The history of African village chickens: an archaeological and molecular perspective

The history of the introduction and dispersal of village chickens across the African continent is a subject of intense debate and speculation among scholars. Here, we synthesize and summarise the current scientific genetic and nongenetic knowledge in relation to the history of the species on the continent. Sociocultural, linguistic, archaeological and historic data all suggest a complex history for the species in Africa, characterized by multiple maritime and/or terrestrial introductions over time and several dispersal routes towards and within Africa. Molecular genetics information supports these observations and in addition suggests possible Asian centers of origin for African domestic chickens, including South Asia and Island Southeast Asia. However, both sets of data were until now too limited in their geographic scope, both within Africa and in comparison with chickens from Asia, to unravel the history of the species in detail. We anticipate that further continent-wide studies combining archaeological, ancient and/or modern genetic information may shed new insights on the history of the species. These will contribute to a deeper understanding of the history of trading networks and human interactions within Africa and between African and Asian societies, at the root of the development and expansion of African civilizations

Reconstructing the origin and dispersal patterns of village chickens across East Africa: insights from autosomal markers

Unravelling the genetic history of any livestock species is central to understanding the origin, development and expansion of agricultural societies and economies. Domestic village chickens are widespread in Africa. Their close association with, and reliance on, humans for long-range dispersal makes the species an important biological marker in tracking cultural and trading contacts between human societies and civilizations across time. Archaezoological and linguistic evidence suggest a complex history of arrival and dispersion of the species on the continent, with mitochondrial DNA (mtDNA) D-loop analysis revealing the presence of five distinct haplogroups in East African village chickens. It supports the importance of the region in understanding the history of the species and indirectly of human interactions. Here, through a detailed analysis of 30 autosomal microsatellite markers genotyped in 657 village chickens from four East African countries (Kenya, Uganda, Ethiopia and Sudan), we identify three distinct autosomal gene pools (I, II and III). Gene pool I is predominantly found in Ethiopia and Sudan, while II and III occur in both Kenya and Uganda. A gradient of admixture for gene pools II and III between the Kenyan coast and Uganda's hinterland (P = 0.001) is observed, while gene pool I is clearly separated from the other two. We propose that these three gene pools represent genetic signatures of separate events in the history of the continent that relate to the arrival and dispersal of village chickens and humans across the region. Our results provide new insights on the history of chicken husbandry which has been shaped by terrestrial and maritime contacts between ancient and modern civilizations in Asia and East Africa

The History of African Village Chickens: an Archaeological and Molecular Perspective

Abstract The history of the introduction and dispersal of village chickens across the African continent is a subject of intense debate and speculation among scholars. Here, we synthesize and summarise the current scientific genetic and nongenetic knowledge in relation to the history of the species on the continent. Sociocultural, linguistic, archaeological and historic data all suggest a complex history for the species in Africa, characterized by multiple maritime and/or terrestrial introductions over time and several dispersal routes towards and within Africa. Molecular genetics information supports these observations and in addition suggests possible Asian centers of origin for African domestic chickens, including South Asia and Island Southeast Asia. However, both sets of data were until now too limited in their geographic scope, both within Africa and in comparison with chickens from Asia, to unravel the history of the species in detail. We anticipate that further continent-wide studies combining archaeological, ancient and/or modern genetic information may shed new insights on Afr Archaeol Rev (2013) 30:97-11

Assessment of OvineSNP50 in Nigerian and Kenyan sheep populations

Deciphering genomic information requires markers that are polymorphic and sufficient enough to capture its vast array of genetic data. Polymorphic loci can differ greatly between breeds of the same species and the exclusion of the Nigerian and some African sheep breeds during the development of the OvineSNP50 chip necessitated the validation of SNPs included on the chip to allow for genomic applications of the excluded breeds. A total of sixty sheep samples were genotyped [10 each of the Balami, Uda, West African Dwarf and Yankasa from Nigeria, Dorper and Red Maasai from Kenya (East Africa)] using the Ovine 50k Illumina SNP bead chip. Results revealed that 33,994 SNPs (97.47%) of the called 34,876 SNPs were validated for downstream analysis. Mean heterozygosity values of 0.154 and 0.153 were obtained for polymorphic SNPs on sex and autosomal chromosomes respectively, while the values of 0.662 and 0.054 were obtained on the sex and autosomal chromosomes respectively for the mean identity-bystate (IBS). Six and three individuals violated the per ID and identity-by-state (IBS) thresholds, respectively. It was observed that the Ovine 50k Illumina SNP bead chip wasinformative in the Nigerian and East African sheep that were studied, and should be useful in examining the underlying genetic variation.Keywords: Sheep, OvineSNP50, genome-wide, call rate, minor allele frequenc

DNA species surveillance: Monitoring bushmeat poaching and trading in Kenya using partial cytochrome b gene

DNA species identification has applications in such areas as forensic science, systematics, conservation genetics and agriculture. One key anthropogenic activity threatening large wildlife fauna is illegal exploitation. In Kenya, species identification of raw and processed meat products remains a constraint to effective enforcement of illegal trade in game meat (bushmeat) and products. We tested the reliability of a 321 bp mitochondrial cytochrome b (cyt b) region as a species identification tool for application in wildlife forensics. Query sequences were generated from known specimens of 14 Eastern African wildlife species, 13 representing commonly poached ungulates, and three domesticated species. These were compared, using Basic Local Alignment Search Tool (BLAST) algorithm, with NCBI GenBank reference sequences for species identity. These query sequences were subsequently deposited on Genbank. They represent a contribution to a diagnostic internal East African Wildlife reference cyt b database. The test species comprised: Cape buffalo, bushbuck, Guenther’s dik-dik, common duiker, common eland, Grant’s gazelle, hartebeest, impala, lesser kudu, plains zebra, Thomson’s gazelle, common warthog, wildebeest, Maasai ostrich, cattle, goat and sheep. Additionally, cooked beef and pork samples were analyzed. The results show that, when conspecific sequences were available in the database, species discrimination was 100%. Phylogeny clustering of the species by maximum likelihood supported the species determination by BLAST. The second part of the study carried out a preliminary survey of the prevalence of illegal game meat sold in the dispersal area of Tsavo National Park, Kenya. Sixty two raw meat samples were randomly collected from small roadside retail outlets along the Nairobi-Mombasa highway (A109), a major transnational highway that transverses Tsavo National Park. The results indicate a 9.7% (n = 6) illegal game meat sale, comprising five Guenther’s dik-diks and a Beisa oryx. A 2 km radius hotspot, with 83% (n = 5) of the bushmeat sales was identified just south of Tsavo East National Park.Key words: East Africa, Kenya, bushmeat, poaching, wildlife conservation, species identification, mitochondrial cytochrome b gene

Genomic markers associated with antibody response to Newcastle disease virus of Sasso chickens raised in Ethiopia

Newcastle disease virus (NDV) is one of the highly contagious avian pathogens that threatens poultry producers in endemic zones due to its epidemic potential. Selection for antibody (Ab) response can effectively improve disease resistance in chickens. However, the molecular basis of the variation in Ab response to NDV is unclear. This study aimed to detect genomic markers and genes modulating Ab response to NDV in chickens reared under tropical, outdoor conditions. A genome-wide association study (GWAS) was conducted on Sasso T451A chickens that were naturally exposed to infectious diseases from 56 to 112 days of age to identify regions associated with Ab response to NDV. Phenotypic immune data from 935 chickens, monitored in two batches, and genotyping data of these chickens based low-pass sequencing (2,676,181 single nucleotide polymorphisms, SNPs) were used. BioMart data mining and variant effect predictor tools were used to annotate SNPs and candidate genes, respectively. A total of five SNPs (rs316795557 (FOXP2), chr 1; rs313761644 (CEP170B), chr 5; rs733628728, chr 13; and two unnamed SNPs, chr 30 and chr 33) were associated with the chicken antibody response to NDV at the suggestive significance level. These SNPs are located on chromosomes 1, 5, and 13 and are in genomic regions that contain several genes with roles in the regulation of the immune response. The results of this study pave the path for more investigation into the host immune response of chickens to NDV.</p

Patterns in Age-Seroprevalence Consistent with Acquired Immunity against Trypanosoma brucei in Serengeti Lions

Trypanosomes cause disease in humans and livestock throughout sub-Saharan Africa. Although various species show evidence of clinical tolerance to trypanosomes, until now there has been no evidence of acquired immunity to natural infections. We discovered a distinct peak and decrease in age prevalence of T. brucei s.l. infection in wild African lions that is consistent with being driven by an exposure-dependent increase in cross-immunity following infections with the more genetically diverse species, T. congolense sensu latu. The causative agent of human sleeping sickness, T. brucei rhodesiense, disappears by 6 years of age apparently in response to cross-immunity from other trypanosomes, including the non-pathogenic subspecies, T. brucei brucei. These findings may suggest novel pathways for vaccinations against trypanosomiasis despite the notoriously complex antigenic surface proteins in these parasites

Bluetongue and Epizootic Haemorrhagic Disease virus in local breeds of cattle in Kenya

AbstractThe presence of bluetongue virus (BTV) and Epizootic Haemorrhagic Disease virus (EHDV) in indigenous calves in western Kenya was investigated. Serum was analysed for BTV and EHDV antibodies. The population seroprevalences for BTV and EHDV for calves at 51weeks of age were estimated to be 0.942 (95% CI 0.902–0.970) and 0.637 (95% CI 0.562–0.710), respectively, indicating high levels of circulating BTV and EHDV. The odds ratio of being positive for BTV if EHDV positive was estimated to be 2.57 (95% CI 1.37–4.76). When 99 calves were tested for BTV and EHDV RNA by real-time RT-PCR, 88.9% and 63.6% were positive, respectively. Comparison of the serology and real-time RT-PCR results revealed an unexpectedly large number of calves that were negative by serology but positive by real-time RT-PCR for EHDV. Eight samples positive for BTV RNA were serotyped using 24 serotype-specific real-time RT-PCR assays. Nine BTV serotypes were detected, indicating that the cattle were infected with a heterogeneous population of BTVs. The results show that BTV and EHDV are highly prevalent, with cattle being infected from an early age