SNP matrices and vcf files for phylogenetic, genetic structure and historical demographic analyses of Podocarpus from Hispaniola

Aim: Hispaniola is the second largest island in the Caribbean and a
hotspot of biodiversity. The island was formed by the fusion of a northern
and southern palaeo-islands during the mid-Miocene (15 Ma). The historical
split of Hispaniola together with repeated marine incursions during the
Pleistocene are known to have influenced lineage divergence and genetic
structure in a few birds and mammals, but the effect on vascular plants is
less understood. The conifer genus Podocarpus has two species, P.
hispaniolensis and P. buchii, that are endemic to the mountains of
Hispaniola and are IUCN endangered. The former occurs in the mountains of
the north, and the latter in the south, with a region of sympatry in the
Central Cordillera. Here we evaluate the historical split of the two
palaeo-islands, and repeated marine incursions as dispersal barriers to
the geographical distribution of genetic diversity, genetic structure,
divergence patterns, and the historical demography of the two species.
Location: Hispaniola island, Caribbean. Methods: Using Genotyping by
Sequencing in 47 Podocarpus samples we identified two sets of single
nucleotide polymorphisms for our analyses (74,260 and 22,657 SNPs).
Results: The results show a population genetic structure that corresponds
to the geographic distribution of the species in mountainous areas.
Podocarpus in Hispaniola followed a stepping-stone colonization pattern
with bottlenecks at each mountain colonization event. Main conclusions:
The historical events in question did not seem to have influenced the
genetic structure, diversity, or demography of Podocarpus, instead the
current geographic barriers imposed by lowland xeric valleys did. The
clear divergence between species together with the elevated
within-population genetic diversity and significant genetic structure call
for a multi-population in situ conservation of each species.