East Asian origin of the widespread alpine snow‐bed herb, <i>Primula cuneifolia</i> (Primulaceae), in the northern Pacific region

Ikeda, Hajíme; Yakubov, V. V.; Barkalov, Vyacheslav Yu.; Sato, Kazuhiro; Fujii, Norihiko

doi:10.1111/jbi.13918

Cited by 18 publications

(19 citation statements)

References 81 publications

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“…SNP analyses were performed with three methods using Stacks v. 2.5 [ 25 ]. Stacks is a method developed for the RAD analysis and has also been applied to PCR-based methods such as MIG-Seq and GRAS-Di [ 16 , 26 ]. In the first method, the denovo_map pl mapping protocol (hereafter referred to as de_novo ) was used.…”

Section: Methodsmentioning

confidence: 99%

Genetic Diversity and Genetic Structure of the Wild Tsushima Leopard Cat from Genome-Wide Analysis

Itô

Nakajima

Onuma

et al. 2020

Animals

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The Tsushima leopard cat (Prionailurus bengalensis euptilurus) lives on Tsushima Island in Japan and is a regional population of the Amur leopard cat; it is threatened with extinction. Its genetic management is important because of the small population. We used genotyping by random amplicon sequencing-direct (GRAS-Di) to develop a draft genome and explore single-nucleotide polymorphism (SNP) markers. The SNPs were analyzed using three genotyping methods (mapping de novo, to the Tsushima leopard cat draft genome, and to the domestic cat genome). We examined the genetic diversity and genetic structure of the Tsushima leopard cat. The genome size was approximately 2.435 Gb. The number of SNPs identified was 133–158. The power of these markers was sufficient for individual and parentage identifications. These SNPs can provide useful information about the life of the Tsushima leopard cat and the pairings and for the introduction of founders to conserve genetic diversity with ex situ conservation. We identified that there are no subpopulations of the Tsushima leopard cat. The identifying units will allow for a concentration of efforts for conservation. SNPs can be applied to the analysis of the leopard cat in other regions, making them useful for comparisons among populations and conservation in other small populations.

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Section: Methodsmentioning

confidence: 99%

Genetic Diversity and Genetic Structure of the Wild Tsushima Leopard Cat from Genome-Wide Analysis

Itô

Nakajima

Onuma

et al. 2020

Animals

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“…In phylogeographic studies of the Japanese archipelago, there is a relatively large number of studies that inferred migration history through the Sakhalin and the Kuril Islands in the north (Fujii and Senni 2006;Hata et al 2017;Ikeda et al 2018Ikeda et al , 2020 and the Ryukyu Islands in the south (Nakamura et al 2010;Setoguchi et al 2006Setoguchi et al , 2008. However, few studies dealt with grassland plants with a migration history through the Korean Peninsula, such as the Mansen elements.…”

Section: Origin and Migration History Of V Orientalismentioning

confidence: 99%

“…However, these studies have not sufficiently examined whether the origin of the plant species is on the continent or in Japan itself, which is an unresolved issue. Several studies suggest a Japanese origin rather than a continental origin for these species (Ikeda et al 2018(Ikeda et al , 2020Xia et al 2021).…”

Section: Introductionmentioning

confidence: 99%

Phylogeography of the East Asian grassland plant, Viola orientalis (Violaceae), inferred from plastid and nuclear restriction site-associated DNA sequencing data

et al. 2021

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To elucidate the origin and migration history of the "Mansen elements," a group of temperate grassland plants mainly distributed in northeastern Asia, phylogeographic analyses based on chloroplast DNA markers and double-digest restriction site-associated DNA sequencing (ddRAD-seq) data were performed on Viola orientalis, one of the representative species of the group. Phylogenetic analyses using ddRAD-seq data revealed that the populations of V. orientalis were clustered into five clades, among which the continental clades made of populations from Russia and Korea diverged more than 100,000 years earlier than the Japanese clades. The Japanese clade likely diverged during the last glacial period, followed by a further postglacial divergence into the Kyushu and the Honshu subclades. Our study demonstrated that V. orientalis originated in the continental area of northeastern Asia and, during the last glacial period, has spread southward through the Korean Peninsula across the Japanese Islands. This finding supports the previously proposed evolutionary hypothesis regarding the origin and migration routes of the Mansen elements.

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“…This approach was coined by Knowles and Maddison (2002) as "statistical phylogeography" and will be referred to as such henceforth. Examples of its application in alpine phylogeography include Theodoridis et al (2017), Fu et al (2018), Wang et al (2019) and Ikeda et al (2020). For further reviews on statistical phylogeography and how it is applied see Knowles (2004) and Knowles (2009).…”

Section: From Non-spatial To Spatially Explicitmentioning

confidence: 99%

“…The progress of alpine phylogeography has seen our understanding of where alpine plants survived during the last glacial period (LGP, ka) develop from tentative suggestions using qualitative data, usually derived from various nuclear and plastid markers under neutral evolution (Stehlik et al 2001;Schönswetter et al 2002;Kropf et al 2003;Puşcaş et al 2008;Ronikier et al 2012;Gizaw et al 2013;Wang et al 2014), to explicit testing of hypotheses using sophisticated statistical models applied to large numbers of single nucleotide polymorphisms (SNPs) obtained from next generation sequencing (NGS) data (Theodoridis et al 2017;Westergaard et al 2019;Ikeda et al 2020). This progress is also owed to the growing urgency to improve our insights into the phylogeographic histories of alpine plants: As many alpine species are under threat from the ongoing climate change (Freeman et al 2018), comprehending how alpine plants survived past climate change may help us foresee if and how they will cope with future climate change.…”

Section: Introductionmentioning

confidence: 99%

Addressing alpine plant phylogeography using integrative distributional, demographic and coalescent modeling

2021

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Phylogeographic studies of alpine plants have evolved considerably in the last two decades from ad hoc interpretations of genetic data to statistical model-based approaches. In this review we outline the developments in alpine plant phylogeography focusing on the recent approach of integrative distributional, demographic and coalescent (iDDC) modeling. By integrating distributional data with spatially explicit demographic modeling and subsequent coalescent simulations, the history of alpine species can be inferred and long-standing hypotheses, such as species-specific responses to climate change or survival on nunataks during the last glacial maximum, can be efficiently tested as exemplified by available case studies. We also discuss future prospects and improvements of iDDC.

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East Asian origin of the widespread alpine snow‐bed herb, Primula cuneifolia (Primulaceae), in the northern Pacific region

Cited by 18 publications

References 81 publications

Genetic Diversity and Genetic Structure of the Wild Tsushima Leopard Cat from Genome-Wide Analysis

Genetic Diversity and Genetic Structure of the Wild Tsushima Leopard Cat from Genome-Wide Analysis

Phylogeography of the East Asian grassland plant, Viola orientalis (Violaceae), inferred from plastid and nuclear restriction site-associated DNA sequencing data

Addressing alpine plant phylogeography using integrative distributional, demographic and coalescent modeling

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