Next-Gen phylogeography of rainforest trees: measuring landscape-level cpDNA variation from whole-genome sequencing.

Standardized phylogeographic studies across co-distributed taxa can identify important refugia and biogeographic barriers, and potentially uncover how changes in adaptive constraints through space and time impact on the distribution of genetic diversity. The combination of Next Generation Sequencing and methodologies that enable uncomplicated analysis of the full chloroplast genome may provide an invaluable resource for such studies. Here we assess the potential of a shotgun-based method across twelve non-model rainforest trees sampled from two evolutionary distinct regions. Whole genomic shotgun sequencing libraries consisting of pooled individuals were used to assemble species-specific chloroplast references (in silicio). For each species the pooled libraries allowed for the detection of variation within and between datasets (each representing a geographic region). The potential use of nuclear rDNA as an additional marker from the NGS libraries was investigated by mapping reads agains...