Allele-frequency clines
We observed a highly significant allele-frequency cline between 24.9 °S
and 4.8 °N for both the DE and SAE alleles (P <0.0001;
DE loci: adjusted R 2 = 0.78, SAE loci: adjustedR 2 = 0.77; Figure 2, Table S2). The two slopes
were similar, differing by a factor of only 1.2. Predicted DE allele
frequencies decreased from 0.75 (95% CI: 0.72-0.77) at 24.9 °S to 0.46
(95% CI: 0.42-0.51) at 4.8 °N (a decrease of 0.0095 per degree
latitude). Predicted SAE allele frequencies decreased from 0.40 (95%
CI: 0.37-0.43) at 24.9 °S to 0.17 (95% CI: 0.13-0.20) at 4.8 °N (a
decrease of 0.0079 per degree latitude). When considered together, the
clines were significantly stronger than clines expected under a random
selection of alleles (DE loci: P = 0.081, SAE loci: P =
0.043, all loci: P = 0.013), which indicates that they cannot be
explained by genetic drift. The cline based on both the DE and SAE
alleles explained as much as 87% of the variation (adjustedR 2; Figure 3, Table S2). Predicted allele
frequencies decreased from 0.57 (95% CI: 0.55-0.59) at 24.9 °S to 0.29
(95% CI: 0.27-0.32) at 4.8 °N (a decrease of 0.0091 per degree
latitude). No clines were observed for the remaining alleles, which were
not associated with male-deleterious traits (negative adjustedR 2 values). Frequencies of DE alleles, but not
SAE alleles, in East and central Africa were significantly higher than
pooled frequencies based on a random selection of alleles (six DE
alleles: multiply the 1-sided P = 0.013 by 2, nine SAE alleles:
1-sided P = 0.70).
The populations from HiP and Nairobi NP deviated from the cline, showing
relatively low DE and SAE allele frequencies that were close to the
frequencies of the remaining microsatellite alleles. In HiP 18 out of 20
and in Nairobi NP 16 out of 20 of the non-pooled
male-deleterious-trait-associated alleles at the microsatellites
analysed in both populations showed relatively low frequencies compared
to nearby populations (HiP: compared with northern and southern KNP,
Nairobi NP: compared with other East African populations; Table S3). Low
frequencies were observed for most non-pooled alleles, which is not
expected under genetic drift (Wilcoxon signed rank exact test; HiP:P = 0.0010; Nairobi NP: P = 0.0083, Holm-Šidák correction
based on 12 possible focal populations: P = 0.095, Table S3). In
HiP, low frequencies have earlier been attributed to negative selection
(van Hooft et al., 2019).