Habitat Selection by African Buffalo (Syncerus caffer) in Response to Landscape-Level Fluctuations in Water Availability on Two Temporal Scales

Seasonal fluctuations in water availability cause predictable changes in the profitability of habitats in tropical ecosystems, and animals evolve adaptive behavioural and spatial responses to these fluctuations. However, stochastic changes in the distribution and abundance of surface water between years can alter resource availability at a landscape scale, causing shifts in animal behaviour. In the Okavango Delta, Botswana, a flood-pulsed ecosystem, the volume of water entering the system doubled between 2008 and 2009, creating a sudden change in the landscape. We used African buffalo (Syncerus caffer) to test the hypotheses that seasonal habitat selection would be related to water availability, that increased floodwater levels would decrease forage abundance and affect habitat selection, and that this would decrease buffalo resting time, reduce reproductive success and decrease body condition. Buffalo selected contrasting seasonal habitats, using habitats far from permanent water during the rainy season and seasonally-flooded habitats close to permanent water during the early and late flood seasons. The 2009 water increase reduced forage availability in seasonally-flooded habitats, removing a resource buffer used by the buffalo during the late flood season, when resources were most limited. In response, buffalo used drier habitats in 2009, although there was no significant change in the time spent moving or resting, or daily distance moved. While their reproductive success decreased in 2009, body condition increased. A protracted period of high water levels could prove detrimental to herbivores, especially to smaller-bodied species that require high quality forage. Stochastic annual fluctuations in water levels, predicted to increase as a result of anthropogenically-induced climate change, are likely to have substantial impacts on the functioning of water-driven tropical ecosystems, affecting environmental conditions within protected areas. Buffer zones around critical seasonal resources are essential to allow animals to engage in compensatory behavioural and spatial mechanisms in response to changing environmental conditions.     

Pan-African Genetic Structure in the African Buffalo (Syncerus caffer): Investigating Intraspecific Divergence

The African buffalo (Syncerus caffer) exhibits extreme morphological variability, which has led to controversies about the validity and taxonomic status of the various recognized subspecies. The present study aims to clarify these by inferring the pan-African spatial distribution of genetic diversity, using a comprehensive set of mitochondrial D-loop sequences from across the entire range of the species. All analyses converged on the existence of two distinct lineages, corresponding to a group encompassing West and Central African populations and a group encompassing East and Southern African populations. The former is currently assigned to two to three subspecies (S. c. nanus, S. c. brachyceros, S. c. aequinoctialis) and the latter to a separate subspecies (S. c. caffer). Forty-two per cent of the total amount of genetic diversity is explained by the between-lineage component, with one to seventeen female migrants per generation inferred as consistent with the isolation-with-migration model. The two lineages diverged between 145 000 to 449 000 years ago, with strong indications for a population expansion in both lineages, as revealed by coalescent-based analyses, summary statistics and a star-like topology of the haplotype network for the S. c. caffer lineage. A Bayesian analysis identified the most probable historical migration routes, with the Cape buffalo undertaking successive colonization events from Eastern toward Southern Africa. Furthermore, our analyses indicate that, in the West-Central African lineage, the forest ecophenotype may be a derived form of the savanna ecophenotype and not vice versa, as has previously been proposed. The African buffalo most likely expanded and diverged in the late to middle Pleistocene from an ancestral population located around the current-day Central African Republic, adapting morphologically to colonize new habitats, hence developing the variety of ecophenotypes observed today.     

Basic haematological values in the African buffalo (Syncerus caffer caffer) and in the red buffalo (Syncerus caffer nanus)

Basic haematological values in 13 African buffaloes (Syncerus caffer caffer), 11 cows and 2 bulls, and in 2 red buffaloes (Syncerus caffer nanus), 1 bull and 1 cow, are reported. In the African buffalo, the erythrocyte count--mean 9.76 X 10(12) 1(-1)--ranged from 6.72 to 12.42 X 10(12) 1(-1), the haematocrit values--mean 0.391--varied from 0.32 to 0.47 and the haemoglobin content--mean 148.17--was in the range from 122.1 to 172.5 g 1(-1). For the red buffalo only individual values are given. In the African buffaloes, the leukocyte counts--mean 7.39 X 10(9) 1(-1)--ranging from 5.1 to 12.4 X 10(9) 1(-1) were slightly increased compared with man. For the red buffalo only individual values are reported. These values are compared with data abstracted from the literature for related buffalo species. The age-dependent decrease of erythrocyte counts and the age-dependent rise of the eosinophile proportion in the differential count are discussed.     

Habitat preferences of the secretive forest buffalo (Syncerus caffer nanus) in Central Africa

The forest buffalo Syncerus caffer nanus is one of the three subspecies of African buffalo inhabiting the rainforests of Western and Central Africa. Because of its secretive behaviour and main habitat (dense rainforests), there is little quantitative information on the habitat preferences of this buffalo. We present here the first data on the frequencies of this species along a habitat gradient ranging from clearings and rivers to forests, as well as the characteristics of the buffalo's resting places. We recorded information from a buffalo herd during the period January 2002–January 2004 in the Bai-Hokou area (Dzanga-Ndoki National Park, Central African Republic). Resting places were firstly compared with available habitat (i.e. resting vs. random sites) and, successively, comparisons were made between diurnal versus nocturnal and wet versus dry season resting places. Forest buffalos were found to be highly dependent on clearings, as well as on the more open forest stands, characterized by large trees and open canopy. Such preferences could be due to the tendency of the buffalos to rest all together; open patches are likely to facilitate social interactions between the members of the herd.     

Novel SNP Discovery in African Buffalo,Syncerus caffer,Using High-Throughput Sequencing

The African buffalo, Syncerus caffer, is one of the most abundant and ecologically important species of megafauna in the savannah ecosystem. It is an important prey species, as well as a host for a vast array of nematodes, pathogens and infectious diseases, such as bovine tuberculosis and corridor disease. Large-scale SNP discovery in this species would greatly facilitate further research into the area of host genetics and disease susceptibility, as well as provide a wealth of sequence information for other conservation and genomics studies. We sequenced pools of Cape buffalo DNA from a total of 9 animals, on an ABI SOLiD4 sequencer. The resulting short reads were mapped to the UMD3.1 Bos taurus genome assembly using both BWA and Bowtie software packages. A mean depth of 2.7× coverage over the mapped regions was obtained. Btau4 gene annotation was added to all SNPs identified within gene regions. Bowtie and BWA identified a maximum of 2,222,665 and 276,847 SNPs within the buffalo respectively, depending on analysis method. A panel of 173 SNPs was validated by fluorescent genotyping in 87 individuals. 27 SNPs failed to amplify, and of the remaining 146 SNPs, 43–54% of the Bowtie SNPs and 57–58% of the BWA SNPs were confirmed as polymorphic. dN/dS ratios found no evidence of positive selection, and although there were genes that appeared to be under negative selection, these were more likely to be slowly evolving house-keeping genes.     

Evaluation of a Real-Time PCR Test for the Detection and Discrimination of Theileria Species in the African Buffalo (Syncerus caffer)

A quantitative real-time PCR (qPCR) assay based on the cox III gene was evaluated for the simultaneous detection and discrimination of Theileria species in buffalo and cattle blood samples from South Africa and Mozambique using melting curve analysis. The results obtained were compared to those of the reverse line blot (RLB) hybridization assay for the simultaneous detection and differentiation of Theileria spp. in mixed infections, and to the 18S rRNA qPCR assay results for the specific detection of Theileria parva. Theileria parva, Theileria sp. (buffalo), Theileria taurotragi, Theileria buffeli and Theileria mutans were detected by the cox III assay. Theileria velifera was not detected from any of the samples analysed. Seventeen percent of the samples had non-species specific melting peaks and 4.5% of the samples were negative or below the detection limit of the assay. The cox III assay identified more T. parva and Theileria sp. (buffalo) positive samples than the RLB assay, and also detected more T. parva infections than the 18S assay. However, only a small number of samples were positive for the benign Theileria spp. To our knowledge T. taurotragi has never been identified from the African buffalo, its identification in some samples by the qPCR assay was unexpected.Because of these discrepancies in the results, cox III qPCR products were cloned and sequenced. Sequence analysis indicated extensive inter- and intra-species variations in the probe target regions of the cox III gene sequences of the benign Theileria spp. and therefore explains their low detection. The cox III assay is specific for the detection of T. parva infections in cattle and buffalo. Sequence data generated from this study can be used for the development of a more inclusive assay for detection and differentiation of all variants of the mildly pathogenic and benign Theileria spp. of buffalo and cattle.     

Food selection and competition in the East African buffalo (Syncerus caffer Sparrman)

Rumen samples collected at different times of the year from buffalo in the Serengeti, were analysed with respect to proportions of plant parts present. Buffalo were almost exclusive grazers and were capable of selecting for grass leaf. At certain times of year it was the dominant food intake component but declined to only 11% of the diet by the end of the dry season. The amount of leaf in the diet was determined by the amount of rainfall which governed the growth of the food grasses. Experimental preference tests with tame animals indicated that they were capable of selecting for different grass species. The preferences were, however, for those species with a higher leaf: stem ratio. The mechanism of selection is discussed. The function of the behavioural selection appeared to be concerned with maximizing the nutrient quality of the food requirements. It appeared that ecological separation had evolved through interspecific competition.     

Neutralising antibodies to parainfluenza 3 virus in African wildlife, with special reference to the Cape buffalo (Syncerus caffer).

As part of a study to assess the prevalence of common viral agents in African wildlife, nearly 3,300 sera from 44 different wild species, from eight African countries, have been examined for neutralising antibodies to parainfluenza 3 (PI3) virus. Antibody was demonstrated in 20 of the 44 species examined, including seven species not previously reported as sero-positive. Sera were collected between 1963 and 1977 and results indicated that infection has been widespread for a considerable time. The high prevalence of antibody, and the range of titres, to PI3 virus found in free-living populations of buffalo suggest that this species is particularly important as a reservoir of infection in the wild.     

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.     

Palatability factors and nutritive values of the food of buffaloes (Syncerus caffer) in Uganda

The food preferences of tame buffaloes grazing different vegetation types were recorded. The effects of fire and rainfall were investigated. By initiating a new growth cycle, fire altered the food habits of large herbivores and also the distribution of small mammals. Seasonal variations in the effect of rainfall on plant growth explains why preferences did not change in proportion to precipitation. The more important grasses were collected and their parts analysed physically and chemically. Their stem to leaf ratio is considered to have influenced the species eaten by coarse grazers such as buffalo. A broad correlation was obtained between buffalo preferences and the percentage green leaf of Hyparrhenia filipendula and Themeda triandra. This correlation was improved when preferences were compared with the number of grams green leaf carbohydrate per 100 g dry grass. There was a negative response to the silica present in dead leaves, but stem fibre appeared to have little effect on preferences. A grazing animal experiences a combination of attractants and repellants, i.e. green leaf carbohydrate and protein less stem fibre and dead leaf silica. Other palatability factors were noted, in particular tannins and oils in grasses of the tribe Andropogoneae. These may act as repellants, possibly only when the grazing animal has alternative vegetation from which to choose. The mineral content of grasses appeared to be adequate and calcium and phosphorus were present in about the required proportions. The observations support the belief that selective grazing enables a herbivore to consume a diet of significantly higher nutritive value than that of the average sward. Browsing and new growth after fire help compensate for the low nutritive value of pasture during the dry season. The nutritive value of the diet is considered to be the proximal factor in the seasonal cycle of reproduction of the buffalo and probably the ultimate factor in the reproduction of certain other ungulates and rodents.     

Immobilization of African buffaloes (Syncerus caffer coffer) in large numbers for veterinary research

Four hundred and eleven African buffaloes were immobilized with etorphine hydrochloride (M99, Reckitts) and sampled under difficult conditions in North Western Botswana. The buffaloes were darted from a helicopter in 36 days. 584 darts were fired giving a success rate of 70-5%. Various age groups in three separate buffalo populations were included. The technique and difficulties encountered when working from a helicopter are described. Mechanical failure of the darting equipment was negligible. A breakdown of the costs involved is given and a comparison made with similar work carried out solely from land vehicles.     

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.     

Ecological cues, gestation length, and birth timing in African buffalo (Syncerus caffer)

We examined annual variation in the timing of conception andparturition in the African buffalo (Syncerus caffer) and thesynchrony of birth timing with resource cues, using 8 yearsof monthly birth, rainfall, and vegetation data, measured asNormalized Difference Vegetation Index (NDVI). Monthly birthshad the strongest significant correlations with NDVI and rainfalllevels 12 and 13 months in the past, respectively. In addition,the synchrony of current year births corresponds most stronglyto the synchrony of the previous year's NDVI distribution. Becausethe gestation period of buffalo has been estimated to be around11 months, these findings suggest that improved protein levels,occurring approximately a month after the first green flushof the wet season, are either a trigger for conception or conceptionhas evolved to be synchronous with correlated environmentalcues that ensure females enter a period of peak body conditionaround the time of conception and/or parturition. With a gestationperiod of approximately 340 days, parturition occurs to takeadvantage of the period when forage has its highest proteincontent. A comparative analysis of gestation periods withinthe subfamily Bovinae indicates that African buffalo have aprotracted gestation for their body size, which we suggest isan adaptation to their seasonal environment. We also found thatinterannual variation in the birth distribution suggests a degreeof plasticity in the date of conception, and variation in thenumber of calves born each year suggest further synchrony ata timescale longer than a single year.