from
 Ghezelayagh et. al. (2022) 6:1211-1220. in Newick format used in hemiplasy
 risk factor analysis (Fig. 4 & Fig. S6). * GhezelayaghTips.csv: CSV
 file with columns for the tip/species, family, and pharyngognath status
 used to subset the Ghezelayagh2022_Tree_Rooted.tre for hemiplasy risk
 factor analysis (Fig. 4 & Fig. S6). * Species: Species name * Family:
 Family assignment * PJ: Binary presence (1) or absence (0) of
 pharyngognathy for each species in the phylogeny. *
 HPC_script_examples.Rmd: R Markdown file containing bash scripts for
 genomic assemblies, alignment, phylogenetic breakpoints, coalescent tree
 construction, and analysis of gene tree-species tree discordance. *
 Hughes2018_RootedNames.tre: ASTRAL derived coalescent tree from Hughes et.
 al. (2018) Proc. Natl. Acad. Sci., 115:6249-6254. in Newick format used in
 hemiplasy risk factor analysis (Fig. 4 & Fig. S4). * HughesTips.csv:
 CSV file with columns for the tip/species, family, and pharyngognath
 status used to subset the Hughes2018_RootedNames.tre for hemiplasy risk
 factor analysis (Fig. 4 & Fig. S4). * Species: Species name * Family:
 Family assignment * PJ: Binary presence (1) or absence (0) of
 pharyngognathy for each species in the phylogeny. *
 HPC_script_examples.Rmd: R Markdown file containing bash scripts for
 genomic assemblies, alignment, phylogenetic breakpoints, coalescent tree
 construction, and analysis of gene tree-species tree discordance. *
 s0.0005_results.csv: Output from HeIST using a mutation rate of 0.0005. *
 Tree: Tree ID for trees with correct evolutionary history from HeIST
 simulations * NumberMutations: The number of mutations on a given tree *
 s0.005_results.csv: Output from HeIST using a mutation rate of 0.005. *
 Tree: Tree ID for trees with correct evolutionary history from HeIST
 simulations * NumberMutations: The number of mutations on a given tree *
 s0.05_results.csv: Output from HeIST using a mutation rate of 0.005. *
 Tree: Tree ID for trees with correct evolutionary history from HeIST
 simulations * NumberMutations: The number of mutations on a given tree *
 sCF_GTR_F0_R8_Rooted.tre: IQ-Tree2 phylogeny derived from site-concordance
 factors with branch lengths estimated under GTR+F0+R8 substitution model
 in Newick format (Fig. S1). #### Megaphylogeny: Data used in constructing
 the megaphylogeny ##### Files * Calibrations.docx: Table and references
 for calibrations used for time-calibration. *
 PJA_Accessions_MegaPhylo.csv: Accession table for BOLD and NCBI accessions
 used to generate the phylogeny PJA_Tree.tree used in analyses. * Taxon:
 Species name * 12S RNA: Accessions for 12S rRNA * 16S RNA: Accessions for
 12S rRNA * ATP6: Accessions for mitochondrially encoded ATP synthase
 membrane subunit 6 * ATP8: Accessions for 'mitochondrially encoded
 ATP synthase membrane subunit 8 * CYTB: Accessions for Cytochrome b *
 UBE3A: Accessions for ubiquitin protein ligase E3A * COI: Accessions for
 Cytochrome oxidase subunit I * COII: Accessions for Cytochrome oxidase
 subunit II * COIII: Accessions for Cytochrome oxidase subunit III *
 D-loop: Accessions for the mitochondria D-loop/control region * ENC1:
 Accessions for Ectoderm-Neural Cortex 1 * FICD: Accessions for FIC domain
 protein adenylyltransferase * GCS1: Accessions for GCS1 * GLYT: Accessions
 for glycine transporter 1 * GPR85: Accessions for G Protein-Coupled
 Receptor 85 * H3: Accessions for histone 3A * KIAA: Accessions for KIAA *
 MYH6: Accessions formyosin heavy chain 6 * ND1: Accessions for NADH
 dehydrogenase 1 * ND2: Accessions for NADH dehydrogenase 2 * ND3:
 Accessions for NADH dehydrogenase 3 * ND4: Accessions for NADH
 dehydrogenase 4 * ND4l: Accessions for NADH dehydrogenase 4L * ND5:
 Accessions for NADH dehydrogenase 5 * ND6: Accessions for NADH
 dehydrogenase 6 * PANX2: Accessions for Pannexin 2 * PLAGL2: Accessions
 for Zinc finger protein PLAGL2 * PTR: Accessions for patched
 domain-containing 4 * RAG1: Accessions for Recombination activating gene 1
 * RAG2: Accessions for Recombination activating gene 2 * RIPK4: Accessions
 for Receptor Interacting Serine/Threonine Kinase 4 * RNF213: Accessions
 for Ring finger protein 213 * SIDKEY: Accessions for sidkey * SLC10A3:
 Accessions for Solute Carrier Family 10 Member 3 * SNX33: Accessions for
 Sorting Nexin 33 * SVEP1: Accessions for Sushi, Von Willebrand Factor Type
 A, EGF And Pentraxin Domain Containing 1 * TBR1: Accessions for T-box
 brain 1 * TMO-4C4: Accessions for TMO-4C4 * VCPIP: Accessions for Valosin
 Containing Protein Interacting Protein * ZIC1: Accessions for zinc finger
 protein 1 * ZNF503: Accessions for Zinc Finger Protein 503 *
 PJA_MitogenomeAccessions_MegaPhylo.csv: Mitogenome accession numbers used
 to generate the phylogeny PJA_Tree.tree used in analyses. * Species:
 Species name * Accession: Accession for mitogenome used in generating
 megaphylogeny ### **Change Log:** 9/18/25: Ghezelayagh2022_Tree_Rooted.tre
 while described in the README was accidentally omitted and missing from
 the submitted zip archive while all remaining files/scripts to analyze
 that dataset were included. This has been resolved and the tree has now
 added to the archive.