Positive selection of deleterious alleles through interaction with a sex-ratio suppressor gene in African Buffalo: a plausible new mechanism for a high frequency anomaly

Abstract

Although generally rare, deleterious alleles can become common through genetic drift, hitchhiking or reductions in selective constraints. Here we present a possible new mechanism that explains the attainment of high frequencies of deleterious alleles in the African buffalo (Syncerus caffer) population of Kruger National Park, through positive selection of these alleles that is ultimately driven by a sex-ratio suppressor. We have previously shown that one in four Kruger buffalo has a Y-chromosome profile that, despite being associated with low body condition, appears to impart a relative reproductive advantage, and which is stably maintained through a sex-ratio suppressor. Apparently, this sex-ratio suppressor prevents fertility reduction that generally accompanies sex-ratio distortion. We hypothesize that this body-condition-associated reproductive advantage increases the fitness of alleles that negatively affect male body condition, causing genome-wide positive selection of these alleles. To investigate this we genotyped 459 buffalo using 17 autosomal microsatellites. By correlating heterozygosity with body condition (heterozygosity-fitness correlations), we found that most microsatellites were associated with one of two gene types: one with elevated frequencies of deleterious alleles that have a negative effect on body condition, irrespective of sex; the other with elevated frequencies of sexually antagonistic alleles that are negative for male body condition but positive for female body condition. Positive selection and a direct association with a Y-chromosomal sex-ratio suppressor are indicated, respectively, by allele clines and by relatively high numbers of homozygous deleterious alleles among sex-ratio suppressor carriers. This study, which employs novel statistical techniques to analyse heterozygosity-fitness correlations, is the first to demonstrate the abundance of sexually-antagonistic genes in a natural mammal population. It also has important implications for our understanding not only of the evolutionary and ecological dynamics of sex-ratio distorters and suppressors, but also of the functioning of deleterious and sexually-antagonistic alleles, and their impact on population viability.

Figure 1. Correlation between LBC-minus-HBC group difference in PL-H _e and baseline PL-H _e.

Baseline PL-H _e (expected heterozygosity per locus): PL-H _e of the pooled group of LBC and HBC individuals, error bars: 95% CI, vertical axis: 2(SE² _LBC + SE² _HBC)^0.5, horizontal axis: 2SE; Spearman rank correlation coefficient: ρ = 0.80, n _LBC = 230, n _HBC = 90, n _{microsatellites} = 17, P _{randomization between body condition classes} = 0.00034. Data are from southern Kruger. This figure shows that it was the microsatellites with low baseline PL-H _e (<0.56) that were associated with effects on body condition, i.e. a relatively large PL-H _e decrease in the LBC (low body condition) group relative to the HBC (high body condition) group. The positive correlation indicates that the HFCs (heterozygosity-fitness correlations) in southern Kruger can only be explained by LD between microsatellites and expressed genes.

Figure 2. Proportion of LBC individuals for different classes of single-locus genotypes.

Error bars: Wilson 95% CI, *: P _{randomization}<0.033 compared to each of the other genotype classes. Data are from southern Kruger and only from those microsatellites that contained a majority allele. The high numbers of observations are due to the fact that the bars represent single-locus genotypes (eight times number of individuals). The single-locus genotypes could be pooled across microsatellites because there was no significant LD. This figure shows that only the homozygous majority alleles were associated with LBC (low body condition). The proportion of LBC individuals was significantly higher among majority-allele homozygotes than among any other class of single-locus genotype. Furthermore, the positive association between effect size and allele frequency (i.e. only significant effect with majority alleles) suggests that the majority alleles are linked to alleles at expressed genes under positive selection.

Figure 3. Negative correlation between males and females in LBC-minus-HBC allele frequency difference.

Spearman rank correlation: ρ = −0.46, n _{microsatellites} = 9 (without majority allele), n _alleles = 53 excluding rare alleles (frequency <0.05) to prevent low sample size bias, n _{LBC females} = 138, n _{HBC females} = 48, n _{LBC males} = 92, n _{HBC males} = 42, P _{randomization between body condition classes per sex} = 0.0024. Data are from southern Kruger. The opposite sex effect (negative correlation), i.e. relatively high microsatellite allele frequencies in LBC (low body condition) males relative to HBC (high body condition) males and vice versa in females, indicates that the linked expressed gene alleles are sexually antagonistic.

Figure 4. Allele frequency difference between low ML-H _e and high ML-H _e group correlated against baseline allele frequency.

Low ML-H _e (multilocus expected heterozygosity) group: LBC males and HBC females (opposite body condition classes were combined because of sexual antagonism, see Figure 3), high ML-H _e group: HBC males and LBC females, baseline allele frequency: allele frequency among pooled LBC and HBC individuals of both sexes, Y-axis: allele frequencies were averaged across sexes, Spearman rank correlation coefficient: ρ = 0.32, n _{microsatellites} = 9 (without majority allele), n _alleles = 53 excluding rare alleles (frequency <0.05) to prevent low sample size bias, n _{LBC males} = 92, n _{HBC males} = 42, n _{LBC females} = 138, n _{HBC females} = 48, P _{randomization between body condition classes per sex} = 0.027. Data are from southern Kruger. The positive allele frequency differences at high baseline values indicate that most high-frequency alleles were associated with LBC (low body condition) in males and HBC (high body condition) in females. Furthermore, the positive correlation between effect size and baseline allele frequency suggests that most high-frequency alleles are linked to alleles at expressed genes under positive selection.

Figure 5. Allele clines in Kruger for two classes of microsatellites.

Allele frequencies were averaged across individuals and across microsatellites. Black diamonds: average majority allele frequency per herd, Z = 3.51, P _Stouffer-Z = 0.00044, n _{microsatellites} = 8, ρ = −0.60, n _herds = 30, n _individuals = 459; grey diamonds: average frequency per herd of the pooled three most frequent alleles per microsatellite (microsatellites without majority allele), Z = 3.58, P _Stouffer-Z = 0.00034, n _{microsatellites} = 9, ρ = −0.52, n _herds = 30, n _individuals = 459, latitude <−24: southern Kruger. Allele clines with increasing frequencies going from north to south were observed for all eight autosomal microsatellites with a majority allele and eight out of nine autosomal microsatellites without a majority allele. These allele clines are indicative of positive selection.

Figure 6. Proportion of males carrying Y-chromosomal haplotype 557 in relation to autosomal genotype.

Error bars: Wilson 95% CI. Data are from southern Kruger and from only those microsatellites that contained a majority allele. The high numbers of observations are due to the fact that the bars represent single-locus genotypes (eight times number of individuals). The single-locus genotypes could be pooled across microsatellites because there was no significant LD. This figure shows a direct association at the individual level between autosomal deleterious alleles (in LD with homozygous microsatellite majority alleles) and a Y-chromosomal sex-ratio suppressor (in LD with haplotype 557). The proportion of males carrying haplotype 557 was significantly higher among majority-allele homozygotes than among the other single-locus genotypes (P _{randomization} = 0.019).

Figure 7. A hypothesised mechanism that can explain positive selection of alleles deleterious to male body condition.

A sex-ratio (SR) suppressor, linked to Y-chromosomal haplotype 557, is triggered by low body condition. When active, it prevents a decrease in fertility that is due to SR distortion. Low body condition can be caused by a lack of resources during droughts and by disease. A SR distorter, resulting in a female-biased sex ratio , is assumed to be active in a large fraction of males. Body-condition associated suppressor activity can result in positive selection of deleterious alleles that negatively affect male body condition, provided that the positive effect on relative male fertility is larger than the negative effect on lifetime male mating success and that their effect on female relative fitness is not too negative. Thus there is a trade-off between increased relative fertility and decreased lifetime mating success. Positive selection can occur as long as the net reproductive success is higher for low-heterozygosity males than for high-heterozygosity males. The net reproductive success of low-heterozygosity males is positively correlated with the SR suppressor frequency (relatively high in southern Kruger, Figure S4) and with the negative effect of the SR distorter on male fertility. The latter effect is probably large considering the strong frequency fluctuations (up to a factor of five) of the SR suppressor between wet periods, when it is not active, and dry periods, when it is active .