Data from: Rampant dispersal without gene-flow: Reproductively and geographically isolated lineages of the Supertramp lizard Lamprolepis smaragdina permeate the lesser Sunda Archipelago

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.