Evaluating genetic diversity in two tropical leguminous trees, Dalbergia cochinchinensis and D. nigrescens, in lowland forests in Cambodia and Thailand using MIG-seq

Measuring levels of genetic diversity and differentiation between populations in a species is important to understand the current status and evolution of the species. In this study, we employed MIG-seq, a PCR-based method of reduced-representation sequencing, to assess genetic variation of two tropical leguminous tree species, Dalbergia cochinchinensis and D. nigrescens, in Cambodia and Thailand. Sequence data of about 500 loci, each with the approximate length of 100 bp, were obtained and various statistics of population genetics were computed. The estimates calculated from the sequence data obtained by MIG-seq were compared to those obtained by the Sanger sequencing of 9 nuclear coding genes in D. cochinchinensis in a previous study. The silent nucleotide diversity of the coding regions were slightly lower than that measured by MIG-seq while estimates of FST were generally higher in the coding regions, though the differences were not significant because of the larger variances of the estimates for the coding regions. Because MIG-seq mostly targets non-coding regions, it likely measures neutral genetic variation in the species. Nucleotide diversities within populations of the two species were similar to each other and ca. 0.005. Three and four clusters of populations were genetically recognized in D. cochinchinensis and D. nigrescens, respectively. Although the populations were clearly differentiated from each other, levels of differentiation between populations as measured by FST were higher in D. cochinchinensis than in D. nigrescens, indicating higher levels of gene flow between populations in the latter species. We recommend using MIG-seq for quick survey of genetic variation, because it is cost effective and result in smaller variances of the estimates.