Plio-Pleistocene environmental changes shape present day phylogeography of New Zealand’s southern beeches (Nothofagaceae)

Island ecosystems can be severely affected by climate change as they provide limited opportunities for species to track their habitat. Studying the population dynamics of keystone species from these ecosystems can shed a light on climate – ecosystem interactions. Southern beeches are such keystone species in New Zealand with beech forests constituting the most abundant forest cover on the two main islands. Here we use 2.4 kilobase pairs of chloroplast genetic markers from four species of southern beech across their geographic distribution to help elucidate the Pleistocene history of New Zealand forests, and the processes that led to the present-day distribution of southern beech diversity. Broadly concordant phylogeographic patterns were observed across all beech species analysed. The centre of genetic diversity in silver beech was in the northern South Island, with unique haplotypes in the southern South Island, and southern and northern North Island, separated by known ‘beech gaps’. Significantly less genetic diversity was evident in the subgenus Fuscospora (red, hard, black/mountain beech). All three species shared a single haplotype in the southern South Island, and a unique haplotype north of the central South Island ‘beech gap’. Our study indicates that the present-day distribution of southern beech diversity in New Zealand is largely a result of Plio-Pleistocene environmental changes, with survival in cryptic southern South Island and multiple North Island in situ microrefugia throughout recent glacial cycles. By contrast, the northern South Island was likely the only New Zealand region that supported large (silver) beech populations throughout the Pleistocene. With beech species in New Zealand being keystone forest species, the distribution of the genus throughout the Pleistocene provides a proxy for forest cover at different times. It helps understand the ecological challenges the New Zealand forest fauna and flora were exposed to during the climate oscillations of the ice ages.