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Effects of Pleistocene climate change on genetic structure and diversity of Shorea macrophylla in Kalimantan Rainforest

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The island of Borneo is the diversity center of the Dipterocarpaceae, the most important family of tropical rainforest trees in Southeast Asia. However, changes in land use and climate have affected dipterocarp distributions on the island, raising concerns about the vulnerability (inter alia) of the endemic riparian species Shorea macrophylla. Thus, to aid conservation efforts, we have investigated the genetic diversity, structure, and demographic history of S. macrophylla. The species’ genetic diversity and structure in Kalimantan (part of Indonesia, covering 75% of the island) were explored by examining genotypes of 377 individuals representing 13 populations in three regions (Northeast, Central, and West Kalimantan) using 14 newly developed microsatellite loci. Higher genetic diversity was found, at all loci, in samples from Northeast Kalimantan than in samples from the other regions. Moderate genetic differentiation between populations was detected (FST 0.093). Bayesian clustering, principal coordinate, and neighbor joining tree analyses of the population structure consistently identified two genetically distinct groups, one in the Northeast and the other in the Central and West regions. The higher diversity of the diverged populations in Northeast Kalimantan indicates that the region may have hosted rainforest refugia during the ice age. Accordingly, analysis using DIY ABC software indicated that the Northeast and Central-West Kalimantan groups diverged 194,000 years ago. We conclude that global climate change during the Pleistocene strongly influenced the genetic diversity and structure of S. macrophylla populations in Kalimantan.

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We sincerely thank Prof. Ryo Ohsawa (University of Tsukuba) for providing laboratory facilities for DNA extraction. Thanks are also due to Ghani Purnomo, Sawitri, Dicky Wahono, Intracawood Manufacturing Ltd., Wana Inti Kahuripan Ltd., Sari Bumi Kusuma Ltd., Suka Jaya Makmur Ltd., and Intracawood Manufacturing Ltd., for their kind support during the sample collection. A MEXT Japan scholarship supported this study.

Data archiving statement

All genotyping data used in this study was deposited in the Dryad data repository, https://doi.org/10.5061/dryad.92j7j53.

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Correspondence to Yoshihiko Tsumura.

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Communicated by W. Ratnam

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Utomo, S., Uchiyama, K., Ueno, S. et al. Effects of Pleistocene climate change on genetic structure and diversity of Shorea macrophylla in Kalimantan Rainforest. Tree Genetics & Genomes 14, 44 (2018). https://doi.org/10.1007/s11295-018-1261-1

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  • Shorea macrophylla
  • Genetic diversity and structure
  • Pleistocene climate change
  • Refugia
  • Kalimantan