Fig. 4: Increase in putatively deleterious variation in the GOC compared to the ENP fin whales.

Sample sizes: Gulf of California (GOC) N = 17, Eastern North Pacific (ENP) N = 27. A The GOC fin whales contain significantly fewer heterozygous and more homozygous derived genotypes in all four functional categories of variants. B Only putatively deleterious nonsynonymous alleles (DEL) are significantly elevated (two-tailed MWU test p < 0.001; Table S15) in the GOC compared with the ENP population. The ENP and GOC fin whales contain similar numbers of derived neutral alleles (SYN: synonymous and TOL: tolerated nonsynonymous), and putatively deleterious loss-of-function (LOF) alleles. For A and B, we used two-tailed Mann-Whitney U tests without multiple testing adjustment (the exact p values for the Mann–Whitney U tests are given in Table S15 in the supplementary material). In the boxplots, the notch indicates the median, and the boxes represent the 25th and 75th percentiles. The whiskers extend to data points no >1.5 * IQR (inter-quantile range) from the hinges and the points show outliers beyond the whiskers. C \({R}_{{XY}}\) and \({R}_{{XY}}^{2}\) statistics in GOC (X) and ENP (Y) populations. \({R}_{{XY}} > 1\) (dashed gray line) indicates a relative accumulation of the corresponding mutation category in the GOC population. Similarly, \({R}_{{XY}}^{2} > 1\) indicates relative accumulation of homozygous mutations. The 2x standard error based on the jackknife distribution is denoted as error bar, the circles in the center of the error bars represent the R_XY or R²_XY values. For C we used a two-tailed Z score test without multiple testing adjustment (R_XY Z-test significant values: p_SYN = 0.61, p_DEL = 0.02, p_TOL = 0.98, p_LOF = 0.88; R²_XY Z-test significant values: p_SYN = 0, p_DEL = 2.60e-142, p_TOL = 3.73e-234, p_LOF = 9.91e-17). Significance levels: ns, not significant; *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001. Source data are provided as a Source Data file.