Isotopic signatures of methane emissions from tropical fires, agriculture and wetlands: the MOYA and ZWAMPS flights

We report methane isotopologue data from aircraft and ground measurements in Africa and South America. Aircraft campaigns sampled strong methane fluxes over tropical papyrus wetlands in the Nile, Congo and Zambezi basins, herbaceous wetlands in Bolivian southern Amazonia, and over fires in African woodland, cropland and savannah grassland. Measured methane δ 13 C CH 4 isotopic signatures were in the range −55 to −49‰ for emissions from equatorial Nile wetlands and agricultural areas, but widely −60 ± 1‰ from Upper Congo and Zambezi wetlands. Very similar δ 13 C CH 4 signatures were measured over the Amazonian wetlands of NE Bolivia (around −59‰) and the overall δ 13 C CH 4 signature from outer tropical wetlands in the southern Upper Congo and Upper Amazon drainage plotted together was −59 ± 2‰. These results were more negative than expected. For African cattle, δ 13 C CH 4 values were around −60 to −50‰. Isotopic ratios in methane emitted by tropical fires depended on the C3 : C4 ratio of the biomass fuel. In smoke from tropical C3 dry forest fires in Senegal, δ 13 C CH 4 values were around −28‰. By contrast, African C4 tropical grass fire δ 13 C CH 4 values were −16 to −12‰. Methane from urban landfills in Zambia and Zimbabwe, which have frequent waste fires, had δ 13 C CH 4 around −37 to −36‰. These new isotopic values help improve isotopic constraints on global methane budget models because atmospheric δ 13 C CH 4 values predicted by global atmospheric models are highly sensitive to the δ 13 C CH 4 isotopic signatures applied to tropical wetland emissions. Field and aircraft campaigns also observed widespread regional smoke pollution over Africa, in both the wet and dry seasons, and large urban pollution plumes. The work highlights the need to understand tropical greenhouse gas emissions in order to meet the goals of the UNFCCC Paris Agreement, and to help reduce air pollution over wide regions of Africa. This article is part of a discussion meeting issue 'Rising methane: is warming feeding warming? (part 2)'.

Assessment of the Risk of Foot and Mouth Disease among Beef Cattle at Slaughter from East African Production Systems

Endemic foot and mouth disease (FMD) in East African cattle systems is one factor that limits access to export markets. The probability of FMD transmission associated with export from such systems have never been quantified and there is a need for data and analyses to guide strategies for livestock exports from regions where FMD remains endemic. The probability of infection among animals at slaughter is an important contributor to the risk of FMD transmission associated with the final beef product. In this study, we built a stochastic model to estimate the probability that beef cattle reach slaughter while infected with FMD virus for four production systems in two East African countries (Kenya and Uganda). Input values were derived from the primary literature and expert opinion. We found that the risk that FMD-infected animals reach slaughter under current conditions is high in both countries (median annual probability ranging from 0.05 among cattle from Kenyan feedlots to 0.62 from Ugandan semi-intensive systems). Cattle originating from feedlot and ranching systems in Kenya had the lowest overall probabilities of the eight systems evaluated. The final probabilities among cattle from all systems were sensitive to the likelihood of acquiring new infections en route to slaughter and especially the probability and extent of commingling with other cattle. These results give insight into factors that could be leveraged by potential interventions to lower the probability of FMD among beef cattle at slaughter. Such interventions should be evaluated considering the cost, logistics, and tradeoffs of each, ultimately guiding resource investment that is grounded in the values and capacity of each country.

Genome-wide local ancestry and direct evidence for mitonuclear co-adaptation in African hybrid cattle populations (Bos taurus/indicus)

Domestic cattle have a key economic role in African societies, providing an important source of mobile wealth through supply of meat, milk, cowhide, fuel, transport, and traction. The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions and complex patterns of admixture between the humpless Bos taurus (taurine) and humped Bos indicus (zebu) subspecies, which share a common ancestor 150-500 thousand years ago. Human migration and trade from Asia have left a peak of zebu nuclear ancestry in East Africa and most cattle populations across the continent have a hybrid genetic composition. Notwithstanding this, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu nuclear ancestry. In this regard, the efficient functioning of the mitochondrion relies on a network of biochemical interactions between the products of 37 mitochondrial genes and more than one thousand nuclear genes; therefore, admixed African cattle represent ideal populations for evaluating mitonuclear interactions and mismatch between the nuclear and mitochondrial genomes. Using high-density SNP array data from 18 different cattle populations, including ten African admixed breeds, we find strong evidence for mitonuclear coevolution in hybrid African cattle with significant retention of Bos taurus alleles at mitochondrially-targeted nuclear genes, particularly those genes with products that directly interact with mtDNA-encoded protein subunits in OXPHOS and ribosomal complexes, or that have functions in mtDNA replication. We also show that subspecific local ancestry varies substantially across the genomes of admixed populations, with a marked signal of taurine ancestry at the major histocompatibility (MHC) gene cluster, which likely reflects adaptation to infectious disease challenges facing African livestock. Our results demonstrate that African admixed cattle represent an excellent comparative model for studying the phenotypic consequences of mitonuclear mismatch and genomic introgression in humans and other large mammals.

A locus conferring tolerance to Theileria infection in African cattle

East Coast fever, a tick-borne cattle disease caused by the Theileria parva parasite, is among the biggest natural killers of cattle in East Africa, leading to over 1 million deaths annually. Here we report on the genetic analysis of a cohort of Boran cattle demonstrating heritable tolerance to infection by T. parva (h2 = 0.65, s.e. 0.57). Through a linkage analysis we identify a 6 Mb genomic region on Bos taurus chromosome 15 that is significantly associated with survival outcome following T. parva exposure. Testing this locus in an independent cohort of animals replicates this association with survival following T. parva infection. A stop gained polymorphism in this region was found to be highly associated with survival across both related and unrelated animals, with only one of the 20 homozygote carriers (T/T) of this change succumbing to the disease in contrast to 44 out of 97 animals homozygote for the reference allele (C/C). Consequently, we present a genetic locus linked to tolerance of one of Africa's most important cattle diseases, raising the promise of marker-assisted selection for cattle that are less susceptible to infection by T. parva.

Pastoralism in Africa

To find the origins of African pastoralism it is important archaeologists look for the wild progenitors of animals. The wild sheep of Africa (Ammotragus lervia) were never domesticated, so all domestic sheep and goats came from the Near East. There has been some debate over whether there was an independent domestication of African cattle, because wild cattle (Bos primigenius) remains have been found in the Nile Valley. Genetic evidence shows that the source of African domesticated cattle was the Levant, some 8,000 years ago. Cattle spread across the Sahara as the environment was conducive to pastoralism, being well watered at this time. This lasted until after 5000 bp when the Intertropical Convergence Zone (ITCZ) retreated and the Sahara dried up to its present condition. The tsetse barrier also retreated at this time, allowing pastoralists to move south into West Africa and, via the Ethiopian highlands, to East Africa, arriving c.4500 bp, although it took another 1,000 years for them to fully adapt to the grasslands of southern Kenya and Tanzania. Domestic stock then went on to southern Africa via a tsetse-free corridor, arriving around 2000 bp. The effect of herding societies on local hunters throughout Africa appears to have been an initial rapprochement, with a later hardening of relations. In East Africa, this was probably due to the need to learn about the new environment with the help of local hunters and to adjust to new epizootic diseases. In southern Africa, the first pastoralists were primarily sheep herders during the 1st millennium bce, with few cattle bones being found from this time. Pastoralists only became fully fledged cattle herdsmen around 1000 bp when they developed the attributes of the historic Khoekhoen. A further debate existed in southern Africa over whether pastoralism there was the result of immigrant herders who arrived in the northern Kalahari and then spread to the Cape, or if local hunters took up sheep herding.

Identification of MHC Alleles Associated With Disease Resistance/Susceptibility In Smallholder Cattle In Zambia

Background: The occurrence of Major Histocompatibility complex (MHC) alleles associated with resistance to Mastitis, Bovine Leukaemia Virus (BLV), Theileriosis, Foot and Mouth Disease (FMD) and susceptibility Dermatophilosis in African cattle is ill defined. Methods: Here, we used manual annotation to screen for five MHC alleles previously known to be associated with resistance/susceptibility to these diseases from a database of alleles sequenced from 846 cattle in Zambia. Results: Overall, we found 28 (3.3%), 21 (2.6%), 55 (6.5%), and 15 (1.8%) animals with resistance alleles to Mastitis, BLV, Theileriosis, FMD and 39 (4.6%) animals with susceptibility alleles to Dermatophilosis, respectively. Conclusion: This study provides the first evidence of resistance/susceptibility alleles in smallholder cattle in Zambia and the data could aid strategies for breeding cattle with enhanced resistance to disease in endemic countries.

Genetic variation of Nigerian cattle inferred from maternal and paternal genetic markers

The African cattle provide unique genetic resources shaped up by both diverse tropical environmental conditions and human activities, the assessment of their genetic diversity will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the genetic diversity of cattle samples from Nigeria using both maternal and paternal DNA markers. Nigerian cattle can be assigned to 80 haplotypes based on the mitochondrial DNA (mtDNA) D-loop sequences and haplotype diversity was 0.985 + 0.005. The network showed two major matrilineal clustering: the dominant cluster constituting the Nigerian cattle together with other African cattle while the other clustered Eurasian cattle. Paternal analysis indicates only zebu haplogroup in Nigerian cattle with high genetic diversity 1.000 ± 0.016 compared to other cattle. There was no signal of maternal genetic structure in Nigerian cattle population, which may suggest an extensive genetic intermixing within the country. The absence of Bos indicus maternal signal in Nigerian cattle is attributable to vulnerability bottleneck of mtDNA lineages and concordance with the view of male zebu genetic introgression in African cattle. Our study shades light on the current genetic diversity in Nigerian cattle and population history in West Africa.

Feed Quality and Feeding Level Effects on Faecal Composition in East African Cattle Farming Systems

Effects of feeding levels below maintenance requirements of metabolizable energy (MER) and of feed supplementation on fecal nutrient and microbial C concentrations were evaluated. In experiment 1, Rhodes grass hay only was offered to Boran steers at 80%, 60%, and 40% of individual MER, while steers at 100% MER additionally received a concentrated mixture. This reduction in MER decreased N, increased fungal C but did not affect bacterial C concentrations in feces. In experiment 2, Holstein × Boran heifers were offered a poor-quality roughage diet without supplement, with sweet potato vine silage or with a urea-molasses block. These two supplements did not affect the fecal chemical composition or fungal C but increased bacterial C concentrations in feces. Across all data, the fungal C/bacterial C ratio was positively related to N and negatively to neutral detergent fiber concentrations in feces, indicating diet-induced shifts in the fecal microbial community.

Population Structure Assessed Using Microsatellite and SNP Data: An Empirical Comparison in West African Cattle

A sample of 185 West African cattle belonging to nine different taurine, sanga, and zebu populations was typed using a set of 33 microsatellites and the BovineHD BeadChip of Illumina. The information provided by each type of marker was summarized via clustering methods and principal component analyses (PCA). The aim was to assess differences in performance between both marker types for the identification of population structure and the projection of genetic variability on geographical maps. In general, both microsatellites and Single Nucleotide Polymorphism (SNP) allowed us to differentiate taurine cattle from zebu and sanga cattle, which, in turn, would form a single population. Pearson and Spearman correlation coefficients computed among the admixture coefficients (fitting K = 2) and the eigenvectors corresponding to the first two factors identified using PCA on both microsatellite and SNP data were statistically significant (most of them having p < 0.0001) and high. However, SNP data allowed for a better fine-scale identification of population structure within taurine cattle: Lagunaire cattle from Benin were separated from two different N’Dama cattle samples. Furthermore, when clustering analyses assumed the existence of two parental populations only (K = 2), the SNPs could differentiate a different genetic background in Lagunaire and N’Dama cattle. Although the two N’Dama cattle populations had very different breeding histories, the microsatellite set could not separate the two N’Dama cattle populations. Classic bidimensional dispersion plots constructed using factors identified via PCA gave different shapes for microsatellites and SNPs: plots constructed using microsatellite polymorphism would suggest the existence of weakly differentiated, highly intermingled, subpopulations. However, the projection of the factors identified on synthetic maps gave comparable images. This would suggest that results on population structuring must be interpreted with caution. The geographic projection of genetic variation on synthetic maps avoids interpretations that go beyond the results obtained, particularly when previous information on the analyzed populations is scant. Factors influencing the performance of the projection of genetic parameters on geographic maps, together with restrictions that may affect the election of a given type of markers, are discussed.