Abstract
Geranium erianthum is an alpine plant growing in dry habitats, which is distributed from East Asia to northern coastal regions of the northern Pacific. The ice-free area around the current Bering Strait (i.e., Beringia) had played an important role in range expansion into neighboring regions such as East Asia and North America for some alpine plants. However, recent studies suggest that some alpine plants in snowbed environment spread from East Asia to northern coastal regions of the northern Pacific. In this study, we investigated phylogenetic relationships and genetic differentiations among populations of G. erianthum and the related species using the chloroplast genome and single-nucleotide polymorphisms, to evaluate the alternative biogeographic hypotheses in which region of Beringia, British Columbia or East Asia is probable for its distributional origin. Range reconstruction based on phylogenetic tree of chloroplast genome indicated G. erianthum and related species originated in East Asia, from where G. erianthum migrated eastward into Beringia and British Columbia. In addition, nuclear genome-wide SNPs indicated that no significant genetic differentiation was detected between Japanese and Beringian populations. The lack of genetic differentiation suggests that the current range of G. erianthum resulted from rapid range expansion during the latter period of the last glacial era. Overall, the East Asian refugium hypothesis was applicable to the alpine plant G. erianthum in dry habitat, indicating that range expansion pattern from East Asia into the northern Pacific may be more common rather than limited for snowbed species.
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The chloroplast genome sequence results are deposited in DDBJ (Accession numbers: DRA010649). SNPs data from MIG-seq analysis are also deposited in DDBJ (Accession numbers: DRA010651).
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Acknowledgements
The authors thank Dr. Kenji Horie, Dr. Naoyuki Nakahama, Dr. Sachiko Nishida, and Tomohiro Kawai for granting access to their collection of materials. We also thank the Ministry of the Environment, and the prefectural offices of Hokkaido, Nagano, and Yamanashi for granting us permission to conduct surveys. We thank The University Museum, University of Tokyo (TI) for granting access to their specimen collections.
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This study was partly supported by JSPS KAKENHI Grant Number JP16H04827 and the National BioResource Project (18km0210136j0002) from AMED.
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SK, SS, HI and MI to conceived the ideas; SKH and YS performed MIG-seq experiment; OK supported to detect genotype and SNP calling from next-generation sequencing data; SK and SS designed the study and genetic analyses. All authors contributed to interpret the analysis results and write the manuscript.
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Online Resource 1. DDBJ and voucher specimen numbers for chloroplast genome sequencing.
Online Resource 2. Voucher specimen numbers for MIG-seq analyses.
Online Resource 3. Nucleotide substitution models in RAxML-NG, MrBayes, and BEAST.
Online Resource 4. Sequence alignments of 40 taxa chloroplast genome. The 68 coding sequences are concatenated.
Online Resource 5. Bayesian inference tree based on the chloroplast genome. Numbers above branches are posterior probabilities.
Online Resource 6. Results of SNPs detection of Geranium erianthum, which are based on MIG-seq analysis of the nuclear genome.
Online Resource 7. ΔK and mean estimated LnP(D) in STRUCTURE analysis.
Online Resource 8. Accession numbers of Geraniaceae and Francoaceae species.
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Kurata, S., Sakaguchi, S., Ikeda, H. et al. From East Asia to Beringia: reconstructed range dynamics of Geranium erianthum (Geraniaceae) during the last glacial period in the northern Pacific region. Plant Syst Evol 308, 28 (2022). https://doi.org/10.1007/s00606-022-01820-4
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DOI: https://doi.org/10.1007/s00606-022-01820-4