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Table and Figure Legend
Figure 1. Locations of provenances of Quercus mongolicavar. crispula (Qc , red), Q. ×angustilepidota (green), and Q. dentata (Qd , blue), which were planted in the inland site (a) and the coastal site (b). Provenances are categorized into southwestern (inverse triangles), northwestern (triangles), northern (diamonds), eastern (squares) districts of the northernmost area of Hokkaido and other areas of Hokkaido (circles). Enlarged symbols indicate reference individuals ofQc and Qd for inferring local ancestry. Locations of the inland site (red arrow head) and the coastal site (blue arrow head) are shown.
Figure 2. Quercus dentata ancestry (S ) and inter-ancestry heterozygosity (H ) of sampled trees in the inland site (a) and the coastal site (b). Ancestral populations of Q. mongolica var. crispula are S = 0 and H = 0, and those of Q. dentata are S = 0 and H = 0. Solid lines indicate backcrossing from F1 hybrids (S = 0.5 and H = 1) to ancestral populations, and a dotted curve indicate random mating between the ancestral populations. Symbols are shown in the same way as Figure 1.
Figure 3. Principal component analysis for phenotypes of eight morphological traits of leaves and shoots. Proportion (%) of variances for the first five principal components (PCs) and vectors (arrows) of the traits contributing to the first and second PCs are shown (a). Coordination of sampled trees in the inland site (b) and the coastal site (c) on the first and second PCs are shown. Symbols are shown in the same way as Figure 1.
Figure 4. Relationship between Quercus dentata ancestry and the first principal component of phenotypic variation of sampled trees in the inland site (a) and the coastal site (b). Solid and dotted lines are fitted to observations in the focal site and the other site, respectively, using the lowess method. Symbols are shown in the same way as Figure 1.
Figure 5. Relationship between mean values of the first principal component of phenotypic variation of sampled trees and mean values of the stem basal area of recorded trees at plantation rows in the inland site (a) and the coastal site (b). Solid and dotted lines are fitted to observations in the focal site and the other site, respectively, using the lowess method. Symbols are shown in the same way as Figure 1.
Figure 6. Genome-wide patterns of local ancestry (a) and mean number of Quercus dentata alleles in admixed individuals (b). Along vertical axis (a), Q. dentata reference individuals (white), admixed individuals sorted by Quercus dentata ancestry, and Q. mongolica var. crispula reference individuals (black) are arranged. White, black, and grey bars (a) indicate homozygote of Q. dentata alleles, homozygote of Q. mongolica var. crispula alleles, and heterozygote of both alleles, respectively, in admixed individuals. Blue vertical lines indicate borders of chromosomes, and red vertical lines indicate positions of loci potentially associated with traits shown in Figure 7 and Table S2.
Figure 7. Manhattan plots of likelihood of genome-wide association with eight morphological traits of leaves and shoots. Left panels (a, c, e, g, i, k, m, o) are association of SNP genotypes (association mapping), and right panels (b, d, f, h, j, l, n, p) are association of local ancestry (admixture mapping). Taxon-specific traits: relative lead width (a, b), lateral vein interval (c, d), tooth angle (e, f), and stellate hair length (g, h); and habitat-specific traits: stellate hair density (i, j), leaf mass per area (k, l), shoot diameter (m, n), and scale bud number (o, p) are shown. Black and grey circles indicate loci in different chromosomes, and green circles indicate loci potentially associated with traits (FDR < 0.15).
Supporting Information
Table S1. Provenances of sampled trees in inland and coastal sites.
Figure S1. Photographs of inland site (a) and coastal site (b) in 2017.
Figure S2. Locations and sizes of trees planted in three blocks (a–c) in inland site. Solid circles, circles with crosses, and open circles indicate sampled reference, sampled non-reference, and non-sampled living trees, respectively. Crosses, + and ×, indicate dead and thinned trees, respectively. Triangles indicate non-experimental trees. Colors indicate taxa: Quercus mongolica var. crispula (red),Q. × angustilepidota (green), and Q. dentata(blue).
Figure S3. Locations and sizes of trees planted in two blocks (a, b) in coastal site. Solid circles, circles with crosses, and open circles indicate sampled reference, sampled non-reference, and non-sampled living trees, respectively. Crosses, + and ×, indicate dead and thinned trees, respectively. Triangles indicate non-experimental trees. Colors indicate taxa: Quercus mongolica var. crispula (red),Q. × angustilepidota (green), and Q. dentata(blue).
Figure S4. Measurements for morphological traits of leaves and shoots.
Figure S5. Bayesian clustering of SNP genotypes at ddRAD loci of sampled trees in both inland and coastal sites. Log likelihood when the number of clusters (K ) are 1, 2, and 3 (a). Genetic differentiation (F ST) between clusters when K = 2 andK = 3 (b). Bar plots of ancestry proportions of trees sorted by the ancestry proportion of clusters, when K = 2 (c) and K= 3 (d). Colors correspond to clusters (b, c, d). Colors of circles indicate taxa: Quercus mongolica var. crispula (red),Q. × angustilepidota (green), and Q. dentata(blue), and enlarged symbols indicate reference samples (e).
Figure S6. Frequency distributions (scatter plots) and correlations (histograms) for pairs of shoot hair (0: absent and 1: present) and eight morphological traits: relative leaf width, lateral vein interval (mm), tooth angle (˚), loge length (mm) and loge density (mm–2) of stellate hair on lower leaf surface, lead mass per area (mg mm–2), shoot diameter (mm), and loge number of axillary buds at bud-scale scars. Numbers indicate Kendall’s correlation coefficients, and red lines indicate linear regression lines.
Figure S7. Patterson’s D statistics at neighboring 101 ddRAD loci along chromosomes. Positive D values indicate introgression fromQuercus dentata to Q. mongolica var. crispula . Red vertical lines indicate positions of trait-associated loci shown in Figure 7 and Table S2.
Figure S8. Phenotypic values of four taxon-specific traits in inland (left) and coastal (middle) sites and those values scaled in each site and pooled together (right) in relation to Quercus dentataancestry. Solid and dotted lines are fitted to observations in the focal site and the other site, respectively, using the lowess method. Symbols are shown in the same way as Figure 1.
Figure S9. Phenotypic values of four habitat-specific traits in inland (left) and coastal (middle) sites and those values scaled in each site and pooled together (right) in relation to Quercus dentataancestry. Solid and dotted lines are fitted to observations in the focal site and the other site, respectively, using the lowess method. Symbols are shown in the same way as Figure 1.
Figure S10. Principal component analysis for SNP genotypes at ddRAD loci of sampled trees in both inland and coastal sites. Proportion (%) of variances for the first 10 principal components (PCs) are shown (a). Coordination of sampled trees on the first and second PCs (b), the first and third PCs (c), and the first and fourth PCs (d) are shown. Symbols are shown in the same way as Figure 1.
Figure S11. Q-Q plots of expected and observed –log10p values for four taxon-specific traits. Red lines indicate identical expected and observed –log10 p values.
Figure S12. Q-Q plots of expected and observed –log10p values for four habitat-specific traits. Red lines indicate identical expected and observed –log10 p values.
Table S2. ddRAD loci of SNP genotypes (G) and local ancestry (A) associated with traits (FDR < 0.15) and proteins nearest to or between trait-associated loci obtained from PM1N v2.3 Quercus robur annotation database.
Data S1. Data of phenotypes of morphological traits of leaves and shoots and performance of trees in plantation rows in inland and coastal common gardens.