Koichi Kamiya

Phylogenetic Relationships of Diploxylon Pines (Subgenus Pinus) Based on Plastid Sequence Data

The plastid DNA sequences of rbcL, matK, the trnV intron, and the rpl20‐rps18 spacer in 38 species of subgenus Pinus, representing all recognized subsections, were analyzed. Combined data sets of 3230 bp were used to assess relationships with maximum parsimony, neighbor joining, and maximum likelihood algorithms. Subgenus Pinus splits into two distinct lineages, corresponding to Eurasia and North America (“New World hard pines”). The Eurasian lineage differentiated into two clades: the Mediterranean pines, including the Himalayan pine P. roxburghii (subsections Canarienses, Halepenses, and Pinaster), and subsection Pinus. Two North American pines, P. tropicalis and P. resinosa, are typical members of subsection Pinus but are not closely related to each other. Subsection Contortae occupied the basal position in the “New World hard pines” followed by subsection Ponderosae. Of the remaining “New World hard pines” subsections, Attenuatae was a monophyletic group and Oocarpae, Australes, and Leiophyllae were poorly resolved. The eastern Cuban pines, P. cubensis and P. maestrensis, formed a subgroup within Australes. matK evolved much faster than rbcL, and the noncoding regions evolved more slowly than rbcL and matK synonymous sites. The divergence times for each subsection were estimated from the rbcL sequence data calibrated by fossil data.

Phylogeny of PgiC gene in Shorea and its closely related genera (Dipterocarpaceae), the dominant trees in Southeast Asian tropical rain forests

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.

Short-term drought causes synchronous leaf shedding and flushing in a lowland mixed dipterocarp forest, Sarawak, Malaysia

Tropical rain forests are evergreen and experience a climate suitable for plant growth year round (Whitmore 1998). However, most tropical rain-forest trees display periodic shoot growth (Borchert 1991) and show synchronous leaf flushing at the community level (Itioka & Yamauti in press, Medway 1972, Ng 1981). Synchronous leaf flushing may have a great impact on animal population such as herbivores, because young leaves are suitable food resources for many herbivores (Aide 1988, 1992; Coley 1983, Itioka & Yamauti 2004, Lowman 1985).

Molecular database for classifying Shorea species (Dipterocarpaceae) and techniques for checking the legitimacy of timber and wood products.

The extent of tropical forest has been declining, due to over-exploitation and illegal logging activities. Large quantities of unlawfully extracted timber and other wood products have been exported, mainly to developed countries. As part of the export monitoring effort, we have developed methods for extracting and analyzing DNA from wood products, such as veneers and sawn timbers made from dipterocarps, in order to identify the species from which they originated. We have also developed a chloroplast DNA database for classifying Shorea species, which are both ecologically and commercially important canopy tree species in the forests of Southeast Asia. We are able to determine the candidate species of wood samples, based on DNA sequences and anatomical data. The methods for analyzing DNA from dipterocarp wood products may have strong deterrent effects on international trade of illegitimate dipterocarp products. However, the method for analyzing DNA from wood is not perfect for all wood products and need for more improvement, especially for plywood sample. Consequently, there may be benefits for the conservation of tropical forests in Southeast Asia.

Wide Host Ranges of Herbivorous Beetles? Insights from DNA Bar Coding

There are very few studies that have investigated host-specificity among tropical herbivorous insects. Indeed, most of the trophic interactions of herbivorous insects in Southeast Asian tropical rainforests remain unknown, and whether polyphagous feeding is common in the herbivores of this ecosystem has not been determined. The present study employed DNA bar coding to reveal the trophic associations of adult leaf-chewing chrysomelid beetles in a Bornean rainforest. Plant material ingested by the adults was retrieved from the bodies of the insects, and a portion of the chloroplast rbcL sequence was then amplified from this material. The plants were identified at the family level using an existing reference database of chloroplast DNA. Our DNA-based diet analysis of eleven chrysomelid species successfully identified their host plant families and indicated that five beetle species fed on more than two families within the angiosperms, and four species fed on several families of gymnosperms and/or ferns together with multiple angiosperm families. These findings suggest that generalist chrysomelid beetles associated with ecologically and taxonomically distant plants constitute a part of the plant-insect network of the Bornean rainforest.

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

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.

Population structure of two closely related pelagic cichlids in Lake Victoria, Haplochromis pyrrhocephalus and H. laparogramma.

Cichlid fishes in Lake Victoria show spectacular diversification that is thought to be recent. Therefore, by investigating those fishes, we may be able to elucidate recently completed or ongoing speciation processes. We studied the population structures of two closely related pelagic cichlid species, Haplochromis pyrrhocephalus and H. laparogramma, using a mitochondrial DNA locus and 12 nuclear microsatellite loci as putative neutral markers. Ten and two populations of H. pyrrhocephalus and H. laparogramma, respectively, were sampled from the southern part of Lake Victoria. We grouped those 12 populations into four mutually differentiated regional populations, one of which consisted of the two H. laparogramma populations. The levels of differentiation were substantial at the mitochondrial locus (F(ST) = 0.03-0.54), but very low at microsatellite loci (R(ST) = 0.008-0.116). The data from both types of loci indicated that the regional population of H. laparogramma was first separated from those of H. pyrrhocephalus if we set aside one erratic population of H. pyrrhocephalus. The data also suggested recent population expansions of the two species, the time scales for which were estimated to be on the order of 10(4)-10(5) years. These data suggested that dynamic speciation processes accompanied occasional spawning of new species and population size changes in this lake.

High population differentiation and unusual haplotype structure in a shade‐intolerant pioneer tree species, Zanthoxylum ailanthoides (Rutaceae) revealed by analysis of DNA polymorphism at four nuclear loci

Differences in demographic history, life‐history traits, and breeding systems affect nucleotide variation patterns. It is expected that shade‐intolerant pioneer tree species have different patterns of genetic polymorphism and population structure than climax species. We studied patterns of nucleotide polymorphism at four putative starch pathway loci (agpSA, agpSB, agpL, and GBSSI) in Zanthoxylum ailanthoides, a shade‐intolerant pioneer tree species that occupies forest gaps in warm‐temperate forests of East Asia. Genetic diversity was lower within each population than among populations, and differentiation among populations was high across the loci (FST = 0.32–0.64), as expected from the insect‐pollinated breeding system and the metapopulation structure of this pioneer species. Numbers of haplotypes were smaller than those expected from the observed numbers of segregating sites. Single haplotypes accounted for more than 47% of all the sampled genes at the respective loci. These variation patterns were incompatible with neutral predictions for populations of a finite island model. Complex population dynamics, such as bottleneck and/or admixture, in the history of this pioneer tree species might have resulted in the observed patterns of genetic variation and population structure, which are different from those of climax wind‐pollinated tree species, such as conifers. In contrast to the other loci investigated in this study, agpL showed nearly no variation in Z. ailanthoides (one singleton only), but there was some extent of variation in a closely related species, Zanthoxylum schinifolium. This suggests possibly a recent selective sweep at or near the locus in Z. ailanthoides.

Evolutionary Relationships in the Drosophila ananassae Species Cluster Based on Introns of Multiple Nuclear Loci

The Drosophila ananassae species cluster includes D. ananassae, D. pallidosa, D. parapallidosa, and the cryptic species “pallidosa-like”, “pallidosa-like Wau” and “papuensis-like” Some of the taxa are sympatric in the South Pacific, Papua New Guinea, and Southeast Asia, and gene flow between different taxa has been suspected for a handful of genes. In the present analysis, we examined DNA sequences of introns in four loci: alpha actinin (Actn) on XL, white (w) on XR, CG7785 on 2L, and zinc ion transmembrane transporter 63C (ZnT63C) on 2R. Phylogenetic trees (neighbor-joining and haplotype network) were inconsistent among these loci. Some haplotypes shared between taxa were found for w, CG7785, and ZnT63C, suggesting recent gene flow. However, no haplotypes were shared, for example, between D. ananassae and D. pallidosa for CG7785, which is close to the proximal breakpoint of In(2L)D. This suggests that taxon-specific inversions prevent gene flow, as predicted by the chromosomal speciation hypothesis.

Geographical variation in soil bacterial community structure in tropical forests in Southeast Asia and temperate forests in Japan based on pyrosequencing analysis of 16S rRNA

Geographical variation in soil bacterial community structure in 26 tropical forests in Southeast Asia (Malaysia, Indonesia and Singapore) and two temperate forests in Japan was investigated to elucidate the environmental factors and mechanisms that influence biogeography of soil bacterial diversity and composition. Despite substantial environmental differences, bacterial phyla were represented in similar proportions, with Acidobacteria and Proteobacteria the dominant phyla in all forests except one mangrove forest in Sarawak, although highly significant heterogeneity in frequency of individual phyla was detected among forests. In contrast, species diversity (α-diversity) differed to a much greater extent, being nearly six-fold higher in the mangrove forest (Chao1 index = 6,862) than in forests in Singapore and Sarawak (~1,250). In addition, natural mixed dipterocarp forests had lower species diversity than acacia and oil palm plantations, indicating that aboveground tree composition does not influence soil bacterial diversity. Shannon and Chao1 indices were correlated positively, implying that skewed operational taxonomic unit (OTU) distribution was associated with the abundance of overall and rare (singleton) OTUs. No OTUs were represented in all 28 forests, and forest-specific OTUs accounted for over 70% of all detected OTUs. Forests that were geographically adjacent and/or of the same forest type had similar bacterial species composition, and a positive correlation was detected between species divergence (β-diversity) and direct distance between forests. Both α- and β-diversities were correlated with soil pH. These results suggest that soil bacterial communities in different forests evolve largely independently of each other and that soil bacterial communities adapt to their local environment, modulated by bacterial dispersal (distance effect) and forest type. Therefore, we conclude that the biogeography of soil bacteria communities described here is non-random, reflecting the influences of contemporary environmental factors and evolutionary history.