Geographical distribution of two haplotypes of chloroplast DNA in four oak species (Quercus) in Japan

Kanno, Munetake; Yokoyama, Jun; Suyama, Yoshihisa; Ohyama, Motonari; Itoh, Takaò; Suzuki, Mitsuo

doi:10.1007/s10265-004-0160-8

Cited by 75 publications

(84 citation statements)

References 22 publications

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“…The populations are dense and continuous in northern Japan but sparse and commonly isolated in small patchy forests at elevations 4800 m in the south (Figure 1). cpDNA data (Kanno et al, 2004;Okaura et al, 2007) are consistent with palynological data (Hibino and Takeuchi, 1998;Miyoshi, 1998;Morita et al, 1998), suggesting a recent colonization history (from 8000 to 12000 years ago) for the northern Japan (approximately more than 351 N) populations. The southern populations are shown to have remained in situ during the last glacial maximum (LGM) and lasted from 20 000 to 18 000 years BP.…”

Section: Introductionsupporting

confidence: 75%

Nucleotide variation in Quercus crispula Blume

2008

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Quercus is attractive for evolutionary studies, primarily for developing the concepts of the species, speciation and adaptation; however, remarkably little is known about levels of nucleotide polymorphism in the nuclear functional genes of this genus. This article provides the first characterization of levels of nucleotide polymorphism in 11 gene fragments in natural populations of a Quercus species, Quercus crispula Blume. Results show that the level of nucleotide variation in this oak is generally higher than that in conifers, as high as that in a European oak, but lower than that in an aspen. The level of population recombination is relatively high. Withinpopulation inbreeding is negligible and between-population differentiation is modest. The decay of linkage disequilibrium is significantly faster in the species-wide samples and the three northernmost populations than in the other populations. Statistical tests support the hypothesis of a recent bottleneck for several populations in the southern part of Japan. The amounts and patterns of nucleotide variation, recombination and linkage disequilibrium, and genetic differentiation observed among populations of this species are contradictory to our expectations, given the recent colonization history of the northern Japan populations.

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Section: Introductionsupporting

confidence: 75%

Nucleotide variation in Quercus crispula Blume

2008

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“…Even though the Tsugaru and Soya Straits had opened approximately 8000 y ago (Minato and Ijiri, 1984), the range was not sufficiently wide to prevent birds from carrying seeds (18 and 42 km, respectively, at the shortest paths). The distribution of the new haplotype found by Kanno et al (2004) shows the same trend.…”

Section: Discussionsupporting

confidence: 58%

“…Recently, Kanno et al (2004) reported cpDNA variations in the 4 aforementioned Japanese oaks. They investigated 5 regions with a total length of 3396 bp and found a single nucleotide substitution (T/C) at the trnQ-trnS intergenic spacer, resulting in 2 haplotypes.…”

Section: Introductionmentioning

confidence: 99%

Phylogeographic structure and late Quaternary population history of the Japanese oak Quercus mongolica var. crispula and related species revealed by chloroplast DNA variation

et al. 2007

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Generally, oaks dominate the broadleaf deciduous forests in Japan. The genetic variation in 6 cpDNA regions (trnT-trnL, trnL-trnF, atpB-rbcL, and trnHpsbA speacers, trnL intron, and matK gene) with regard to the Japanese oak (Quercus mongolica var. crispula) and 3 related species in the section Prinus (Q. serrata, Q. dentata and Q. aliena) was investigated in 598 trees belonging to 44 populations distributed throughout the Japanese archipelago. Additional samples were collected from Korea, China, and Russia (Sakhalin). Thirteen haplotypes (I to XIII) were identified on the bases of 15 nucleotide substitutions and 3 indels. Haplotypes I and II were discovered in northeastern Japan, whereas haplotypes III to IX were distributed in southwestern Japan. The boundary distinguishing these 2 groups was located in central Japan coincident with the Itoigawa-Shzuoka tectonic line. Haplotype I was also found in Sakhalin, whereas haplotypes VI, VII, VIII, X, XI, XII, and XIII were found in Korea and China. Four oak species in the same location shared identical haplotypes, suggesting cpDNA introgression by occasional hybridization. Both the values of total haplotype diversity (H T ) and haplotype diversity within populations (H S ) in Q. mongolica var. crispula were higher in the southwestern populations than in the northeastern populations. A haplotype network indicated that haplotype VI is the ancestral haplotype. The presence of identical haplotypes in Korea, China, and Japan suggested that the haplotypes diversified on the Eurasian continent before the last glacial period. The difference in genetic structure between the northeastern and southwestern regions indicates a difference in the history of migration and recolonization in Japan during the last glacial period.

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“…Specifically, the genetic diversity of species such as Japanese beech (Fagus crenata; Tomaru et al, 1998;Fujii et al, 2002), an endemic deciduous shrub (Stachyurus praecox; Ohi et al, 2003) and oak species (Quercus spp. ; Kanno et al, 2004) is lower in the northern part of Honshu than in the southern part due to the founder effect that followed rapid postglacial expansion of these species.…”

Section: Introductionmentioning

confidence: 93%

The influence of climatic oscillations during the Quaternary Era on the genetic structure of Asian black bears in Japan

et al. 2009

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The Asian black bear (Ursus thibetanus) inhabits two of the main islands, Honshu and Shikoku, in Japan. To determine how climatic oscillations during the Quaternary Era affected the genetic structure of the black bear populations in Japan, we examined their phylogeographic relationships and compared their genetic structure. We analysed an approximately 700-bp sequence in the D-loop region of mitochondrial DNA collected from 589 bears in this study with 108 bears from a previous study. We observed a total of 57 haplotypes and categorized them into three clusters (Eastern, Western and Southern) based on the spatial distribution of the haplotypes. All but 2 of the 41 haplotypes in the Eastern cluster were distributed locally. Genetic diversity was generally low in northern Japan and high in central Japan.Demographic tests rejected the expansion model in northern populations. Haplotypes of the Western and Southern clusters were unique to local populations. We conclude that the extant genetic structure of the Asian black bear populations arose as follows: first, populations became small and genetic drift decreased genetic diversity in the northern area during the last glacial period, whereas large continuous populations existed in the southern part of central Japan. These patterns were essentially maintained until the present time. In western and southern Japan, the effects of climatic oscillations were smaller, and thus, local structure was maintained.

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Geographical distribution of two haplotypes of chloroplast DNA in four oak species (Quercus) in Japan

Cited by 75 publications

References 22 publications

Nucleotide variation in Quercus crispula Blume

Nucleotide variation in Quercus crispula Blume

Phylogeographic structure and late Quaternary population history of the Japanese oak Quercus mongolica var. crispula and related species revealed by chloroplast DNA variation

The influence of climatic oscillations during the Quaternary Era on the genetic structure of Asian black bears in Japan

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