DOI: 10.5061/dryad.4tmpg4fjr
title: Data from: Iguanas rafted more than 8,000 km from North America to Fiji

description: Founder-event speciation can occur when one or more organisms colonize a
 distant, unoccupied area via long-distance dispersal, leading to the
 evolution of a new species lineage. Species radiations established by
 long-distance, and especially transoceanic, dispersal can cause
 substantial shifts in regional biodiversity. Here, we investigate the
 occurrence and timing of the greatest known long-distance oceanic
 dispersal event in the history of terrestrial vertebrates—the rafting of
 iguanas from North America to Fiji. Iguanas are large-bodied herbivores
 that are well-known overwater dispersers, including species that colonized
 the Caribbean and the Galápagos islands. However, the origin of Fijian
 iguanas had not been comprehensively tested. We estimated the phylogenetic
 rela- tionships and evolutionary timescale of the iguanid lizard radiation
 using genome-wide exons and ultraconserved elements (UCEs). Those data
 indicate that the closest living relative of extant Fijian iguanas is the
 North American desert iguana and that the two taxa likely diverged during
 the late Paleogene near or after the onset of volcanism that produced the
 Fijian archipelago. Biogeographic models estimate North America as the
 most probable ancestral range of Fijian iguanas. Our analyses support the
 hypothesis that iguanas reached Fiji via an extraordinary oceanic
 dispersal event from western North America, and which spanned a fifth of
 the earth’s circumference (&gt;8,000 km). Overwater rafting of iguanas
 from North America to Fiji strengthens the importance of founder-event
 speciation in the diversification of iguanids and elucidates the scope of
 long-distance dispersal across terrestrial vertebrates.
description: This dataset includes all files to reproduce the results from
 Scarpetta et al. 2025. This includes multiple sequence alignments,
 biogeographic analysis files, species-tree and divergence time analysis
 files, and resulting treefiles. The dataset also includes a baits file for
 target sequence capture, a file of the targets, and a spreadsheet of
 distance data used to create Figure 4 in the main text.
description: # Data from: Iguanas rafted more than 8,000 km from North America to Fiji
 \[[https://doi.org/10.5061/dryad.4tmpg4fjr](https://doi.org/10.5061/dryad.4tmpg4fjr)] **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, Fisher RN, Karin BR, Niukula J, Corl A, Jackman TR, McGuire JA. Iguanas rafted more than 8000 km from North America to Fiji. 2025. Proceedings of the National Academy of Sciences of the United States of America. ``` ``` https://doi.org/10.1073/pnas.2318622122 ``` **Dataset overview** This dataset includes all files to reproduce the results from Scarpetta et al. 2025. This includes multiple sequence alignments, biogeographic analysis files, species-tree and divergence time analysis files, and resulting treefiles. The dataset also includes a baits file for target sequence capture, a file of the targets, and a spreadsheet of distance data used to create Figure 4 in the main text. **Supplemental Dataset Legends** **Supplemental Dataset 1.** FASTA file of the tiled baits produced by Arbor Biosciences to capture the target loci. **Supplemental Dataset 2.** Zipped directory of all individual locus alignments for the autosomal dataset, and concatenated alignments of each marker type and the entire dataset. The compressed directory **Supplemental_Data_2_iguana_autosomal_data.tar.gz** contains all `*.fasta` files for the autosomal data to perform the phylogenomic analyses. The overarching directory is **iguana_autosomal_data**. The subdirectories are **iguana_autosomal_all_loci_final**, **iguana_autosomal_concatenated_datasets**, and **iguanas_RELEC_OG_test_FINAL**. ``` iguana_autosomal_data ├── iguana_autosomal_all_loci_final ├── iguana_autosomal_concatenated_datasets │ ├── AHE │ ├── CONCAT_ALL_autosomal │ ├── RELEC │ ├── UCE │ └── Wiens [the ToL loci] └── iguanas_RELEC_OG_test_FINAL ``` \#"iguana_autosomal_all_loci_final" contains *.fasta files for each individual AHE, RELEC, ToL (Wiens), and UCE alignment \#"iguana_autosomal_concatenated_datasets" contains *.phylip alignment files and *.charset character set files for each concatenated alignment contained in the following subdirectories (see line below) \#"iguana_autosomal_concatenated_datasets" contains five subdirectories, "AHE", "CONCAT_ALL_autosomal" (all autosomal alignments concatenated), "RELEC", "UCE", and "Wiens" (the ToL loci) \#"iguanas_RELEC_OG_test_FINAL" contains *.fasta files for each individual RELEC alignment for the test analyses that had five additional outgroups **Supplemental Dataset 3.** Zipped directory of all individual locus alignments for the entire X-chromosome dataset and the filtered dataset containing exons &gt;500 bp that have at least 75% taxa per locus, and concatenated alignments of each of those datasets. The compressed directory **Supplemental_Data_3_iguana_Xchr_data.tar.gz** contains all `*.fasta` files for the X-chromsome data to perform the phylogenomic analyses. The overarching directory is **iguana_Xchr_data**. The subdirectories are **iguana_xchr_fastas_final_trimal**, **iguana_xchr_fastas_final_trimal_75pertaxa_500bpmin**, **iguana_xchr_fastas_final_trimal_75pertaxa_500bpmin_CONCAT**, and **iguana_xchr_fastas_final_trimal_CONCAT**. ``` iguana_Xchr_data ├──iguana_xchr_fastas_final_trimal ├──iguana_xchr_fastas_final_trimal_75pertaxa_500bpmin ├──iguana_xchr_fastas_final_trimal_75pertaxa_500bpmin_CONCAT └──iguana_xchr_fastas_final_trimal_CONCAT ``` \#"iguana_xchr_fastas_final_trimal" contains *.fasta files for each individual X-chromosome alignment \#"iguana_xchr_fastas_final_trimal_75pertaxa_500bpmin" contains *.fasta files for each individual X-chromosome alignment in the 75% complete, minimum 500 base pairs per locus filtered dataset \#"iguana_xchr_fastas_final_trimal_75pertaxa_500bpmin_CONCAT" contains the concatenated nexus file of all X-chromosome alignments \#"iguana_xchr_fastas_final_trimal_CONCAT" contains the concatenated nexus file of all X-chromosome alignments in the 75% complete, minimum 500 base pairs per locus filtered dataset **Supplemental Dataset 4.** Zipped directory of all treefiles from phylogenomic analyses. This includes all individual genetrees, collated gene tree files, concatenated maximum likelihood tree files, ASTRAl III and ASTRAL-Hybrid tree files, all files from concordance factor analyses, and treefiles from StarBeast3 and BEAST2. The compressed directory **Supplemental_Data_4_all_treefiles.tar.gz** contains all tree files. The overarching directory is **Brachy_all_treefiles**. The subdirectories are **ASTRAL-HYB_trees**, **ASTRAL_trees**, **BEAST2_FBD_trees**, **BEAST2_trees**, **Boottrees**, **Concat_trees**, **Concordance**, **Outgroup_test**, and **STARBEAST_TREES**. ``` Brachy_all_treefiles ├── ASTRAL_trees ├── ASTRAL-HYB_trees ├── BEAST2_FBD_trees ├── BEAST2_trees ├── Boottrees ├── Concat_trees │ ├── AHE_concat │ ├── Autosomal_concat │ ├── RELEC_concat │ ├── RELEC_concat_OG_test │ ├── UCE_concat │ ├── Wiens_concat [ToL concat] │ ├── Xchr_75per_500bpmin_concat │ └── Xchr_all_concat ├── Concordance │ ├── astral-astralHYB_AHE │ ├── astral-astralHYB_RELEC │ ├── astral-astralHYB_autosomal_AHE_RELEC_UCE_Wiens │ ├── astralHYB_RELEC_200bp_gCF │ ├── astralHYB_RELEC_OG_test_200bp_gCF │ ├── astralHYB_RELEC_OG_test_gCF │ ├── astralHYB_UCE │ ├── astralHYB_Wiens │ ├── astralHYB_Xchr_75pertaxa_500bpmin │ ├── astral_UCE │ ├── astral_Wiens │ ├── concat_AHE │ ├── concat_RELEC │ ├── concat_UCE │ ├── concat_Xchr_75pertaxa_500bpmin │ ├── concat_Xchr_all_SCF-only │ ├── concat_autosomal_AHE_RELEC_UCE_Wiens │ └── concat_wiens ├── Outgroup_test └── STARBEAST_TREES ``` \#"ASTRAL-HYB_trees" contains all phylogenetic tree *.tre files estimated in ASTRAL-Hybrid \#"ASTRAL_trees" contains all phylogenetic tree *.tre files estimated in ASTRAL III \#"BEAST2_FBD_trees" contains all phylogenetic timetree *.tre files estimated in BEAST2 under the fossilized birth death process using genomic and morphological data \#"BEAST2_trees" contains all phylogenetic timetree *.tre files estimated in BEAST2 \#"Boottrees" contains all phylogenetic tree *.tre files, each of which contains all of the individual gene tree files used to estimate trees in ASTRAL \#"Concat_trees" contains all phylogenetic tree files for all concatenated analyses and associated output from IQTREE2. The *.contree file is the file that contains the maximum likelihood estimate and bootstrap values \#"Concordance" contains all site and gene concordance factor analyses for each of the uncalibrated trees (i.e., those in "ASTRAL-HYB_trees", "ASTRAL_trees", and "Concat_trees"). When the ASTRAL-Hybrid and ASTRAL III tree were the same topology, concordance factors were calculated only once. The values are in the *.tree files \#"Outgroup_test" contains all phylogenetic tree *.tre files for the RELEC outgroup test analyses, including an anlysis in ASTRAL-Hybrid a gene trees file, and a concatenated tree \#"STARBEAST_TREES" contains all phylogenetic timetree *.tre files estimated in StarBeast3 **Supplemental Dataset 5.** Zipped directory of all data, files, and code for statistical biogeographic analysis in BioGeoBears. The compressed directory **Supplemental_Data_5_BioGeoBears_files_data_code.tar.gz** contains all input files for analyses in BioGeoBears. The overarching directory is **BGB**. The subdirectories are **moreroutes_2laurasia_2_out**, **moreroutes_2laurasia_9_out**, **moreroutes_2laurasia_no_out**, **moreroutes_2laurasia_9_out_direct_route_comparison**, **no_out**, **outgroup_test_2_out**, and **outgroup_test_9_out**. Each folder 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. ``` BGB ├── moreroutes_2laurasia_2_out ├── moreroutes_2laurasia_9_out ├── moreroutes_2laurasia_9_out_direct_route_comparison ├── moreroutes_2laurasia_no_out ├── no_out ├── outgroup_test_2_out └── outgroup_test_9_out ``` \#moreroutes_2laurasia_2_out contains all files for the analyses with additional areas and two outgroups \#moreroutes_2laurasia_9_out contains all files for the analyses with additional areas and nine outgroups \#moreroutes_2laurasia_9_out_direct_route_comparison contains all files for the analyses with additional areas and nine outgroups directly comparing likelihoods and AIC for all alternative hypothesis. This directory contains additional manual dispersal matrices to constrain analyses for each hypothesis. \#moreroutes_2laurasia_no_out contains all files for the analyses with additional areas and no outgroups \#no_out contains all files for the analyses with no outgroups \#outgroup_test_2_out contains all files for the analyses with two outgroups \#outgroup_test_9_out contains all files for the analyses with nine outgroups **Supplemental Dataset 6.** XML file for StarBeast3 analysis of 100 RELEC loci with Iguanidae calibration and all outgroups included. **Supplemental Dataset 7.** XML file for StarBeast3 analysis of 100 RELEC loci with *Brachylophus*-*Dipsosaurus* calibration and all outgroups included. **Supplemental Dataset 8.** XML file for StarBeast3 analysis of 100 RELEC loci with Iguanidae calibration with only oplurid and leiosaurid outgroups. **Supplemental Dataset 9.** XML file for StarBeast3 analysis of 100 RELEC loci with Iguanidae calibration with only phrynosomatid outgroups. **Supplemental Dataset 10.** XML file for BEAST2 analysis of 100 RELEC loci with Iguanidae calibration and all outgroups included. **Supplemental Dataset 11.** XML for StarBeast3 analysis of 50 loci each of RELEC, UCE, and AHE with Iguanidae calibration and all outgroups included. **Supplemental Dataset 12.** XML for StarBeast3 analysis of 50 loci each of RELEC, UCE, and AHE with *Brachylophus*-*Dipsosaurus* calibration and all outgroups included. **Supplemental Dataset 13.** XML for BEAST2 analysis of 50 loci each of RELEC, UCE, and AHE with Iguanidae calibration and all outgroups included. **Supplemental Dataset 14.** XML file for StarBeast3 analysis of 165 X-chromosome exons with Iguanidae calibration and all outgroups included. **Supplemental Dataset 15.** XML file for StarBeast3 analysis of 165 X-chromosome exons with *Brachylophus*-*Dipsosaurus* calibration and all outgroups included. **Supplemental Dataset 16.** XML file for StarBeast3 analysis of 165 X-chromosome exons with Iguanidae calibration with only oplurid and leiosaurid outgroups. **Supplemental Dataset 17.** XML file for StarBeast3 analysis of 165 X-chromosome exons with Iguanidae calibration with only phrynosomatid outgroups. **Supplemental Dataset 18.** XML file for BEAST2 analysis of 165 X-chromosome exons with Iguanidae calibration and all outgroups included. **Supplemental Dataset 19.** XML file for FBD BEAST2 analysis of 50 loci each of RELEC, UCE, and AHE and all outgroups included, with *Queironius praelapsus* excluded. **Supplemental Dataset 20.** XML file for FBD BEAST2 analysis of 50 loci each of RELEC, UCE, and AHE and all outgroups included. **Supplemental Dataset 21.** XML file for BEAST2 analysis of 100 RELEC and 50 UCEs with nine outgroups included. **Supplemental Dataset 22.** FASTA file of the target loci. **Supplemental Dataset 23.** Data on published dispersal lengths in iguanas and vertebrates broadly. This Excel files contains two sheets. The first "vert" contains dispersal distance data and a source for that distance for each vertebrate taxon that appears in Figure 4b of the main text. The first "iguana" contains dispersal distance data for iguanid taxon that appears in Figure 4a of the main text.