Figure 3
From: Comparative analysis of corrected tiger genome provides clues to its neuronal evolution
The genes showing multiple signatures of adaptation in tiger. (a) The upSet plot of the number of genes shared by the combination of the five methods used to test for adaptive evolution. The matrix layout was constructed using the upSET package in R71. The connection between the red circles shows the intersection of different methods with the intersection value depicted as a bar plot. RTT: higher root-to-tip branch length, USF: Unique substitution with functional impact, HBW: Higher branch dN/dS (ω), PSG: Positively selected genes, PSS: Positively selected sites, GW: Gene-wide, SS: Site-specific. Gene-wide (GW) represents the genes showing all three signs of adaptation among the MSA (HBW, RTT, PSG), which takes into account the evolution of the complete gene. Site-specific (SS) represents the genes showing the two signs of adaptation among the MSA (USF and PSS), which takes into account the evolution of specific sites in a gene. (b) Network diagram of GO biological processes enriched (p-value < 0.01) in the MSA genes. The nodes represent the GO biological processes, and the edges represent the number of MSA genes shared among the enriched categories.
