The widespread distribution of Lithocarpus (ca. 250 spp.) on the continent of Asia and throughout the Malayan Archipelago provides a compelling biogeographical setting to apply genealogical approaches to investigate interspecific patterns of landscape-level molecular differentiation. We specifically address phylogeography and reproductive biology using cpDNA and ITS sequences from 200 individual trees collected from Indochinese and Bornean populations, with emphasis on sympatric zones on Mt. Kinabalu, Borneo. A total of 70 unique haplotyes was determined and these are divided into two lineages, Indochinese and Bornean. A widespread haplotype among Indochinese populations was common in North Borneo as well, but no Bornean haplotypes were found in continental populations. Many haplotypes were trans-specific, suggesting incomplete lineage sorting of a polymorphic ancestral population. The distribution of cpDNA variation also could be influenced localized introgression, but there is limited evidence for interspecific hybridization in the genus. To examine species boundaries, we analyzed ITS sequences from the same plants and resolved regionally distributed species groupings that generally correspond to sections within the genus. ITS data generally identify phylogenetic patterns and broader biogeographic subdivisions. On Mt. Kinabalu where many species co-occur, individuals representing species with highly derived fruit types were monophyletic for ITS. In contrast, the ITS sequences of several species bearing plesiomorphic, acorn-like fruits were more closely related, with few examples of agreement between morpho-species and ITS clades. Overall, the combination of shared, presumably ancestral cpDNA haplotypes with high levels of endemic types suggests long-term persistence of large populations in North Borneo. ITS data suggest species cohesion among individuals with well-defined apomorphic fruit; whereas, less specialized species do not appear to be reproductively isolated.

Key words: biogeography, Malayan Archipelago, reproduction, tropical trees