Fig. 1: Population structure, genetic admixture, and heterozygosity of east Asian citrus.
From: Diversification of mandarin citrus by hybrid speciation and apomixis
a Multidimensional scaling (MDS) plot of 51 citrus accessions. Projection onto the first two principal coordinates (upper panel) shows C. ryukyuensis as a distinct population from tachibana, shiikuwasha, and other Ryukyuan hybrids (yukunibu and deedee). The third principal coordinate (lower panel) separates the two Mangshan wild mandarins (MS) from other mandarins. It also separates tachibana from shiikuwasha. For easier visualization, accessions with significant pummelo ancestry (pummelos, oranges, some mandarins, yukunibus) are not shown in the lower panel. See Supplementary Data 1 and 3 for accession code and names. b Four-way admixture plot of 53 citrus accessions based on local ancestry inference. PU=pummelo (C. maxima), RK=C. ryukyuensis, MS=mangshanyeju, MA=common mandarin, MM=generic C. reticulata without subspecies assignment (MS vs MA), UNK=unknown. Note that tachibana has more MS alleles than shiikuwasha and other Ryukyuan hybrids. Some wild mandarins (M01, M04) are hybrids with nearly equal contribution from the two subspecies of MS and MA. Common mandarins display varying degree of MS admixture. c Heterozygosity distribution violin plot for the same accessions as in b), for non-overlapping windows of 500,000 callable sites. C. ryukyuensis shows the lowest heterozygosity compared to tachibana, shiikuwasha and other hybrid types as well as accessions from C. reticulata and C. maxima. Median and quartiles are denoted by the white dot and black bar limits respectively, and whiskers are 1.5× inter-quartile range. Source data are provided as a Source Data file.
