Datasets for Draco lineatus phylogenomics study

The biota of Sulawesi is noted for its high degree of endemism and for its
substantial levels of in situ biological diversification. While the
island’s long period of isolation and dynamic tectonic history have been
implicated as drivers of regional diversification, this has rarely been
tested in the context of an explicit geological framework. Here we provide
a tectonically-informed biogeographical framework that we use to explore
the diversification history of Sulawesi flying lizards (the Draco lineatus
Group), a radiation that is endemic to Sulawesi and its surrounding
islands. We employ a framework for inferring cryptic speciation that
involves phylogeographic and genetic clustering analyses as a means of
identifying potential species followed by population demographic
assessment of divergence-timing and rates of bi-directional migration as
means of confirming lineage independence (and thus species status). Using
this approach, phylogenetic and population genetic analyses of
mitochondrial sequence data obtained for 613 samples, a 50-SNP data set
for 370 samples, and a 1249-locus exon-capture data set for 106 samples
indicate that the current taxonomy substantially understates the true
number of Sulawesi Draco species, that both cryptic and arrested
speciation have taken place, and that ancient hybridization confounds
phylogenetic analyses that do not explicitly account for reticulation. The
Draco lineatus Group appears to comprise 15 species – nine on Sulawesi
proper and six on peripheral islands. The common ancestor of this group
colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two
ancestral islands, and began to radiate ~6 Ma as new islands formed and
were colonized via overwater dispersal. The enlargement and amalgamation
of many of these proto-islands into modern Sulawesi, especially during the
past 3 Ma, set in motion dynamic species interactions as once-isolated
lineages came into secondary contact, some of which resulted in lineage
merger, and others surviving to the present.