Demographic history and interspecific hybridization of four Shorea species (Dipterocarpaceae) from Peninsular Malaysia inferred from nucleotide polymorphism in nuclear gene regions

Shorea acuminata Dyer, Shorea curtisii Dyer ex King, Shorea leprosula Miq., and Shorea parvifolia Dyer are dominant tree species in the tropical rainforest of Peninsular Malaysia, which experienced several climatic changes during Pleistocene. To investigate the current population structure and demographic history of these species, we analyzed levels and patterns of nucleotide polymorphism of the nuclear gene region PgiC. We also used sequence data of the GapC gene region obtained in our previous study. Negative Tajima's D values observed in both investigated gene regions for S. curtisii, S. leprosula, and S. parvifolia implied that all three species have experienced population expansion events. Little to moderate levels of population differentiation in S. acuminata and S. curtisii suggested recent divergence of the investigated populations after postglacial colonization of the Peninsular Malaysia. In addition, some haplotypes were similar or identical to haplotypes of the other species. The existence of such haplotypes could be partially explained by interspecific hybridization. Indeed, we found some putative hybrid individuals. Interspecific hybridization among closely related species might have contributed to the polymorphism of the investigated species

PCR-RFLP analysis of cpDNA in the genus Abies

We used PCR-RFLP analysis of the chloroplast DNA of the genus Abies (family Pinaceae), to determine if the method could be employed to detect inter-specific variation in this genus and to study how the variation was distributed in different regions of the genome. Ten different chloroplast DNA regions, consisting of coding and non-coding DNA sequences, were amplified with specific primers in ten different Abies taxa. The amplification products were digested with several restriction enzymes. The results showed that the chloroplast genome is highly variable in most of the investigated taxa and contains multiple variable regions that appear to be distributed throughout the whole genome. Species-diagnostic markers were found for four of the ten investigated species. Unexpectedly, intra-specific variation was also detected in four species. It is likely that further studies, including larger sample sizes and/or more powerful methods for the detection of chloroplast DNA variation will reveal additional variation for this genus

nDNA PAL1 sequences

nDNA sequences (.fas) of the phenylalanine ammonia-lyase (PAL1) gene, partial cds. 48 sequences. Alignment length: 940bp

Data from: Molecular identification of natural mangrove hybrids of Rhizophora in Peninsular Malaysia

Natural hybridization is common in plants. Very often, the identity of a putative hybrid is inferred based on the observation of morphological features intermediate between two possible parental species occurring in a specific location. However, due to plasticity of morphological features and the co-occurrence of more than two possible parental species, molecular markers would be most useful to establish the origin of a putative hybrid. In mangroves, three Rhizophora species (Rhizophora apiculata, Rhizophora mucronata, and Rhizophora stylosa) and two putative hybrids (Rhizophora × lamarckii and Rhizophora × annamalayana) are distributed in the Indo-West Pacific region. Leaf samples of Rhizophora were obtained from two locations in Peninsular Malaysia, namely, Bagan Lalang and Pulau Burung, where all three species grow in sympatry. We analyzed sequences of one chloroplast and six nuclear DNA regions. Our results confirmed earlier claims that the morphologically identified putative hybrids growing in Pulau Burung are R. × lamarckii, a cross between R. apiculata and R. stylosa. Our data also pointed to the possible discovery of a new Rhizophora hybrid—a cross between R. mucronata and R. stylosa—the identification of which would have been difficult based on morphological features alone. The directions and the stages of hybridization are also discussed

nDNA DLDH sequences

nDNA sequences (.fas) of the dihydrolipoamide dehydrogenase (DLDH) gene, partial cds. 48 sequences. Alignment length: 1221bp

nDNA SBE2 sequences

nDNA sequences (.fas) of the starch branching enzyme II (SBE2) gene, partial cds. 48 sequences. Alignment length: 947bp

Genetic variation of Abies alba in Italy

Italy represents the southern limit of Abies alba (Mill.) (silver fir) distribution in Europe. In this region, populations are widely spread in different and isolated habitats. We used allozyme markers to study the genetic structure of ten natural populations of this species from the northern, central, and southern parts of Italy. Mean expected heterozygosity ranged from 0.129 to 0.180 and was similar to that found in other conifers. In contrast to other conifers, all the populations investigated in the present study showed a deficiency of heterozygotes. Partial inbreeding due to restricted pollen dispersal and Wahlund effect could be responsible for this situation. The central populations harboured more variability than the populations from other parts of Italy. The present study revealed significant differentiation among the investigated populations. The average genetic distance for all pair-wise comparisons between the ten populations was 0.014. Populations from the central Italy showed closer affinity to the southern populations than to the populations from the northern Italy. Our results suggest that the A. alba populations in central Italy have originated either through a postglacial blending of two different populations or through expansion of the southern populations. In addition, they confirm distinct character of populations from the southern Italy

cpDNA atpB-rbcL sequences

cpDNA sequences (.fas) of the atpB-rbcL intergenic spacer and rbcL gene, partial cds. 48 sequences. Alignment length: 840bp