Incongruent patterns of nuclear and chloroplast variation in Correa (Rutaceae): introgression and biogeography in south-eastern Australia

Correa (family Rutaceae) is a genus endemic to southern Australia, in which chloroplast introgression between species has previously been inferred. The current study aimed to document the extent of incongruence between molecular markers and taxonomy, describe patterns of geographic variation, and infer genetic and biogeographic processes important in the history of the genus. Sampling focused on subg. Correa (nine species) and included 166 samples from 95 localities. Samples were genotyped at the chloroplast loci trnL-trnF and trnK and the nuclear ITS regions, either by direct sequencing or by restriction digests of PCR products. Both chloroplast and ITS datasets resolved subg. Persistens (two species mostly from wet forests) as distinct from those of subg. Correa. Within subg. Correa chloroplast and ITS lineages were largely incongruent with each other and with current taxonomy, but both datasets showed similar geographic patterns. In each dataset there was one lineage mostly restricted to western South Australia and Western Australia, and one lineage widespread in eastern South Australia, Victoria, Tasmania, New South Wales and Queensland. The split between these geographic lineages occurs in South Australia, on the western side of the Murray basin; it is sharply defined in the chloroplast results, whereas the distributions of ITS lineages overlap. The geographic patterns and incongruence exhibited by both ITS and chloroplast markers provide evidence for substantial chloroplast and nuclear introgression between species. Geographic distributions of genetic lineages are consistent with divergence caused by a historical vicariance event across the lower Murray basin and subsequent reconnection of populations.