The stone oaks (Lithocarpus) form the largest genus (300 spp.) in the insect-pollinated chestnut subfamily in the Fagaceae and produce fruit with similar ecological characteristics as Quercus acorns. These trees are largely restricted to mesic habitats throughout much of Southeast Asia and have two centers of diversity: Indochina and the island of Borneo. To investigate whether current landscape level genetic variation might indicate historical migration routes and refugia, we sequenced an intergenic region (rbcL-atpBE) on the chloroplast genome from 166 individuals in eight different locations. Our taxonomic sampling included 49 species in at least eight sections to address the question of interspecific introgression. We found 66 unique genotypes, which exhibited strong phylogenetic and geographic structure. Two major lineages, one shared between Indochina and Borneo ("continental") and one found only on Borneo ("Bornean"), contained roughly equal numbers of individuals. Numerous transpecific polymorphisms were observed and only one species was fixed on a type, which was shared with other species. In general, individuals from a single location were more closely related than expected, indicating limited seed migration. Populations found in the northwest part of the island possessed the highest degree of overall diversity and appeared to lie nearest the center of origin of the group. The presence of a shared ancestral genotype between China and Borneo suggests limited genetic drift and persistence of a neutral transpecific polymorphism through a time span perhaps exceeding ten million years. A number of macroevolutionary processes, acting simultaneously and at different times in the past, are responsible for the observed patterns, including incomplete lineage sorting, introgressive hybridization, local population dynamics, and isolation by distance. Further sampling of the other Southeast Asian landmasses will be necessary to pinpoint migration routes and refugia and to calibrate the timing of these events.

Key words: Borneo, Fagaceae, interspecific phylogeography, Lithocarpus, Southeast Asia, transpecific polymorphisms