The genetic structure of Quercus crispula in northeastern Japan as revealed by nuclear simple sequence repeat loci

Ohsawa, Takafumi; Tsuda, Yoshiaki; Saito, Yoko; Ide, Yuji

doi:10.1007/s10265-010-0402-x

Cited by 25 publications

(28 citation statements)

References 54 publications

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“…On the other hand, the Central populations were the largest; they showed a high mixing degree and the lowest differentiation. In general, the population that is capable of maintaining its level of genetic diversity is often the largest population group [62]. Therefore, as expected, the Central group showed the highest capacity to maintain its level of genetic diversity.…”

Section: Genetic Differentiationsupporting

confidence: 56%

Genetic Diversity and Structure of Natural Quercus variabilis Population in China as Revealed by Microsatellites Markers

Shi

Wen

et al. 2017

Forests

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Quercus variabilis is a tree species of ecological and economic value that is widely distributed in China. To effectively evaluate, use, and conserve resources, we applied 25 pairs of simple sequence repeat (SSR) primers to study its genetic diversity and genetic structure in 19 natural forest or natural secondary forest populations of Q. variabilis (a total of 879 samples). A total of 277 alleles were detected. Overall, the average expected heterozygosity (H e ) was 0.707 and average allelic richness (AR) was 7.79. Q. variabilis manifested a loss of heterozygosity, and the mean of inbreeding coefficient (F IS ) was 0.044. Less differentiation among populations was observed, and the genetic differentiation coefficient (F ST ) was 0.063. Bayesian clustering analysis indicated that the 19 studied populations could be divided into three groups based on their genetic makeup, namely, the Southwest group, Central group, and Northeastern group. The Central group, compared to the populations of the Southwest and Northeast group, showed higher genetic diversities and lower genetic differentiations. As a widely distributed species, the historical migration of Q. variabilis contributed to its genetic differentiation.

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Section: Genetic Differentiationsupporting

confidence: 56%

Genetic Diversity and Structure of Natural Quercus variabilis Population in China as Revealed by Microsatellites Markers

Shi

Wen

et al. 2017

Forests

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“…; Ohsawa et al. ). Previous phylogeographic studies of Japanese broad‐leaved trees ( Fagus crenata , Okaura and Harada ; Betula maximowicziana , Tsuda and Ide ; Quercus mongolica var.…”

Section: Introductionmentioning

confidence: 97%

Comparative phylogeographic study of Hosta sieboldiana and Hosta albomarginata (Asparagaceae) in Japan

Lee

Maki

2013

Ecology and Evolution

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We analyzed variations in chloroplast DNA (cpDNA) in the widespread herbaceous species Hosta sieboldiana and Hosta albomarginata across large portions of their geographic ranges in the Japanese archipelago. Our objective was to compare the phylogeographic histories and phylogeographic structures of the two congeneric species in the Japanese archipelago. The location of the study is Japanese archipelago. We sequenced 1380 bp of noncoding cpDNA from 45 populations of H. sieboldiana (n = 362) and 55 populations of H. albomarginata (n = 436) to assess genetic variations within and among populations across almost the entire distributions of the species in Japan. Extant patterns of geographic structure were analyzed using statistical parsimony networks and spatial analysis of molecular variance (SAMOVA). We also used Monmonier's algorithm to detect genetic barriers between regions. Relationships between the populations were examined using a neighbor-joining (NJ) method. Four haplotypes were found for H. sieboldiana, whereas eight haplotypes were identified for H. albomarginata. Total genetic haplotype diversity (hT) and within-population haplotype diversity (hS) for H. sieboldiana were 0.352 and 0.040, respectively, while the values for H. albomarginata were 0.529 and 0.085, respectively. The population differentiations (GST) for H. sieboldiana and H. albomarginata were 0.839 and 0.886, respectively. The SAMOVA analysis revealed two clusters in H. sieboldiana and four clusters in H. albomarginata. Differentiations between and among the clusters were supported by the BARRIER analysis and the NJ tree. We detected differences in the population genetic structure between the two species. We found that H. sieboldiana had lower haplotype diversity than H. albomarginata. These results may be partially explained by the difference in ecological habitats and geographic distributions between the species. Hosta albomarginata is more widely distributed than H. sieboldiana in East Asia including Russia, and this large distribution range would enable more chances to intraspecific gene flow.

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“…Most of these studies examined cpDNA or mitochondrial (mt)DNA variation (Tomaru et al, 1998;Fujii et al, 2002;Okaura & Harada, 2002;Ohi et al, 2003;Aizawa et al, 2007;Okaura et al, 2007;Saeki & Murakami, 2009;Ohsawa et al, 2011;Iwasaki et al, 2012), although some studies have used microsatellite markers (Tsuda & Ide, 2005;Aizawa et al, 2009;Hiraoka & Tomaru, 2009a, b;Hu et al, 2010). Most of these studies examined cpDNA or mitochondrial (mt)DNA variation (Tomaru et al, 1998;Fujii et al, 2002;Okaura & Harada, 2002;Ohi et al, 2003;Aizawa et al, 2007;Okaura et al, 2007;Saeki & Murakami, 2009;Ohsawa et al, 2011;Iwasaki et al, 2012), although some studies have used microsatellite markers (Tsuda & Ide, 2005;Aizawa et al, 2009;Hiraoka & Tomaru, 2009a, b;Hu et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Pattern of population genetic structure revealed by nuclear simple sequence repeat markers in the understory perennialVeratrum albumssp.oxysepalum(Melanthiaceae) with a disjunct pattern of chloroplast DNA haplotypes

Kikuchi

Pak

Takahashi

et al. 2012

Biol J Linn Soc Lond

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Compared to tree species, there still remains a very limited number of phylogeographical studies on temperate forest perennials. In the present study, we used nuclear microsatellite markers to detect extant patterns of population genetic structure of the perennial plant Veratrum album ssp. oxysepalum in the understory of temperate forests, aiming to provide insights into the post-glacial history of the species and the reasons for the disjunct distribution of chloroplast DNA (cpDNA) haplotypes found in a previous study. We examined eight polymorphic nuclear microsatellite loci to examine genetic variation within and among 32 populations of V. album ssp. oxysepalum and seven populations of Veratrum stamineum. The population of V. album ssp. oxysepalum was split into two groups: those in the northern part of the Japanese Archipelago and all others. In addition, each population group was split into two subgroups. Only one population of V. stamineum included a substantial number of individuals categorized as V. album ssp. oxysepalum. The population genetic structure revealed by nuclear microsatellites suggests that V. album ssp. oxysepalum migrated from Eurasia into the Japanese Archipelago at least twice before the last glacial era through two different land bridges: the Korean Peninsula and Sakhalin. In addition, there appeared to be at least two refugia of V. album ssp. oxysepalum in each of the areas, dominated by the two different lineages from Eurasia during the last glacial era. The disjunct geographical pattern found in cpDNA variation in a previous study was blurred in the genetic structure as revealed by microsatellite markers, probably as a result of extensive gene flow via pollen. Currently, one-directional introgressive hybridization occurs from V. album ssp. oxysepalum to V. stamineum at only one locality; there is no evidence of the opposite pattern.

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The genetic structure of Quercus crispula in northeastern Japan as revealed by nuclear simple sequence repeat loci

Cited by 25 publications

References 54 publications

Genetic Diversity and Structure of Natural Quercus variabilis Population in China as Revealed by Microsatellites Markers

Genetic Diversity and Structure of Natural Quercus variabilis Population in China as Revealed by Microsatellites Markers

Comparative phylogeographic study of Hosta sieboldiana and Hosta albomarginata (Asparagaceae) in Japan

Pattern of population genetic structure revealed by nuclear simple sequence repeat markers in the understory perennialVeratrum albumssp.oxysepalum(Melanthiaceae) with a disjunct pattern of chloroplast DNA haplotypes

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