A continent-wide high genetic load in African buffalo revealed by clines in the frequency of deleterious alleles, genetic hitchhiking and linkage disequilibrium

dc.contributor.authorVan Hooft, Pim
dc.contributor.authorGetz, Wayne Marcus
dc.contributor.authorGreyling, Barend J.
dc.contributor.authorZwaan, Bas
dc.contributor.authorBastos, Armanda D.S.
dc.date.accessioned2022-10-05T11:09:45Z
dc.date.available2022-10-05T11:09:45Z
dc.date.issued2021-12-09
dc.descriptionS1 Text. Allele size standardization.en_US
dc.descriptionS1 Table. Earlier reported associations of microsatellite alleles with low body condition and bovine tuberculosis (BTB) infection risk.en_US
dc.descriptionS2 Table. Allele size standardization.en_US
dc.descriptionS3 Table. Overview of alleles selected for analysis.en_US
dc.descriptionS4 Table. p-MDTA allele frequencies per population.en_US
dc.descriptionS5 Table. Per-locus Pearson correlation between ‘p-MDTA minus p-wildtype’ allele frequency difference and latitude, and between He and latitude.en_US
dc.descriptionS6 Table. He per locus per population.en_US
dc.descriptionS7 Table. Linkage disequilibrium per population.en_US
dc.descriptionS8 Table. He per locus in KNP, HiP and Addo NP.en_US
dc.descriptionS1 Fig. Increase of pairwise FST with geographic distance.en_US
dc.descriptionS2 Fig. Multilocus-He cline based on twelve microsatellites per locality.en_US
dc.descriptionS3 Fig. Multilocus-He cline based on seven microsatellites analysed in both East and southern Africa (microsatellite sets A, B and D) plus ABS010 and AGLA293.en_US
dc.descriptionS4 Fig. Correlation between per-locus southern/northern KNP He ratio and He-latitude Pearson correlation, based on 19 microsatellites.en_US
dc.description.abstractA high genetic load can negatively affect population viability and increase susceptibility to diseases and other environmental stressors. Prior microsatellite studies of two African buffalo (Syncerus caffer) populations in South Africa indicated substantial genome-wide genetic load due to high-frequency occurrence of deleterious alleles. The occurrence of these alleles, which negatively affect male body condition and bovine tuberculosis resistance, throughout most of the buffalo’s range were evaluated in this study. Using available microsatellite data (2–17 microsatellite loci) for 1676 animals from 34 localities (from 25˚S to 5˚N), we uncovered continent-wide frequency clines of microsatellite alleles associated with the aforementioned male traits. Frequencies decreased over a south-to-north latitude range (average per-locus Pearson r = -0.22). The frequency clines coincided with a multilocus-heterozygosity cline (adjusted R2 = 0.84), showing up to a 16% decrease in southern Africa compared to East Africa. Furthermore, continent-wide linkage disequilibrium (LD) at five linked locus pairs was detected, characterized by a high fraction of positive interlocus associations (0.66, 95% CI: 0.53, 0.77) between male-deleterious-trait-associated alleles. Our findings suggest continent-wide and genome-wide selection of male-deleterious alleles driven by an earlier observed sex-chromosomal meiotic drive system, resulting in frequency clines, reduced heterozygosity due to hitchhiking effects and extensive LD due to male-deleterious alleles co-occurring in haplotypes. The selection pressures involved must be high to prevent destruction of allele-frequency clines and haplotypes by LD decay. Since most buffalo populations are stable, these results indicate that natural mammal populations, depending on their genetic background, can withstand a high genetic load.en_US
dc.description.departmentZoology and Entomologyen_US
dc.description.librarianam2022en_US
dc.description.urihttp://www.plosone.orgen_US
dc.identifier.citationVan Hooft, P., Getz, W.M., Greyling, B.J., Zwaan, B. & Bastos, A.D.S. (2021) A continent-wide high genetic load in African buffalo revealed by clines in the frequency of deleterious alleles, genetic hitchhiking and linkage disequilibrium. PLoS ONE 16(12): e0259685. https://DOI.org/10.1371/journal.pone.0259685.en_US
dc.identifier.issn1932-6203 (online)
dc.identifier.other10.1371/journal.pone.0259685
dc.identifier.urihttps://repository.up.ac.za/handle/2263/87520
dc.language.isoenen_US
dc.publisherPublic Library of Scienceen_US
dc.rights© 2021 van Hooft et al. This is an open access article distributed under the terms of the Creative Commons Attribution License.en_US
dc.subjectGenetic loaden_US
dc.subjectClinesen_US
dc.subjectAllelesen_US
dc.subjectAfrican buffalo (Syncerus caffer)en_US
dc.titleA continent-wide high genetic load in African buffalo revealed by clines in the frequency of deleterious alleles, genetic hitchhiking and linkage disequilibriumen_US
dc.typeArticleen_US

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