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Large-scale genetic structure revealed in tree populations in SE Asia, as well as in many temperate forests, has been shaped by climatic fluctuation in the late Pleistocene, most importantly by that in the last glacial period. In a comparative study of the phylogeographic patterns of two closely related dipterocarp species, Dryobalanops aromatica C.F.Gaertn. and D. beccarii Dyer, we investigated how changes in land area associated with changes in climate affected large-scale genetic structure. We examined the genetic variation of D. aromatica, collected from nine populations throughout the Sundaic region, and of D. beccarii, collected from 16 populations mainly in Borneo, using seven polymorphic microsatellite markers. The two species were clearly distinguishable in the STRUCTURE analysis, although hybridisation probably occurred in sympatric populations and also in several other populations. The D. aromatica populations were divided into two main groups by the STRUCTURE analysis: Malay–Sumatra and Borneo. Mixing of the Sumatra and Borneo clusters occurred on the Malay Peninsula, supporting the hypothesis that tropical rainforests expanded over a dried Sunda Shelf during the last glacial period. The two main genetic clusters might have been formed by repeated cycles of fluctuation in land area. The D. beccarii populations in Borneo were divided into four geographically distinct groups: western Sarawak, central inland Sarawak, central coastal Sarawak and Sabah. The population on the Malay Peninsula (Gunung Panti) was an admixture of the four Bornean clusters. This suggests that this population is a relic of the recent range expansion of D. beccarii during the last glacial period.

Genetic variation and structure of Ubame oak (Quercus phillyraeoides A. Gray), a shrub tree on the Pacific coast of Japan, were examined to elucidate historical population dynamics using five chloroplast DNA (cpDNA) marker regions and 11 nuclear microsatellite loci. Three cpDNA haplotypes (A, B and C) were identified in a screen of 41 populations across the entire distribution range in Japan. Haplotype A was the most prevalent and was found in the entire range. Haplotype B was locally restricted to the Kii Peninsula, while haplotype C was restricted to the southwestern part of Japan. These haplotypes corresponded with the nuclear genetic constitution revealed by microsatellite markers. Two genetically differentiated major groups were identified by STRUCTURE analysis applied to 536 individuals from 28 populations, and they mostly corresponded with the two major cpDNA haplotypes, A and C. These populations were further divided into three geographically identified groups: group 1 in the area including Kanto and Tokai regions, the Kii Peninsula and the Muroto-misaki Cape on the Pacific coast; group 2 in the Bungo-suido Channel area; and group 3 in southern Kyushu and Okinawa. Populations in the Seto Inland Sea were divided into two groups: one was included in group 1 and appears to have originated from last glacial maximum (LGM) refugia located in the Kii Peninsula, while the other was included in group 2 and appears to have originated from LGM refugia located in southern Kyushu. These groups can be considered as conservation units for the preservation of unique seashore ecosystems, or as a seed source to foster coastal protection forests and next-generation production forests. Considerable care should be taken to protect isolated populations that may be specialized to unique local environments, such as those on the islands of Koshikijima and Izenajima.

Manurung J, Siregar IZ, Kusmana C, Dwiyanti FG. 2017. Genetic variation of the mangrove species Avicennia marina in heavy metal polluted estuaries of Cilegon Industrial Area, Indonesia. Biodiversitas 18: 1109-1115. Mangrove forests are often facing various anthropogenic disturbances, particularly in the industrial area. However, information on the status of industrial heavy metal pollution and its impact on the genetic variation of mangrove species, such as Avicennia marina, particularly in Indonesian industrial area has not been assessed. In this study, the classification of heavy metals in two estuaries of Cilegon Industrial Area (Pelabuhan Warna Sari and Krakatau) and one estuary outside Cilegon Industrial Area (Pulau Sangiang) were determined by Sediment Quality Guidelines- States Environment Protection Agency (SQGs-USEPA). Furthermore, the genetic diversity of 72 individuals of A. marina in the three estuaries were examined using four microsatellite loci (M3, M64, M81 and M98). The results showed that Krakatau area was the heavily polluted estuary based on SQGs-USEPA and have a lower genetic variation (He= 0.54) than Pelabuhan Warna Sari (moderately polluted, He= 0.56) and Pulau Sangiang (non-polluted, He= 0.60) suggesting a notable of deficiencies of genetic variation of A. marina in heavy polluted estuary compared to moderately and non-polluted estuary. Considering the low level of genetic variation in heavily polluted area, transplantation among estuaries and introduction of propagules from non-polluted estuary or other regions are needed as one of the conservation efforts.

Genetic variation and structure of Ubame oak (Quercus phillyraeoides A. Gray), a shrub tree on the Pacific coast of Japan, were examined to elucidate historical population dynamics using five chloroplast DNA (cpDNA) marker regions and 11 nuclear microsatellite loci. Three cpDNA haplotypes (A, B and C) were identified in a screen of 41 populations across the entire distribution range in Japan. Haplotype A was the most prevalent and was found in the entire range. Haplotype B was locally restricted to the Kii Peninsula, while haplotype C was restricted to the southwestern part of Japan. These haplotypes corresponded with the nuclear genetic constitution revealed by microsatellite markers. Two genetically differentiated major groups were identified by STRUCTURE analysis applied to 536 individuals from 28 populations, and they mostly corresponded with the two major cpDNA haplotypes, A and C. These populations were further divided into three geographically identified groups: group 1 in the area including Kanto and Tokai regions, the Kii Peninsula and the Muroto-misaki Cape on the Pacific coast; group 2 in the Bungo-suido Channel area; and group 3 in southern Kyushu and Okinawa. Populations in the Seto Inland Sea were divided into two groups: one was included in group 1 and appears to have originated from last glacial maximum (LGM) refugia located in the Kii Peninsula, while the other was included in group 2 and appears to have originated from LGM refugia located in southern Kyushu. These groups can be considered as conservation units for the preservation of unique seashore ecosystems, or as a seed source to foster coastal protection forests and next-generation production forests. Considerable care should be taken to protect isolated populations that may be specialized to unique local environments, such as those on the islands of Koshikijima and Izenajima.