Genetic variation of the genus <i>Shorea</i> (Dipterocarpaceae) in Indonesia

Abstract

This dissertation is composed of three parts using the AFLP marker technique to characterize genetic variation of Indonesian dipterocarps, a dominant tree family in Asian tropical rainforests: (1) genetic variation of Dipterocarpaceae and its relation to molecular phylogenies and taxonomic subdivisions; (2) genetic diversity within and among populations of two common dipterocarps, Shorea leprosula Miq. and S. parvifolia Dyer, in Indonesia; (3) genetic variation in nine Shorea species in Indonesia. Part 1: A total of 81 samples of dipterocarp trees (Dipterocarpaceae; subfamily Dipterocarpoideae) from Indonesia belonging to 54 species in all nine genera native to the country were investigated at 125 AFLP loci in order to assess genetic differentiation among species. The resultant UPGMA tree clearly separated all investigated dipterocarps into two major groups corresponding to tribe Dipterocarpeae with base chromosome number of x = 11 and to tribe Shoreae with x = 7. The results of this study using the AFLP marker technique are in accordance with the topology of molecular phylogenetic trees derived from PCR-RFLP and sequence analysis of chloroplast DNA (with a few exceptions) and generally support the traditional taxonomic subdivisions of Dipterocarpoideae. Part 2: AFLPs were used to assess the genetic diversity and differentiation in the most common and widespread emergent dipterocarp tree species - Shorea leprosula Miq. and S. parvifolia Dyer - from Indonesia. A total of 268 individuals from natural populations in Sumatra and Borneo and from a plantation on Java were analysed at 56 AFLP loci. S. leprosula is genetically more variable than S. parvifolia. AMOVA analysis at two hierarchical levels exhibited that most genetic variation resided within populations with a proportion of 70.2% for S. leprosula and 66.2% for S. parvifolia. The observed genetic diversity within populations and genetic differentiation among populations agreed with the life history traits of Shorea species. Some private markers with high frequencies were found, which can serve as diagnostic markers for the identification of wood of different species from different islands and regions. Part 3: Genetic variation in nine Shorea species from two different locations, namely Nanjak Makmur on Sumatra and Sumalindo on Kalimantan (Borneo), was evaluated using AFLP markers. A total of 274 trees were investigated at 85 polymorphic AFLP loci. The results indicated that the six species from Nanjak Makmur Sumatra and the five species from Sumalindo Borneo showed similar levels of genetic variation. The hypothesis that uncommon species (S. blumutensis and S. dasyphylla) show a lower level of genetic variation than widespread species (e.g., S. leprosula and S. parvifolia) is rejected. AMOVA analysis revealed that the genetic variation was mainly found among species, both in Nanjak Makmur Sumatra (57.7%) and in Sumalindo Borneo (56.3%). The UPGMA dendrogram of all samples revealed an almost complete separation of clusters according to species affiliation. Thus, AFLP markers proved suitable to dissect phylogenetic relationships among Shorea species confirming the validity of results of the first part. Species-specific markers with high frequencies (> 80%) have been detected in two species (S. platyclados and S. johorensis). Several other markers showed high frequency differences among species, and between regions within species (for S. leprosula and S. parvifolia that are represented in both regions). The homology of equal-sized AFLP fagments has to be confirmed by sequencing. Sequence information can be used to develop specific PCR markers for the identification of the origin of wood. In conclusion, AFLPs proved to be suitable tools to analyse phylogenetic relationships among species of the Dipterocarpaceae and to investigate patterns of genetic diversity within and among populations of one species. Results can be applied within the context of the development of strategies for the conservation of genetic resources of dipterocarps, and as a basis for development of molecular tools to identify the origin of dipterocarp wood.