Genetic diversity and the genetic structure of natural populations of Chamaecyparis obtusa: implications for management and conservation

Abstract

We investigated 25 natural populations of Chamaecyparis obtusa using 51 cleaved amplified polymorphic sequence (CAPS) markers, which were developed using information on sequence-tagged sites (STS) in Cryptomeria japonica. Most CAPS markers have codominant expression patterns, and are suitable for population studies because of their robustness and convenience. We estimated various genetic diversity parameters, including average heterozygosity (H e ) and allelic richness and found that the more peripheral populations tended to have lower genetic diversity than central populations, in agreement with a previous theoretical study. The overall genetic differentiation between populations was low, but statistically significant (G ST ¼ 0.039), and similar to the level reported in a previous allozyme study. We attempted to detect non-neutral loci associated with local adaptation to clarify the relationship between the fixation index (F ST ) and H e values for each locus and found seven candidates non-neutral loci. Phylogenetic tree analysis of the populations and Bayesian clustering analysis revealed a pattern of gradually increasing isolation of populations with increasing geographical distance. Three populations had a high degree of linkage disequilibrium, which we attribute to severe bottlenecks due to human disturbance or competition with other species during their migration from refugia after the most recent glaciation. We concluded that the small populations in western Japan and in Kanto district are more important, from a conservation perspective, than the populations in central Japan, due to their genetic divergence, relatively small sizes and restricted areas.

Genome Scan to Detect Genetic Structure and Adaptive Genes of Natural Populations of Cryptomeria japonica

“…IBD was demonstrated in the C. japonica populations, especially among geographically close populations, but the IBD appears to be weaker in this species than in C. obtusa (Tsumura et al 2007). The genetic isolation of the Yakushima populations from the others contributed strongly to the IBD, but significant IBD was still detected when Yakushima populations were excluded.…”

Genetic relationships and origin of commercial clones of Nangouhi, a vegetatively propagated cultivar of hinoki cypress (Chamaecyparis obtusa)

“…Since these populations are close to the Aso area where Nangouhi is used geographically, Nangouhi likely originated from one or more natural populations located somewhere in Kyushu; however, the suggestion that the source of a Nangouhi population be assigned to the Hikosan population needs careful scrutiny. Tsumura et al (2007) reported that the allele frequency of the Hikosan population was more similar to that of the Tanakamiyama population in Kinki compared to that of other populations in Kyushu. Nevertheless, hinoki populations tend to be clustered genetically within the same district or group of districts (see Fig.…”

“…1). Tsumura et al (2007) also argued that some individuals in the Hikosan population may have been introduced by humans.…”

“…Tsumura et al (2007) investigated the genetic structure of 25 natural populations of hinoki and concluded that genetic differentiation among populations was significant, but low. In particular, most of the possible source populations listed in Table 4 (Hikosan, Besshiyama, Misasa, and Tanakamiyama) were clustered genetically in the phylogenetic tree in Tsumura et al (2007); therefore, several hypervariable markers would be needed to attain the objective. Otherwise, organelle DNA variation would be effective for identifying the source population of Nangouhi.…”

“…2.9.3 (Goudet 2001). Tsumura et al (2007) investigated the genetic diversity and genetic structure of 25 natural populations of hinoki using 51 cleaved amplified polymorphic sequence (CAPS) markers (Fig. 1).…”