Male-deleterious-trait associations
Alleles at the seventeen microsatellite loci (dataset A) have previously been shown to be significantly associated with two deleterious traits in male buffalo from southern KNP (i.e., south of the Olifants River): 1) low body condition and 2) BTB infection (van Hooft et al., 2018; van Hooft et al., 2014). BTB was present only in southern KNP at the time of sampling, except for three BTB-positive individuals in the north. Here we considered all microsatellite alleles from southern KNP, after excluding rare alleles (observed <15 times), as being potentially associated with male-deleterious traits when they had a higher frequency among low-body-condition, BTB-positive males than among high-body-condition, BTB-negative males. The sample sizes of these two male groups were similar, N = 35 and N = 39 respectively. As argued in an earlier study, comparison of allele frequencies between the two male groups probably constitutes a reliable indicator of association strength with male-deleterious traits (van Hooft et al., 2019). In contrast to that study, we did not make a further distinction among alleles according to their association with female-beneficial traits. Thus, as discussed elsewhere (van Hooft et al., 2019), we assumed two alleles per coding gene with the aforementioned sexually-antagonistic trait associations due to linkage with a second coding gene.
As in earlier studies, we made a distinction between two groups of microsatellites based on whether their alleles showed highest frequency in low or high body-condition individuals from southern KNP (van Hooft et al., 2018; van Hooft et al., 2019; van Hooft et al., 2014). From our first group of eight microsatellites (BM3517 , BM4028 ,ETH010 , ETH225 , INRA006 , INRA128 ,TGLA227 and TGLA263 ) we identified eight high-frequency alleles, one at each locus (frequency > 0.63 in all eight cases), that were associated with low body condition in both sexes and thus likely linked to sex-independent deleterious alleles (van Hooft et al., 2014). As in earlier studies, we refer to this group as the deleterious-effect-associated loci (DE loci) (van Hooft et al., 2018; van Hooft et al., 2019; van Hooft et al., 2014). From our second group of nine microsatellites (BM0719 , BM1824 , BM3205 ,CSSM019 , DIK020 , ILSTS026 , SPS115 ,TGLA057 and TGLA159 ) we identified a number of alleles (36 out of 53, excluding rare alleles with frequency <0.05) that showed sexually antagonistic associations. They were either associated with low body condition in males and high body condition in females (19 alleles) or vice versa (17 alleles). Alleles of this second group are assumed to be linked to haplotypes consisting of closely linked male-specific deleterious and female-specific beneficial alleles (van Hooft et al., 2019; van Hooft et al., 2014). As in earlier studies, we refer to the second group as the sexually-antagonistic-effect-associated loci (SAE loci) (van Hooft et al., 2018; van Hooft et al., 2019; van Hooft et al., 2014). The two microsatellite groups are largely independent because only two out of 72 DE-SAE locus pairs (INRA006 -ILSTS026 and TGLA057 -INRA128 ) are characterized by an interlocus distance <29 Megabase (Mb).