DOI: 10.5061/dryad.bzkh189mn
title: Data from: Rampant dispersal without gene-flow: Reproductively and geographically isolated lineages of the Supertramp lizard Lamprolepis smaragdina permeate the lesser Sunda Archipelago

description: We investigated the biogeographical patterns of a widespread arboreal
 lizard found throughout Wallacea and the western Pacific islands. Wallacea
 contains longstanding oceanic currents that flow from the Pacific Ocean
 into the Indian Ocean, known as the Indonesian Throughflow. Using genetic
 data, we aim to estimate the timing and sequence of island colonization in
 the Lesser Sunda archipelago of southern Wallacea and to determine the
 proportion of dispersal events that may have been aided by ocean currents.
 Levels of gene flow are also explored in the context of island
 arrangement, past connectivity (ex. Pleistocene land bridges), and ocean
 currents. Location- Southern Wallacea (Indonesia, Timor-Leste) Taxon-
 Emerald Tree Skink (Lamprolepis smaragdina) Methods- We estimated a
 mitochondrial DNA phylogeny from southern Wallacean populations to
 identify divergent populations and to guide sample selection for
 genomic-scale data collection. These genomic data were used to estimate 1)
 phylogenetic relationships of island populations using both concatenated
 Maximum Likelihood, summary coalescent, and multispecies coalescent
 methods, 2) levels of genetic connectivity between lineages using genetic
 clustering and migration analyses, and 3) to reconstruct their dispersal
 history using ancestral range reconstruction analysis. Results- We found
 that the Emerald Tree Skinks of southern Wallacea diverged from a
 population on Peleng Island ~1.25 Ma and that Lesser Sunda populations
 diverged between ~1–0.4 Ma. MtDNA data are insufficient to estimate the
 relationships of each population and find one island to be paraphyletic
 and two to be polyphyletic. Genomic data find that Timor Island is
 polyphyletic while all other islands are recovered as monophyletic. Gene
 flow is minimal or absent across the archipelago, even between islands
 that become periodically land-bridged. More than half of the estimated
 over-water dispersal events occurred perpendicular to or against ocean
 currents. Main Conclusions- Despite this species’ over-water dispersal
 abilities island populations are genetically isolated from one another,
 even on adjacent islands that become periodically land bridged. This
 suggests that species formation is complete. The inferred dispersal
 history involved many paths that would be difficult to complete given the
 direction of ocean currents, indicating that historical ocean currents are
 more dynamic than currently understood.
description: Transcriptomes from the liver tissues of two Lesser Sunda
 Lamprolepis smaragdina were used to design RNA probes for a
 targeted-capture experiment. 1364 nuclear loci (1726310 base pairs total)
 were sequenced for 104 individual Lamprolepis samples. These data were
 analyzed in a phylogenomic, population genomic, and biogeographical
 framework. Detailed methods on marker development, the exon-capture
 experiement, and data filtering and processing are found in the
 supplemental methods document.
description: # Rampant dispersal without gene-flow: Reproductively and geographically
 isolated lineages of the Supertramp lizard Lamprolepis smaragdina permeate
 the lesser Sunda Archipelago #### Reilly SB, Kaiser H, Karin BR, Arifin U,
 Stubbs AL, Arida E, Hamidy A, Iskandar DT, McGuire JA (2025) Journal of
 Biogeography,
 [https://doi.org/10.1111/jbi.15087](https://doi.org/10.1111/jbi.15087)
 Transcriptomes from the liver tissues of two Lesser Sunda Lamprolepis
 smaragdina were used to design RNA probes for a targeted-capture
 experiment. 1364 nuclear loci (1726310 base pairs total) were sequenced
 for 104 individual lizards. These data were analyzed in a phylogenomic,
 population genomic, and biogeographical framework. ## Description of the
 data and file structure **File: Lamprolepis annotated transcriptome
 (MVZ294396_Flores).fasta** Description: Annotated transcriptome loci in a
 fasta format. **File: Lamprolepis annotated transcriptome
 (MVZ294410_Lembata).fasta** Description: Annotated transcriptome loci in a
 fasta format. **File: Lamprolepis (MVZ294396) RNA baits for target
 capture.fasta** Description: 120 base pair, 4.8x tiled RNA bait designs
 from a single reference transcript (sample MVZ:Herp:294396 from Flores
 Island, Indonesia) in fasta format. **File: Lamprolepis Concatenated
 Alignment.phylip** Description: 1364 concatenated loci for 104
 Cyrtodactylus samples in phylip format. The alignment totals 1716310 base
 pairs. This file was used for Maximum-Likelihood phylogenetic estimation
 with the software IQTree2. **File: Lamprolepis Concatenated Alignment
 Partitions.txt** Description: The partitions of the 1364 loci in the
 concatenated alignment "Lamprolepis Concatenated
 Alignment.phylip". **File: Lamprolepis BEAST ML_topology.xml**
 Description: XML file used to run the BEAST time-calibrated phylogenetic
 analysis with the topology of Clades 1-4 fixed to match that of the
 Maximum Likelihood (IQTree2) tree. **File: Lamprolepis BEAST
 coalescent_topology.xml** Description: XML file used to run the BEAST
 time-calibrated phylogenetic analysis with the topology of Clades 1-4
 fixed to match that of the summary coalescent (ASTRAL3) and multi-species
 coalescent (SNAPP) trees. **File: Lamprolepis ASTRAL input.tre**
 Description: Individual Maximum-Likelihood gene trees for 1335 nuclear
 loci generated with the software IQTree2. This file serves as the input
 for the summary coalescent species tree software ASTRAL3. **File:
 Lamprolepis ASTRAL Map File.txt** Description: Map file for the ASTRAL3
 software species tree analysis. The file tells ASTRAL3 which samples from
 the are to be grouped together. **File: Lamprolepis_ML.tre** Description:
 Simplified phylogeny produced by the BEAST2 software with relationships of
 Clades 1-4 fixed to match the Maximum Likelihood tree. This file serves as
 the tree for ancestral range estimation analyses in the software
 BioGeoBEARS. **File: Lamprolepis_coalescent.tre** Description: Simplified
 phylogeny produced by the BEAST2 software with relationships of Clades 1-4
 fixed to match the coalescent trees. This file serves as the tree for
 ancestral range estimation analyses in the software BioGeoBEARS. **File:
 Lamprolepis_distances.txt** Description: Distances between regions in
 kilometers, estimated using Google Earth. This file scales dispersal
 probability for ancestral range estimation in the software BioGeoBEARS.
 **File: Lamprolepis_areas.txt** Description: 12 regions defined for
 ancestral range estimation in the software BioGeoBEARS. The file then
 lists all samples and which regions they occur in. **File:
 Lamprolepis_BioGeoBears.R** Description: R code used to run the
 BioGeoBEARS analyses. Change the names of the input trees
 (Lamprolepis_ML.tre or Lamprolepis_coalescent.tre) for each analysis.
 **File: Lamprolepis_STRUCTURE.stru** Description: Biallelic single
 nucleotide polymorphism (snps) data from 98 Lamprolepis smaragdina from
 the Lesser Sunda Islands. This file contains 18362 snps and serves as the
 input for genetic clustering analysis with the software STRUCTURE. The
 linkage of the snps is indicated on the first line with "-1"
 indicating the start of a new locus. **File: Lamprolepis_ADEGENET.txt**
 Description: Biallelic single nucleotide polymorphism (snps) data from 98
 Lamprolepis smaragdina from the Lesser Sunda Islands. This file contains
 18362 snps and serves as the input for PCA and isolation-by-distance
 analyses with the R package ADEGENET. **File: Lamprolepis_GPHOCS.aln**
 Description: Flanking (intron) sequence data for 500 loci for all 104
 samples. This file served as the input for the software G-PhoCS. **File:
 Lamprolepis_ND2.nex** Description: Alignment of the mitochondrial ND2 gene
 and associated tRNAs. The file contains up to 1426 base pairs for 174
 samples. **File: Lamprolepis mtDNA partitions.txt** Description: Gene
 partitions for the alignment "Lamprolepis_ND2.nex" **File:
 Lamprolepis_SNAPP.xml** Description: XML file used to run the SNAPP
 multispecies coalescent species tree analysis in BEAST. The file contains
 1334 independent snps for 57 samples. ## Sharing/Access information Links
 to other publicly accessible locations of the raw data: Sequence data for
 the ND2 mitochondrial gene have been submitted to the GenBank database
 under accession numbers OR130303–OR130453. Sequencing data from the
 exon‐capture experiment have been submitted to the NCBI sequence read
 archive under accession number PRJNA983734. Data was derived from the
 following sources: Voucher specimens and frozen tissue samples are housed
 at the Museum of Vertebrate Zoology, UC Berkeley, USA, or the Museum
 Zoologicum Bogoriense, Cibinong, Indonesia. Mitochondrial and exon-capture
 data were derived from samples listed in Table S1 of the published paper.