Genetic variation of Indonesian dipterocarps assessed by amplified fragment length polymorphisms

Genetic variation of Indonesian dipterocarps assessed by amplified fragment length polymorphisms

Iskandar Z. Siregar 1, U.J. Siregar1, C.P. Cao2, O. Gailing2 and R. Finkeldey2

1Department of Silviculture, Faculty of Forestry, Bogor Agricultural University, Kampus IPB Darmaga, PO Box 168 Bogor 16680, Indonesia.

2Institute of Forest Genetics and Forest Tree Breeding, University of Goettingen, Buesgenweg 2, 37077 Goettingen, Germany.


The dipterocarp forests of Indonesia are centres of global biodiversity. The design of efficient conservation strategies requires an understanding of this diversity and its dynamics in time and space at all levels. Variation within species, i.e. genetic variation, is largely unknown for Indonesian dipterocarps, and even patterns of genetic differentiation among species are poorly described. The amplified fragment length polymorphism (AFLP) technique was used to observe genome-wide genetic differentiation among Indonesian dipterocarps and to study levels of genetic diversity and differentiation among populations of two closely related, widely distributed species: Shorea leprosula and S. parvifolia . The results generally support the taxonomic classification within the subfamily Dipterocarpoideae based on morphological traits and previous molecular studies of chloroplast DNA (cpDNA). Considerable genetic variation was observed within the population for both species (mean H e = 0.161 for S. leprosula and 0.138 for S. parvifolia ). Ranking of locations with regard to variation levels revealed a similar trend; the populations in a single location on Sumatra (“Asialog”) had the highest variation. Genetic differentiation among populations was high (GST = 25% for S. leprosula and 31% for S. parvifolia ). The results will help to efficiently select and design genetic resources of Indonesian dipterocarps and contribute to the sustainable utilization of genetic resources. In combination with ongoing studies on the extraction of DNA from dipterocarp wood they will be useful to develop reliable molecular tools to identify the origin of dipterocarp timber and processed wood. These tools are expected to gain importance for the international trade of wood and wood products from dipterocarps and for the observation of the chain-of-custody (COC) within the context of forest certification.

Key words : Dipterocarpaceae, phylogeny, Shorea leprosula, Shorea parvifolia, AFLP, genetic variation, Indonesia


The Asian dipterocarp forests are widely recognized as global centres of biodiversity. The Dipterocarpaceae is a species-rich tree family with close to 500 species mainly distributed in Southeast Asia. They are dominant components of species-rich forest communities in lowland evergreen forests of the central tropics as well as in monsoon forests. Indonesia is the country with the highest species diversity of dipterocarps. However, the genetic diversities within and among Indonesian dipterocarps have not yet been investigated in detail.

Conservation of genetic resources requires at least a basic understanding of the diversity that we wish to conserve (Bawa and Krugman 1990). Selection of genetic resources should be based on an understanding of patterns of genetic variation within and among populations

(Finkeldey and Gregorius 1994). In situ conservation of genetic resources requires knowledge on the temporal dynamics of genetic structures (Hattemer 1995), and the efficiency of sampling strategies for ex situ collections is enhanced by an understanding of the genetic diversity of the target species (Dvorak et al. 1999).

The genetic implications of forest management, and in particular harvesting operations, are frequently overlooked. However, management systems such as target diameter felling may compromise the adaptive potential of populations and the ability to produce particular phenotypes (FAO 1993). Forest management endangering genetic resources and thus violating the principles of sustainability are particularly common and have strong negative impacts on tropical forests (Finkeldey and Hattemer 1993). For example, Murawski et al. (1994) found evidence for increased selfing in Shorea megistophylla after selective logging of a dipterocarp forest in Sri Lanka.

The above considerations point towards the importance to improve our understanding of the spatial and temporal dynamics of genetic structures of dipterocarps in their diversity center. Since genetic variation of Indonesian dipterocarps is virtually unexplored, we initially investigated patterns of genetic differentiation among 54 dipterocarp species from all nine genera native to Indonesia at a large number of gene loci using the amplified fragment length polymorphism (AFLP) technique. AFLPs are anonymous “genetic fingerprints” which are expected to give information on genome-wide patterns of genetic differentiation. Specifically, we tested the hypothesis that the taxonomic classification of the “Asian” subfamily Dipterocarpoideae into tribes, genera, sections, etc. (Ashton 1982), which is largely in accordance with molecular phylogenies based on chloroplast DNA (Tsumura et al. 1996, Kajita et al. 1998, Kamiya et al.1998, Indrioko 2005) and partial DNA sequences of a few selected genes (Kamiya et al. 2005), is also reflected at a highly variable marker system. The application of taxonomic classifications or molecular phylogenies based on a single or few genes for the conservation of genetic resources is only justified, if the observed patterns are representative for the genome-wide variation among species.

In a second step, we selected two important dipterocarps from Indonesia, Shorea leprosula and S. parvifolia, and investigated their variation in more detail. We sampled several natural populations from both species on Sumatra and Borneo and a plantation on Java, and used AFLPs to analyze variation of both species within and among populations. We tested the hypotheses that the species exhibit similar levels of genetic variation, that populations do not significantly differ from each other with regard to the amount variation, and that populations are not significantly differentiated from each other.

Finally, we examined the usefulness of the observed molecular variation patterns to identify the origin of material from dipterocarps. “Genetic fingerprints” are potentially reliable and non-manipulable tools to identify the origin of tropical timber and wood products and hence of interest for the international trade with tropical timber and for the observation of the chain-of-custody (COC) within the context of forest certification.

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