Geographic patterns of genetic variation in nuclear and chloroplast genomes of two related oaks (Quercus aliena and Q. serrata) in Japan: implications for seed and seedling transfer

Jose-Maldia, Lerma San; Matsumoto, Asako; Ueno, S.; Kanazashi, Ayako; Kanno, Munetake; Namikawa, Kanji; Yoshimaru, Hiroshi; Tsumura, Yoshihiko

doi:10.1007/s11295-017-1202-4

Cited by 16 publications

(26 citation statements)

References 83 publications

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“…Northeast/southwest divergence with a boundary in central Honshu, as found for lineage A, was also previously reported for several animals and plants from Japan (Okaura, Quang, Ubukata, & Harada, ; Jose‐Maldia et al, ; Sekiné et al, ; Shoda‐Kagaya et al, ; Suzuki et al, ; Watanabe et al, ). This phenomenon was presumably explained by the separation by the sea channel of Fossa Magna in the Miocene, or by subsequent orogenic movements that occurred during the Quaternary, which formed mountain chains over 3,000 m high and that currently run north to south in central Honshu.…”

Section: Discussionsupporting

confidence: 80%

“…Northeast/southwest divergence with a boundary in central Honshu, as found for lineage A, was also previously reported for several animals and plants from Japan (Okaura, Quang, Ubukata, & Harada, 2007;Jose-Maldia et al, 2017;Sekiné et al, 2013;Shoda-Kagaya et al, 2010;Suzuki et al, 2002;Watanabe et al, 2006). This Figure 5).…”

Section: Phylogeographical History Of Haemadipsa Japonica In Japansupporting

confidence: 82%

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Nuclear microsatellite and mitochondrial DNA analyses reveal the regional genetic structure and phylogeographical history of a sanguivorous land leech, Haemadipsa japonica, in Japan

Morishima

Aizawa

2019

Ecology and Evolution

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Recent molecular studies have indicated that phylogeographical history of Japanese biota is likely shaped by geohistory along with biological events, such as distribution shifts, isolation, and divergence of populations. However, the genetic structure and phylogeographical history of terrestrial Annelida species, including leech species, are poorly understood. Therefore, we aimed to understand the genetic structure and phylogeographical history across the natural range of Haemadipsa japonica , a sanguivorous land leech species endemic to Japan, by using nine polymorphic nuclear microsatellites (nSSR) and cytochrome oxidase subunit one (COI) sequences of mitochondrial DNA (mtDNA). Analyses using nSSR revealed that H . japonica exhibited a stronger regional genetic differentiation among populations ( G ' ST = 0.77) than other animal species, probably because of the low mobility of land leech. Analyses using mtDNA indicated that H . japonica exhibited two distinct lineages (A and B), which were estimated to have diverged in the middle Pleistocene and probably because of range fragmentation resulting from climatic change and glacial and interglacial cycles. Lineage A was widely distributed across Japan, and lineage B was found in southwestern Japan. Analyses using nSSR revealed that lineage A was roughly divided into two population groups (i.e., northeastern and southwestern Japan); these analyses also revealed a gradual decrease in genetic diversity with increasing latitude in lineage A and a strong genetic drift in populations of northeastern Japan. Combined with the largely unresolved shallow polytomies from the mtDNA phylogeny, these results implied that lineage A may have undergone a rapid northward migration, probably during the Holocene. Then, the regional genetic structure with local unique gene pools may have been formed within each lineage because of the low mobility of this leech species.

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Section: Discussionsupporting

confidence: 80%

“…Northeast/southwest divergence with a boundary in central Honshu, as found for lineage A, was also previously reported for several animals and plants from Japan (Okaura, Quang, Ubukata, & Harada, 2007;Jose-Maldia et al, 2017;Sekiné et al, 2013;Shoda-Kagaya et al, 2010;Suzuki et al, 2002;Watanabe et al, 2006). This Figure 5).…”

Section: Phylogeographical History Of Haemadipsa Japonica In Japansupporting

confidence: 82%

Nuclear microsatellite and mitochondrial DNA analyses reveal the regional genetic structure and phylogeographical history of a sanguivorous land leech, Haemadipsa japonica, in Japan

Morishima

Aizawa

2019

Ecology and Evolution

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“…These results suggest that genetic variation in the northern lineage has been affected by severe genetic drift during one or more past glacial periods. The significant genetic differentiation between the northern and southern lineages, and the lower level of genetic diversity in the northern lineage, that we observed in M. kobus are common trends among temperate tree species that are widely distributed along the Japanese archipelago (Hiraoka and Tomaru 2009;Sakaguchi et al 2011;San Jose-Maldia et al 2017;Tamaki et al 2018;Tsumura et al 2007Tsumura et al , 2014. However, the locations of boundaries between northern and southern lineages are different among species.…”

Section: What Factors Contributed To Producing the Current Genetic Vamentioning

confidence: 52%

Population genetic structure and demography of Magnolia kobus: variety borealis is not supported genetically

et al. 2019

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Species delimitations by morphological and by genetic markers are not always congruent. Magnolia kobus consists of two morphologically different varieties, kobus and borealis. The latter variety is characterized by larger leaves than the former. For the conservation of M. kobus genetic resources in natural forests, the relationships between morphological and genetic variation should be clarified. We investigated variations in nuclear microsatellites, chloroplast DNA (cpDNA) sequences and leaf morphological traits in 23 populations of M. kobus over the range of species. Two genetically divergent lineages, northern and southern were detected and their geographical boundary was estimated to be at 39°N. The northern lineage consisted of two genetic clusters and a single cpDNA haplotype, while the southern one had multiple genetic clusters and cpDNA haplotypes. The northern lineage showed significantly lower genetic diversity than the southern. Approximate Bayesian computation indicated that the northern and southern lineages had experienced, respectively, population expansion and long-term stable population size. The divergence time between the two lineages was estimated to be 565,000 years ago and no signature of migration between the two lineages after divergence was detected. Ecological niche modeling showed that the potential distribution area in northern Japan at the last glacial maximum was very small. It is thus considered that the two lineages have experienced different population histories over several glacial-inter-glacial cycles. Individuals of populations in the central to northern part of Honshu on the Sea of Japan side and in Hokkaido had large leaf width and area. These leaf characteristics corresponded with those of variety borealis. However, the delimitation of the northern and southern lineages detected by genetic markers (39°N) was not congruent with that detected by leaf morphologies (36°N). It is therefore suggested that variety borealis is not supported genetically and the northern and southern lineages should be considered separately when identifying conservation units based not on morphology but on genetic markers.

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“…crispula (Blume) Ohashi, Quercus dentata Thunb. ex Murray, and Quercus aliena Blume in Japan, Korea, China, and Russia (Kanno et al, 2004 ; Okaura et al, 2007 ), geographic patterns of genetic variation in nuclear and chloroplast genomes of two related oaks ( Q. aliena and Q. serrata ) in Japan (San Jose-Maldia et al, 2017 ), differentiation of three closely related Japanese oak species and detection of interspecific hybrids using AFLP markers (Matsumoto et al, 2009 ) and exploring the species limits and dynamics of speciation in the two closely related Chinese oaks Q. mongolica and Q. liaotungensis Koidz. (Zeng et al, 2010 , 2011 ).…”

Section: Introductionmentioning

confidence: 99%

Species Boundaries Between Three Sympatric Oak Species: Quercus aliena, Q. dentata, and Q. variabilis at the Northern Edge of Their Distribution in China

et al. 2018

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Oaks are important timber trees with wide distributions in China, but few genetic studies have been conducted on a fine scale. In this study, we seek to investigate the genetic diversity and differentiation of three sympatric oak species (Quercus aliena Blume, Quercus dentata Thunb. ex Murray, and Quercus variabilis Blume) in their northern distribution in China using 17 bi-parentally inherited nSSRs markers and five maternally inherited chloroplast DNA (cpDNA) fragments. Both the cpDNA and the nSSRs show a high level of genetic differentiation between different oak sections. The chloroplast haplotypes are clustered into two lineages. Clear species boundaries are detected between Q. variabilis and either Q. aliena or Q. dentata. The sharing of chloroplast haplotype H1 between Q. aliena and Q. dentata suggests very recent speciation and incomplete lineage sorting or introgression of H1 from one species to another. The nSSRs data indicate a complete fixation of variation within sites for all three oak species, and that extensive gene flow occurs within species whereas only limited gene flow is detected between Q. aliena and Q. dentata and nearly no gene flow can be detected between Q. aliena and Q. variabilis and between Q. dentata and Q. variabilis. Prezygotic isolation may have contributed to the species boundaries of these three sympatric oak species.

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Geographic patterns of genetic variation in nuclear and chloroplast genomes of two related oaks (Quercus aliena and Q. serrata) in Japan: implications for seed and seedling transfer

Cited by 16 publications

References 83 publications

Nuclear microsatellite and mitochondrial DNA analyses reveal the regional genetic structure and phylogeographical history of a sanguivorous land leech, Haemadipsa japonica, in Japan

Nuclear microsatellite and mitochondrial DNA analyses reveal the regional genetic structure and phylogeographical history of a sanguivorous land leech, Haemadipsa japonica, in Japan

Population genetic structure and demography of Magnolia kobus: variety borealis is not supported genetically

Species Boundaries Between Three Sympatric Oak Species: Quercus aliena, Q. dentata, and Q. variabilis at the Northern Edge of Their Distribution in China

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