title: Mitogenomes from Egyptian Cattle Breeds: New Clues on the Origin of Haplogroup Q and the Early Spread of Bos taurus from the Near East.
abstract: BACKGROUND
  Genetic studies support the scenario that Bos taurus domestication occurred in the Near East during the Neolithic transition about 10 thousand years (ky) ago, with the likely exception of a minor secondary event in Italy. However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of taurine cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas. Egypt is in close geographic and cultural proximity to the Near East, in particular the Nile Delta region, and was one of the first neighboring areas to adopt the Neolithic package. Thus, a survey of mitogenome variation of autochthonous taurine breeds from the Nile Delta region might provide new insights on the early spread of cattle rearing outside the Near East.
  
  
  METHODS
  Using Illumina high-throughput sequencing we characterized the mitogenomes from two cattle breeds, Menofi (N = 17) and Domiaty (N = 14), from the Nile Delta region. Phylogenetic and Bayesian analyses were subsequently performed.
  
  
  CONCLUSIONS
  Phylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago. Comparisons of Nile Delta mitogenomes with those from other geographic areas revealed that (i) most Egyptian mtDNAs are probably direct local derivatives from the founder domestic herds which first arrived from the Near East and the extent of gene flow from and towards the Nile Delta region was limited after the initial founding event(s); (ii) haplogroup Q1 was among these founders, thus proving that it underwent domestication in the Near East together with the founders of the T clades.
authors.affiliation: Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.
authors.forename: Anna
authors.initials: A
authors.lastname: Olivieri
authors.affiliation: Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy; School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, United Kingdom.
authors.forename: Francesca
authors.initials: F
authors.lastname: Gandini
authors.affiliation: Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy; Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Achilli
authors.affiliation: Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Fichera
authors.affiliation: Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate (Milano), Italy; Fondazione Telethon, Milano, Italy.
authors.forename: Ermanno
authors.initials: E
authors.lastname: Rizzi
authors.affiliation: Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.
authors.forename: Silvia
authors.initials: S
authors.lastname: Bonfiglio
authors.affiliation: Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.
authors.forename: Vincenza
authors.initials: V
authors.lastname: Battaglia
authors.affiliation: Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.
authors.forename: Stefania
authors.initials: S
authors.lastname: Brandini
authors.affiliation: Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.
authors.forename: Anna
authors.initials: A
authors.lastname: De Gaetano
authors.affiliation: Animal Production Research Institute (APRI), Ministry of Agriculture, Cairo, Egypt.
authors.forename: Ahmed
authors.initials: A
authors.lastname: El-Beltagi
authors.affiliation: Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy.
authors.forename: Hovirag
authors.initials: H
authors.lastname: Lancioni
authors.affiliation: Department of Animal Production, Faculty of Agriculture, Ain Shams University, Cairo, Egypt.
authors.forename: Saif
authors.initials: S
authors.lastname: Agha
authors.affiliation: Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.
authors.forename: Ornella
authors.initials: O
authors.lastname: Semino
authors.affiliation: Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Ferretti
authors.affiliation: Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.
authors.forename: Antonio
authors.initials: A
authors.lastname: Torroni
mesh_terms: D000818:Animals; D000829:Animals, Domestic; D001499:Bayes Theorem; D001947:Breeding; D002417:Cattle; D019143:Evolution, Molecular; D014644:Genetic Variation; D005828:Genetics, Population; D054629:Genome, Mitochondrial; D023281:Genomics; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D058974:Phylogeography