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Genetic variation and population structure of a threatened timber tree Dalbergia cochinchinensis in Cambodia

Abstract

Dalbergia cochinchinensis Pierre ex Laness. (Fabaceae) is a commercially important tree in Southeast Asia. Although this species is under legal protections, illegal logging and disorderly developments have reduced its populations, and the conservation of this species is currently of much concern. In this study, we determined nucleotide sequences at six chloroplasts and ten nuclear loci in four populations of D. cochinchinensis in Cambodia, followed by population genetic analyses. The average silent nucleotide diversity over the nuclear loci, excluding one with an exceptionally high value, was 0.0057 in the entire population, and the mean F ST across the nuclear loci between each population pair was between 0.135 and 0.467. Thus, the nucleotide diversity in the studied populations was not low compared with that in other tree species, and the level of population differentiation was high. Neutrality test statistics indicated a recent reduction of population size and a subdivision of the population within this species. The divergence times and migration rates were estimated with a likelihood-based method assuming the isolation with migration model. Based on the results, the three populations split 68,000–138,000 years ago, possibly corresponding to the start of the last glacial period, and the level of gene flow among the populations was very low thereafter. Moreover, after the split, population sizes were reduced considerably. Notably, the nucleotide diversity in an insertion sequence in a noncoding region of nuclear C4H was much higher than the mean nucleotide diversity in silent sites across other nuclear genes, indicating that the region was affected by selection.

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Acknowledgements

We cordially thank the Forestry Administration of Cambodia for the permits and support of our fieldwork in Cambodia.

Data archiving statement

All sequences are deposited with EMBL/GenBank/DDBJ under the accession numbers AB850618–AB850637 for the chloroplast loci and KX428531–KX429590 for the nuclear loci.

Funding

The Environment Research and Technology Development Fund (S9) of the Ministry of Environment, Japan, and JSPS KAKENHI grant numbers JP26291082 and JP16H02553 supported this research.

Author information

Correspondence to Hidenori Tachida.

Additional information

Communicated by D. B. Neale

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Moritsuka, E., Chhang, P., Tagane, S. et al. Genetic variation and population structure of a threatened timber tree Dalbergia cochinchinensis in Cambodia. Tree Genetics & Genomes 13, 115 (2017). https://doi.org/10.1007/s11295-017-1199-8

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Keywords

  • Divergence time
  • Genetic divergence
  • Genetic diversity
  • IM model
  • Population size reduction
  • Siamese rosewood