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. 2020 Jan 14;11:253. doi: 10.1038/s41467-019-14213-y

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a Geographical origin of the Lotus accessions. b Principal component analysis (PCA) based on the genotypes of the Lotus accessions. a–b Accessions are colored according to their grouping in the PCA plot. c Pairwise sequentially Markovian coalescent (PSMC) curves based on pseudo-diploids generated by merging alignments of pairs of accessions. Each curve indicates the inferred population size history through time for pseudodiploid pairs including MG063 and MG126, respectively. The horizontal gray line indicates an effective population size of 5 × 10⁴. d The lower panel shows a heatmap of divergence times (years ago) for pseudodiploid pairs as estimated from the PSMC analysis with a population size cutoff of 5 × 10⁴. Accession colors are matched in a–e. e Heatmap showing the genetic distances between pairs of accessions. Genetic distance indicates the average number of allelic differences per polymorphic site in a pairwise comparison. d, e Accessions MG152 and MG154 from Tsushima Island (green), MG110 and MG111 (gray) and MG112 (blue) from central Kyushu, MG126 from northern Japan, and M063 from eastern Kyushu are highlighted as indicated in e. The accessions are shown in the same order in d and e. Source data underlying d and e are provided as a Source Data file.