Forensic DNA profiling of tropical timber species in Peninsular Malaysia.

Illegal logging poses a significant threat to the sustainability of tropical forest ecosystems. By using Neobalanocarpus heimii (Dipterocarpaceae) as an example, the study assessed the feasibility of using short tandem repeats (STRs) as a tool to identify the source of illegally logged timber. Thirty natural populations of N. heimii were profiled using 12 STRs to develop the DNA profiling databases. As the cluster analysis divided the 30 populations into three genetic clusters, corresponding to three subregions within Peninsular Malaysia. The DNA databases were characterised at the levels of population, subregion and Peninsular Malaysia. Independence tests within and among loci were violated in all the databases due to significant levels of population differentiation and inbreeding. Thus, the effects of population substructure and inbreeding should be incorporated into the calculation of random match probability. The random match probabilities estimated using subpopulation and subpopulation-cum-inbreeding models were biased in favour of the defendant, whereas the random match probabilities estimated using product rule were biased in favour of the prosecutor. The conservativeness tests showed that the subregion and Peninsular Malaysia databases were conservative, and these databases should be able to provide legal evidence for court proceedings against illegal loggers in Peninsular Malaysia

Highly variable STR markers of Neobalanocarpus heimii (Dipterocarpaceae) for forensic DNA profiling

Neobalanocarpus heimii, locally known as chengal, is an important timber species in Peninsular Malaysia. Owing to the high demand for its valuable timber, N. heimii is subjected to illegal logging and this species may become endangered in the near future. The present study was designed to identify a set of highly polymorphic short tandem repeat (STR) markers for timber tracking of N. heimii. An extensive evaluation of 51 STRs developed for Dipterocarpaceae managed to identify 12 STR loci (Nhe004, Nhe005, Nhe011, Nhe015, Nhe018, Hbi161, Sle392, Sle605, Slu044a, Shc03, Shc04 and Shc07), which showed specific amplification, high polymorphism, single-locus mode of inheritance, absence of null alleles and absence of mononucleotide repeat motifs in N. heimii. These loci can be readily used to establish a linkage between the evidentiary sample and the source, thus providing a useful set of markers for individual identification in N. heimii

Estimation of outcrossing rates in Koompassia malaccensts from an open-pollinated population in Peninsular Malaysia using microsatellite markers

Koompassia malaccensis (Leguminosae), locally known as kempas, is an important tropical timber species in South-East Asia. Although studies have shown that most tropical tree species are predominantly outcrossing, there is no empirical support for this species prior to this study, with regard to its mating system. Information on its reproductive biology is also scanty. We report the estimation of the outcrossing rates of K. malaccensis using microsatellite markers, based on a fruiting season at the Semangkok Forest Reserve, Selangor. Microsatellite analysis was performed for an average of 46 seeds each from nine adult K. malaccensis trees, using four polymorphic microsatellite loci (Kma050, Kma067, Kma147 and Kma180). Single and multilocus population outcrossing estimates (ts and tm respectively) were determined using the software MLTR version 3.0. Results showed that this timber species was predominantly outcrossing (tm = 0.890). Biparental mating (tm – ts) was very low, only 0.026, suggesting low tendency of mating between relatives. Outcrossing estimates obtained for individual mother trees were in the range of 0.637 to 0.994. The relatively lower outcrossing rates exhibited by a few progeny arrays indicated that K. malaccensis was not completely self-incompatible

Evidence for a higher number of species of Odontotermes (Isoptera) than currently known from Peninsular Malaysia from mitochondrial DNA phylogenies

Termites of the genus Odontotermes are important decomposers in the Old World tropics and are sometimes important pests of crops, timber and trees. The species within the genus often have overlapping size ranges and are difficult to differentiate based on morphology. As a result, the taxonomy of Odontotermes in Peninsular Malaysia has not been adequately worked out. In this study, we examined the phylogeny of 40 samples of Odontotermes from Peninsular Malaysia using two mitochondrial DNA regions, that is, the 16S ribosomal RNA and cytochrome oxidase subunit I genes, to aid in elucidating the number of species in the peninsula. Phylogenies were reconstructed from the individual gene and combined gene data sets using parsimony and likelihood criteria. The phylogenies supported the presence of up to eleven species in Peninsular Malaysia, which were identified as O. escherichi, O. hainanensis, O. javanicus, O. longignathus, O. malaccensis, O. oblongatus, O. paraoblongatus, O. sarawakensis, and three possibly new species. Additionally, some of our taxa are thought to comprise a complex of two or more species. The number of species found in this study using DNA methods was more than the initial nine species thought to occur in Peninsular Malaysia. The support values for the clades and morphology of the soldiers provided further evidence for the existence of eleven or more species. Higher resolution genetic markers such as microsatellites would be required to confirm the presence of cryptic species in some taxa

Are patterns of fine-scale spatial genetic structure consistent between sites within tropical tree species?

JRS was funded by the Swiss National Science Foundation (SNF) (http://www.snf.ch/en/Pages/default.aspx) grant number PDFMP3_132479 / 1 awarded to JG. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Ti: Genetic diversity assessment of Koompassia malaccensis

A genetic diversity study of Koompassia malaccensis based on 19 populations from 18 forest reserves in Peninsular Malaysia is reported. The genetic diversity assessment was based on six polymorphic microsatellites. Overall, all the populations showed high levels of genetic diversity. The allelic richness ranged from 6.0 (Pekan) to 9.3 (Lenggor) whereas the gene diversity ranged from 0.683 (Pekan) to 0.859 (Lenggor). The estimated coefficient of population differentiation (R st) was 0.07, implying that 93% of the genetic diversity was partitioned within populations, with only 75% distributed among populations. From the cluster analysis among the populations, the two peat swamp populations (Pekan and Kuala Langat Selatan) formed a tight cluster even though they are not adjacuet to one another. Further analysis including more populations and applying more microsatellites will generate more comprehensive genetic information

Genetic diversity of two tropical tree species of the Dipterocarpaceae following logging and restoration in Borneo: high genetic diversity in plots with high species diversity

Background: The impact of logging and restoration on species diversity has been well studied in tropical forests. However, little is known about their effects on genetic diversity within species. Aims: We assess the degree of genetic diversity among dipterocarp seedlings used for enrichment planting of selectively logged forests in Sabah, Malaysia, and compare it with diversity in naturally regenerating seedlings. Methods: We sampled young leaf tissues from seedlings of Shorea leprosula and Parashorea malaanonan for DNA genotyping, using microsatellite markers. Results: The levels of genetic diversity (expected heterozygosity and rarefied allelic richness) of naturally regenerating seedlings were statistically indistinguishable among unlogged, once logged and repeatedly logged forest areas. Enrichment-planted seedlings of P. malaanonan exhibited similar levels of genetic diversity to naturally regenerating seedlings whereas those of S. leprosula had significantly lower genetic diversity than natural seedlings. Interestingly, reduction of genetic variation was consistently observed in single-species plots relative to mixed-species plots among enrichment-planted seedlings. Conclusions: There was no reduction of genetic variation in naturally regenerating dipterocarp seedlings in areas of selective logging. However, genetic variation of enrichment-planted seedlings was lower in single-species plots relative to mixed-species plots. This suggests that enrichment-planting strategies should adopt diverse mixtures that should promote levels of both species richness and genetic diversity within species

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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10265-010-0348-z) contains supplementary material, which is available to authorized users

The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests

Hyperdiverse tropical rainforests, such as the aseasonal forests in Southeast Asia, are supported by high annual rainfall. Its canopy is dominated by the species-rich tree family of Dipterocarpaceae (Asian dipterocarps), which has both ecological (e.g., supports flora and fauna) and economical (e.g., timber production) importance. Recent ecological studies suggested that rare irregular drought events may be an environmental stress and signal for the tropical trees. We assembled the genome of a widespread but near threatened dipterocarp, Shorea leprosula, and analyzed the transcriptome sequences of ten dipterocarp species representing seven genera. Comparative genomic and molecular dating analyses suggested a whole-genome duplication close to the Cretaceous-Paleogene extinction event followed by the diversification of major dipterocarp lineages (i.e. Dipterocarpoideae). Interestingly, the retained duplicated genes were enriched for genes upregulated by no-irrigation treatment. These findings provide molecular support for the relevance of drought for tropical trees despite the lack of an annual dry season.ISSN:2399-364

Development of Microsatellites in <i>Labisia pumila</i> (Myrsinaceae), an Economically Important Malaysian Herb

Premise of the study: The exploitation of Labisia pumila for commercial demand is gradually increasing. It is therefore important that conservation is prioritized to ensure sustainable utilization. We developed microsatellites for L. pumila var. alata and evaluated their polymorphism across var. alata, var. pumila, and var. lanceolata. Methods and Results: Ten polymorphic microsatellites of L. pumila were developed using the magnetic bead hybridization selection approach. A total of 84, 48, and 66 alleles were observed in L. pumila var. alata, var. pumila, and var. lanceolata, respectively. The species is likely a tetraploid, with the majority of the loci exhibiting up to four alleles per individual. Conclusions: This is the first report on the development of microsatellites in L. pumila. The microsatellites will provide a good basis for investigating the population genetics of the species and will serve as a useful tool for DNA profiling