Microsatellite markers reveal high allelic variation in natural populations of Cryptomeria japonica near refugial areas of the last glacial period

Abstract

Using 11 microsatellite markers, we investigated the allelic variation and genetic structure of Cryptomeria japonica, across most of its natural distribution. The markers displayed high levels of polymorphism (average gene diversity=0.77, average number of alleles=24.0), in sharp contrast to the lower levels of polymorphism found in allozyme and cleaved amplified polymorphic sequence markers in previous studies. Little genetic differentiation was found among populations (F(ST)=0.028, P<0.001), probably because the species is wind-pollinated and long-lived. No clear relationship between Nei's genetic distances and geographical locations of the populations were found using the principal coordinate and unweighted pair-group method with arithmetic averaging analyses. The lack of such trends might be due partly to microsatellite homoplasy arising from mutation blurring the genealogical record. However, there was a trend towards high allelic diversity in five populations (Ashitaka, Ashiu, Oki-Island, Yakushima-Island-1 and -2), which are very close to, or in, refugial areas of the last glacial period as defined by Tsukada based on pollen analysis data and current climatic divisions. We postulate that these refugial populations might have been less affected by genetic drift than the other populations due to their relatively large size.

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

“…According to fossil pollen data (Tsukada 1983(Tsukada , 1988, the refugial areas of this species in the last glacial period ($18,000 years ago) were located in the Izu peninsula, along the Wakasa Bay to Oki Island, Yakushima Island, and (probably) the southern Kii peninsula and Shikoku Island (Figure 1). Most of these refugia were in western parts of Japan, in accordance with both our data and the results of a previous microsatellite marker-based population study (Takahashi et al 2005). The populations in the refugia of the last glacial period still show higher than average genetic diversity.…”

“…6) populations, and others located at high elevations or more marginal areas such as peninsulas showed lower genetic diversity. A previous population analysis using microsatellite markers showed similar results, especially in the frequencies of rare alleles (Takahashi et al 2005). These northern populations are thought to have been established $6000 years ago by migration from refugial areas, based on inferences from fossil pollen data (Tsukada 1986).…”

“…In the last glacial period, no C. japonica populations are thought to have been present on Kyushu Island, so C. japonica forests on Yakushima Island have presumably been isolated for a long time from those of the mainland. Consequently, this forest has a unique structure and higher diversity than the other natural forests (Tsumura and Ohba 1993;Takahashi et al 2005) because the area of natural C. japonica forest on this island is quite large, $6000 ha, and the species is dominant in this forest.…”

Genome scanning for detecting adaptive genes along environmental gradients in the Japanese conifer, Cryptomeria japonica

“…The R s values also varied, from 1.569 to 1.794 with an average of 1.721, and the H e values ranged from 0.292 to 0.320 with an average of 0.311 (Table 2). In contrast to findings from previous studies, these parameters do not reveal any clear geographical trends (Takahashi et al, 2005;Tsumura et al, 2007). The average F IS value for all loci was not significantly different from expectations under the Hardy-Weinberg equilibrium except for one locus, SNPg04215.…”

Primer Note: Development of Highly Polymorphic Nuclear Microsatellite Markers for Hinoki (Chamaecyparis obtusa)

“…It has also been important to conserve the natural genetic resources and the within-population genetic diversity against potential depletion or contamination through overcutting or plantation practices. Highly polymorphic microsatellite (simple sequence repeat; SSR) markers have enhanced molecular studies of Japanese conifer species, in particular, genotypic discrimination of clones (e.g., HIRAO et al, 2006), gene flow in seed orchards and natural populations (e.g., MORIGUCHI et al, 2005;GOTO et al, 2005;IWAIZUMI et al, 2007;LIAN et al, 2008), and inter-population genetic structure (e.g., TAKAHASHI et al, 2005).…”