Figure 1.

The genomic substrate for rock vs. sand evolution. (A) A maximum likelihood phylogeny of eight rock- and 14 sand-dwelling species, based on variable sites (informative SNP and InDels) identified throughout the genome. “Sand” species contain representatives of the lineages “shallow benthic, deep benthic and utaka” from Ref.³², while the “rock” species correspond to the “mbuna” lineage. (B) A plot of Z-F_ST (F_ST normalized using Fisher’s Z-transformation) across the genome (ggplot2 v3.3.3https://ggplot2.tidyverse.org/), plotting genomic divergence between rock- vs. sand-dwelling groups. Single nucleotide polymorphisms (SNPs) summed over 10 kb bins and insertion-deletion mutations (InDels) are shown on the same scale. Numbers along the x-axis refer to linkage groups (i.e., chromosomes) and threshold lines indicate 2.5% FDR. (C) Evolutionary conservation (PhastCons) scores were calculated for each nucleotide across the genome, subdivided by genome annotation and plotted by bins of increasing F_ST. The PhastCons score for each genome category is significantly higher for increasing bins of F_ST (pairwise Wilcoxon rank sum p value < 2e−16 for each pair of bins).