History and genetic diversity of African sheep: Contrasting phenotypic and genomic diversity

Abstract

Domesticated sheep have adapted to contrasting and extreme environments and continue to play important roles in local community-based economies throughout Africa. Here we review the Neolithic migrations of thin-tailed sheep and the later introductions of fat-tailed sheep into eastern Africa. According to contemporary pictorial evidence, the latter occurred in Egypt not before the Ptolemaic period (305-25 BCE). We further describe the more recent history of sheep in Egypt, the Maghreb, west and central Africa, central-east Africa, and southern Africa. We also present a comprehensive molecular survey based on the analysis of 50 K SNP genotypes for 59 African breeds contributed by several laboratories. We propose that gene flow and import of fat-tailed sheep have partially overwritten the diversity profile created by the initial migration. We found a genetic contrast between sheep north and south of the Sahara and a west-east contrast of thin- and fat-tailed sheep. There is no close relationship between African and central and east Asian fat-tailed breeds, whereas we observe within Africa only a modest effect of tail types on breed relationships.

Keywords: Africa; adaptation; fat tail; history; phylogeography; sheep; thin tail.

FIGURE 1

Current density of sheep (Gilbert et al., 2018) and approximate locations of continental African sheep breeds with colors indicating the types of sheep. See Table S1 for details and references. Breed codes: ADA, Adane; ADI, Adile; AFA, Afar; AGU, Akele Guzai; AHS, Abour‐Halai‐Shalat; AKM, Abudeleik Kanzi Maenit; ALH, Al Ahamda; ALL, Angola Long‐legged; AMA, Angola Maned; ARA, Ara‐Ara; ARB, Arsi Bale; ARO, Arabo; ARR, Arrit; ASH, Shugar; BAG, Bagarra; BAH, Bahu; BAL, Balami; BAR, Barbarine; BAS, Basotho; BBA, Bali‐Bali; BEG, Begait; BER, Berber; BGU, Beni Guil; BHP, Black‐headed Persian; BHS, Black‐headed Somali; BIJ, Bija; BJA, Boujaad; BKA, Baraka; BLB, Baluba; BNA, Beni Ahsen; BON, Bonga; BTI, Black Thibar; BUZ, Buzee; CAM, Cameroon Dwarf; CLL, Congo Long‐legged; CPP, Chi Pepo; DAM, Damara; DAN, Dangila; DJA, Djallonke; DME, Döhne Merino; DMN, D'man; DON, Dongola; DOU, Doukkala; DOY, Doyogena; DRP, Dorper; DUB, Dubasi; DZA, Dané Zaqla; EAB, East African Blackheaded; EBI, Barki; FEL, Fellahi; FRF, Farafra; FRT, Farta; GGD, Gumuz Gesses Dibate; GHI, Ghimi; GND, Goundoun; GOU, Gourane; GUZ, Gumz; GWA, Gafera Washera; HAD, Hadina; HAM, Hammari; HMA, Hamra; HOR, Horro; IBE, Ibeidi; IFI, Ifilène; ING, Ingessana; KD, Kido; KEF, Kefis; KIR, Kirdi; KSH, Kabashi; KUM, Kumumava; KUR, Kurassi; LAD, Ladoum; LND, Landim; LOY, Loya; MAC, Macina; MAU, Black Maure; MBO, Mbororo; MDM, Mondombe; MEI, Meidob; MFT, Malawi Fat‐tailed; MKE, Mayo‐Kebbi; MMA, Meatmaster; MNG, Mongalla; MNZ, Menz; MOS, Mossi; NGU, Nguni; NIL, Nilotic; NMA, Nuba Maned; NQA, Namaqua Afrikaner; ODF, ODJ, Ouled Djellal; OSS, Ossimi; PED, Pedi; PEU, Peul‐Peul; PVO, Peul Voltaique; RAH, Rahalya; RAS, Rashaidi; RDA, Ronderib Afrikaner; REZ, Rezegat; RHM, Rahmani; RIO, Rio d'Oro; RMA, Red Maasai; RMB, Rembi; RWB, Rwanda‐Burundi; SAB, Sabi; SAH, Sahelian; SAI, Saidi; SAM, South African Merino; SAMM, SouthAfrican Mutton Merino; SAR, Sardi; SDN, Sidaoun; SHA, Shanbali; SHG, Shubi Gemo; SMA, South Sudanese; SMO, South Moroccan; SOA, Somali Arab; SOU, Souhagi; SSC, SiciloSarde; SWA, Swakara; SWZ, Swazi; TDL, Tadla; TDM, Tadmit; TLT, Tanzania Long‐tailed; TMA, Timahdite; TOP, Toposa; TOR, Toronké; TOU, Touabire; TSW, Tswana; TUA, Tuareg; TUC, Tucur; TZG, Tazegzawt; UDA, Uda; VEN, Venda; VOG, Vogan; WAD, West African Dwarf; WAT, Watish; WOL, Wollo; WKA, West Kanem; WOL, Wollo; WTT, Western Thin‐tailed; YAN, Yankasa; ZAG, Zaghawa; ZAI, Zaian; ZEM, Zemmour.

FIGURE 2

Archeological sites with ovine remains (Table S4). Datings may be based on the analysis of animal remains, food remains, or on the age of the site and are shown in 1000 years BCE or, if indicated, 1000 years CE. Per site and per region, only the oldest reported date is shown.

FIGURE 3

NeighborNet graph of F _ST distances between 57 indigenous African sheep breeds (984 individuals).

FIGURE 4

NeighborNet graph of F _ST distances between 21 European, Asian and African regional clusters (see Table S3) of closely related breeds of African and Asian sheep breeds, suggesting a relationship of Italian and Spanish breed with the Maghreb and Barbarine sheep and a partial separation of breeds according to the tail type. In this figure central‐east African sheep are represented by Ethiopian sheep. Colors correspond to those in Figures 1 and S4.

FIGURE 5

Blue arrows indicate Neolithic migrations in Africa inferred from datings of sheep remains. The broad lines with colors corresponding to those in Figure 1 indicate gene flow inferred from genetic distances between modern sheep breeds.