Fig. 3: Hominid ILS.
From: A high-quality bonobo genome refines the analysis of hominid evolution
a, A whole-genome ILS cladogram analysis (left) for bonobo–human (red) and chimpanzee–human (blue) and a schematic map (right) of clustered ILS segments (500-bp resolution) specifically for chromosomes 3, 4 and 7. The lighter density plot represents the clustered ILS events mapping to intragenic regions, whereas the vertical lines represent the subset that overlap with protein-coding exons. b, Distribution of distances between ILS segments (inter-ILS) (500-bp resolution) compared with a simulated (null) expectation (from 400,000 simulations) reveals a bimodal pattern with a subset (26%) that is clustered and significantly non-randomly distributed. A two-sample Wilcoxon rank-sum test was used to calculate the P value in R. c, ILS exons show a significant excess of amino acid replacement (dN/dS) for both human–bonobo (H–B; red line; P = 0.004778) and human–chimpanzee (H–C; blue line; P = 0.03924) ILS. In particular, exons mapping to the ILS clustered segments (b) show the most significant excess of amino acid replacements dN/dS (dotted purple line; P = 0.001015) compared to the genome-wide null distribution (grey density plot). This shift is not observed for the non-clustered ILS segments (NC ILS; dotted black line; P = 0.3161). Significance was analysed using the one-sample Student’s t-test in R. The silhouette of the chimpanzee in a is created by T. Michael Keesey and Tony Hisgett (http://phylopic.org/; image is under a Creative Commons Attribution 3.0 Unported licence); silhouettes of bonobo and gorilla are from http://phylopic.org/ under a Public Domain Dedication 1.0 licence.
