Recent distribution changes affect geographic clines in genetic diversity and structure of Pinus densiflora natural populations in Japan

Iwaizumi, Masakazu G.; Tsuda, Yoshiaki; Ohtani, Mitsuaki; Tsumura, Yoshihiko; Takahashi, Makoto

doi:10.1016/j.foreco.2013.05.026

Cited by 30 publications

(17 citation statements)

References 54 publications

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“…According to Wright [42], the level of genetic differentiation among populations is low when the coefficient of genetic differentiation (F ST ) is less than 0.25. Our results showed that the genetic differentiation level of P. koraiensis was very low (F ST ranging from 0.007 to 0.021), and the AMOVA results showed that only 2.35% of the total genetic variation occurred among populations, which was consistent with conifers often showing low levels of genetic differentiation among populations [35,36,43,44]. Due to their wind pollination and high out-crossing rates, Pinus species, such as P. koraiensis often exhibit high gene flow among populations [45][46][47] and, consequently, a low level of genetic differentiation.…”

Section: Genetic Differentiation and Population Structuresupporting

confidence: 69%

Genetic Diversity and Population Structure of Natural Pinus koraiensis Populations

Tong

Lewis

Zhou

et al. 2019

Forests

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Studying the genetic diversity and population structure of natural forest populations is essential for evaluating their ability to survive under future environmental changes and establishing conservation strategies. Pinus koraiensis is a conifer species with high ecological and economic value in Northeast China. However, its natural forests have been greatly reduced in recent years, mostly due to over exploitation and over utilization. Here, we evaluated the genetic diversity and population structure of seven populations of P. koraiensis located throughout its native distribution. A total of 204 samples were genotyped with nine polymorphic nuclear SSR (simple sequence repeat) markers. The results showed high genetic diversity in all populations, with an average expected heterozygosity of 0.610, and the northern-most populations (Dailin (DL) and Fenglin (FL)) showed slightly higher diversity than the other five populations. The level of genetic differentiation among populations was very low (FST = 0.020). Analysis of molecular variance (AMOVA) showed that only 2.35% of the genetic variation existed among populations. Moreover, STRUCTURE analysis clearly separated the seven populations into two clusters. Populations DL and FL from the Xiaoxinganling Mountains comprised cluster I, while cluster II included the five populations from the Changbai Mountains and adjacent highlands. Our research on the genetic diversity and population structure of P. koraiensis in natural forests of China can provide a basis for the implementation of programs for the conservation and utilization of P. koraiensis genetic resources in the future.

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Section: Genetic Differentiation and Population Structuresupporting

confidence: 69%

Genetic Diversity and Population Structure of Natural Pinus koraiensis Populations

Tong

Lewis

Zhou

et al. 2019

Forests

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“…ellipticus (Aoki et al 2004b), Photinia glabra (Aoki et al 2006), Myrsine seguinii (Aoki et al 2011), and Camellia japonica (Ueno 2015) for plant species, C. hilgendorfi; a specific predator of C. sieboldii seeds (Aoki et al 2008) and Rhynchaenus dorsoplanatus; a specific leaf miner of C. sieboldii leaves (Aoki et al 2010) for insect species. Genetic boundaries between several species of warm to cool temperate zones in Japan also appear to be located in this region, for example, Pinus (Miyata and Ubukata 1994;Iwaizumi et al 2013), Cerasus (Tsuda et al 2009), Zanthoxylum (Yoshida et al 2010), Padus, Carpinus, and Magnolia (Iwasaki et al 2010(Iwasaki et al , 2012, and Acer (Yoshimaru and Matsumoto 2015) for plant species; Curculio (Aoki et al 2009) for insect species; and Cervus (Nagata et al 1999), Macaca (Kawamoto et al 2007), Petaurista (Oshida et al 2009), Ursus (Yasukochi et al 2009), and Lepus (Nunome et al 2010) for mammal species. The common geographic differentiation among multiple codistributed taxa may help efforts to elucidate the relative influence of major historical events such as climate changes during the glacial and interglacial periods (Avise 2000).…”

Section: Discussionmentioning

confidence: 99%

Approximate Bayesian computation analysis of EST-associated microsatellites indicates that the broadleaved evergreen tree Castanopsis sieboldii survived the Last Glacial Maximum in multiple refugia in Japan

et al. 2018

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Climatic changes have played major roles in plants' evolutionary history. Glacial oscillations have been particularly important, but some of their effects on plants' populations are poorly understood, including the numbers and locations of refugia in Asian warm temperate zones. In the present study, we investigated the demographic history of the broadleaved evergreen tree species Castanopsis sieboldii (Fagaceae) during the last glacial period in Japan. We used approximate Bayesian computation (ABC) for model comparison and parameter estimation for the demographic modeling using 27 EST-associated microsatellites. We also performed the species distribution modeling (SDM). The results strongly support a demographic scenario that the Ryukyu Islands and the western parts in the main islands (Kyushu and western Shikoku) were derived from separate refugia and the eastern parts in the main islands and the Japan Sea groups were diverged from the western parts prior to the coldest stage of the Last Glacial Maximum (LGM). Our data indicate that multiple refugia survived at least one in the Ryukyu Islands, and the other three regions of the western and eastern parts and around the Japan Sea of the main islands of Japan during the LGM. The SDM analysis also suggests the potential habitats under LGM climate conditions were mainly located along the Pacific Ocean side of the coastal region. Our ABC-based study helps efforts resolve the demographic history of a dominant species in warm temperate broadleaved forests during and after the last glacial period, which provides a basic model for future phylogeographical studies using this approach.

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“…The genetic diversity of T . koraiensis was slightly lower than that of conifer species that have widespread geographic ranges, including Thuja occidentalis (mean N A = 8.83; H E = 0.64 in the core populations; mean N A = 6.64; H E = 0.60 in the peripheral populations) [ 68 ], Pinus densiflora (mean N A =14.6; H E = 0.873 within 1883 individuals from 62 natural populations) [ 69 ], and P . orientalis (mean N A = 8.945; H E = 0.832 from 21 populations) [ 70 ].…”

Section: Discussionmentioning

confidence: 99%

Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing

Hou

Cui

et al. 2018

Genes

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Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR) were detected based on 875,792 de novo-assembled contigs using a restriction-associated DNA (RAD) approach. Among these SSRs, 300 were randomly selected to test for polymorphisms and 96 obtained loci were able to amplify a fragment of expected size. Twelve polymorphic SSR markers were developed to analyze the genetic diversity and population structure of three natural populations. High genetic diversity (mean NA = 5.481, HE = 0.548) and moderate population differentiation (pairwise Fst = 0.048–0.078, Nm = 2.940–4.958) were found in this species. Molecular variance analysis suggested that most of the variation (83%) existed within populations. Combining the results of STRUCTURE, principal coordinate, and neighbor-joining analysis, the 232 individuals were divided into three genetic clusters that generally correlated with their geographical distributions. Finally, appropriate conservation strategies were proposed to protect this species. This study provides genetic information for the natural resource conservation and utilization of T. koraiensis and will facilitate further studies of the evolution and phylogeography of the species.

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Recent distribution changes affect geographic clines in genetic diversity and structure of Pinus densiflora natural populations in Japan

Cited by 30 publications

References 54 publications

Genetic Diversity and Population Structure of Natural Pinus koraiensis Populations

Genetic Diversity and Population Structure of Natural Pinus koraiensis Populations

Approximate Bayesian computation analysis of EST-associated microsatellites indicates that the broadleaved evergreen tree Castanopsis sieboldii survived the Last Glacial Maximum in multiple refugia in Japan

Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing

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