Phylogenetic divergence associated with climate oscillations and topology illustrates the dispersal history of Formosan sambar deer ( Rusa unicolor swinhoii ) in Taiwan

The island of Taiwan represents an ideal context for studying the effects of climatic oscillations and topographic variation on large herbivores due to its varied tropical to sub-tropical climate zones at different elevational ranges. We explored the phylogenetics of Formosan sambar deer ( Rusa unicolor swinhoii ) using the control region of the mitochondrial genome. We detected 18 haplotypes among 454 sequences across the island and grouped them into six regions based on SAMOVA, with 68.78% variance among regions. A Bayesian phylogenetic dendrogram revealed two spatially segregated genetic clades. Neutrality tests and Bayesian skyline plots uncovered different demographic expansion histories for the two clades. We further tested divergence times and chronology to propose potential phylogenetic scenarios, which were examined using approximate Bayesian computation. Finally, we present a credible hypothesis for a glacial refugium in the northern part of the Central Mountain Range. Subsequent secondary contact between the two clades during interglacial periods has led to the extant genetic structure of Formosan sambar deer.