Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in South‐East Asia

Abstract

Tropical rainforests in South-East Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag-based simple sequence repeats and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the south-western part of Borneo, genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28-0.09 million years before present and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.

Patterns of avian diversification in Borneo: The case of the endemic Mountain Black-eye (Chlorocharis emiliae)

“….2% for mitochondrial coding genes . These divergence values are more in accord with the division of dipterocarps into eastern and western groups in the mid-Pleistocene (Iwanaga et al 2012, Ohtani et al 2013). Subsequent to glacial periods, when lowland forest reoccupied central Borneo (Cannon et al 2009), populations of birds from the eastern and western lowland refugia would have expanded along with lowland forest habitat and come into contact.…”

“…First, paleo-climatic and vegetation modeling must address geologic events earlier than the LGM. Based on genetic divergence values in a wide variety of studies in addition to our own (e.g., Gorog et al 2004, den Tex et al 2010, Ohtani et al 2013, the timescale of Borneo's avifaunal division is two orders of magnitude older than the LGM, perhaps nearer one million years than 10,000 years. Thus, models explaining the state of geography at the LGM, although extremely helpful in indicating what may happen to habitats during glacial cycles, may not apply to the mid or early Pleistocene.…”

“…From work on lowland taxa and preliminary studies of montane populations (Moyle et al 2005, Moyle et (Sheldon et al 2009, Irham et al 2012. Substantial evidence indicates that lowland bird populations were subdivided, presumably during one or more glacial periods, into forest refugia in western Sundaland and eastern Borneo, as were other groups of Sundaic organisms (e.g., Brandon-Jones 1998, Thomas 2000, Gathorne-Hardy et al 2002, Gorog et al 2004, Bänfer et al 2006, Iwanaga et al 2012, Ohtani et al 2013). This subdivision would have occurred as lowland forest retreated or shifted position and montane forest expanded and dominated central Borneo ( Figure 2B).…”

Current Genetic Structure of Teak (Tectona Grandis) in Myanmar Based on Newly Developed Chloroplast Single Nucleotide Polymorphism and Nuclear Simple Sequence Repeat Markers

“…Chloroplast DNA (cpDNA) variation-based haplotype distribution reflects the phylogeographic structure [17]. Among these markers, chloroplast single nucleotide polymorphisms (cpSNP) are very useful for clarifying phylogeographic patterns because of their slow rate of sequence evolution, small organelle DNA genome size, and absence of recombination [18], and cpSNP variations are known to be structured geographically in plant species [19].…”

Population Genetic Diversity in The Genus Dryoblanops Gaertn. f. (Dipterocarpaceae) Based on Nucler Microsatellite Markers

“…This result is consistent with genetic diversity at the species level, which showed that the mean observed heterozygosity (H O ) ranged from 0.378 in D. beccarii to 0.578 in D. aromatica and the mean expected heterozygosity was lowest in D. rappa (H E = 0.392) and highest in D. aromatica (H E = 0.635) ( Table 3). The estimates of genetic diversity for the six Dryobalanops species in this study were comparable to those of other dipterocarp species studied using microsatellite, such as Shorea leprosula [24], which occurs in the Malay Peninsula, Sumatra and Borneo and Shorea javanica [25], which occurs in Sumatra. However, this study also showed that the levels of genetic diversity in Dryobalanops species were lower than Shorea lumutensis [26], which occurs in the Malay Peninsula.…”