Fig. 3: Rhoiptelea chiliantha shares the juglandoid whole-genome duplication (WGD) with the rest Juglandaceae species, but exhibits much slower evolution following the polyploidization event.
a Dot plot showing homologous chromosomes of R. chiliantha and J. regia. Syntenic blocks are plotted with their colors indicating their median Ks values. Each pair of homoeologous chromosomes in one species shows collinear relationships with one homologous pair in another. The dot colors distinguish between orthologous (yellow: smaller Ks) and paralogous (green: larger Ks) relationships, pointing to the WGD shared by the two species. b Phylogenies from the three types of gene families (see main text). The phylogenetic trees at the top, middle, and bottom are from gene families of type 1, 2 and 3, respectively. For the scores shown in parentheses, the denominator is the total number of gene trees with bootstrap values ≥80 (2655 trees) and the numerator represents the number of gene trees displaying the respective topology with bootstrap values ≥80. The phylogenetic trees on the left (2464 trees) support a shared WGD, those on the right (123 trees) an independent WGD. The red star in (b) and (c) marks the WGD event, and the red circles indicate speciation events. c Relative rate tests used to estimate the evolutionary rate of the different species. Rch1 and Rch2 are the WGD-derived homoeologs of R. chiliantha, Jre1 and Jre2 are the WGD-derived homoeologs of J. regia; Rch1-Jre1 and Rch2-Jre2 are the orthologous gene pairs due to speciation. Ks(S1-Rch1) is the expected number of substitutions per synonymous site in Rch1 since the speciation event (labeled S1), and other Ks estimates are similarly defined. d A comparison of the molecular evolutionary rates for R. chiliantha and J. regia using the two-tailed two-sample Wilcoxon rank-sum test (Mann–Whitney test). ***P < 0.001. Source data are provided as a Source Data file.
