DOI: 10.5061/dryad.ngf1vhj62
title: Data from: The evolutionary history of dragon lizards (Squamata: Agamidae) revealed by phylogenomics

description: Dragon lizards (Squamata: Agamidae) are a species-rich, ecologically and
 morphologically diverse group that is broadly distributed across the
 eastern hemisphere. Here, we present a phylogenomic study of this major
 clade of lizards to elucidate their biogeographic history, understand how
 dispersal and vicariance generated modern species distributions, and
 examine whether ecological opportunities encountered during agamid
 evolutionary history shaped speciation rates. We generated genome-wide
 sequence data for 42 species representing 40 genera to infer the
 evolutionary relationships and timescale of dragon lizards. The phylogeny
 was largely concordant across several different types of genetic loci, but
 rapidly evolving long exons had better support values across gene and
 species trees compared to other datasets. We also inferred a supermatrix
 tree and timetree for 433 (72% of described species) species to perform
 taxonomically well-sampled biogeographic and macroevolutionary analyses.
 These analyses inferred that agamids originated during the Late Cretaceous
 and in Laurasia, and that Southeast Asia has been a major source of agamid
 diversity. Rate analyses found that neither individual biogeographic and
 cladogenetic events nor ecological opportunities appear to have resulted
 in structured variation in speciation rates when considering all agamid
 lizards. Our study refutes supercontinental vicariance as a driving
 mechanism for speciation in Agamidae and provides a case of a broadly
 distributed and diverse clade with weak evidence for variation in
 speciation rates.
description: # Data from: The evolutionary history of dragon lizards (Squamata:
 Agamidae) revealed by phylogenomics ```
 https://doi.org/10.5061/dryad.ngf1vhj62] ``` **Corresponding author
 information** ``` Name: Simon Scarpetta ORCID:
 https://orcid.org/my-orcid?orcid=0000-0003-0976-9337 Affiliation:
 Department of Environmental Science, University of San Francisco, San
 Francisco, California email: sscarpetta@usfca.edu alternate email:
 sgscarp@gmail.com ``` **Funding information** ``` This work was funded by
 an NSF postdoctoral research fellowship in Biology to SGS (DBI # 2109461).
 ``` **Related publication** ``` Scarpetta SG, Karin BR, Corl A, McGuire
 JA. The evolutionary history of dragon lizards (Squamata: Agamidae)
 revealed by phylogenomics. 2025. Systematic Biology. ``` ```
 https://doi.org/10.1093/sysbio/syaf088 ``` #### **Dataset overview** This
 dataset includes all files to reproduce the results from Scarpetta et al.
 2025. This includes supplemental figures, multiple sequence alignments,
 biogeographic analysis files, divergence time analysis files, treefiles,
 and diversification analysis files and scripts. **Supplemental
 Dataset/File Legends** **Supplemental File 1.** Supporting Information.
 **Supplemental File 2.** Figure S1 Supermatrix phylogeny of 433 agamid
 lizard species, estimated in IQ-TREE2 from 38 nuclear (ToL) and 6
 mitochondrial loci. **Supplemental File 3.** Figure S2 Supermatrix
 timetree of 433 agamid lizard species, estimated in TreePL based on fixed
 supermatrix topology. **Supplemental File 4.** Table S2
 **Supplemental_File4_Table_S2_GenBank_Accession_Table.csv** GenBank
 accession numbers for agamid lizard sequences used in supermatrix
 analyses, as well as those for chameleon outgroups. **Supplemental File
 5.** Table S11
 **Supplemental_File5_Table_S11_Agamid_PGLS_results_Dryad.xlsx** Results of
 PGLS analyses of agamid lizards testing correlations between DR statistic
 speciation tip rates and environmental/ecological variables. Contains
 results in three tabs: opportunities and interactions with environmental
 covariates, subfamily-specific analyses, and whole family results with
 bioclim variables (covariates) only. The sheet named key explains the
 column headers. The unavailable values are represented as – **Supplemental
 File 6.** Figs_S30–S35. Time-stratified BioGeoBEARS analyses on
 supermatrix timetree using original manual dispersal matrix and an areas
 allowed matrix, in a single PDF file. FIGURE S30. Results of DEC analysis.
 FIGURE S31. Results of DEC+J analysis. FIGURE S32. Results of DIVAlike
 analysis. FIGURE S33. Results of DIVAlike+J analysis. FIGURE S34. Results
 of BAYAREAlike analysis. FIGURE S35. Results of BAYAREAlike+J analysis.
 **Supplemental File 7.** Figs_S36–S41. Time-stratified BioGeoBEARS
 analyses on supermatrix timetree using alternative manual dispersal matrix
 and an areas allowed matrix, in a single PDF file. FIGURE S36. Results of
 DEC analysis. FIGURE S37. Results of DEC+J analysis. FIGURE S38. Results
 of DIVAlike analysis. FIGURE S39. Results of DIVAlike+J analysis. FIGURE
 S40. Results of BAYAREAlike analysis. FIGURE S41. Results of BAYAREAlike+J
 analysis. **Supplemental Dataset 8.** Zipped directory of all individual
 locus alignments for the autosomal dataset and the additional exons, and
 concatenated supermatrix alignment. The compressed directory
 **Supplemental_File_8_Alignments.tar.gz** contains all `*.fasta` and
 `*.nex` files to perform the phylogenomic analyses. The overarching
 directory is **Supplemental_File_8_Alignments**. The subdirectories/files
 are **Acro_addexons_200bp_50percomp.tar.gz**,
 **Acro_addexons_400bp_100percomp.tar.gz**,
 **Acro_addexons_400bp_50percomp.tar.gz**,
 **Acro_addexons_concatexons_200bp_50percomp.tar.gz**,
 **Acro_addexons_concatexons_400bp_100percomp.tar.gz**,
 **Acro_addexons_concatexons_400bp_50percomp.tar.gz**,
 **Acro_addexons_unfiltered.tar.gz**,
 **Acro_autosomal_loci_withSanger.tar.gz**,
 **Acro_autosomal_trimal_200bp_50percomp.tar.gz**,
 **Acro_autosomal_trimal_400bp_100percomp.tar.gz**,
 **Acro_autosomal_trimal_400bp_50percomp.tar.gz**,
 **Acro_autosomal_trimal_unfiltered.tar.gz**, and
 **Acro_supermatrix_concat_v3.nex**. ``` Supplemental_File_8_Alignments ├──
 Acro_addexons_200bp_50percomp.tar.gz ├──
 Acro_addexons_400bp_100percomp.tar.gz ├──
 Acro_addexons_400bp_50percomp.tar.gz ├──
 Acro_addexons_concatexons_200bp_50percomp.tar.gz ├──
 Acro_addexons_concatexons_400bp_100percomp.tar.gz ├──
 Acro_addexons_concatexons_400bp_50percomp.tar.gz ├──
 Acro_addexons_unfiltered.tar.gz ├── Acro_autosomal_loci_withSanger.tar.gz
 ├── Acro_autosomal_trimal_200bp_50percomp.tar.gz ├──
 Acro_autosomal_trimal_400bp_100percomp.tar.gz ├──
 Acro_autosomal_trimal_400bp_50percomp.tar.gz ├──
 Acro_autosomal_trimal_unfiltered.tar.gz └── Acro_supermatrix_concat_v3.nex
 ``` **Supplemental Dataset 9.** Zipped directory of all tree files
 including all concatenated tree, species tree, gene tree, gene concordance
 factor, and divergence time analysis files. The compressed directory
 **Supplemental_File_9_Trees.tar.gz** contains all `*.tre`, `*.tree`, and
 associated files resulting from phylogenomic analyses. The overarching
 directopry is **Supplemental_File_9_Trees** and the main subdirectories
 are **Additional_exons**, **Autosomal**, **BEAST2**, and **Supermatrix**.
 ``` Supplemental_File_9_Trees ├── Additional_exons │   ├──
 concord_ASTRALHyb_addexons_Acrodonta_200bp_50percomp │   ├──
 concord_ASTRALHyb_addexons_Acrodonta_400bp_100percomp │   ├──
 concord_ASTRALHyb_addexons_Acrodonta_400bp_50percomp │   ├──
 concord_ASTRALHyb_addexons_Acrodonta_concatgenes_200bp_50percomp │   ├──
 concord_ASTRALHyb_addexons_Acrodonta_concatgenes_400bp_100percomp │   └──
 concord_ASTRALHyb_addexons_Acrodonta_concatgenes_400bp_50percomp ├──
 Autosomal │   ├── ASTRAL-Hybrid │   │   ├──
 Acro_ASTRAL-Hybrid_200bp_50percomp │   │   │   ├──
 concord_ASTRALHyb_Acro_AHE_200bp_50percomp │   │   │   ├──
 concord_ASTRALHyb_Acro_AHE_RELEC_UCE_Wiens_200bp_50percomp_FINAL │   │  
 │   ├── concord_ASTRALHyb_Acro_RELEC_200bp_50percomp │   │   │   ├──
 concord_ASTRALHyb_Acro_ToL_200bp_50percomp │   │   │   └──
 concord_ASTRALHyb_Acro_UCE_genesortr750_200bp_50percomp │   │   ├──
 Acro_ASTRAL-Hybrid_400bp_100percomp │   │   │   ├──
 concord_ASTRALHyb_Acro_AHE_400bp_100percomp │   │   │   ├──
 concord_ASTRALHyb_Acro_AHE_RELEC_UCE_Wiens_400bp_100percomp_FINAL │   │  
 │   ├── concord_ASTRALHyb_Acro_RELEC_400bp_100percomp │   │   │   ├──
 concord_ASTRALHyb_Acro_ToL_400bp_100percomp │   │   │   └──
 concord_ASTRALHyb_Acro_UCE_genesortr750_400bp_100percomp │   │   ├──
 Acro_ASTRAL-Hybrid_400bp_50percomp │   │   │   ├──
 concord_ASTRALHyb_Acro_AHE_400bp_50percomp │   │   │   ├──
 concord_ASTRALHyb_Acro_AHE_RELEC_UCE_Wiens_400bp_50percomp_FINAL │   │  
 │   ├── concord_ASTRALHyb_Acro_RELEC_400bp_50percomp │   │   │   ├──
 concord_ASTRALHyb_Acro_ToL_400bp_50percomp │   │   │   └──
 concord_ASTRALHyb_Acro_UCE_genesortr750_400bp_50percomp │   │   ├──
 Acro_ASTRAL-Hybrid_unfiltered │   │   │   ├── Concord_ASTRALHyb_Acro_AHE
 │   │   │   ├── Concord_ASTRALHyb_Acro_AHE_RELEC_UCE_Wiens_FINAL │   │  
 │   ├── Concord_ASTRALHyb_Acro_RELEC │   │   │   ├──
 Concord_ASTRALHyb_Acro_ToL │   │   │   └── Concord_ASTRALHyb_Acro_UCE │  
 │   └── Acro_ASTRAL-Hybrid_unfiltered_withSanger │   └──
 IQTREE_Concatenated │   ├── Concat_AHE_200bp_50percomp │   ├──
 Concat_AHE_400bp_100percomp │   ├── Concat_AHE_400bp_50percomp │   ├──
 Concat_AHE_unfiltered │   ├── Concat_Autosomal_200bp_50percomp │   ├──
 Concat_Autosomal_400bp_100percomp │   ├── Concat_Autosomal_400bp_50percomp
 │   ├── Concat_Autosomal_unfiltered │   ├── Concat_RELEC_200bp_50percomp
 │   ├── Concat_RELEC_400bp_100percomp │   ├── Concat_RELEC_400bp_50percomp
 │   ├── Concat_RELEC_unfiltered │   ├──
 Concat_ToL_200bp_50percomp_400bp_50percomp_400bp_100percomp │   ├──
 Concat_ToL_unfiltered │   ├── Concat_UCE_genesortr750_200bp_50percomp │  
 ├── Concat_UCE_genesortr750_400bp_100percomp │   ├──
 Concat_UCE_genesortr750_400bp_50percomp │   ├──
 Concat_UCE_genesortr750_unfiltered │   ├──
 Concat_withSanger_Autosomal_unfiltered │   ├──
 Concat_withSanger_RELEC_unfiltered │   └──
 Concat_withSanger_ToL_unfiltered ├── BEAST2 └── Supermatrix ├── IQTREE └──
 TreePL ``` **Supplemental Dataset 10.** Zipped directory of all files
 needed for BioGeoBEARS analysis on phylogenomic timetrees. The compressed
 directory **Supplemental_File_10_BGB_phylogenomic.tar.gz** contains
 contains the input R script, geographic range data, and the input tree,
 and for time-stratified analyses, a time slice file, an areas allowed
 file, and a manual dispersal matrix. ```
 Supplemental_File_10_BGB_phylogenomic ├── Acrodonta_areas_FINAL.txt ├──
 acro_BGB_FINAL.R ├── acro_divtime_BGB.tre ├──
 acro_divtime_hydrofix_BGB.tre ├── acrodonta_areas_allowed.txt ├──
 acrodonta_manual_dispersal_time_strat_NEW.txt └──
 acrodonta_timeperiods_NEW.txt ``` **Supplemental Dataset 11.** Zipped
 directory of all files needed for BioGeoBEARS analysis on supermatrix
 timetrees. The compressed directory
 **Supplemental_File_11_BGB_supermatrix.tar.gz** contains contains the
 input R script, geographic range data, and the input tree, and for
 time-stratified analyses, a time slice file, an areas allowed file, and a
 manual dispersal matrix. The overarching directory is
 **Supplemental_File_11_BGB_supermatrix** and the two subdirectories are
 **main_text** and **multiplier_test**. ```
 Supplemental_File_11_BGB_supermatrix ├── main_text │   ├──
 Acrodonta_supermatrix_areas.txt │   ├── acro_BGB_supermatrix_Final.R │  
 ├── acro_calib_pruned.tre │   ├── acrodonta_supermatrix_areas_allowed.txt
 │   ├── acrodonta_supermatrix_manual_dispersal_time_strat.txt │   └──
 acrodonta_supermatrix_timeperiods.txt └── multiplier_test ├──
 Acrodonta_supermatrix_areas.txt ├──
 acro_BGB_supermatrix_Final_alternative.R ├── acro_calib_pruned.tre ├──
 acrodonta_supermatrix_areas_allowed.txt ├──
 acrodonta_supermatrix_manual_dispersal_time_strat_alternative.txt └──
 acrodonta_supermatrix_timeperiods.txt ``` **Supplemental Dataset 12.**
 Zipped directory of all files and scripts needed for diversification
 analyses on the supermatrix timetree. These include PGLS, BAMM, RPANDA,
 CLaDS, MiSSE, phylogenetic ANOVA, CoMET, RPANAD environmental, and castor
 analyses. The compressed directory
 **Supplemental_File_12_Diversification_analyses.tar.gz** contains all
 input R scripts, spreadsheets, and tree files to perform diversification
 analyses. The overarching directory is
 **Supplemental_File_11_BGB_supermatrix** and the subdirectories are
 **1_PGLS**, **2_BAMM**, **3_RPANDA_CLaDS_MiSSE**, **4_Phy_ANOVA**,
 **5_CoMET**, **6_RPANDA_Env**, and **7_PSR**. ```
 Supplemental_File_12_Diversification_analyses ├── 1_PGLS │   ├──
 Agamid_PGLS_FINAL.R │   ├── Agamid_traits_V4.xlsx │   └──
 acro_BAMM_pruned.tre ├── 2_BAMM │   ├── Acro_Bamm_v3_FINAL.R │   ├──
 acro_BAMM_pruned.tre │   ├── acro_diversification_v3.txt │   └──
 myPriors.txt ├── 3_RPANDA_CLaDS_MiSSE │   ├──
 Agamidae_clade_specific_rates_RPANDA_FINAL.R │   ├──
 Agamidae_taxa_Final.xlsx │   └── acro_BAMM_pruned.tre ├── 4_Phy_ANOVA │  
 ├── acro_BAMM_pruned.tre │   ├── agamid_speciation_anova_FINAL.R │   └──
 speciation_rates_ANOVA.csv ├── 5_CoMET │   ├── TESS_CoMET_agamid_FINAL.R
 │   └── acro_BAMM_pruned.tre ├── 6_RPANDA_Env │   ├──
 01_diversification_arid_amphib_FINAL.R │   ├──
 02_diversification_tempmean_amphib_FINAL.R │   ├── Agamid_traits_V4.xlsx
 │   ├── Australia_climate_data_45Mya_Scotese.csv │   └──
 acro_BAMM_pruned.tre └── 7_PSR ├── Acro_diversification_PSR.R └──
 acro_BAMM_pruned.tre ``` **Supplemental Dataset 13.** Zipped directory
 of all files required to produce the supermatrix timetree using penalized
 likelihood in treePL, including the fixed supermatrix `.tre` file, the
 calibrations `.txt` file, and the `.sh` wrapper script for treePL. The
 compressed directory is **Supplemental_File_13_treePL.tar.gz**. ```
 Supplemental_File_13_treePL ├── Acrodonta_treePL_wrapper.txt ├──
 supermatrix_concat_partitions_contree.tre └── treepl_wrapper.sh* ```
 **Supplemental Dataset 14.** XML file
 **Supplemental_File_14_50RELEC_50UCE_BEAST2_HAmphib.xml** for BEAST2
 analysis of 50 RELEC and 50 UCE loci and a pure-birth tree prior.
 **Supplemental Dataset 15.** XML file
 **Supplemental_File_15_50RELEC_50UCE_BEAST2_HOut.xml** for BEAST2 analysis
 of 50 RELEC and 50 UCE loci fixing the position of Hydrosaurus and a
 pure-birth tree prior. **Supplemental Dataset 16.** XML file
 **Supplemental_File_16_Addexons_50per_400bp_BEAST2.xml** for BEAST2
 analysis of additional exons with 50% taxon completness and &gt;400 base
 pairs and a pure-birth tree prior. **Supplemental Dataset 17.** XML file
 **Supplemental_File_17_50RELEC_50UCE_BEAST2_HOut_diffuse_clockprior.xml**
 for BEAST2 analysis of 50 RELEC and 50 UCE loci with a more diffuse clock
 rate prior and a pure-birth tree prior. **Supplemental Dataset 18.** XML
 file **Supplemental_File_18_50RELEC_50UCE_BEAST2_HOut_BD_treeprior.xml**
 for BEAST2 analysis of 50 RELEC and 50 UCE loci and a birth-death tree
 prior.