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

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dc.contributor.author Van Hooft, Pim
dc.contributor.author Getz, Wayne Marcus
dc.contributor.author Greyling, Barend J.
dc.contributor.author Zwaan, Bas
dc.contributor.author Bastos, Armanda D.S.
dc.date.accessioned 2022-10-05T11:09:45Z
dc.date.available 2022-10-05T11:09:45Z
dc.date.issued 2021-12-09
dc.description S1 Text. Allele size standardization. en_US
dc.description S1 Table. Earlier reported associations of microsatellite alleles with low body condition and bovine tuberculosis (BTB) infection risk. en_US
dc.description S2 Table. Allele size standardization. en_US
dc.description S3 Table. Overview of alleles selected for analysis. en_US
dc.description S4 Table. p-MDTA allele frequencies per population. en_US
dc.description S5 Table. Per-locus Pearson correlation between ‘p-MDTA minus p-wildtype’ allele frequency difference and latitude, and between He and latitude. en_US
dc.description S6 Table. He per locus per population. en_US
dc.description S7 Table. Linkage disequilibrium per population. en_US
dc.description S8 Table. He per locus in KNP, HiP and Addo NP. en_US
dc.description S1 Fig. Increase of pairwise FST with geographic distance. en_US
dc.description S2 Fig. Multilocus-He cline based on twelve microsatellites per locality. en_US
dc.description S3 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.description S4 Fig. Correlation between per-locus southern/northern KNP He ratio and He-latitude Pearson correlation, based on 19 microsatellites. en_US
dc.description.abstract A 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.department Zoology and Entomology en_US
dc.description.librarian am2022 en_US
dc.description.uri http://www.plosone.org en_US
dc.identifier.citation Van 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.issn 1932-6203 (online)
dc.identifier.other 10.1371/journal.pone.0259685
dc.identifier.uri https://repository.up.ac.za/handle/2263/87520
dc.language.iso en en_US
dc.publisher Public Library of Science en_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.subject Genetic load en_US
dc.subject Clines en_US
dc.subject Alleles en_US
dc.subject African buffalo (Syncerus caffer) en_US
dc.title A continent-wide high genetic load in African buffalo revealed by clines in the frequency of deleterious alleles, genetic hitchhiking and linkage disequilibrium en_US
dc.type Article en_US


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