From East Asia to Beringia: reconstructed range dynamics of Geranium erianthum (Geraniaceae) during the last glacial period in the northern Pacific region

Kurata, Seikan; Sakaguchi, Shota; Ikeda, Hajíme; Hirota, Shun K.; Kurashima, Osamu; Suyama, Yoshihisa; Itô, Motomi

doi:10.1007/s00606-022-01820-4

Cited by 3 publications

(6 citation statements)

References 65 publications

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“…After removal of unnecessary reads, the total and mean numbers of reads obtained from MIG‐seq for G. krameri and G. shikokianum were 33,665,376 (mean: 1,402,724 per sample) and 64,911,152 (mean: 1,352,316), respectively. The remaining reads were assembled for each species using the Stacks components ( ustacks , cstacks , sstacks , and Populations ) of Stacks 1.48 (Catchen et al, 2013) with parameter settings of the components similar to those in the previous study by Kurata et al (2022). Parameter settings of each component are as follows: in ustacks , ‐M 2, ‐m 3, ‐N 2; in Populations , ‐r 0.1, ‐‐min‐maf 0.01, ‐‐max‐obs‐het 0.5.…”

Section: Methodsmentioning

confidence: 99%

“…Trimming of sequencing reads was performed using Trimmomatic‐0.39 (Bolger et al, 2014) with the following parameter setting: SLIDINGWINDOW: 4:15; LEADING: 20; TRAILING: 20; MINLEN: 30. A de novo assembly using NOVOPlasty (Dierckxsens et al, 2017) was carried out with the same settings as in the previous study of Kurata et al (2022). A plastid sequence of G. incanum (NC_030045.1) and 10 gene loci ( atpA , ccsA , cemA , ndhF , ndhJ , psaA , psbB , psbZ , rbcL , and rpoC1 ) were assigned as a reference sequence and seed sequences, respectively, for de novo assembly of chloroplastic reads.…”

Section: Methodsmentioning

confidence: 99%

“…Each gap originating from inversions or deletions was eliminated, and phylogenetic analyses were performed using RAxML‐NG (Kozlov et al, 2019) and MrBayes version 3.2.7a (Ronquist et al, 2012) after estimating nucleotide substitution models of 10 gene loci using ModelTest‐NG v.0.1.6 (Darriba et al, 2020). Phylogenetic analyses were performed with the same parameter settings of Kurata et al (2022): that is, the number of bootstrap replicates was set to 100 in the maximum likelihood (ML) phylogenetic analysis; the number of Markov chain Monte Carlo (MCMC) simulations after a burn‐in of 100,000 iterations was set to 1,000,000, and samples were collected every 1000 cycles, and diagnostics were performed every 10,000 cycles in the Bayesian phylogenetic analysis. The bootstrap supports for ML phylogenetic tree were calculated using the pgsumtree option of Phylogears2 (Tanabe, 2008).…”

Section: Methodsmentioning

confidence: 99%

“…Low-quality bases of raw reads and the primer sequence region were removed using FASTX-toolkit (http:// hannonlab.cshl.edu/fastx_toolkit/) and TagDust (Lassmann et al 2009) under the parameter settings applied in the previous study of Kurata et al (2022): the minimum quality score to remove low-quality sequences of raw reads and the primer sequence region were set to 30 (Àq 30) and 40 (Àp 40), respectively. After removal of unnecessary reads, the total and mean numbers of reads obtained from MIG-seq for G. krameri and G. shikokianum were 33,665,376 (mean: 1,402,724 per sample) and 64,911,152 (mean: 1,352,316), respectively.…”

Section: Snp Detectionmentioning

confidence: 99%

“…After SNP calling, SNP filtering was performed for the two species. We used PLINK 1.9 (Purcell et al, 2007) and filtered the data by removing individuals with >80% missing data, loci held by <30% of individuals (--mind 0.8, --geno 0.3), and markers with a minor allele frequency <3% (--maf 0.03), which were modified parameter settings of Kurata et al (2022). After filtering, individuals with >50% missing data were removed.…”

Section: Snp Detectionmentioning

confidence: 99%

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Phylogeographic incongruence between two related Geranium species with divergent habitat preferences in East Asia

Kurata,

Sakaguchi,

Hirota

et al. 2024

Ecological Research

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Plant species with overlapping distributions are expected to experience the same historical events. In contrast, species with different preferred habitat types may exhibit incongruent phylogeographic patterns because of their habitat‐dependent demographic changes in spite of their overlapping distributions. On the western side of the Japanese Archipelago, boreal forest and non‐forest vegetation were dominant during the last glacial period; subsequently, temperate forests expanded, and open vegetation (e.g., grasslands) decreased. Such vegetation shifts can result in incongruent phylogeographic patterns among temperate forest and grassland species; however, few phylogeographic studies have investigated this hypothesis. Here, we evaluated the phylogeographic structure of two related Geranium species that occur in grassland (Geranium krameri) and temperate forest (Geranium shikokianum) habitats using chloroplast genome sequencing and nuclear genome‐wide single‐nucleotide polymorphisms genotyping. The phylogeographic structure was stronger for the temperate forest species than the grassland species, despite its currently scattered distribution for grassland species. The observed patterns indicate that the phylogeographic histories of these species were influenced by their habitat configurations since the last glacial period. During the ice age, grasslands in Japan were much more widespread than today; this would have enabled the grassland species to form a continuous distribution, leading to low divergence among regional populations. In contrast, the significant genetic divergence within the forest species can be attributed to the glacial isolation of regional populations. Our genetic results suggest that vegetation transitions have variously controlled the population dynamics of two species with overlapping distributions.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Snp Detectionmentioning

confidence: 99%

Section: Snp Detectionmentioning

confidence: 99%

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Phylogeographic incongruence between two related Geranium species with divergent habitat preferences in East Asia

Kurata,

Sakaguchi,

Hirota

et al. 2024

Ecological Research

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The migration history of the Kamchatka rhododendron (Therorhodion camtschaticum s.l.) indicates two distinct dispersal routes towards Eastern Beringia

Polezhaeva,

Modorov,

Mochalova

et al. 2024

Botanical Journal of the Linnean Society

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The Kamchatka rhododendron (Therorhodion camtschaticum s.l.) is a small, cold-resistant arcto-alpine shrub species with a controversial taxonomy and a wide Beringian distribution, from northern Eurasia to Arctic North America. Some authors regard T. camtschaticum and the closely related Therorhodion glandulosum as separate species while others suggest that they represent regionally differentiated subspecies. In order to resolve this relationship, we sampled 33 populations within the native species ranges, using three fragments of plastid DNA (ptDNA) and ten nuclear microsatellites (nSSR). We recovered two genetic lineages consistent with species rather than subspecies. The distribution of these genetic lineages are consistent with two different migration pathways of species from western Beringia to eastern Beringia: (i) for T. glandulosum a northern pathway from northern East Asia to the Seward Peninsula in northern Alaska; and (ii) for T. camtschaticum a southern pathway from the southern part of western Beringia to the Aleutian Islands and the seashore of south-east Alaska. The northern route extends from the Okhotsk seashore through the Kolyma region, Chukotka, and central and northern Kamchatka. The southern route begins at the Sikhote-Alin ridge, and goes through Sakhalin Island, the Kuril Islands, and southern Kamchatka. Demographic analysis using nSSR data inferred a divergence time between T. camtschaticum and T. glandulosum long before the Last Glacial Maximum.

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Contribution of genetic analyses to semi‐natural grassland biodiversity conservation in Japan

Nakahama

Kurata

Ushimaru

2023

Plant Species Biology

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Semi-natural grasslands maintained by moderate anthropogenic disturbance have been rapidly declining worldwide in recent decades, resulting in the progressive degradation of biodiversity therein. Similarly, in Japan, many semi-natural grassland organisms are threatened with extinction owing to the decline of semi-natural grasslands, and their conservation and management has attracted considerable attention. Although ecological studies using genetic information are expected to contribute to the conservation of semi-natural grassland organisms, no reviews have been conducted on the potential roles of these studies in grassland conservation in Japan. Here, we review the current trends in conservation-ecological study on Japanese semi-natural grassland organisms using genetic information by grouping into five categories: (1) monitoring of genetic diversity and spatial genetic structure, (2) exploration of the genetic consequences of management practices, (3) prevention of genetic disturbance, (4) elucidation of natural history traits, and (5) estimation of the origin and demography. Furthermore, the applicability of studies using high-throughput sequencing, which has been rapidly progressing in recent years, is highlighted. This review provides the methods and perspectives on the use of genetic information to conserve biodiversity in semi-natural grasslands.

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From East Asia to Beringia: reconstructed range dynamics of Geranium erianthum (Geraniaceae) during the last glacial period in the northern Pacific region

Cited by 3 publications

References 65 publications

Phylogeographic incongruence between two related Geranium species with divergent habitat preferences in East Asia

Phylogeographic incongruence between two related Geranium species with divergent habitat preferences in East Asia

The migration history of the Kamchatka rhododendron (Therorhodion camtschaticum s.l.) indicates two distinct dispersal routes towards Eastern Beringia

Contribution of genetic analyses to semi‐natural grassland biodiversity conservation in Japan

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