Fig. 3: High incongruence in gene-tree phylogenies.
From: Genomic evidence for homoploid hybrid speciation between ancestors of two different genera
a, b Phylogenetic topologies (a) and the corresponding numbers (shown on the top of bar charts in (b) revealed from the phylogenies of 4769 strictly orthologous nuclear gene pairs with high-confidence support values (≥50). The number for Topology II was significantly more (P = 3.11 × 10−79) than that for Topology III. c Simulations under solely ILS scenario. The red arrow indicates the observed ratio (Topology III/Topology II) from 4769 ortholog groups (see in b). The gray bars are a histogram of the ratios obtained in 10,000 simulated datasets. The solely ILS hypothesis was strongly rejected due to a significant difference (P = 0) between observed and simulated ratios. d Genome-wide distribution of Topologies I (blue bars) and II (green bars). Statistical significance was determined by a two-tailed one-sample binomial test (b) and a two-tailed one-sample Student’s t test (c). Significant differences are indicated with asterisks (***P < 0.001). Source data are provided as a Source Data file.
