Abstract
Aim To date, there have been few studies investigating the phylogeography of forest trees that are widely distributed in New Zealand. Our main objective was to examine the phylogeographic distribution of chloroplast DNA from New Zealand Sophora trees with respect to known biogeographical regions, proposed refugia and species boundaries. A second objective was to investigate the origins of the southern and Chatham Island populations of Sophora chathamica , which have been proposed to derive from Māori translocation. Location The New Zealand archipelago coastal and lowland forests. Methods We sequenced the chloroplast trnQ5′‐rps16 intergenic spacer from 416 samples of Sophora , representing all of the New Zealand species. A median‐joining network was used to analyse haplotype relationships. Phylogeographic structuring was assessed with G ST and N ST calculations and spatial analysis of molecular variance ( SAMOVA ). Analyses of molecular variance were used to test partitioning schemes including species divisions and proposed biogeographical boundaries. Results A total of 22 haplotypes were recovered. Moderate genetic differentiation was detected and it had a phylogeographic component but no higher level groupings were found with a SAMOVA . Very little of the chloroplast variation was partitioned by species boundaries or geography. Haplotype diversity decreased from north to south but was not higher in proposed major lowland forest glacial refugia. Populations of Sophora chathamica suggested to derive from Māori translocations contained a haplotype not detected from the proposed natural range of the species. Main conclusions Sophora survived the Last Glacial Maximum in widespread populations throughout much of the country, although our data did not provide evidence for survival in the southern South Island. Chloroplast sharing among New Zealand Sophora species likely results from hybridization and introgression. Our results indicate that the occurrence of S. chathamica in the southern North Island, northern South Island and Chatham Islands is likely to be natural, although the planting by Māori of some of the individuals in the southern North Island and Chatham Islands cannot be excluded.