Chloroplast phylogeography of New Zealand Sophora trees (Fabaceae): extensive hybridization and widespread Last Glacial Maximum survival

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 GST and NST 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.

Genetic Variation and Hybridisation among Eight Species of kōwhai (Sophora: Fabaceae) from New Zealand Revealed by Microsatellite Markers

“…However, S. molloyi appeared to be similar in assignment to S. microphylla , and S. godleyi comprised individuals with a range of assignment values as well as samples that appeared to be uniquely assigned to S. godleyi (pink samples in Figure 2 ). The close relationship between S. microphylla and S. molloyi is a similar result to that of Shepherd et al [ 10 ] who showed that in the southern North Island the two species share haplotype K and in the southern part of Cook Strait they share haplotype F. Sophora microphylla and S. molloyi are distinguished by their growth habit, leaf characters and ecological preferences as presented in the taxonomic revision [ 6 ].…”

“…This is a significant result since, prior to the recent taxonomic revision of Sophora in New Zealand [ 4 , 6 ], S. chathamica was not an accepted species and S. fulvida and S. longicarinata were treated as varieties of S. microphylla [ 25 ]. In contrast, S. prostrata , with its divaricate growth habit, small and few leaflets, and resupinate flower, has long been accepted as a distinct species, and in previous genetic studies, it is one of the few species to have been distinguished [ 9 , 10 ], a result supported in this study. However, S. molloyi appeared to be similar in assignment to S. microphylla , and S. godleyi comprised individuals with a range of assignment values as well as samples that appeared to be uniquely assigned to S. godleyi (pink samples in Figure 2 ).…”

“…Other attempts to establish species relationships have unsuccessfully used enzyme electrophoresis [ 8 ] and amplified fragment length polymorphism (AFLP) markers [ 9 ]. Inter simple sequence repeats (ISSR) markers resolved Sophora prostrata samples as a group, but the samples of the other species did not form discrete species groups [ 9 ]; a similar result was obtained with more recently generated AFLP data [ 10 ]. Another recent study [ 11 ] used the same ISSR markers as [ 9 ] and reported that S. prostrata individuals were mixed up with individuals of Sophora microphylla and Sophora tetraptera .…”

“…A phylogeographic study [ 10 ] of 416 samples representing the eight New Zealand species using 22 chloroplast trnQ-5′rps16 haplotypes concluded that little of the genetic variation was partitioned by species boundaries or geography, haplotype diversity decreased from North Island (20 haplotypes, nine haplotypes unique) to South Island (11 haplotypes, two haplotypes unique), and chloroplast sharing among the New Zealand species most probably results from hybridisation and introgression. A phylogenetic analysis of Sophora sect.…”

“…The failure of the earlier genetic studies—e.g., [ 1 , 3 , 7 , 8 , 9 , 11 ]—to elucidate species relationships, and setting aside the more informative recent analyses [ 2 , 10 , 12 ], prompted the development of 12 microsatellite markers [ 13 ]. These microsatellite markers discriminated 14 individuals of Sophora chathamica and four populations of S. microphylla and have provided tools that will enable genetic variation among individual plants to be studied.…”