Some Examples of Studies on Forest Trees

Phylogeography

Example I
Shorea acuminata, S. curtisii, S. leprosula and S. parvifolia 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 two nuclear gene regions PgiC and GapC. Negative Tajima's D values observed in both investigated gene regions for S. curtisii, S. leprosula and S. parvifolia implied that both 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.

Example II
The distributions of tropical rainforests in Southeastern Asia have changed over geological time scale, due to global climatic changes and coinciding sinking and re-exposure of the continental shelf by changing sea levels. We studied the levels and patterns of nucleotide polymorphism in five nuclear gene regions of Shorea parvifolia to infer its population structure and demographic history. Shorea parvifolia is one of most common tropical rainforest tree species in this area. We detected two major genetically different groups of populations, and estimated their divergence time during the Pleistocene. The first group included populations from the Borneo island. The second group included all Peninsular Malaysia populations and one population from the Sumatra island. Migration events following divergence of these two groups were detected. We also found populations representing admixture of the two groups. These admixed populations seem to be products of recent migration event after Last Glacial Maximum.

Hybrid speciation

In plants, interspecific hybridization is known to initiate stable speciation events. Hybrid speciation through polyploidy is much more common than hybrid speciation without an increase in ploidy, because the duplication in chromosome number provides the hybrid with an effective means of reproductive isolation from its parental species. Pinus densata, is a pine distributed in southwestern China and the Tibetan plateau. It has been suggested, following analysis of morphological characters that it arose as the product of natural hybridization between P. tabulaeformis and P. yunnanensis. Like other pines, P. densata is diploid (2N = 24). Thus, its evolution does not involve polyploidy. We used Southern analysis of chloroplast (cp) DNA to analyze cpDNA variation in populations of Pinus tabulaeformis, and P. yunnanensis (Wang and Szmidt, 1994). Several fragment patterns distinguished between the two species. The obtained markers were subsequently used to examine cpDNA variation of P. densata. The analysis demonstrated that P. densata populations harbor three different haplotypes. Two of these haplotypes are characteristic of P. tabulaeformis and P. yunnanensis. However, the third haplotype is absent in other Asian Pinus species. These results suggest that P. densata populations are result of past hybridization involving P. tabulaeformis, P. yunnanensis and a third unknown or extinct taxon.

Molecular systematics of tropical trees

Pinus krempfii is morphologically very unique as compared to other Pinus species by having flat leaf-like needles (Fig. 1). Its taxonomic position has been problematic ever since its discovery in 1921. We investigated the taxonomic status of P. krempfii through analysis of sequence variation in chloroplast (cp) DNA. First, analysis was conducted using 10 representatives of the two Pinus subgenera: Strobus and Pinus. In addition, to infer the position of P. krempfii in Pinaceae in relation with other genera, 14 representatives of eight additional genera were included in the analysis (Wang et al. 2000). The results indicated that: 1) P. krempfii clearly belongs to the genus Pinus; 2) Within the genus Pinus, P. krempfii is more allied with species in subgenus Strobus and differs distinctly from species in subgenus Pinus; 3) Despite the similarity in certain morphological and anatomical leaf and wood characters to Keteleeria and Pseudolarix, the cpDNA data do not support the hypothesis for close relationship between P. krempfii and these two genera suggested by some authors. Our second study involved analysis of sequence divergence of rbcL, matK, trnV intron and rpl20-rps18 spacer regions among 32 Pinus species and representatives of six other genera in Pinaceae (Wang et al. 1999). As before, phylogenetic analyses based on these four sequences placed P. krempfii in subgen. Strobus.

Effects of RNA editing on the evolution of plant mitochondrial DNA

In plants, mitochondrial genetic information is modified by RNA editing. Namely, specific cytidines (C's) in the primary transcripts are changed to uridines (U's) in the mature mRNAs. This results in critical changes in codons, leading to amino-acid sequences that are more conserved in evolution than those encoded in the genomic DNA. This phenomenon may release the selection pressure on the DNA sequence and accelerate the rate of nucleotide substitutions, which can be particularly important for species that harbour many edited sites such as some gymnosperms. Various lines of evidence suggest the possibility of the transfer of mitochondrial sequences to the nucleus or back to the mitochondria. Such sequences, if derived from edited mitochondrial transcripts would be expected to lack edited sites. Our sequence analysis of the mitochondrial coxI gene in eight gymnosperm species revealed a high rate of non-synonymous nucleotide substitutions with a strong (98%) predominance of C-T substitutions (Lu et al. 1998; Szmidt et al. 2001). Furthermore, we found that all the non-synonymous C-T changes in the coxI genomic DNA sequences were eliminated by RNA editing. Pronounced variation in the number and location of edited sites was found among species. Most species had a relatively large number of edited sites. However, no RNA editing of the coxI sequence was found in Gingko biloba and Larix sibirica. The sequence composition of the investigated coxI fragment suggests that the coxI gene in G. biloba and L. sibirica originated from edited mitochondrial coxI transcripts by reverse transcription followed by insertion into the nuclear genome or back into the mitochondrial genome. Our results also demonstrate that where there are a large number of edited sites, RNA editing can accelerate the divergence of sequences among species.

References

  1. Ishiyama, H., Inomata, N., Yamazaki, T., Ab Shukor, N. A. and Szmidt, A. E. (2008). Demographic history and interspecific hybridization of four Shorea species (Dipterocarpaceae) from Peninsular Malaysia inferred from nucleotide polymorphism in nuclear gene regions. Canadian Journal of Forest Research: 38(5): 996-1007.
  2. Wang, X-R. and Szmidt, A. E., (1994). Hybridisation and chloroplast DNA variation in a Pinus species complex from Asia. Evolution 48: 1020-1031.
  3. Wang, X-R., Szmidt, A. E. and Nguyen, H-N. (2000). The phylogenetic position of the endemic flat-needle pine Pinus krempfii (Le., Pinaceae) from Vietnam. Plant Systematics and Evolution 220: 21-36.
  4. Wang, X-R., Tsumura, Y., Yoshimaru, H., Nagasaka, K. and Szmidt, A. E. (1999). Phylogenetic relationships of Eurasian pines (Pinus, Pinaceae) based on chloroplast rbcL, matK, rpl20-rps18 spacer and trnV intron sequences. American Journal of Botany 86: 1742-1753.
  5. Lu, M-Z, Szmidt, A. E. and Wang, X-R. (1998). RNA editing in gymnosperms and its impact on the evolution of the mitochondrial coxI gene. Plant Molecular Biology 37: 225-234.
  6. Szmidt, A. E., Lu, M-Z., and Wang, X-R. (2001). Effects of RNA editing on the coxI evolution and phylogeny reconstruction. Euphytica 118: 9-18.
  7. Ma, X-F., Szmidt, A. E. and Wang, X-R. (2006). Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from nucleotide variation at seven gene loci. Molecular Biology and Evolution 23 (4): 807-816.

by Alfred E. Szmidt. All Rights Reserved.