Phylogeny, population structure, diversity, and dynamic history of wild walnuts.
(A) Geographic distribution, population structure, and phylogenetic tree analysis of wild Persian walnut accessions plus outgroups. Each of the six regional walnut populations are indicated by different colors. EA: Eastern Asia; YG: Yunnan-Kweichow Plateau; XJ: Xinjiang province; SA: southern Asia; WA: western Asia; EU: Europe. The basemap and distribution of all sampling points were plotted in ArcGIS v10.2 (ESRI Inc., Redlands, California, USA). The world map was downloaded from the Natural Earth (https://www.naturalearthdata.com/downloads/10m-cultural-vectors). The grey line indicates the country region border shape in the map. (B) Summary of nucleotide diversity (θπ) and population divergence (FST) across groups. The size of each circle represents the nucleotide diversity (θπ)for the group, and values on the line between pairs indicate the population divergence (FST). (C) Comparisons among wild Persian walnut groups (EA, YG, XJ, SA, WA, and EU) based on D statistics. The grey dotted line indicates where a Z-score is more than 3. (D) Pairwise sequentially Markovian coalescent (PSMC) estimates of the changes in the effective population size over time for 12 individuals of Persian walnut. Each line represents one individual. 10*6 = 1.0 Ma; Persian walnut Ne curves converged 1.0 million years ago, probably reflecting the time when all sources of J. regia last shared a common ancestor. “Az”-Landrace from Azerbaijan; Ji-Cultivar Jiling province, China; Jg-cultivar from Beijing, China; Gu-wild walnut from Guizhou province, China; Qi-wild walnut from Qinling mountains, China; Jp-landrace from Japan; Pk-wild walnut from Pakistan; Sk-landrace from South Korea; Lu-cultivar from Shandong province, China; Xj-cultivar from Xinjiang province, China; Ia-wild walnut from Iran; Sx-wild walnut from Shaanxi province, China.