Phylogeny ofPgiC gene inShoreaand its closely related genera (Dipterocarpaceae), the dominant trees in Southeast Asian tropical rain forests

Abstract

Dipterocarpaceae, trees that dominate tropical rain forests in Southeast Asia consist of many economically and ecologically important species. We determined partial sequences of the PgiC gene from species of Shorea, Hopea, Neobalanocarpus, and Parashorea to elucidate phylogenetic relationships among the species of these genera, which have been regarded as interrelated. The sequences generated a gene tree with better resolution than previous cpDNA trees. The PgiC tree is essentially consistent with cpDNA trees, except for the placement of Neobalanocarpus. The PgiC tree shows that Neobalanocarpus is nested within White Meranti of Shorea, whereas this genus forms a clade with Hopea in cpDNA trees. This conflict suggests that Neobalanocarpus is derived via hybridization between White Meranti of Shorea and Hopea. Species belonging to each of three timber groups (Yellow Meranti, Balau, and Red Meranti) within Shorea are monophyletic. Together they form a monophyletic clade distinct from White Meranti. Botanical sections within Red Meranti appear not to be monophyletic. An extensive number of shared polymorphisms among species and consequential lack of monophyly of intraspecific haplotypes are found in Red Meranti. Potential causes of this phenomenon, including persistence of ancestral polymorphisms and gene flow via interspecific hybridization, are discussed.

Height growth, wood density and molecular markers to distinguish five tree species of Dipterocarpaceae grown at same site

“…Cao et al, 2006;Indrioko et al, 2006;Tsumura et al, 1996) and earlier morphological examinations (Symington, 1943) showed a close affinity between the genus Parashorea and the speciesrich genus Shorea. Similar to our results on S. contorta, the diagnostic haplotypes of Shorea fallax fell into 5 different subclades throughout the clade of Red meranti in a phylogenetic tree derived from the nuclear gene PgiC suggesting interspecific hybridization or ancestral polymorphisms (Kamiya et al, 2005). These examples underline that in some cases it is difficult to distinguish unambiguously some tropical species, even with current molecular techniques.…”

“…A number of methods have been applied to clarify the phylogeny of Dipterocarpaceae, e.g. by using restriction fragment length polymorphism (RFLP) markers and nucleotide sequences of chloroplast cp(DNA) genes Indrioko et al, 2006;Kajita et al, 1998;Morton et al, 1999;Tsumura et al, 1996), random amplified polymorphic DNA (RAPD) markers (Rath et al, 1998) or partial sequences of nuclear genes (Kamiya et al, 2005).…”

Application of DNA barcoding markers to the identification of Hopea species

“…However, phylogenetic analysis of Dipterocarpaceae species based on sequencing of the genomic regions trnL-trnF, matK, and trnL indicated that Hopea was closest to Neobalanocarpus heimii and independent of Shorea (Gamage et al, 2006). Analyses of the Dipterocarpaceae suggests that there is a low level of genetic variation among species in this family (Yamazaki et al, 1999;Kamiya et al, 2005) Therefore, it is important to use a combination of gene markers for identifying species and to support the determinations made by standard morphological methods. In this study, we performed an analysis with three gene sequences, matK, rbcL, and trnH-psbA, and our results using pairs of sequences reinforce this conclusion.…”

Comprehensive Molecular Phylogeny of the Sub-Family Dipterocarpoideae (Dipterocarpaceae) Based on Chloroplast DNA Sequences

“…Since then, several other phylogenetic studies on Dipterocarpaceae were reported based on chloroplast (cp) DNA sequences Gamage et al, 2003;Kajita et al, 1998;Kamiya et al, 1998;Morton et al, 1999) and the nuclear gene PgiC (Kamiya et al, 2005). However, previous studies on molecular phylogeny of the Dipterocarpaceae included either limited number of species Morton et al, 1999;Tsumura et al, 1996) or informative sites (Gamage et al, 2003;Kamiya et al, 1998) or both .…”