Data from: Rampant dispersal without gene-flow: Reproductively and geographically isolated lineages of the Supertramp lizard Lamprolepis smaragdina permeate the lesser Sunda Archipelago
Data files
Jan 20, 2025 version files 339.91 MB
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Lamprolepis_(MVZ294396)_RNA_baits_for_target_capture.fasta
5.88 MB
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Lamprolepis_ADEGENET.txt
5.55 MB
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Lamprolepis_annotated_transcriptome_(MVZ294396_Flores).fasta
14.79 MB
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Lamprolepis_annotated_transcriptome_(MVZ294410_Lembata).fasta
13.85 MB
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Lamprolepis_areas.txt
394 B
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Lamprolepis_ASTRAL_input.tre
8.70 MB
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Lamprolepis_ASTRAL_Map_File.txt
1.82 KB
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Lamprolepis_BEAST_coalescent_topology.xml
30.92 MB
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Lamprolepis_BEAST_ML_topology.xml
30.92 MB
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Lamprolepis_BioGeoBears.R
52.60 KB
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Lamprolepis_coalescent.tre
451 B
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Lamprolepis_Concatenated_Alignment_Partitions.txt
39.44 KB
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Lamprolepis_Concatenated_Alignment.phylip
178.50 MB
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Lamprolepis_distances.txt
584 B
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Lamprolepis_GPHOCS.aln
42.80 MB
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Lamprolepis_ML.tre
451 B
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Lamprolepis_mtDNA_partitions.txt
184 B
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Lamprolepis_ND2.nex
252.22 KB
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Lamprolepis_SNAPP.xml
93.82 KB
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Lamprolepis_STRUCTURE.stru
7.54 MB
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README.md
5.78 KB
Abstract
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.
README: 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
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.
Methods
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.