Genetic variation, structure and dispersal among Cape buffalo populations from the Hluhluwe-Imfolozi and Kruger National Parks of South Africa

Genetic variation, structure and dispersal among Cape buffalo populations from the Hluhluwe-Imfolozi and Kruger National Parks of South Africa Barend Jacobus (Ben) Greyling Doctor of Philosophy (Zoology) Department of Zoology and Entomology Supervisor: Prof. Armanda Slager-Bastos Co-supervisor: Dr. Pim van Hooft 2007 The research reported on in this thesis is aimed at quantifying and qualifying, using a molecular genetics approach, some of the factors that influence the population dynamics of Cape buffalo (Syncerus caffer caffer) from the Kruger National Park (KNP) and Hluhluwe-imFolozi park (HiP) in South Africa. Prior to large-scale genotyping of animals sampled from these parks, a high-throughput, cost- and time-effective profiling system was developed. The system, based on a panel of 17 microsatellites (Msats), was found to be quite suitable for the intended application, since it uncovered substantial genetic variation, while exclusion probabilities were in excess of 0.999 and a random match probability of 6.5 x 10-17 was obtained. Inter-population level analyses revealed that the two populations were significantly differentiated (Msat data: FST = 0.159; mtDNA data: FST = 0.275), while little or no differentiation could be demonstrated among most herds and subpopulations. It seems that while drift has played a major role in divergence of the two populations, gene flow is the primary driving force behind the maintenance of genetic variation among herds and subpopulations. A striking feature was that HiP exhibited significant lower levels of genetic variation than KNP, which is reflected by the fact that a mere 4 haplotypes could be found in HiP compared to 34 identified in KNP. The absence of geographic partitioning and small genetic distances separating the haplotypes may be attributed to genetic contact between the respective populations in the distant past. The reduced levels of genetic variation in HiP may be the remnants of the rinderpest bottleneck. HiP also displayed signals of a population contraction, while KNP is in equilibrium and seems to have retained substantial levels of genetic variation. HiP also experienced a steady decline in genetic variation from 1986 to 2004, while sex-biased dispersal was less pronounced in HiP than in KNP, possibly due to the lack of mtDNA diversity and the small size of the park. The results presented here provide valuable baseline information for making conservation management decisions from a genetic point of view.Thesis (PhD (Zoology))--University of Pretoria, 2007.Zoology and Entomologyunrestricte

A natural gene drive system influences bovine tuberculosis susceptibility in African buffalo : possible implications for disease management

Bovine tuberculosis (BTB) is endemic to the African buffalo (Syncerus caffer) of HluhluweiMfolozi Park (HiP) and Kruger National Park, South Africa. In HiP, the disease has been actively managed since 1999 through a test-and-cull procedure targeting BTB-positive buffalo. Prior studies in Kruger showed associations between microsatellite alleles, BTB and body condition. A sex chromosomal meiotic drive, a form of natural gene drive, was hypothesized to be ultimately responsible. These associations indicate high-frequency occurrence of two types of male-deleterious alleles (or multiple-allele haplotypes). One type negatively affects body condition and BTB resistance in both sexes. The other type has sexually antagonistic effects: negative in males but positive in females. Here, we investigate whether a similar gene drive system is present in HiP buffalo, using 17 autosomal microsatellites and microsatellite-derived Y-chromosomal haplotypes from 401 individuals, culled in 2002– 2004. We show that the association between autosomal microsatellite alleles and BTB susceptibility detected in Kruger, is also present in HiP. Further, Y-haplotype frequency dynamics indicated that a sex chromosomal meiotic drive also occurred in HiP. BTB was associated with negative selection of male-deleterious alleles in HiP, unlike positive selection in Kruger. Birth sex ratios were female-biased. We attribute negative selection and female-biased sex ratios in HiP to the absence of a Y-chromosomal sex-ratio distorter. This distorter has been hypothesized to contribute to positive selection of male-deleterious alleles and male-biased birth sex ratios in Kruger. As previously shown in Kruger, microsatellite alleles were only associated with male-deleterious effects in individuals born after wet pre-birth years; a phenomenon attributed to epigenetic modification. We identified two additional allele types: male-specific deleterious and beneficial alleles, with no discernible effect on females. Finally, we discuss how our findings may be used for breeding disease-free buffalo and implementing BTB test-and-cull programs.S1 Text. Sex chromosomal meiotic drive can explain genome-wide high-frequency occurrence of male-deleterious alleles.S2 Text. Frequency differences of DEmajority and SAEpooled alleles between HiP and Kruger.S1 Fig. Map with sampling localities.S2 Fig. Monthly rainfall in HiP.S3 Fig. Annual rainfall in HiP in the period 1979–2004.S4 Fig. Frequencies of DEmajority and SAEpooled alleles in HiP compared with Kruger.S5 Fig. Difference in Amale-spec between SAEindvN alleles from Kruger observed and not observed in HIP.S6 Fig. Allele frequency differences between northern Kruger and HiP per SAE allele type.S1 Table. List of SAEpooled and DEmajority alleles.S2 Table. List of individual alleles at the DE microsatellite loci.S3 Table. List of individual alleles at the SAE microsatellite loci.S4 Table. List of individual alleles at the SAE microsatellite loci with unknown linkage.S5 Table. Logistic regression of BTB-infection risk for each sex separately.S6 Table. Logistic regression of BTB-infection risk for dry and wet pre-birth years separately.S7 Table. Logistic regression between sex (dependent) and age and 3yr-pre-birth rainfall.The US NSF Division of Environmental Biology (Grant number 0090323 awarded to Dr Wayne M. Getz) and the M3B2 DST/NRF SARChI Chair, University of Pretoria.http://www.plosone.orgam2019Mammal Research InstituteZoology and Entomolog

Genetic responsiveness of African buffalo to environmental stressors : a role for epigenetics in balancing autosomal and sex chromosome interactions?

In the African buffalo (Syncerus caffer) population of the Kruger National Park (South Africa) a primary sex-ratio distorter and a primary sex-ratio suppressor have been shown to occur on the Y chromosome. A subsequent autosomal microsatellite study indicated that two types of deleterious alleles with a negative effect on male body condition, but a positive effect on relative fitness when averaged across sexes and generations, occur genome-wide and at high frequencies in the same population. One type negatively affects body condition of both sexes, while the other acts antagonistically: it negatively affects male but positively affects female body condition. Here we show that high frequencies of male-deleterious alleles are attributable to Y-chromosomal distorter-suppressor pair activity and that these alleles are suppressed in individuals born after three dry pre-birth years, likely through epigenetic modification. Epigenetic suppression was indicated by statistical interactions between pre-birth rainfall, a proxy for parental body condition, and the phenotypic effect of homozygosity/heterozygosity status of microsatellites linked to male-deleterious alleles, while a role for the Y-chromosomal distortersuppressor pair was indicated by between-sex genetic differences among pre-dispersal calves. We argue that suppression of male-deleterious alleles results in negative frequencydependent selection of the Y distorter and suppressor; a prerequisite for a stable polymorphism of the Y distorter-suppressor pair. The Y distorter seems to be responsible for positive selection of male-deleterious alleles during resource-rich periods and the Y suppressor for positive selection of these alleles during resource-poor periods. Male-deleterious alleles were also associated with susceptibility to bovine tuberculosis, indicating that Kruger buffalo are sensitive to stressors such as diseases and droughts. We anticipate that future genetic studies on African buffalo will provide important new insights into gene fitness and epigenetic modification in the context of sex-ratio distortion and infectious disease dynamics.S1 Fig. Map with locations of the rainfall stations and the sampled herds.S2 Fig. Regression between fraction HBC among BTB-negative females and BTB prevalence per herd.S1 Table. Logistic regression southern females with body condition status as dependent variable (highest ranking model).S2 Table. Logistic regression southern males with body condition status as dependent variable (highest ranking model).S3 Table. Logistic regression southern females with BTB status as dependent variable (highest ranking model).S4 Table. Logistic regression southern males with BTB status as dependent variable (highest ranking model).S5 Table. Logistic regression northern females with body condition status as dependent variable (highest ranking model).S6 Table. Logistic regression southern males with BTB status as dependent variable (Evidence Ratio = 1.9).S7 Table. Logistic regression northern males with body condition status as dependent variable (Evidence Ratio = 2.1).S8 Table. Significance of the genetic-measure by annual-rainfall interaction per single year.S9 Table. Logistic regression northern females with body condition status as dependent variable (Evidence Ratio = 1.8).S10 Table. Results Hedges' g analyses (group differences with respect to MDLmale and MDLfemale).S1 Text. Consistency of the model outcomes.Laboratory analyses were supported by US NIH/NSF Ecology of Infectious Disease Grant GM83863 awarded to WMG.http://www.plosone.orgam2018Mammal Research InstituteZoology and Entomolog

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

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 bodycondition- 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 sexuallyantagonistic alleles, and their impact on population viability.US NIH/NSF Ecology of Infectious Disease Grant GM83863 awarded to WMG.http://www.plosone.orgam201

The design and evaluation of a genetic probe for Megasphaera elsdenii

M.Sc.The remarkable adaptability of the ruminant with respect to the variety of feeds of different composition which it can utilize is attributable to the presence, in the rumen, of a complex microbial population with diverse nutritional requirements and enzymatic activities. For economic reasons it is essential in feedlot practice to meet, as closely as possible, the energy requirements of ruminants being rounded off for slaughter purposes. This necessitates adapting the animals in the shortest possible time from predominantly pasture to high-concentrate diets, i.e. diets containing a high proportion of readily fermentable carbohydrates. However, a very rapid transition between these diets frequently results in a perturbation of the microbial population of the rumen. In particular, the sudden increase in the concentration of readily fermentable carbohydrates favours the proliferation of lactic acid-producing species, whereas the numbers of lactic acid-utilizing species increase more slowly. The resulting accumulation of lactic acid in the rumen causes a marked drop in pH which has an adverse effect on digestive processes in general. In mild cases, this may merely have a temporary negative effect on food intake and growth of the animal, but in the worst cases it may lead to ruminal stasis, cause permanent damage to the lining of the rumen wall and even result in death. Even though the incidence and severity of acute lactic acidosis may be restricted through careful diet formulation and inclusion of buffers and ionophore antibiotics in the diet, a small proportion of the animals brought into feedlots do not adapt readily to the highconcentrate diets and the performance of a larger proportion is probably negatively affected by sub-acute acidosis. The Nutritional Microbiology Section of the ARC Animal Nutrition and Animal Products Institute at Irene therefore embarked on the development of an alternative preventative and therapeutic treatment against lactic acidosis, viz. the administration of live, laboratory-grown cultures of highly-active lactate utilizers, specially selected for their potential for survival and multiplication in the rumen of animals on feedlot diets. By selective enrichment and extensive screening procedures a collection of phenotypically similar isolates of anaerobic, large, Gram-negative, acid-tolerant and ionophore-resistant cocci was obtained, which were presumptively identified as strains of Megasphaera elsdenii. These organisms utilized both L(+) and D(-) lactate and showed high specific growth rates on relatively inexpensive media even at low pH values, and they appeared to hold good promise for the intended application. In order to test the effectiveness of treatment of acidosis-compromised animals with cultures of these bacteria, information on their persistence in the rumen was required. Conventional microbiological counting methods were unsuitable for this purpose because of slowness and unsatisfactory specificity and precision. The present investigation deals primarily with the design and evaluation of a speciesspecific 16S rRNA probe for M elsdenii. It was intended for following the contribution of this species to the total microbial population of the rumen, as affected by the sudden exposure to high-concentrate diets. Furthermore, the phylogenetic relationship between the recent isolates, the type strain and previously sequenced strains of M elsdenii and M cerevisiae, as well as representatives of other rumen bacteria was investigated. In conclusion, the method for measuring the relative abundance of M elsdenii in rumen microbial populations with the aid of a custom-designed rRNA probe satisfactorily met the requirements of the proposed application

Development of a high-throughput microsatellite typing approach for forensic and population genetic analysis of wild and domestic African Bovini

Conservation management and forensic traceability of African buffalo and cattle rely on the timely provision of unbiased and accurate genetic information. An approach in which 17 cattle microsatellite markers are co-electrophoresed, following amplification in three core multiplex reactions was established for this purpose. Mean allelic richness per locus was 8.24 and 6.47, for buffalo and Bonsmara cattle, respectively, whilst an unbiased match probability of 6.5x10-17 and 1.03 x 10-16 was obtained for each. These results confirm the usefulness of this rapid, cost-effective typing approach for forensic, paternity and fine-scale genetic analyses of wild and domestic African Bovini tribe members