Identification of hybridization and introgression between Cinnamomum kanehirae Hayata and C. camphora (L.) Presl using genotyping-by-sequencing
Figures
Figure 1
The gel electrophoresis of InDel,…
Figure 1
The gel electrophoresis of InDel, ZS_CK InDel_1 (mitochondrial DNA) ( A,B ), JLH2_CK…
Figure 1 The gel electrophoresis of InDel, ZS_CK InDel_1 (mitochondrial DNA) (A,B), JLH2_CK InDel_4 (codominant) (C–F) and ZS_CK InDel_2 (chloroplast DNA) (G). M: 100 bp DNA ladder. (A) Lanes 1–14: hybrids, Lanes 15–16: C. camphora. (B) Lanes 1–8: C. kanehirae, Lanes 9–15: C. camphora, Lane 16: hybrid. (C) Lanes 1–12: hybrids, Lanes 13 and 14: C. kanehirae, Lanes 15 and 16: C. camphora. (D) Lanes 1–8: C. kanehirae, Lanes 10–24: C. camphora. (E) Lane 1: C. kanehirae, Lanes 2–14: hybrids, Lanes 15 and 16: C. camphora. (F) Lane 1: C. kanehirae, Lanes 2–14: hybrids, Lane 15 and 16: C. camphora. (G) Lanes 1–8: C. kanehirae, Lanes 9–16: ESW C. camphora. Lanes 17–24: NW C. camphora. The used samples are listed in Supplementary Table S5 online.
Figure 2
Neighbor-joining tree based on 808…
Figure 2
Neighbor-joining tree based on 808 SNPs. Bootstrap values from 1000 replicates are shown…
Figure 2 Neighbor-joining tree based on 808 SNPs. Bootstrap values from 1000 replicates are shown on the nodes. Colors on branches are colored by clusters. C. kanehirae is in red, putative hybrids are in orange, and C. camphora is in green.
Figure 3
Principal coordinates analysis (PCoA) based…
Figure 3
Principal coordinates analysis (PCoA) based on the Nei’s pairwise genetic distances of C.…
Figure 3 Principal coordinates analysis (PCoA) based on the Nei’s pairwise genetic distances of C. kanehirae, C. camphora and hybrids (75 samples). Colored symbols inside each oval are represented as in the legend. Samples are as in Supplementary Table S4 online.
Figure 4
Identification and classification of hybrids.…
Figure 4
Identification and classification of hybrids. STRUCTURE results showing the proportion of the genome…
Figure 4 Identification and classification of hybrids. STRUCTURE results showing the proportion of the genome of every individual originating from each of the inferred clusters (K = 2); red is cluster 1 (C. kanehirae) and green is cluster 2 (C. camphora); the hybrids are mixed with red and green. STRUCTURE of K = 3, 23 accessions of the green cluster were divided into the blue cluster. All ESW C. camphora have high Q-values in the green cluster. STRUCTURE of K = 4, only the red cluster was divided into the yellow cluster in C. kanehirae and putative hybrids. The dotted lines are classified by morphological characteristics and phylogenetic analysis.
Figure 5
NewHybrids results with the putative…
Figure 5
NewHybrids results with the putative pedigrees for all 75 individuals and posterior probabilities…
Figure 5 NewHybrids results with the putative pedigrees for all 75 individuals and posterior probabilities for a given class in different color bars.