DOI: 10.5061/dryad.nk1mt6b
title: Data from: Leap-frog dispersal and mitochondrial introgression: phylogenomics and biogeography of Limnonectes fanged frogs in the Lesser Sundas Archipelago of Wallacea

description: Aim: The Lesser Sunda Islands are situated between the Sunda and Sahul
 Shelves, with a linear arrangement that has functioned as a two-way filter
 for taxa dispersing between the Asian and Australo-Papuan biogeographic
 realms. Distributional patterns of many terrestrial vertebrates suggest a
 stepping-stone model of island colonization. Here we investigate the
 timing and sequence of island colonization in Asian-origin fanged frogs
 from the volcanic Sunda Arc islands with the goal of testing the
 stepping-stone model of island colonization. Location: The Indonesian
 islands of Java, Lombok, Sumbawa, Flores, and Lembata. Taxon: Limnonectes
 dammermani and L. kadarsani (Family: Dicroglossidae) Methods:
 Mitochondrial DNA was sequenced from 153 frogs to identify major lineages
 and to select samples for an exon-capture experiment. We designed probes
 to capture sequence data from 974 exonic loci (1,235,981 bp) from 48 frogs
 including the outgroup species, L. microdiscus. The resulting data were
 analyzed using phylogenetic, population genetic, and biogeographical model
 testing methods. Results: The mtDNA phylogeny finds L. kadarsani
 paraphyletic with respect to L. dammermani, with a pectinate topology
 consistent with the stepping-stone model. Phylogenomic analyses of 974
 exons recovered the two species as monophyletic sister taxa that diverged
 ~7.6 Ma with no detectable contemporary gene flow, suggesting
 introgression of the L. dammermani mitochondrion into L. kadarsani on
 Lombok resulting from an isolated ancient hybridization event ~4 Ma.
 Within L. kadarsani, the Lombok lineage diverged first while the Sumbawa
 and Lembata lineages are nested within a Flores assemblage composed of two
 parapatrically distributed lineages meeting in central Flores.
 Biogeographical model comparison found strict stepping-stone dispersal to
 be less likely than models involving leap-frog dispersal events. Main
 conclusions: These results suggest that the currently accepted
 stepping-stone model of island colonization might not best explain the
 current patterns of diversity in the archipelago. The high degree of
 genetic structure, large divergence times, and absent or low levels of
 migration between lineages suggests that L. kadarsani represents five
 distinct species.
description: Limnonectes 16S
 mitochondrial DNA alignment16S mitochondrial DNA
 alignment for Limnonectes kadarsani, L. dammermani, and L.
 microdiscus.Limnonectes_16S.nexLimnonectes Exon-Capture alignmentA concatenated phylip alignment file of 974 genes (exons+introns) for Limnonectes kadarsani, L. dammermani, and L. microdiscus. These data were collected using MYbaits in-solution exon-capture experiment.Limno_Exon-Capture.phylipASTRAL Input TreesIndividual RAxML phylogenies for 974 genes that are used as the input for the summary coalescent software ASTRAL-II.Limno_TF_refined_ASTRAL_input.treG-PhoCS Input FileIndividual alignments for the flanking regions (introns) of 659 genes used as the input file for demographic analyses performed by the software G-PhoCS.Limno_GPhocsInput.alnScaled Distances for BioGeoBears analysisScaled geographic distances between islands or island regions for biogeographical model testing analyses in BioGeoBears.geographic-distances-scaled.txtDefined areas for BioGeoBearsThe defined islands or island regions used in biogeographical model testing analyses for BioGeoBears.geographicAreas.txtGuide tree for BioGeoBearsAn ultrametric tree of the relationships between major clades of Limnonectes from the Lesser Sundas used as a guide tree for biogeographical model testing analyses in BioGeoBears.clade-tree-ultrametric.treBioGeoBears Model 1The stepping-stone model tested in BioGeoBears.model1-steppingstone.txtBioGeoBears Model 2The BioGeoBears model allowing stepping-stone plus one leap-frog dispersals.model2-steppingstone+1leapfrog.txtBioGeoBears Model 3The BioGeoBears model allowing stepping-stone plus one or two leap-frog dispersals.model3-steppingstone+1leapfrog+2leapfrog.txtBioGeoBears Model 4The BioGeoBears model allowing stepping-stone plus up to three leap-frog dispersals.model4-steppingstone+1leapfrog+2leapfrog+3leapfrog.txtBioGeoBears Model 5The BioGeoBears model allowing stepping-stone plus up to four leap-frog dispersals.model5-steppingstone+1leapfrog+2leapfrog+3leapfrog+4leapfrog.txt