Applicability of bovine microsatellite markers for population genetic studies on African buffalo (Syncerus caffer)

The applicability of bovine autosomal microsatellite markers for population genetic studies on African buffalo was investigated. A total of 168 microsatellite markers were tested for PCR amplification on a test panel of seven African buffalo. Amplification was observed for 139 markers (83%), and 101 markers were studied further with 91 (90%) being polymorphic. The mean number of alleles per marker was 5.0 (SE = 0.2) and the mean heterozygosity per marker was 0.61 (SE = 0.03). Considering the overall high level of polymorphism, it was concluded that most bovine microsatellite markers are applicable in African buffalo.     

A reliable body condition scoring technique for estimating condition in African buffalo

Evaluating animal body condition is a necessary component of many ecological studies. Although many methods for assessing animal body condition have been developed, relatively few can be used for estimating condition on live animals. Noninvasive body condition scoring techniques have been developed for assessing condition in livestock and more recently such techniques have been applied to wild ungulates. In this study, we examined the reliability of a body condition scoring technique for assessing condition in African buffalo (Syncerus caffer caffer). We compared a body condition score (BCS) based on visual assessment and manual palpation of an animal’s body to two standard metrics of condition widely used in mammals: kidney fat index (KFI) and haematocrit (HCT). Across all buffalo, BCS was significantly and positively correlated with both KFI and HCT. For HCT, this pattern was observed among adults, juveniles, males and females; and in the wet season but not in the dry season. For KFI, BCS was significantly and positively correlated with KFI among adults, juveniles and males, but not in females. Overall, our results suggest that the BCS technique can serve as a useful method for estimating body condition in buffalo.     

Population structure of African buffalo inferred from mtDNA sequences and microsatellite loci: high variation but low differentiation

The African buffalo ( Syncerus caffer ) is widespread throughout sub-Saharan Africa and is found in most major vegetation types, wherever permanent sources of water are available, making it physically able to disperse through a wide range of habitats. Despite this, the buffalo has been assumed to be strongly philopatric and to form large aggregations that remain within separate home ranges with little interchange between units, but the level of differentiation within the species is unknown. Genetic differences between populations were assessed using mitochondrial DNA (control region) sequence data and analysis of variation at six microsatellite loci among 11 localities in eastern and southern Africa. High levels of genetic variability were found, suggesting that reported severe population bottlenecks due to outbreak of rinderpest during the last century did not strongly reduce the genetic variability within the species. The high level of genetic variation within the species was found to be evenly distributed among populations and only at the continental level were we able to consistently detect significant differentiation, contrasting with the assumed philopatric behaviour of the buffalo. Results of mtDNA and microsatellite data were found to be congruent, disagreeing with the alleged male-biased dispersal. We propose that the observed pattern of the distribution of genetic variation between buffalo populations at the regional level can be caused by fragmentation of a previous panmictic population due to human activity, and at the continental level, reflects an effect of geographical distance between populations.     

Microsatellite analysis of genetic diversity in African buffalo (Syncerus caffer) populations throughout Africa

Genetic diversity in nine African buffalo (Syncerus caffer) populations throughout Africa was analysed with 14 microsatellites to study the effects of rinderpest epidemics and habitat fragmentation during the 20th century. A gradient of declining expected heterozygosity was observed among populations in Save Valley Conservancy (Zimbabwe), and northern and southern Kruger National Park (South Africa). This was explained by a high mortality in northern Kruger National Park during the rinderpest pandemic at the end of the 19th century followed by recolonization from neighbouring populations, resulting in intermediate heterozygosity levels in northern Kruger National Park. In other populations expected heterozygosity was very high, indicating that rinderpest and recent habitat fragmentation had a limited effect on genetic diversity. From expected heterozygosity, estimates of long-term effective population size were derived. Migration rates among populations in eastern and southern Africa were very high, as shown by a weak isolation by distance and significant correlation in allele frequencies between populations. However, there were indications that dry habitats could limit migration. Genetic distances within buffalo in central Africa were relatively large, supporting their status as distinct subspecies. Finally, it was observed that the higher polymorphic microsatellites were less sensitive at detecting isolation by distance and differences in Ne, which may be a result of the high mutation pressure at these loci.     

Phylogeography of the African buffalo based on mitochondrial and Y-chromosomal loci: Pleistocene origin and population expansion of the Cape buffalo subspecies

Population genetics and phylogeography of the African buffalo (Syncerus caffer) are inferred from genetic diversity at mitochondrial D-loop hypervariable region I sequences and a Y-chromosomal microsatellite. Three buffalo subspecies from different parts of Africa are included. Nucleotide diversity of the subspecies Cape buffalo at hypervariable region I is high, with little differentiation between populations. A mutation rate of 13-18% substitutions/million years is estimated for hypervariable region I. The nucleotide diversity indicates an estimated female effective population size of 17 000-32 000 individuals. Both mitochondrial and Y-chromosomal diversity are considerably higher in buffalo from central and southwestern Africa than in Cape buffalo, for which several explanations are hypothesized. There are several indications that there was a late middle to late Pleistocene population expansion in Cape buffalo. This also seems to be the period in which Cape buffalo evolved as a separate subspecies, according to the net sequence divergence with the other subspecies. These two observations are in agreement with the hypothesis of a rapid evolution of Cape buffalo based on fossil data. Additionally, there appears to have been a population expansion from eastern to southern Africa, which may be related to vegetation changes. However, as alternative explanations are also possible, further analyses with autosomal loci are needed.     

The utility of normalized difference vegetation index for predicting African buffalo forage quality

Many studies of mammalian herbivores have employed remotely sensed vegetation greenness, in the form of Normalized Difference Vegetation Index (NDVI) as a proxy for forage quality. The assumption that reflected greenness represents forage quality often goes untested, and limited data exist on the relationships between remotely sensed and traditional forage nutrient indicators. We provide the first study connecting NDVI and forage nutrient indicators within a free-ranging African herbivore ecosystem. We examined the relationships between fecal nutrient levels (nitrogen and phosphorus), forage nutrient levels, body condition, and NDVI for African buffalo (Syncerus caffer) in a South African savanna ecosystem over a 2-year period (2001 and 2002). We used an information-theoretic approach to rank models of fecal nitrogen (N_f) and phosphorus (P_f) as functions of geology, season, and NDVI in each year separately. For each year, the highest ranked models for N_f accounted for 61% and 65% of the observed variance, and these models included geology, season, and NDVI. The top-ranked model for P_f in 2001, although capturing 54% of the variability, did not include NDVI. In 2002, we could not identify a top ranking model for phosphorus (i.e., all models were within 2 AIC_c of each other). Body condition was most highly correlated ( ; P ≤ 0.001) with NDVI at a 1 month time lag and with N_f at a 3 months time lag ( ; P ≤ 0.001), but was not significantly correlated with P_f. Our findings suggest that NDVI can be used to index nitrogen content of forage and is correlated with improved body condition in African buffalo. Thus, NDVI provides a useful means to assess forage quality where crude protein is a limiting resource. We found that NDVI accounted for more than a seasonal effect, and in a system where standing biomass may be high but of low quality, understanding available nutrients is useful for management. © 2012 The Wildlife Society.     

Genetic diversity and isolation in African Buffalo (Syncerus caffer)

We studied genetic diversity in 58 buffalo from the Kruger National Park (KNP) and Willem Pretorius Nature Reserve (WPNR). Thirty-three protein-encoding loci were resolved; three were polymorphic. Average heterozygosity (H) values did not differ substantially between adult and sub-adult animals from the KNP (2.65 and 2.89%, respectively), but were lower in animals from the isolated WPNR herd (H = 1.48% and only 3% polymorphic loci compared to 9.1%). Representative levels of genetic diversity exist in the large but disease-carrying herd, whereas the smaller disease-free herds available for translocations appear less polymorphic.     

Effects of Chemical Immobilization on Survival of African Buffalo in the Kruger National Park

ABSTRACT Capturing, immobilizing, and fitting radiocollars are common practices in studies of large mammals, but success is based on the assumptions that captured animals are representative of the rest of the population and that the capture procedure has negligible effects. We estimated effects of chemical immobilization on mortality rates of African buffalo (Syncerus caffer) in the Kruger National Park, South Africa. We used a Cox proportional hazards approach to test for differences in mortality among age, sex, and capture classes of repeatedly captured radiocollared buffalo. Capture variables did not improve model fit and the Cox regression did not indicate increased risk of death for captured individuals up to 90 days postcapture [exp (β) = 1.07]. Estimated confidence intervals, however, span from a halving to a doubling of the mortality rate (95% CI = 0.56–2.02). Therefore, capture did not influence survival of captured individuals using data on 875 captures over a 5-year period. Consequently, long-term research projects on African buffalo involving immobilization, such as associated with research on bovine tuberculosis, should result in minimal capture mortality, but monitoring of possible effects should continue.     

Genetic structure of African buffalo herds based on variation at the mitochondrial D-loop and autosomal microsatellite loci: Evidence for male-biased gene flow

Sexual differences in herding behaviour ofAfrican buffalo (Syncerus caffer) werestudied by analysing at the herd levelmitochondrial D-loop hypervariable region I andfourteen autosomal microsatellites. Three herdsfrom Arusha National Park in Tanzania wereanalysed with mtDNA and five herds from KrugerNational Park in South Africa with mtDNA andmicrosatellites. Significant mtDNAdifferentiation was observed among herds inArusha NP (F_ST = 0.12, based on haplotypefrequencies). Assignment tests withmicrosatellite data from Kruger NP showed thatmost frequent migration between herds is bymales two years. This was confirmed bytests for herd differentiation and analyseswith Lynch and Ritland's relatedness estimator.Within a herd, males younger than two years andfemales showed a higher relationship through acommon father rather than a common mother,indicating that female herd members mate withonly a few dominant males. This in turnsuggests a female:male sex ratio larger than5:1. The migration rate per generation betweenherds was estimated to be 5–2% for femalesand close to 100% for males. Finally, theimplications for the management of buffalopopulations are being discussed.     

Current population estimate and distribution of the African buffalo in Chebera Churchura National Park,Ethiopia

An investigation into the population status and distribution of the African buffalo (Syncerus caffer Sparrman, 1779) in Chebera Churchura National Park, Ethiopia, was carried out during the wet and dry seasons of 2012–2015. This study tested the hypothesis that buffalo would demonstrate seasonal habitat preferences and changes in population density. Sample counts were carried out in an area of 1215 km². The estimated buffalo population was 5193 individuals, with the population density of 4.3/km². The population showed an increase from 2617 to 5194 individuals during 2006–2015. Males comprised 42.6%, while females 46.7% of the population. Age structure was dominated by adults, which constituted 52.5% of the total population. Subadults comprised 24.3% and young 12.4% of the population. Larger herds of up to 30 individuals were observed during the wet season, and smaller herds of a minimum of four individuals were seen during the dry season. The mean herd sizes during the wet and dry seasons were 29.59 and 16.95, respectively. They were observed more in the riverine vegetation types during the dry season. Of the total, 57.6% utilized riverine habitat during the dry season, whereas 39.8% used this habitat during the wet season. Relative abundance of food sources, green vegetation cover and availability of water were the major factors governing their distribution in the present study area.     

Diurnal activity budget of African buffalo (Syncerus caffer Sparrman, 1779) in Chebera Churchura National Park,Ethiopia

One of the fundamental questions in animal ecology concerns the activity pattern of animals and the environmental and intrinsic factors that influence such dynamics. This study tested the hypotheses that activity time budgets of the African buffalo appeared to vary by season and times of day and predicted that buffalo would express unequal proportion of time for different activity patterns during the wet and dry seasons in Chebera Churchura National Park (CCNP). An investigation on the diurnal activity budget of the African buffalo was carried out during the wet and dry seasons of 2012–2014 in the Chebera Churchura National Park, Ethiopia, using focal‐animal sampling method. Buffalo spent a greater proportion of the time in feeding and resting/ruminating activities in both the wet and dry seasons. Feeding and resting (lying down and standing) were the predominant activities (87.14% of the diurnal active period), 48.95% time spent feeding during the dry season and 44.91% during the wet season. There was a significant decrease in feeding and an increase in resting from dry seasons to wet seasons. Daytime grazing and resting periods during the wet season were estimated to be 5.39 h and 4.98 h, respectively. Morning and the late afternoon activity peaks were more pronounced during the dry season than the wet season. Therefore, feeding and resting time was influenced by the time of day and the seasons. But there were no significant difference in time allocation for other activities in both the wet and dry seasons. The study has implications for understanding animal activity budget across species, particularly relationships between temperature and season.     

Demographics and parasites of African buffalo (Syncerus caffer Sparrman, 1779) in Ruaha National Park,Tanzania

The number of African buffaloes (Syncerus caffer Sparrman, 1779) inhabiting Ruaha National Park, Tanzania, is thought to be declining, but little data exist to determine whether the population is actually in decline. As an initial phase of collecting population data, we conducted demographic surveys, faecal egg counts and gastrointestinal parasite identification in Ruaha's buffalo herds in September 2011 and 2013. Most herds encountered in the two surveys appeared to be in good health, but with fewer calves in 2013 compared with 2011. The herd‐level body condition score was positively associated with the number of calves per 100 cows after adjusting for year, and the lower number of offspring in 2013 could possibly be associated with a below average rainfall in the 2012–2013 rainy season. Mean herd‐level egg counts ranged from 83 to 140 and from 28 to 113 eggs per g faeces in 2011 and 2013, respectively. Haemonchus, Nematodirus, Cooperia and Oesophagostomum spp., as well as coccidian oocysts, were detected in the population. Monitoring herd demographics and baseline health parameters over time will provide insight into population performance, increase the understanding of population stressors and contribute to buffalo conservation within Ruaha National Park and other protected areas of Africa.     

Population structure and ecology of the African buffalo (Syncerus caffer Sparrman, 1779) in Chebera Churchura National Park,Ethiopia

An investigation of population structure and ecology of the African buffalo (Syncerus caffer Sparrman, 1779) was carried out in the Chebera Churchura National Park, Ethiopia during the wet and dry seasons of 2005–2006. Sample counts of African buffaloes were carried out in an area of 1,215 km². The estimated population of buffalo was 2,617 individuals. Males comprised 35.0%, while females 52.8% of the population. The remaining 12% of the population was young of both sexes and of all ages of unknown sex. It was difficult to categorize the young into male and female in the field, as their primary sexual characteristics were not easily visible. Male to female sex ratio was 1.00 : 1.51. Age structure was dominated by adults, which constituted 72.06% of the total population. Subadults comprised 22.02%, and young accounted for 5.9% of the population. Larger herds of up to 27 individuals were observed during the wet season and smaller herds of eight individuals during the dry season. The mean herd size during wet and dry seasons was 24.81 and 7.77, respectively. The African buffaloes were distributed in four habitat types such as grasslands, woodlands, montane forests and riverine habitat in the study area. They were observed more in the riverine vegetation types during the dry season. Relative abundance of food resources, green vegetation cover and water availability in the area were the major factors governing their distribution in the present study area. They spent a greater proportion of the time in feeding and resting/ruminating activities. On the average, 49.7% of the daytime was spent in feeding, and 38.75% of the day on resting (lying down and standing). Morning and the late afternoon activity peaks were more pronounced during the dry season than the wet season.     

Necropsy and parasitic findings from an adult forest buffalo (Syncerus caffer nanus) found dead in the Republic of Congo

A field necropsy was performed on a recently dead adult forest buffalo, Syncerus caffer nanus, found in the Nouabalé-Ndoki National Park, Republic of Congo. Based on the gross and histological lesions, the cause of death was determined to be conspecific fighting. Ectoparasites collected from this forest buffalo were Amblyomma sp. (larvae) and Rhipicephalus ziemanni Neumann. Endoparasites collected included a paramphistomid trematode, Carmyerius gregarius, and oocysts of Eimeria spp., paramphistomid eggs (presumably from C. gregarius), metastrongylid lungworm larvae, and strongylid eggs. Parasitic findings from this forest buffalo were compared to previous reports from savanna and forest buffalo.     

Ancient diversity and geographical sub-structuring in African buffalo Theileria parva populations revealed through metagenetic analysis of antigen-encoding loci

An infection and treatment protocol involving infection with a mixture of three parasite isolates and simultaneous treatment with oxytetracycline is currently used to vaccinate cattle against Theileria parva. While vaccination results in high levels of protection in some regions, little or no protection is observed in areas where animals are challenged predominantly by parasites of buffalo origin. A previous study involving sequencing of two antigen-encoding genes from a series of parasite isolates indicated that this is associated with greater antigenic diversity in buffalo-derived T. parva. The current study set out to extend these analyses by applying high-throughput sequencing to ex vivo samples from naturally infected buffalo to determine the extent of diversity in a set of antigen-encoding genes. Samples from two populations of buffalo, one in Kenya and the other in South Africa, were examined to investigate the effect of geographical distance on the nature of sequence diversity. The results revealed a number of significant findings. First, there was a variable degree of nucleotide sequence diversity in all gene segments examined, with the percentage of polymorphic nucleotides ranging from 10% to 69%. Second, large numbers of allelic variants of each gene were found in individual animals, indicating multiple infection events. Third, despite the observed diversity in nucleotide sequences, several of the gene products had highly conserved amino acid sequences, and thus represent potential candidates for vaccine development. Fourth, although compelling evidence for population differentiation between the Kenyan and South African T. parva parasites was identified, analysis of molecular variance for each gene revealed that the majority of the underlying nucleotide sequence polymorphism was common to both areas, indicating that much of this aspect of genetic variation in the parasite population arose prior to geographic separation.     

Effects of gonadotrophins, growth hormone, and activin A on enzymatically isolated follicle growth, oocyte chromatin organization, and steroid secretion

So far, standard follicle culture systems can produce blastocyst from less than 40% of the in vitro matured oocytes compared to over 70% in the in vivo counterpart. Because the capacity for embryonic development is strictly associated with the terminal stage of oocyte growth, the nuclear maturity status of the in vitro grown oocyte was the subject of this study. Mouse early preantral follicles (100-130 microm) and early antral follicles (170-200 microm) isolated enzymatically were cultured for 12 and 4 days, respectively, in a collagen-free dish. The serum-based media were supplemented with either 100 mIU/ml FSH (FSH only); 100 mIU/ml FSH + 10 mIU/ml LH (FSH-LH); 100 mIU/ml FSH + 1 mIU/ml GH (FSH-GH) or 100 mIU/ml FSH + 100 ng/ml activin A (FSH-AA). Follicle survival was highest in follicle stimulating hormone (FSH)-AA group in both cultured preantral (91.8%) and antral follicles (82.7%). Survival rates in the other groups ranged between 48% (FSH only, preantral follicle culture) and 78.7% (FSH only, antral follicle culture). Estradiol and progesterone were undetectable in medium lacking gonadotrophins while AA supplementation in synergy with FSH caused increased estradiol secretion and a simultaneously lowered progesterone secretion. Chromatin configuration of oocytes from surviving follicles at the end of culture revealed that there were twice more developmentally incompetent non-surrounded nucleolus (NSN) oocytes (>65%) than the competent surrounded nucleolus (SN) oocytes (<34%). We conclude that the present standard follicle culture system does not produce optimum proportion of developmentally competent oocytes.