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 FST 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.
| Original language | English |
|---|---|
| Article number | 115 |
| Journal | Tree Genetics and Genomes |
| Volume | 13 |
| Issue number | 6 |
| DOIs | |
| Publication status | Published - Dec 1 2017 |
Fingerprint
All Science Journal Classification (ASJC) codes
- Forestry
- Molecular Biology
- Genetics
- Horticulture
Cite this
Genetic variation and population structure of a threatened timber tree Dalbergia cochinchinensis in Cambodia. / Moritsuka, Etsuko; Chhang, Phourin; Tagane, Shuichiro; Toyama, Hironori; Sokh, Heng; Yahara, Tetsukazu; Tachida, Hidenori.
In: Tree Genetics and Genomes, Vol. 13, No. 6, 115, 01.12.2017.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Genetic variation and population structure of a threatened timber tree Dalbergia cochinchinensis in Cambodia
AU - Moritsuka, Etsuko
AU - Chhang, Phourin
AU - Tagane, Shuichiro
AU - Toyama, Hironori
AU - Sokh, Heng
AU - Yahara, Tetsukazu
AU - Tachida, Hidenori
PY - 2017/12/1
Y1 - 2017/12/1
N2 - 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 FST 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.
AB - 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 FST 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.
UR - http://www.scopus.com/inward/record.url?scp=85031763153&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85031763153&partnerID=8YFLogxK
U2 - 10.1007/s11295-017-1199-8
DO - 10.1007/s11295-017-1199-8
M3 - Article
VL - 13
JO - Tree Genetics and Genomes
JF - Tree Genetics and Genomes
SN - 1614-2942
IS - 6
M1 - 115
ER -