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).