Domesticating Animals in Africa: Implications of Genetic and Archaeological Findings

Gifford–Gonzalez, Diane; Hanotte, Olivier

doi:10.1007/s10963-010-9042-2

Cited by 201 publications

(161 citation statements)

References 89 publications

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“…Within breeds blocks can extend from 500 Kb to 1 Mb (Sutter et al, 2004;Lindblad-Toh et al, 2005). The median block size of 11-12 Kb across the populations/breeds studied here is consistent with the ancestral block size observed in dogs, despite both domestic species having very distinct genetic histories with the dog having been domesticated several thousands of years before the chicken (Lindblad-Toh et al, 2005;Gifford-Gonzales and Hanotte, 2011).…”

Section: Discussionsupporting

confidence: 81%

“…Both mitochondrial and microsatellite analyses of East African village chickens have revealed several distinct arrivals from Asia of founder stocks and subsequent admixture between them (Mwacharo et al, 2011). The earliest archaeological evidence of domestic chicken in Africa dates back to between 1300 BC and 1400 AD (Gifford-Gonzales and Hanotte, 2011). The origin of South American village chicken remains unclear with their eventual presence on the continent before the arrival of Europeans still the subject of debate (Storey et al, 2007;Gongora et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

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Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

et al. 2012

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Extensive phenotypic variation is a common feature among village chickens found throughout much of the developing world, and in traditional chicken breeds that have been artificially selected for traits such as plumage variety. We present here an assessment of traditional and village chicken populations, for fine mapping of Mendelian traits using genome-wide singlenucleotide polymorphism (SNP) genotyping while providing information on their genetic structure and diversity. Bayesian clustering analysis reveals two main genetic backgrounds in traditional breeds, Kenyan, Ethiopian and Chilean village chickens. Analysis of linkage disequilibrium (LD) reveals useful LD (r 2 X0.3) in both traditional and village chickens at pairwise marker distances of B10 Kb; while haplotype block analysis indicates a median block size of 11-12 Kb. Association mapping yielded refined mapping intervals for duplex comb (Gga 2:38.55-38.89 Mb) and rose comb (Gga 7:18.41-22.09 Mb) phenotypes in traditional breeds. Combined mapping information from traditional breeds and Chilean village chicken allows the oocyan phenotype to be fine mapped to two small regions (Gga 1:67.25-67.28 Mb, Gga 1:67.28-67.32 Mb) totalling B75 Kb. Mapping the unmapped earlobe pigmentation phenotype supports previous findings that the trait is sex-linked and polygenic. A critical assessment of the number of SNPs required to map simple traits indicate that between 90 and 110K SNPs are required for full genome-wide analysis of haplotype block structure/ancestry, and for association mapping in both traditional and village chickens. Our results demonstrate the importance and uniqueness of phenotypic diversity and genetic structure of traditional chicken breeds for fine-scale mapping of Mendelian traits in the species, with village chicken populations providing further opportunities to enhance mapping resolutions.

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Section: Discussionsupporting

confidence: 81%

Section: Introductionmentioning

confidence: 99%

Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

et al. 2012

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“…S4). A seaborne introduction appears likely, because there is increasing evidence that the southern Arabian Peninsula played an important role in domestication [e.g., African wild ass (29)] and in the transfer of crops and livestock [e.g., zebu cattle, fat-tailed sheep (30,31)] between South Asia and the African continent. Additional evidence for a separate introduction might come from socio-ethological observations; today's Eastern African dromedaries are used largely for milk production rather than for riding and transportation, and this use could be rooted in practices associated with the early stage of dromedary husbandry in the southern Arabian Peninsula (1, 7).…”

Section: Resultsmentioning

confidence: 99%

Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

Almathen

Charruau

Mohandesan

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species' range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the "restocking from the wild" hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments.anthropogenic admixture | Camelus dromedarius | demographic history | paleogenetics | wild dromedary T he dromedary (Camelus dromedarius) is one of the largest domestic ungulates and one of the most recent additions to livestock. Known as the "ship of the desert" (1), it enabled the transportation of people and valuable goods (e.g., salt, incense, spices) over long distances connecting Arabia, the Near East, and North Africa. This multipurpose animal has outperformed all other domestic mammals, including the donkey, in arid environments and continues to provide basic commodities to millions of people inhabiting marginal agro-ecological zones. In the current context of advancing desertification and global climate change, there is renewed interest in the biology and production traits of the species (2), with the first annotated genome drafts having been recently released (3, 4). SignificanceThe dromedary is one of the largest domesticates, sustainably used in arid and hostile environments. It provides food and transport to millions of people in marginal agricultural areas. We show how important long-distance and back-and-forth movements in ancient caravan routes shaped the species' genetic diversity. Using a global sample set and ancient mitochondrial DNA analyses, we describe the population structure in modern dromedaries and their wild extinct ancestors. Phylogenetic analyses of ancient and modern dro...

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“…In all these analyses, Kuchi ecotype tended to remain in a distinct group. Ching'wekwe, Morogoro-medium, Unguja and Pemba might have been distributed to Tanzania with the two early main waves of introduction of chickens to Africa in which chickens were introduced along the African East Coast from the Indian Ocean or through Egypt from the Mediterranean before being spread inland through overland routes (MacDonald, 1992;Van Marle-Köster et al, 2008;Gifford-Gonzales & Hanotte, 2011). In contrast, Kuchi seems to have been introduced recently and is highly associated with Shamo gamebirds from Japan.…”

Section: Resultsmentioning

confidence: 99%

Assessing the genetic diversity of five Tanzanian chicken ecotypes using molecular tools

Lyimo¹,

Weigend²,

Janssen-Tapken³

et al. 2014

SA J. An. Sci.

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The study aimed to evaluate the genetic diversity of Tanzanian chicken populations through phylogenetic relationship, and to trace the history of Tanzanian indigenous chickens. Five ecotypes of Tanzanian local chickens (Ching'wekwe, Kuchi, Morogoro-medium, Pemba and Unguja) from eight regions were studied. Diversity was assessed based on morphological measurements and 29 microsatellite markers recommended by ISAG/FAO advisory group on animal genetic diversity. A principal component analysis (PCA) of morphological measures distinguished individuals most by body sizes and body weight. Morogoro Medium, Pemba and Unguja were grouped together, while Ching'wekwe stood out because of their disproportionate short shanks and ulna bones. Kuchi formed an independent group owing to their comparably long body sizes. Microsatellite analysis revealed three clusters of Tanzanian chicken populations. These clusters encompassed i) Morogoro-medium and Ching'wekwe from Eastern and Central Zones ii) Unguja and Pemba from Zanzibar Islands and iii) Kuchi from Lake Zone regions, which formed an independent cluster. Sequence polymorphism of D-loop region was analysed to disclose the likely maternal origin of Tanzanian chickens. According to reference mtDNA haplotypes, the Tanzanian chickens that were sampled encompass two haplogroups of different genealogical origin. From haplotype network analysis, Tanzanian chickens probably originated on the Indian subcontinent and in Southeast Asia. The majority of Kuchi chickens clustered in a single haplogroup, which was previously found in Shamo game birds sampled from Shikoku Island of Japan in the Kōchi Prefecture. Analysis of phenotypic and molecular data, as well as the linguistic similarity of the breed names, suggests a recent introduction of the Kuchi breed to Tanzania.

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Domesticating Animals in Africa: Implications of Genetic and Archaeological Findings

Cited by 201 publications

References 89 publications

Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

Assessing the genetic diversity of five Tanzanian chicken ecotypes using molecular tools

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