Fig. 5: Evidence for coupling within and among chromosomes in the Large-Z effect.
A Density plot of cline slope and center for all ancestry informative variants on the Z chromosome showing hotspots of cline convergence (indicated with white circles); colors represent the density of convergent cline values (number of neighboring points). Points representing variants were downsampled 10-to-1 for visualization purposes; Supplementary Fig. S17 shows non-downsampled version. B Density plots showing the distribution of variants belonging to three hotspots from panel A along the Z chromosome. Arrows from Panel A to B indicate the distribution of SNPs from each hotspot. The green, blue and red rectangles show regions enriched for variants with convergent cline parameters corresponding to hotspots in panel A, a grey rectangle indicates the PAR, and the recent stratum is shown in pink. C Coupling coefficients for 100 kb windows across the Z chromosome, with a black line indicating the smoothed coupling coefficient values. D Cline center across the Z chromosome. E Number of heterospecific recombination events per 100 kb window across the Z chromosome. F Genome-wide intrachromosomal coupling with C. viridis Z-linked interchromosomal LD. The outer track shows mean cline slope over 100 kb windows, and the inner track displays the coupling coefficient over 100 kb windows and a smoothed coupling coefficient line in black. Interchromosomal conspecific LD between the Z and autosomes (above threshold of R2 > 0.7) is shown with green lines at the center of the circle. G Distribution of cline center (left panel) and cline slope (center panel) for variants in C. viridis Z linked conspecific LD and high-FST variants not in LD (for both panels: n = 24,260 for variants in LD and n = 385,351 for uncorrelated variants), along with the distribution of coupling coefficients (right panel) for windows containing at least one variant in C. viridis Z linked conspecific LD compared to windows containing highly differentiated variants without variants in LD (n = 470 and n = 9237, respectively). Boxplots show the median (center line), interquartile range (box), and whiskers extending to the furthest point within 1.5×IQR (outliers not shown) and p-values were obtained from a Wilcoxon test (***p < 0.001).
