Data from: The evolutionary history of Darwin's finches: speciation, gene flow, and introgression in a fragmented landscape

Many classic examples of adaptive radiations take place within fragmented
systems such as islands or mountains, but the roles of mosaic landscapes
and variable gene flow in facilitating species diversification is poorly
understood. Here we combine phylogenetic and landscape genetic approaches
to understand diversification in Darwin's finches, a model adaptive
radiation. We combined sequence data from 14 nuclear introns,
mitochondrial markers, and microsatellite variation from 51 populations of
all 15 recognized species. Phylogenetic species-trees recovered seven
major finch clades: ground, tree, vegetarian, Cocos Island, grey and green
warbler finches, and a distinct clade of sharp-beaked ground finches
(Geospiza cf. difficilis) basal to all ground and tree finches. The ground
and tree finch clades lack species-level phylogenetic structure.
Interisland gene flow and interspecies introgression vary geographically
in predictable ways. First, several species exhibit concordant patterns of
population divergence across the channel separating the Galápagos platform
islands from the separate volcanic province of northern islands. Second,
peripheral islands have more admixed populations while central islands
maintain more distinct species boundaries. This landscape perspective
highlights a likely role for isolation of peripheral populations in
initial divergence, and demonstrates that peripheral populations may
maintain genetic diversity through outbreeding during the initial stages
of speciation.