M. A. Zeder, Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact, Proc Natl Acad Sci, vol.105, issue.33, pp.11597-604, 2008.

M. A. Zeder, Documenting domestication: the intersection of genetics and archaeology, Trends Genet, vol.22, issue.3, pp.139-55, 2006.

Z. Ma, The domestication of animals, J. Anthropol. Res, vol.68, pp.161-190, 2012.

C. Sue, C. James, and S. , The evolution of Neolithic farming from SW Asian origins to NW European limits, European Journal of Archaeology, vol.8, issue.2, pp.137-156, 2005.

H. Epstein, The Awassi sheep with special reference to the improved dairy type. FAO ANIMAL PRODUCTION AND HEALTH PAPER, p.57, 1985.

M. L. Ryder, Sheep and man, 1983.

J. R. Meadows, Five ovine mitochondrial lineages identified from sheep breeds of the near East, Genetics, vol.175, issue.3, pp.1371-1380, 2007.

S. Pedrosa, Evidence of three maternal lineages in Near Eastern sheep supporting multiple domestication events, Proc Biol Sci, vol.272, pp.2211-2218, 1577.

A. Sherratt, Plough and pastoralism: aspects of the secondary products revolution, Pattern of the past: studies in honour of David Clarke, pp.261-305, 1981.

D. Helmer and G. L. , The development of the exploitation of products from Capra and Ovis (meat, milk and fleece) from the PPNB to the Early Bronze in the northern Near East (8700 to 2000 BC cal.). Anthropozoologica, vol.42, pp.41-69, 2007.

S. Hiendleder, Molecular analysis of wild and domestic sheep questions current nomenclature and provides evidence for domestication from two different subspecies, Proc Biol Sci, vol.269, pp.893-904, 1494.

M. Bruford and S. Townsend, Case studies in the genetics of animal domestication: sheep, in Documenting Domestication: New Genetic and Archaeological Paradigms, 2006.

H. R. Rezaei, Evolution and taxonomy of the wild species of the genus Ovis (Mammalia, Artiodactyla, Bovidae), Mol Phylogenet Evol, vol.54, issue.2, pp.315-341, 2010.

J. Clutton-brock, A natural history of domesticated mammals, 1999.

K. Dobney and G. Larson, Genetics and animal domestication: new windows on an elusive process, Journal of Zoology, vol.269, issue.2, pp.261-271, 2006.

M. Tapio, Sheep mitochondrial DNA variation in European, Caucasian, and Central Asian areas, Mol Biol Evol, vol.23, issue.9, pp.1776-83, 2006.

F. Pereira, Genetic signatures of a Mediterranean influence in Iberian Peninsula sheep husbandry, Mol Biol Evol, vol.23, issue.7, pp.1420-1426, 2006.

F. P. Lv and . Wei-feng,

J. ;. Yang, . Zhao, and . Yong-xin,

W. Li,

M. -. Liu,

J. Kantanen, . Han, and . Jian-lin,

M. Li and M. Meta, Analysis Identifies Two Phases of Migration in the History of Eastern Eurasian Sheep, Mol. Biol. Evol, vol.32, issue.10, pp.2515-2533, 2015.

J. M. Davis and J. V. Beckett, Animal husbandry and agricultural improvement: the archaeological evidence from animal bones and teeth, Rural Hist, vol.10, issue.1, pp.1-17, 1999.

A. W. Muigai and O. Hanotte, The Origin of African Sheep: Archaeological and Genetic Perspectives, Afr Archaeol Rev, vol.30, pp.39-50, 2013.

D. Gifford-gonzalez and O. Hanotte, Domesticating Animals in Africa: Implications of Genetic and Archaeological Findings, J World Prehist, vol.24, pp.1-23, 2011.

E. Anati, . Arte-rupestre-nelle, . Regioni, . Della, and . Iberica, , 1968.

M. Ryder, Domestication, history and breed evolution in sheep, 1991.

F. Zeuner, The Mammals of the Palearctic Region: a taxonomic review, 1963.

M. Ryder and . Sheep, Longman Group Limited, Evolution of Domesticated Animals, pp.63-84, 1984.

P. Grubb and . Order-artiodactyla, Mammal Species of the World, pp.267-722, 2005.

V. Geist, On the taxonomy of giant sheep (Ovis ammon Linnaeus, 1766), Can. J. Zool, vol.69, pp.706-723, 1991.

S. Hirsch, Sheep and Goat in palestine, Bulletin of the Palestine Economic Society, 1933.

C. J. Pritchard, A. E. Pennell, and G. L. Williams, A note on the wool characteristics of sheep at the hofuf Agricultural Research Center, 1975.

O. Gürsoy, Small ruminant breeds of Turkey, in Characterization of Small Ruminant Breeds in West Asia, ICARDA, pp.239-416, 2005.

H. Epstein, Domestic animals of China, Commonw. Bur. Anim. Breed. Genet, 1969.

L. Fao, Plan of Action for Resilient Livelihoods, 2014.

M. Hilali, Dietary supplementation with nonconventional feeds from the Middle East: assessing the effects on physicochemical and organoleptic properties of Awassi sheep milk and yogurt, J Dairy Sci, vol.94, issue.12, pp.5737-5786, 2011.

B. W. Hartwell, L. Iniguez, J. Mueller, M. Wurzinger, and W. F. Knaus, Characterization of Awassi lamb fattening systems: a Syrian case study. Trop Anim Health Prod, vol.42, pp.1573-1581, 2010.

S. Galal, O. Gürsoy, and I. Shaat, Awassi sheep as a genetic resource and efforts for their genetic improvement, Small Ruminant Research, vol.23, issue.79, pp.99-108, 2008.

F. R. Asmar, Country Pasture/Forage Resource Profiles, 2011.

L. Iñiguez, Small ruminant breeds of Turkey. Characterization of small ruminant breeds in West Asia, North Africa. ICARDA, vol.1, pp.239-416, 2005.

M. Y. Amin and K. Peters, Awassi Sheep Production and the Development of breeding Program Options in Syria, Prosperity and Poverty in a Globalised World-Challenges for Agricultural Research, 2006.

K. Reiad, W. Al-azzawi, K. Al-najjar, Y. Masri, S. Salhab et al., Factors Influencing the Milk Production of Awassi Sheep in A Flock With the Selected Lines at the Agricultural Scientific Research Centre in Salamieh/Syria. Journal of The Faculty of Veterinary Medecine, kafkas university, vol.16, pp.425-430, 2010.

O. Gürsoy, E. Pekel, L. Özcan, O. Torun, and V. Timon, Genetic selection for milk yield in Awassi sheep. I. Reproduction , Lactation. Doga Turkish Journal of Veterinary, Animal Science, vol.16, issue.3, pp.535-546, 1992.

O. Gürsoy, E. Pekel, L. Özcan, O. Torun, and V. Timon, Comparisons of production traits of Ceylanpinar Awassi sheep with top producing ewes of national flocks in the GAP area. II. Growth performance , carcass traits, Do?a Turkish Journal of Veterinary, vol.17, pp.65-72, 1993.

P. K. Vogt, Historical Introduction to the General Properties of Retroviruses, 1997.

H. Vallée and H. Carré, Sur la nature infectieuse de l'anémie du cheval, C. R. Hebd Seances Acad Sci Ser D Sci Nat, vol.139, pp.331-333, 1904.

V. Ellermann, O. Bang, and E. Leukämie-bei-hühnern, Zentralbl Bakteriol Parasitenkd Infectionskr Hyg Abt Orig, vol.46, pp.595-609, 1908.

P. Rous, A Sarcoma of the Fowl Transmissible by an Agent Separable from the Tumor Cells, J Exp Med, vol.13, issue.4, pp.397-411, 1911.

J. J. Bittner, Some Possible Effects of Nursing on the Mammary Gland Tumor Incidence in Mice, Science, vol.84, p.162, 1936.

L. Gross, Development and serial cellfree passage of a highly potent strain of mouse leukemia virus, Proc Soc Exp Biol Med, vol.94, issue.4, pp.767-71, 1957.

A. Claude and J. G. Murphy, Transmissible tumors of the fowl, Physiol. Rev, vol.13, pp.246-275, 1933.

L. N. Payne, Biology of avian retroviruses, in The retroviridae, pp.299-404, 1992.

E. V. Keogh, Ectodermal lesions produced by the virus of Rous sarcoma, British Journal of experimental pathology, vol.19, pp.1-9, 1938.

D. Baltimore, RNA-dependent DNA polymerase in virions of RNA tumour viruses, Nature, vol.226, issue.5252, pp.1209-1220, 1970.

H. M. Temin and S. Mizutani, RNA-dependent DNA polymerase in virions of Rous sarcoma virus, Nature, vol.226, issue.5252, pp.1211-1214, 1970.

A. J. Dalton, The case for a family of reverse transcriptase viruses: Retraviridae. Intervirology, vol.4, pp.201-207, 1974.

S. M. Murray, Replication in a superficial epithelial cell niche explains the lack of pathogenicity of primate foamy virus infections, J Virol, vol.82, issue.12, pp.5981-5986, 2008.

M. L. Linial, . Foamy, B. N. Fields-virology, D. M. Fields, P. M. Knipe et al., , pp.2245-2263, 2007.

J. M. Coffin, Genetic diversity and evolution of retroviruses, Curr Top Microbiol Immunol, vol.176, pp.143-64, 1992.

V. M. Vogt, Retroviral Virions and Genomes, 1997.

A. L. Payne, D. W. Verwoerd, and H. M. Garnett, The morphology and morphogenesis of jaagsiekte retrovirus (JSRV), Onderstepoort J Vet Res, vol.50, issue.4, pp.317-339, 1983.

J. N. Sfakianos and E. Hunter, M-PMV capsid transport is mediated by Env/Gag interactions at the pericentriolar recycling endosome, Traffic, vol.4, issue.10, pp.671-80, 2003.

P. R. Murcia, F. Arnaud, and M. Palmarini, The transdominant endogenous retrovirus enJS56A1 associates with and blocks intracellular trafficking of Jaagsiekte sheep retrovirus Gag, J Virol, vol.81, issue.4, pp.1762-72, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01601223

H. Yeger, V. I. Kalnins, and J. R. Stephenson, Type-C retrovirus maturation and assembly: post-translational cleavage of the gag-gene coded precursor polypeptide occurs at the cell membrane, Virology, vol.89, issue.1, pp.34-44, 1978.

J. M. Coffin, S. H. Hughes, and H. E. Varmus, The Interactions of Retroviruses and their Hosts, 1997.

R. Swanstrom and J. W. Wills, Synthesis, Assembly, and Processing of Viral Proteins, 1997.

N. Rosenberg and P. Jolicoeur, Retroviral Pathogenesis, pp.475-586, 1997.

J. P. Stoye, Endogenous retroviruses: still active after all these years?, Curr Biol, vol.11, issue.22, pp.914-920, 2001.

J. W. Kijas, Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection, PLoS Biol, vol.10, issue.2, p.1001258, 2012.

F. Arnaud, A paradigm for virus-host coevolution: sequential counteradaptations between endogenous and exogenous retroviruses, PLoS Pathog, vol.3, issue.11, p.170, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01606111

R. E. Tarlinton, J. Meers, and P. R. Young, Retroviral invasion of the koala genome, Nature, vol.442, issue.7098, pp.79-81, 2006.

P. Jern and J. M. Coffin, Effects of retroviruses on host genome function, Annu Rev Genet, vol.42, pp.709-741, 2008.

D. J. Finnegan, Eukaryotic transposable elements and genome evolution, Trends Genet, vol.5, issue.4, pp.103-107, 1989.

A. F. Smit, Interspersed repeats and other mementos of transposable elements in mammalian genomes, Curr Opin Genet Dev, vol.9, issue.6, pp.657-63, 1999.

P. Sanmiguel, The paleontology of intergene retrotransposons of maize, Nat Genet, vol.20, issue.1, pp.43-48, 1998.

E. S. Lander, Initial sequencing and analysis of the human genome, Nature, vol.409, issue.6822, pp.860-921, 2001.

P. Capy, Dynamics and evolution of transposable elements, 1998.

V. V. Kapitonov and J. Jurka, Molecular paleontology of transposable elements in the Drosophila melanogaster genome, Proc Natl Acad Sci, vol.100, issue.11, pp.6569-74, 2003.

C. Biemont and C. Vieira, Genetics: junk DNA as an evolutionary force, Nature, vol.443, issue.7111, pp.521-525, 2006.

M. Bock and J. P. Stoye, Endogenous retroviruses and the human germline, Curr Opin Genet Dev, vol.10, issue.6, pp.651-656, 2000.

K. A. Dunlap, M. Palmarini, and T. E. Spencer, Ovine endogenous betaretroviruses (enJSRVs) and placental morphogenesis, Placenta, vol.27, 2006.

M. Varela, Association of RON tyrosine kinase with the Jaagsiekte sheep retrovirus envelope glycoprotein, Virology, vol.350, issue.2, pp.347-57, 2006.

M. Mura, Late viral interference induced by transdominant Gag of an endogenous retrovirus, Proc Natl Acad Sci U S A, vol.101, issue.30, pp.11117-11139, 2004.

J. D. Boeke and J. P. Stoye, Retrotransposons, Endogenous Retroviruses, and the Evolution of Retroelements, pp.343-436, 1997.

J. Coffin, Retroviridae and their replication, pp.1437-1500, 1990.

J. M. Coffin, Evolution of retroviruses: fossils in our DNA, Proc Am Philos Soc, vol.148, issue.3, pp.264-80, 2004.

J. Denner, . Endogenous, R. Pathogenesis, N. Kurth, and . Bannert, Retroviruses: Molecular biology, genomics, pp.35-69, 2010.

P. Jern, G. O. Sperber, and J. Blomberg, Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy, Retrovirology, vol.2, p.50, 2005.

J. M. Coffin, Structure and classification of retroviruses, in The retroviridae, pp.19-49, 1992.

N. Bannert, U. Fiebig, and O. Hohn, Retroviral particles, proteins and genomes, Retroviruses: Molecular Biology, 2010.

F. H. Lv, Mitogenomic Meta-Analysis Identifies Two Phases of Migration in the History of Eastern Eurasian Sheep, Mol Biol Evol, vol.32, issue.10, pp.2515-2548, 2015.

R. Zheng, T. M. Jenkins, and R. Craigie, Zinc folds the N-terminal domain of HIV-1 integrase, promotes multimerization, and enhances catalytic activity, Proc Natl Acad Sci, vol.93, issue.24, pp.13659-64, 1996.

M. H. Nymark-mcmahon and S. B. Sandmeyer, Mutations in nonconserved domains of Ty3 integrase affect multiple stages of the Ty3 life cycle, J Virol, vol.73, issue.1, pp.453-65, 1999.

C. N. Ting, Endogenous retroviral sequences are required for tissue-specific expression of a human salivary amylase gene, Genes Dev, vol.6, issue.8, pp.1457-65, 1992.

A. M. Schulte, Human trophoblast and choriocarcinoma expression of the growth factor pleiotrophin attributable to germ-line insertion of an endogenous retrovirus, Proc Natl Acad Sci, vol.93, issue.25, pp.14759-64, 1996.

L. K. Johansen and C. D. Morrow, Inherent instability of poliovirus genomes containing two internal ribosome entry site (IRES) elements supports a role for the IRES in encapsidation, J Virol, vol.74, issue.18, pp.8335-8377, 2000.

L. Cavarec, Molecular cloning and characterization of a transcription factor for the copia retrotransposon with homology to the BTB-containing lola neurogenic factor, Mol Cell Biol, vol.17, issue.1, pp.482-94, 1997.
URL : https://hal.archives-ouvertes.fr/hal-01925040

C. Conte, B. Dastugue, and C. Vaury, Promoter competition as a mechanism of transcriptional interference mediated by retrotransposons, EMBO J, vol.21, issue.14, pp.3908-3924, 2002.
URL : https://hal.archives-ouvertes.fr/hal-01924003

L. V. Matyunina, I. K. Jordan, and J. F. Mcdonald, Naturally occurring variation in copia expression is due to both element (cis) and host (trans) regulatory variation, Proc Natl Acad Sci, vol.93, issue.14, pp.7097-102, 1996.

D. B. Smith, Variation of the hepatitis C virus 5' non-coding region: implications for secondary structure, virus detection and typing. The International HCV Collaborative Study Group, J Gen Virol, vol.76, pp.1749-61, 1995.

G. M. Wilson, M. Z. Vasa, and R. G. Deeley, Stabilization and cytoskeletalassociation of LDL receptor mRNA are mediated by distinct domains in its 3' untranslated region, J Lipid Res, vol.39, issue.5, pp.1025-1057, 1998.

D. S. Dimitrov, How do viruses enter cells? The HIV coreceptors teach us a lesson of complexity, Cell, vol.91, issue.6, pp.721-751, 1997.

S. P. Goff, Retroviridae: The retroviruses and their replication, pp.1871-1940, 2001.

S. P. Goff, Host factors exploited by retroviruses, Nat Rev Microbiol, vol.5, issue.4, pp.253-63, 2007.

V. P. Basu, Strand transfer events during HIV-1 reverse transcription, Virus Res, vol.134, issue.1-2, pp.19-38, 2008.

A. Telesnitsky and S. P. Goff, Reverse Transcriptase and the Generation of Retroviral DNA, 1997.

E. Nowak, Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid, Nucleic Acids Res, vol.41, issue.6, pp.3874-87, 2013.

P. O. Brown, Integration, pp.161-204, 1997.

S. F. Yu, Human foamy virus replication: a pathway distinct from that of retroviruses and hepadnaviruses, Science, vol.271, issue.5255, pp.1579-82, 1996.

D. G. Demirov and E. O. Freed, Retrovirus budding. Virus Res, vol.106, pp.87-102, 2004.

M. Palmarini, Jaagsiekte sheep retrovirus is necessary and sufficient to induce a contagious lung cancer in sheep, J Virol, vol.73, issue.8, pp.6964-72, 1999.

M. Palmarini and H. Fan, Retrovirus-induced ovine pulmonary adenocarcinoma, an animal model for lung cancer, J Natl Cancer Inst, vol.93, issue.21, pp.1603-1617, 2001.

R. C. Tustin and J. Ovine, Journal of South African Veterinary Medical Association, vol.40, pp.3-23, 1969.

R. C. Tustin, Experimental transmission of jaagsiekte (ovine pulmonary adenomatosis) to goats, Onderstepoort J Vet Res, vol.55, issue.1, pp.27-32, 1988.

D. F. York and G. Querat, A history of ovine pulmonary adenocarcinoma (jaagsiekte) and experiments leading to the deduction of the JSRV nucleotide sequence, Curr Top Microbiol Immunol, vol.275, pp.1-23, 2003.

D. W. Verwoerd and E. M. De-villiers, On the aetiology of Jaagsiekte, J S Afr Vet Assoc, vol.51, issue.2, pp.71-75, 1980.

J. M. Sharp, Rapid transmission of sheep pulmonary adenomatosis (jaagsiekte) in young lambs, Arch Virol, vol.78, issue.1-2, pp.89-95, 1983.

M. Palmarini, Jaagsiekte retrovirus establishes a disseminated infection of the lymphoid tissues of sheep affected by pulmonary adenomatosis, J Gen Virol, vol.77, pp.2991-2999, 1996.

D. J. Griffiths, H. M. Martineau, and C. Cousens, Pathology and pathogenesis of ovine pulmonary adenocarcinoma, J Comp Pathol, vol.142, issue.4, pp.260-83, 2010.

J. M. Sharp and J. C. Demartini, Natural history of JSRV in sheep, Curr Top Microbiol Immunol, vol.275, pp.55-79, 2003.

M. De-las-heras, L. Gonzalez, and J. M. Sharp, Pathology of ovine pulmonary adenocarcinoma. Current Topics in Microbiology and Immunology, vol.275, pp.25-54, 2003.

O. Oie and . Pulmonary-adenocarcinoma, Terrestrial Manual, 2014.

C. Cousens, Prevalence of ovine pulmonary adenocarcinoma (Jaagsiekte) in a UK slaughterhouse sheep study, Vet Rec, vol.176, issue.16, p.413, 2015.

C. Cousens, Jaagsiekte sheep retrovirus is present at high concentration in lung fluid produced by ovine pulmonary adenocarcinoma-affected sheep and can survive for several weeks at ambient temperatures, Res Vet Sci, vol.87, issue.1, pp.154-160, 2009.

H. Fan, M. Palmarini, and J. C. Demartini, Transformation and oncogenesis by jaagsiekte sheep retrovirus, Curr Top Microbiol Immunol, vol.275, pp.139-77, 2003.

M. Caporale, Infection of lung epithelial cells and induction of pulmonary adenocarcinoma is not the most common outcome of naturally occurring JSRV infection during the commercial lifespan of sheep, Virology, vol.338, issue.1, pp.144-53, 2005.

E. Grego, Colostrum and milk can transmit jaagsiekte retrovirus to lambs, Vet Microbiol, vol.130, pp.247-57, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00532390

M. Caporale, Host species barriers to Jaagsiekte sheep retrovirus replication and carcinogenesis, J Virol, vol.87, pp.10752-62, 2013.

A. Ortin, Lack of a specific immune response against a recombinant capsid protein of Jaagsiekte sheep retrovirus in sheep and goats naturally affected by enzootic nasal tumour or sheep pulmonary adenomatosis, Vet Immunol Immunopathol, vol.61, issue.2-4, pp.229-266, 1998.

T. E. Spencer, Receptor usage and fetal expression of ovine endogenous betaretroviruses: implications for coevolution of endogenous and exogenous retroviruses, J Virol, vol.77, issue.1, pp.749-53, 2003.

S. Sun, J. H. Schiller, and A. F. Gazdar, Lung cancer in never smokers--a different disease, Nat Rev Cancer, vol.7, issue.10, pp.778-90, 2007.

K. Perk, I. Hod, and T. A. Nobel, Pulmonary adenomatosis of sheep (jaagsiekte). I. Ultrastructure of the tumor, J Natl Cancer Inst, vol.46, issue.3, pp.525-562, 1971.

U. Pott, A new Cys2/His2 zinc finger gene, rKr2, is expressed in differentiated rat oligodendrocytes and encodes a protein with a functional repressor domain, J Neurochem, vol.65, issue.5, pp.1955-66, 1995.

M. Palmarini, H. Fan, and J. M. Sharp, Sheep pulmonary adenomatosis: a unique model of retrovirus-associated lung cancer, Trends Microbiol, vol.5, issue.12, pp.478-83, 1997.

C. Leroux, Jaagsiekte Sheep Retrovirus (JSRV): from virus to lung cancer in sheep, Vet Res, vol.38, issue.2, pp.211-239, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00902865

A. D. Miller, Evidence against a role for jaagsiekte sheep retrovirus in human lung cancer, Retrovirology, vol.14, issue.1, p.3, 2017.

M. Palmarini and H. Fan, Molecular biology of jaagsiekte sheep retrovirus, Curr Top Microbiol Immunol, vol.275, pp.81-115, 2003.

D. F. York, Nucleotide sequence of the jaagsiekte retrovirus, an exogenous and endogenous type D and B retrovirus of sheep and goats, J Virol, vol.66, issue.8, pp.4930-4939, 1992.

S. Rosati, An accessory open reading frame (orf-x) of jaagsiekte sheep retrovirus is conserved between different virus isolates, Virus Res, vol.66, issue.1, pp.109-125, 2000.

N. Maeda, Direct transformation of rodent fibroblasts by jaagsiekte sheep retrovirus DNA, Proc Natl Acad Sci, vol.98, issue.8, pp.4449-54, 2001.

M. Varela, T. E. Spencer, M. Palmarini, and F. Arnaud, Friendly viruses: the special relationship between endogenous retroviruses and their host, Ann N Y Acad Sci, vol.1178, pp.157-72, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01608511

J. C. Demartini, Retrovirus-induced lung cancer: mechanisms of transformation of alveolar type II epithelial cells, Chest, vol.125, issue.5, pp.106-113, 2004.

S. K. Wootton, C. L. Halbert, and A. D. Miller, Sheep retrovirus structural protein induces lung tumours, Nature, vol.434, issue.7035, pp.904-911, 2005.

M. Caporale, Expression of the jaagsiekte sheep retrovirus envelope glycoprotein is sufficient to induce lung tumors in sheep, J Virol, vol.80, issue.16, pp.8030-8037, 2006.

J. C. Demartini, Jaagsiekte sheep retrovirus proviral clone JSRV(JS7), derived from the JS7 lung tumor cell line, induces ovine pulmonary carcinoma and is integrated into the surfactant protein A gene, J Virol, vol.75, issue.9, pp.4239-4285, 2001.

S. L. Liu and A. D. Miller, Oncogenic transformation by the jaagsiekte sheep retrovirus envelope protein, Oncogene, vol.26, issue.6, pp.789-801, 2007.

T. E. Allen, The jaagsiekte sheep retrovirus envelope gene induces transformation of the avian fibroblast cell line DF-1 but does not require a conserved SH2 binding domain, J Gen Virol, vol.83, pp.2733-2775, 2002.

S. L. Liu and A. D. Miller, Transformation of madin-darby canine kidney epithelial cells by sheep retrovirus envelope proteins, J Virol, vol.79, issue.2, pp.927-960, 2005.

S. K. Rai, Candidate tumor suppressor HYAL2 is a glycosylphosphatidylinositol (GPI)-anchored cell-surface receptor for jaagsiekte sheep retrovirus, the envelope protein of which mediates oncogenic transformation, Proc Natl Acad Sci, vol.98, issue.8, pp.4443-4451, 2001.

E. Chitra, Generation and characterization of JSRV envelope transgenic mice in FVB background, Virology, vol.393, issue.1, pp.120-126, 2009.

A. Hofacre and H. Fan, Jaagsiekte sheep retrovirus biology and oncogenesis. Viruses, vol.2, pp.2618-2666, 2011.

A. Hofacre and H. Fan, Jaagsiekte sheep retrovirus biology and oncogenesis. Viruses, vol.2, pp.2618-2666, 2010.

M. Cully, Beyond PTEN mutations: the PI3K pathway as an integrator of multiple inputs during tumorigenesis, Nat Rev Cancer, vol.6, issue.3, pp.184-92, 2006.

A. Brunet, Akt promotes cell survival by phosphorylating and inhibiting a Forkhead transcription factor, Cell, vol.96, issue.6, pp.857-68, 1999.

A. Danilkovitch-miagkova, Hyaluronidase 2 negatively regulates RON receptor tyrosine kinase and mediates transformation of epithelial cells by jaagsiekte sheep retrovirus, Proc Natl Acad Sci, vol.100, issue.8, pp.4580-4585, 2003.

S. Hull and H. Fan, Mutational analysis of the cytoplasmic tail of jaagsiekte sheep retrovirus envelope protein, J Virol, vol.80, issue.16, pp.8069-80, 2006.

N. Maeda and H. Fan, Signal transduction pathways utilized by enzootic nasal tumor virus (ENTV-1) envelope protein in transformation of rat epithelial cells resemble those used by jaagsiekte sheep retrovirus, Virus Genes, vol.36, issue.1, pp.147-55, 2008.

C. Murgia, Lung adenocarcinoma originates from retrovirus infection of proliferating type 2 pneumocytes during pulmonary post-natal development or tissue repair, PLoS Pathog, vol.7, issue.3, p.1002014, 2011.

A. Berns, Stem cells for lung cancer? Cell, vol.121, pp.811-814, 2005.

C. F. Kim, Identification of bronchioalveolar stem cells in normal lung and lung cancer. Cell, vol.121, pp.823-858, 2005.

C. Dirks, Mechanism of cell entry and transformation by enzootic nasal tumor virus, J Virol, vol.76, issue.5, pp.2141-2150, 2002.

A. D. Miller, Identification of Hyal2 as the cell-surface receptor for jaagsiekte sheep retrovirus and ovine nasal adenocarcinoma virus, Curr Top Microbiol Immunol, vol.275, pp.179-99, 2003.

G. Lepperdinger, J. Mullegger, and G. Kreil, Hyal2--less active, but more versatile? Matrix Biol, vol.20, pp.509-523, 2001.

V. Vigdorovich, R. K. Strong, and A. D. Miller, Expression and characterization of a soluble, active form of the jaagsiekte sheep retrovirus receptor, Hyal2, J Virol, vol.79, issue.1, pp.79-86, 2005.

V. Vigdorovich, A. D. Miller, and R. K. Strong, Ability of hyaluronidase 2 to degrade extracellular hyaluronan is not required for its function as a receptor for jaagsiekte sheep retrovirus, J Virol, vol.81, issue.7, pp.3124-3133, 2007.

M. Palmarini, The long terminal repeat of Jaagsiekte sheep retrovirus is preferentially active in differentiated epithelial cells of the lungs, J Virol, vol.74, issue.13, pp.5776-87, 2000.

K. Mcgee-estrada and H. Fan, In vivo and in vitro analysis of factor binding sites in Jaagsiekte sheep retrovirus long terminal repeat enhancer sequences: roles of HNF-3, NF-I, and C/EBP for activity in lung epithelial cells, J Virol, vol.80, issue.1, pp.332-373, 2006.

J. Bai, Sequence comparison of JSRV with endogenous proviruses: envelope genotypes and a novel ORF with similarity to a G-protein-coupled receptor, Virology, vol.258, issue.2, pp.333-376, 1999.

M. Palmarini, Molecular cloning and functional analysis of three type D endogenous retroviruses of sheep reveal a different cell tropism from that of the highly related exogenous jaagsiekte sheep retrovirus, J Virol, vol.74, issue.17, pp.8065-76, 2000.

F. Arnaud, Coevolution of endogenous betaretroviruses of sheep and their host, Cell Mol Life Sci, vol.65, issue.21, pp.3422-3454, 2008.

A. Armezzani, Menage a Trois": the evolutionary interplay between JSRV, enJSRVs and domestic sheep. Viruses, vol.6, pp.4926-4971, 2014.

F. Arnaud, P. R. Murcia, and M. Palmarini, Mechanisms of late restriction induced by an endogenous retrovirus, J Virol, vol.81, pp.11441-51, 1920.
URL : https://hal.archives-ouvertes.fr/hal-01601671

A. Armezzani, The signal peptide of a recently integrated endogenous sheep betaretrovirus envelope plays a major role in eluding gag-mediated late restriction, J Virol, vol.85, issue.14, pp.7118-7146, 2011.

B. Chessa, Revealing the history of sheep domestication using retrovirus integrations, Science, vol.324, issue.5926, pp.532-538, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01608619

M. W. Bruford, D. G. Bradley, and G. Luikart, DNA markers reveal the complexity of livestock domestication, Nat Rev Genet, vol.4, issue.11, pp.900-910, 2003.
URL : https://hal.archives-ouvertes.fr/halsde-00294790

E. D. Ladoukakis and E. Zouros, Evolution and inheritance of animal mitochondrial DNA: rules and exceptions, J Biol Res, vol.24, p.2, 2017.

B. Alberts, Molecular biology of the cell, vol.1294, 1994.

J. S. Penta, Mitochondrial DNA in human malignancy, Mutat Res, vol.488, issue.2, pp.119-152, 2001.

R. E. Giles, Maternal inheritance of human mitochondrial DNA, Proc Natl Acad Sci, vol.77, issue.11, pp.6715-6724, 1980.

J. I. Hayashi, Strictly maternal inheritance of rat mitochondrial DNA, Biochem Biophys Res Commun, vol.83, issue.3, pp.1032-1040, 1978.

C. A. Hutchison, Maternal inheritance of mammalian mitochondrial DNA, Nature, vol.251, issue.5475, pp.536-544, 1974.

U. Gyllensten, Paternal inheritance of mitochondrial DNA in mice, Nature, vol.352, issue.6332, pp.255-262, 1991.

G. Piganeau, M. Gardner, and A. Eyre-walker, A broad survey of recombination in animal mitochondria, Mol Biol Evol, vol.21, issue.12, pp.2319-2344, 2004.

G. Piganeau and A. Eyre-walker, A reanalysis of the indirect evidence for recombination in human mitochondrial DNA, Heredity (Edinb), vol.92, issue.4, pp.282-290, 2004.

L. J. Bailey and A. J. Doherty, Mitochondrial DNA replication: a PrimPol perspective, Biochem Soc Trans, vol.45, issue.2, pp.513-529, 2017.

J. W. Taanman, The mitochondrial genome: structure, transcription, translation and replication, Biochim Biophys Acta, vol.1410, issue.2, pp.103-126, 1999.

A. C. Wilson, Mitochondrial DNA and two perspectives on evolutionary genetics, Biological Journal of the Linnean Society, vol.26, issue.4, pp.375-400, 1985.

J. Avise, Intraspecific phylogeography -the mitochondrial-DNA bridge between population genetics and systematics, Annual Review of Ecology and Systematics, vol.18, pp.489-522, 1987.

L. Margulis, Symbiosis and evolution, Sci Am, vol.225, issue.2, pp.48-57, 1971.

M. W. Gray, G. Burger, and B. F. Lang, Mitochondrial evolution, Science, vol.283, issue.5407, pp.1476-81, 1999.

M. W. Gray, Rickettsia, typhus and the mitochondrial connection, Nature, vol.396, issue.6707, pp.109-119, 1998.

S. L. Baldauf, J. D. Palmer, and W. F. Doolittle, The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny, Proc Natl Acad Sci, vol.93, issue.15, pp.7749-54, 1996.

J. K. Harris, The genetic core of the universal ancestor, Genome Res, vol.13, issue.3, pp.407-419, 2003.

C. R. Woese, O. Kandler, and M. L. Wheelis, Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya, Proc Natl Acad Sci U S A, vol.87, issue.12, pp.4576-4585, 1990.

C. J. Cox, The archaebacterial origin of eukaryotes, Proc Natl Acad Sci, vol.105, issue.51, pp.20356-61, 2008.

D. F. Feng, G. Cho, and R. F. Doolittle, Determining divergence times with a protein clock: update and reevaluation, Proc Natl Acad Sci U S A, vol.94, issue.24, pp.13028-13061, 1997.

T. Sicheritz-ponten, C. G. Kurland, and S. G. Andersson, A phylogenetic analysis of the cytochrome b and cytochrome c oxidase I genes supports an origin of mitochondria from within the Rickettsiaceae, Biochim Biophys Acta, vol.1365, issue.3, pp.545-51, 1998.

Y. I. Wolf and E. V. Koonin, Genome reduction as the dominant mode of evolution, Bioessays, vol.35, issue.9, pp.829-866, 2013.

S. B. Vafai and V. K. Mootha, Mitochondrial disorders as windows into an ancient organelle, Nature, vol.491, issue.7424, pp.374-83, 2012.

L. M. Cree, A reduction of mitochondrial DNA molecules during embryogenesis explains the rapid segregation of genotypes, Nat Genet, vol.40, issue.2, pp.249-54, 2008.

S. G. Andersson and C. G. Kurland, Reductive evolution of resident genomes, Trends Microbiol, vol.6, issue.7, pp.263-271, 1998.

J. L. Boore, Animal mitochondrial genomes, Nucleic Acids Res, vol.27, issue.8, pp.1767-80, 1999.

T. Mourier, The Human Genome Project reveals a continuous transfer of large mitochondrial fragments to the nucleus, Mol Biol Evol, vol.18, issue.9, pp.1833-1840, 2001.

S. R. Lee and J. Han, Mitochondrial Nucleoid: Shield and Switch of the Mitochondrial Genome, Oxid Med Cell Longev, p.8060949, 2017.

N. S. Chandel, Evolution of Mitochondria as Signaling Organelles, Cell Metab, vol.22, issue.2, pp.204-210, 2015.

A. Sinha, Improving the vitamin D status of vitamin D deficient adults is associated with improved mitochondrial oxidative function in skeletal muscle, J Clin Endocrinol Metab, vol.98, issue.3, pp.509-522, 2013.

Z. Cheng and M. Ristow, Mitochondria and metabolic homeostasis, Antioxid Redox Signal, vol.19, issue.3, pp.240-242, 2013.

C. S. Ahn and C. M. Metallo, Mitochondria as biosynthetic factories for cancer proliferation, Cancer Metab, vol.3, issue.1, p.1, 2015.

E. D. Robin and R. Wong, Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells, J Cell Physiol, vol.136, issue.3, pp.507-520, 1988.

G. S. Michaels, W. W. Hauswirth, and P. J. Laipis, Mitochondrial DNA copy number in bovine oocytes and somatic cells, Dev Biol, vol.94, issue.1, pp.246-51, 1982.

R. C. Shuster, A. J. Rubenstein, and D. C. Wallace, Mitochondrial DNA in anucleate human blood cells, Biochem Biophys Res Commun, vol.155, issue.3, pp.1360-1365, 1988.

R. J. Wiesner, J. C. Ruegg, and I. Morano, Counting target molecules by exponential polymerase chain reaction: copy number of mitochondrial DNA in rat tissues, Biochem Biophys Res Commun, vol.183, issue.2, pp.553-562, 1992.

N. Galtier, Mitochondrial DNA as a marker of molecular diversity: a reappraisal, Mol Ecol, vol.18, issue.22, pp.4541-50, 2009.

S. Anderson, Sequence and organization of the human mitochondrial genome, Nature, vol.290, issue.5806, pp.457-65, 1981.

R. M. Andrews, Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA, Nat Genet, vol.23, issue.2, p.147, 1999.

S. Hiendleder, The complete mitochondrial DNA sequence of the domestic sheep (Ovis aries) and comparison with the other major ovine haplotype, J Mol Evol, vol.47, issue.4, pp.441-449, 1998.

D. R. Wolstenholme, Animal mitochondrial DNA: structure and evolution, Int Rev Cytol, vol.141, pp.173-216, 1992.

J. Battey and D. A. Clayton, The transcription map of mouse mitochondrial DNA, Cell, vol.14, issue.1, pp.143-56, 1978.

I. Dawid, The Genetic Function of Mitochondrial DNA, C. Saccone and A. Kroon, pp.3-13, 1976.

J. P. Uhler and M. Falkenberg, Primer removal during mammalian mitochondrial DNA replication, DNA Repair (Amst), vol.34, pp.28-38, 2015.

H. Kasamatsu and J. Vinograd, Replication of circular DNA in eukaryotic cells, Annu Rev Biochem, vol.43, issue.0, pp.695-719, 1974.

D. Ojala, J. Montoya, and G. Attardi, tRNA punctuation model of RNA processing in human mitochondria, Nature, vol.290, issue.5806, pp.470-474, 1981.

X. D. Hu and L. Z. Gao, The complete mitochondrial genome of domestic sheep, Ovis aries. Mitochondrial DNA A DNA Mapp Seq Anal, vol.27, pp.1425-1432, 2014.

S. Osawa, Recent evidence for evolution of the genetic code, Microbiol Rev, vol.56, issue.1, pp.229-64, 1992.

I. G. Macreadie, Biogenesis of mitochondria: the mitochondrial gene (aap1) coding for mitochondrial ATPase subunit 8 in Saccharomyces cerevisiae, Nucleic Acids Res, vol.11, issue.13, pp.4435-51, 1983.

A. Chomyn, URF6, last unidentified reading frame of human mtDNA, codes for an NADH dehydrogenase subunit, Science, vol.234, issue.4776, pp.614-622, 1986.

H. Li, Physiology and pathophysiology of mitochondrial DNA, Adv Exp Med Biol, vol.942, pp.39-51, 2012.

R. Kondo, Incomplete maternal transmission of mitochondrial DNA in Drosophila, Genetics, vol.126, issue.3, pp.657-63, 1990.

C. F. Aquadro and B. D. Greenberg, Human mitochondrial DNA variation and evolution: analysis of nucleotide sequences from seven individuals, Genetics, vol.103, issue.2, pp.287-312, 1983.

C. Saccone, G. Pesole, and E. Sbisa, The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern, J Mol Evol, vol.33, issue.1, pp.83-91, 1991.

D. Nesheva, Aspects of ancient mitochondrial DNA analysis in different populations for understanding human evolution, Balkan J Med Genet, vol.17, issue.1, pp.5-14, 2014.

M. Stoneking and H. Soodyall, Human evolution and the mitochondrial genome, Curr Opin Genet Dev, vol.6, issue.6, pp.731-737, 1996.

D. C. Wallace, M. D. Brown, and M. T. Lott, Mitochondrial DNA variation in human evolution and disease, Gene, vol.238, issue.1, pp.211-241, 1999.

C. W. Birky and . Jr, The inheritance of genes in mitochondria and chloroplasts: laws, mechanisms, and models, Annu Rev Genet, vol.35, pp.125-173, 2001.

P. Mishra and D. C. Chan, Mitochondrial dynamics and inheritance during cell division, development and disease, Nat Rev Mol Cell Biol, vol.15, issue.10, pp.634-680, 2014.

M. J. Moses, Spermiogenesis in the crayfish (Procambarus clarkii) II. Description of stages, J Biophys Biochem Cytol, vol.10, pp.301-334, 1961.

H. Ursprung and E. Schabtach, Fertilization in tunicates: loss of the paternal mitochondrion prior to sperm entry, J Exp Zool, vol.159, issue.3, pp.379-83, 1965.

W. Anderson, structure and fate of the parental mitochondrion during early embryogenesis of Paracentrotus lividus, Journal of Ultrastructure Research, vol.24, pp.311-321, 1968.

P. Sutovsky, Ubiquitin tag for sperm mitochondria, Nature, vol.402, issue.6760, pp.371-373, 1999.

M. Sato and K. Sato, Maternal inheritance of mitochondrial DNA by diverse mechanisms to eliminate paternal mitochondrial DNA, Biochim Biophys Acta, vol.1833, issue.8, pp.1979-84, 2013.

L. Piko and L. Matsumoto, Number of mitochondria and some properties of mitochondrial DNA in the mouse egg, Dev Biol, vol.49, issue.1, pp.1-10, 1976.

N. B. Hecht, Maternal inheritance of the mouse mitochondrial genome is not mediated by a loss or gross alteration of the paternal mitochondrial DNA or by methylation of the oocyte mitochondrial DNA, Dev Biol, vol.102, issue.2, pp.452-61, 1984.

M. S. Meusel and R. F. Moritz, Transfer of paternal mitochondrial DNA during fertilization of honeybee (Apis mellifera L.) eggs, Curr Genet, vol.24, issue.6, pp.539-582, 1993.

X. Zhao, Further evidence for paternal inheritance of mitochondrial DNA in the sheep (Ovis aries), vol.93, pp.399-403, 2004.

H. Kaneda, Elimination of paternal mitochondrial DNA in intraspecific crosses during early mouse embryogenesis, Proc Natl Acad Sci, vol.92, issue.10, pp.4542-4548, 1995.

L. Kvist, Paternal leakage of mitochondrial DNA in the great tit (Parus major), Mol Biol Evol, vol.20, issue.2, pp.243-250, 2003.

E. Zouros, Direct evidence for extensive paternal mitochondrial DNA inheritance in the marine mussel Mytilus, Nature, vol.359, issue.6394, pp.412-416, 1992.

M. Schwartz and J. Vissing, Paternal inheritance of mitochondrial DNA, N Engl J Med, vol.347, issue.8, pp.576-80, 2002.

B. Pakendorf and M. Stoneking, Mitochondrial DNA and human evolution, Annu Rev Genomics Hum Genet, vol.6, pp.165-83, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02012633

N. G. Larsson and D. A. Clayton, Molecular genetic aspects of human mitochondrial disorders, Annu Rev Genet, vol.29, pp.151-78, 1995.

N. Howell, Mitochondrial gene segregation in mammals: is the bottleneck always narrow? Hum Genet, vol.90, pp.117-137, 1992.

C. T. Bergstrom and J. Pritchard, Germline bottlenecks and the evolutionary maintenance of mitochondrial genomes, Genetics, vol.149, issue.4, pp.2135-2181, 1998.

J. Felsenstein, The evolutionary advantage of recombination, Genetics, vol.78, issue.2, pp.737-56, 1974.

B. A. Mcleod and B. N. White, Tracking mtDNA heteroplasmy through multiple generations in the North Atlantic right whale (Eubalaena glacialis), J Hered, vol.101, issue.2, pp.235-244, 2009.

W. M. Brown, M. George, J. , and A. C. Wilson, Rapid evolution of animal mitochondrial DNA, Proc Natl Acad Sci, vol.76, issue.4, pp.1967-71, 1979.

M. Ingman, Mitochondrial genome variation and the origin of modern humans, Nature, vol.408, issue.6813, pp.708-721, 2000.

H. J. Muller, The Relation of Recombination to Mutational Advance, Mutat Res, vol.106, pp.2-9, 1964.

R. W. Taylor and D. M. Turnbull, Mitochondrial DNA mutations in human disease, Nat Rev Genet, vol.6, issue.5, pp.389-402, 2005.

M. Krings, Neandertal DNA sequences and the origin of modern humans, Cell, vol.90, issue.1, pp.19-30, 1997.

C. Gissi, Lineage-specific evolutionary rate in mammalian mtDNA, Mol Biol Evol, vol.17, issue.7, pp.1022-1053, 2000.

D. Bensasson, Mitochondrial pseudogenes: evolution's misplaced witnesses, Trends Ecol Evol, vol.16, issue.6, pp.314-321, 2001.

J. W. Ballard and M. C. Whitlock, The incomplete natural history of mitochondria, Mol Ecol, vol.13, issue.4, pp.729-773, 2004.

J. W. Ballard and D. M. Rand, The population biology of mitochondrial DNA and its phylogenetic implications, Annual Review Of Ecology Evolution And Systematics, vol.36, pp.621-642, 2005.

J. C. Avise, Molecular Markers, Natural History, and Evolution, vol.511, 1994.

C. W. Birky, P. Jr, T. Fuerst, and . Maruyama, Organelle gene diversity under migration, mutation, and drift: equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells, and comparison to nuclear genes, Genetics, vol.121, issue.3, pp.613-640, 1989.

G. Leroy, How do introgression events shape the partitioning of diversity among breeds: a case study in sheep, Genet Sel Evol, vol.47, p.48, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01194138

C. Y. Liu, Mitochondrial DNA mutation and depletion increase the susceptibility of human cells to apoptosis, Ann N Y Acad Sci, vol.1011, pp.133-178, 2004.

G. Attardi, Identification and mapping of human mitochondrial genes, Cytogenet Cell Genet, vol.32, issue.1-4, pp.85-98, 1982.

D. L. Nelson and M. M. , Lehninger Principles of Biochemistry, 2000.

P. Linke and H. Weiss, Reconstitution of ubiquinol-cytochrome-c reductase from Neurospora mitochondria with regard to subunits I and II, Methods Enzymol, vol.126, pp.201-211, 1986.

M. D. Crivellone, M. A. Wu, and A. Tzagoloff, Analysis of structural mutants of the yeast coenzyme QH2-cytochrome c reductase complex, J Biol Chem, vol.263, issue.28, pp.14323-14356, 1988.

P. Oudshoorn, Nucleotide sequence of the gene and features of the protein, Eur J Biochem, vol.163, issue.1, pp.97-103, 1987.

A. Tzagoloff, M. A. Wu, and M. Crivellone, Assembly of the mitochondrial membrane system. Characterization of COR1, the structural gene for the 44-kilodalton core protein of yeast coenzyme QH2-cytochrome c reductase, J Biol Chem, vol.261, issue.36, pp.17163-17172, 1986.

M. D. Esposti, Mitochondrial cytochrome b: evolution and structure of the protein, Biochim Biophys Acta, vol.1143, issue.3, pp.243-71, 1993.

M. Wikstrom and K. Krab, The semiquinone cycle. A hypothesis of electron transfer and proton translocation in cytochrome bc-type complexes, J Bioenerg Biomembr, vol.18, issue.3, pp.181-93, 1986.

M. Saraste, Location of haem-binding sites in the mitochondrial cytochrome b, FEBS Lett, vol.166, issue.2, pp.367-72, 1984.

B. L. Trumpower, Cytochrome bc1 complexes of microorganisms, Microbiol Rev, vol.54, issue.2, pp.101-130, 1990.

L. Vigilant, Mitochondrial DNA sequences in single hairs from a southern African population, Proc Natl Acad Sci, vol.86, issue.23, pp.9350-9354, 1989.

D. M. Irwin, T. D. Kocher, and A. C. Wilson, Evolution of the cytochrome b gene of mammals, J Mol Evol, vol.32, issue.2, pp.128-172, 1991.

A. Meyer, Shortcomings Of The Cytochrome-b Gene As A Molecular Marker, Trends In Ecology & Evolution, vol.9, pp.278-280, 1994.

J. Castresana, Cytochrome b phylogeny and the taxonomy of great apes and mammals, Mol Biol Evol, vol.18, issue.4, pp.465-71, 2001.

S. Seddigh and M. Darabi, Functional, structural, and phylogenetic analysis of mitochondrial cytochrome b (cytb) in insects, Mitochondrial DNA A DNA Mapp Seq Anal, pp.1-17, 2017.

H. R. Rezaei, Phylogénie moléculaire du Genre Ovis (Mouton et Mouflons), Implications pour la Conservation du Genre et pour l'Origine de l'Espèce Domestique, in Ecologie, Environnement, p.175, 2007.

V. I. Tsalkin, European and Asian mountain sheep (Gornje barany evropy i asii)

M. Obshchest, . Iss, and . Privody, Moscow Society of Naturalists Zool. Sect.(Moskovskoe Obshchest. Isp. Prirody) Materials for the recognition of the fauna and flora of the USSR 27, 1951.

T. Haltenorth, Klassification der Saugethiere: artiodactyla. Handbuch der Zoologie?, vol.8, 1963.

R. Valdez, The wild sheep of the world, 1982.

D. Wilson and D. Reeder, Mammal species of the world: a taxonomic and geographic reference. Second edn, 1993.

C. F. Nadler, Cytogenetic differentiation, geographic distribution and domestication of palaearctic sheep (Ovis), vol.38, pp.109-125, 1973.

T. J. Nicholls and M. Minczuk, D-loop: 40 years of mitochondrial 7S DNA, vol.56, pp.175-81, 2014.

M. W. Walberg and D. A. Clayton, Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA, Nucleic Acids Res, vol.9, pp.5411-5432, 1920.

J. N. Doda, C. T. Wright, and D. A. Clayton, Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences, Proc Natl Acad Sci, vol.78, issue.10, pp.6116-6136, 1981.

C. Saccone, M. Attimonelli, and E. Sbisa, Structural elements highly preserved during the evolution of the D-loop-containing region in vertebrate mitochondrial DNA, J Mol Evol, vol.26, issue.3, pp.205-216, 1987.

T. A. Brown and D. A. Clayton, Release of replication termination controls mitochondrial DNA copy number after depletion with 2',3'-dideoxycytidine, Nucleic Acids Res, vol.30, issue.9, pp.2004-2014, 2002.

R. Zardoya, Nucleotide sequence of the sheep mitochondrial DNA D-loop and its flanking tRNA genes, Curr Genet, vol.28, issue.1, pp.94-100, 1995.

D. A. Clayton, Transcription and replication of mitochondrial DNA, Hum Reprod, vol.15, issue.2, pp.11-18, 2000.

X. H. Pham, Conserved sequence box II directs transcription termination and primer formation in mitochondria, J Biol Chem, vol.281, issue.34, pp.24647-52, 2006.

J. R. Brown, A. T. Beckenbach, and M. J. Smith, Intraspecific DNA sequence variation of the mitochondrial control region of white sturgeon (Acipenser transmontanus), Mol Biol Evol, vol.10, issue.2, pp.326-367, 1993.

S. K. Sharawat, Mitochondrial D-loop variations in paediatric acute myeloid leukaemia: a potential prognostic marker, Br J Haematol, vol.149, issue.3, pp.391-399, 2010.

E. Mambo, Electrophile and oxidant damage of mitochondrial DNA leading to rapid evolution of homoplasmic mutations, Proc Natl Acad Sci, vol.100, issue.4, pp.1838-1881, 2003.

D. Bogenhagen and D. A. Clayton, Mouse L cell mitochondrial DNA molecules are selected randomly for replication throughout the cell cycle, Cell, vol.11, issue.4, pp.719-746, 1977.

G. S. Shadel and D. A. Clayton, Mitochondrial DNA maintenance in vertebrates, Annu Rev Biochem, vol.66, pp.409-444, 1997.

D. A. Clayton, Transcription and replication of animal mitochondrial DNAs, Int Rev Cytol, vol.141, pp.217-249, 1992.

D. Y. Lee and D. A. Clayton, Properties of a primer RNA-DNA hybrid at the mouse mitochondrial DNA leading-strand origin of replication, J Biol Chem, vol.271, issue.39, pp.24262-24271, 1996.

D. A. Clayton, Replication of animal mitochondrial DNA, Cell, vol.28, issue.4, pp.693-705, 1982.

T. W. Wong and D. A. Clayton, In vitro replication of human mitochondrial DNA: accurate initiation at the origin of light-strand synthesis, Cell, vol.42, issue.3, pp.951-959, 1985.

J. E. Hixson, T. W. Wong, and D. A. Clayton, Both the conserved stem-loop and divergent 5'-flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication, J Biol Chem, vol.261, issue.5, pp.2384-90, 1986.

S. W. Graves, A. A. Johnson, and K. A. Johnson, Expression, purification, and initial kinetic characterization of the large subunit of the human mitochondrial DNA polymerase, Biochemistry, vol.37, issue.17, pp.6050-6058, 1998.

S. Wanrooij and M. Falkenberg, The human mitochondrial replication fork in health and disease, Biochim Biophys Acta, vol.1797, issue.8, pp.1378-88, 2010.

N. Lecrenier and F. Foury, New features of mitochondrial DNA replication system in yeast and man, Gene, vol.246, issue.1-2, pp.37-48, 2000.

E. A. Mckinney and M. T. Oliveira, Replicating animal mitochondrial DNA, Genet Mol Biol, vol.36, issue.3, pp.308-323, 2013.

I. J. Holt, H. E. Lorimer, and H. T. Jacobs, Coupled leading-and lagging-strand synthesis of mammalian mitochondrial DNA, Cell, vol.100, issue.5, pp.515-539, 2000.

M. Y. Yang, Biased incorporation of ribonucleotides on the mitochondrial Lstrand accounts for apparent strand-asymmetric DNA replication, Cell, vol.111, issue.4, pp.495-505, 2002.

T. Yasukawa, Replication of vertebrate mitochondrial DNA entails transient ribonucleotide incorporation throughout the lagging strand, EMBO J, vol.25, issue.22, pp.5358-71, 2006.

J. R. Meadows, S. Hiendleder, and J. W. Kijas, Haplogroup relationships between domestic and wild sheep resolved using a mitogenome panel, Heredity (Edinb), vol.106, issue.4, pp.700-706, 2010.

B. Mw, S. Townsend, and ;. Z. Ma, Mitochondrial DNA diversity in modern sheep: implications for domestication, Documenting domestication. New genetics and archaeological paradigms, pp.306-316, 2006.

S. Pedrosa, Mitochondrial diversity and the origin of Iberian sheep, Genet Sel Evol, vol.39, issue.1, pp.91-103, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00894576

N. J. Wood and S. H. Phua, Variation in the control region sequence of the sheep mitochondrial genome, Anim Genet, vol.27, issue.1, pp.25-33, 1996.

J. Guo, A novel maternal lineage revealed in sheep (Ovis aries), Anim Genet, vol.36, issue.4, pp.331-337, 2005.

S. Y. Chen, Origin, genetic diversity, and population structure of Chinese domestic sheep, Gene, vol.376, issue.2, pp.216-239, 2006.

S. Demirci, Mitochondrial DNA diversity of modern, ancient and wild sheep(Ovis gmelinii anatolica) from Turkey: new insights on the evolutionary history of sheep, PLoS One, vol.8, issue.12, p.81952, 2013.

J. Liu, Genetic Diversity and Phylogenetic Evolution of Tibetan Sheep Based on mtDNA D-Loop Sequences, PLoS One, vol.11, issue.7, p.159308, 2016.

G. Luikart, Multiple maternal origins and weak phylogeographic structure in domestic goats, Proc Natl Acad Sci, vol.98, issue.10, pp.5927-5959, 2001.
URL : https://hal.archives-ouvertes.fr/halsde-00279805

C. Olivieri, Phylogenetic position of a copper age sheep (Ovis aries) mitochondrial DNA, PLoS One, vol.7, issue.3, p.33792, 2012.

J. R. Meadows, Mitochondrial sequence reveals high levels of gene flow between breeds of domestic sheep from Asia and Europe, J Hered, vol.96, issue.5, pp.494-501, 2005.

M. Niemi, Mitochondrial DNA and Y-chromosomal diversity in ancient populations of domestic sheep (Ovis aries) in Finland: comparison with contemporary sheep breeds, Genet Sel Evol, vol.45, p.2, 2013.

F. Sanger, Use of DNA polymerase I primed by a synthetic oligonucleotide to determine a nucleotide sequence in phage fl DNA, Proc Natl Acad Sci, vol.70, issue.4, pp.1209-1222, 1973.

M. Nei, Molecular Evolutionary Genetics, 1987.

M. A. Jobling, M. E. Hurles, and C. Tyler-smith, Human Evolutionary Genetics: origins, peoples and disease, 2004.

Y. X. Fu, Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection, Genetics, vol.147, issue.2, pp.915-940, 1997.

F. Tajima, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, vol.123, issue.3, pp.585-95, 1989.

P. R. Hunter, Reproducibility and indices of discriminatory power of microbial typing methods, J Clin Microbiol, vol.28, issue.9, pp.1903-1908, 1990.

O. Schroeder, Endogenous Retroviral Insertions Indicate a Secondary Introduction of Domestic Sheep Lineages to the Caucasus and Central Asia between the Bronze and Iron Age, Genes, issue.8, 2017.

M. Tapio, Native breeds demonstrate high contributions to the molecular variation in northern European sheep, Mol Ecol, vol.14, issue.13, pp.3951-63, 2005.

M. Nei and W. H. Li, Mathematical model for studying genetic variation in terms of restriction endonucleases, Proc Natl Acad Sci, vol.76, issue.10, pp.5269-73, 1979.

A. R. Rogers and H. Harpending, Population growth makes waves in the distribution of pairwise genetic differences, Mol Biol Evol, vol.9, issue.3, pp.552-69, 1992.

J. R. Meadows, Globally dispersed Y chromosomal haplotypes in wild and domestic sheep, Anim Genet, vol.37, issue.5, pp.444-53, 2006.

M. Uzun, Genetic relationships among Turkish sheep, Genet Sel Evol, vol.38, issue.5, pp.513-537, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00894543

C. Peter, Genetic diversity and subdivision of 57 European and MiddleEastern sheep breeds, Anim Genet, vol.38, issue.1, pp.37-44, 2007.

D. L. Mager and J. P. Stoye, Mammalian Endogenous Retroviruses. Microbiol Spectr, vol.3, issue.1, pp.3-0009, 2015.

?. C. Ayano?lu, . Revealing, . History, . Anatolian, . Domestication et al., THE GRADUATE SCHOOL OF NATURAL AND APPLIED SCIENCES OF MIDDLE EAST TECHNICAL UNIVERSITY, Biology, p.133, 2013.

F. Archer, Alveolar type II cells isolated from pulmonary adenocarcinoma: a model for JSRV expression in vitro, Am J Respir Cell Mol Biol, vol.36, issue.5, pp.534-574, 2007.

E. Ibrahim, A. Sirawan, B. El-bazzal, E. Hage, J. et al., Complete genome sequence of the first H5N1 avian influenza virus isolated from chickens in Lebanon in 2016, Genome Announc, vol.4, issue.5, pp.1062-1078, 2016.

A. E. Romeh, B. Zecchin, A. Fusaro, E. Ibrahim, B. E. Bazzal et al., Highly Pathogenic Avian Influenza H5N1 Clade 2.3.2.1c Virus in Lebanon, vol.61, pp.271-273, 2016.

A. Abi-rizk, T. Kanaan, and J. E. Hage, Seroprevalence of Schmallenberg virus and other Simbu group viruses among the Lebanese sheep, Open Veterinary Journal, vol.7, issue.3, pp.290-293, 2017.

, Complete Genome Sequence of the First H5N1 Avian Influenza Virus Isolated from Chickens in Lebanon, 2016.

, Then, they spread widely and, p.1997

-. , P. A. , P. Ha, and N. A. Np, Germany) according to the manufacturer's protocol. The first-strand cDNA was synthesized using Superscript III reverse transcriptase (Invitrogen, CA) and Uni-12 primer (5= AGCRAAAGCAGG3=) per manufacturer's protocol. Genes were amplified using the Phusion master mix kit (Thermo, MA) and universal primers (4), (H5N1) virus was isolated from infected chickens. Viral RNA was extracted using a QIAamp viral RNA minikit, vol.1, p.542

S. , The virus had an NA substitution V149A that potentially reduced susceptibility to zanamivir (7). Mutations E627K and D701N in the PB2 that facilitate the adaptation of avian viruses to mammals, and increase transmission and/or pathogenicity (8, 9), were not recorded. The BLASTn and phylogenetic analysis of all eight segments revealed that the virus was closely related to the recent clade 2.3.2.1c viruses that circulated in West Africa (Ivory Coast, Niger, and Ghana) and India with high sequence homologies (98 to 99%)

K. F. Shortridge, N. N. Zhou, Y. Guan, P. Gao, T. Ito et al., Characterization of avian H5N1 influenza viruses from poultry in Hong Kong, Virology, vol.252, pp.331-342, 1998.

G. J. Smith and R. O. Donis, World Health Organization/World Organisation for Animal HF, Agriculture Organization HEWG, 2015.

C. Univ and . Bernard, and 2.3.4 during 2013-2014. Influenza Other Respir Viruses, vol.9, pp.271-276, 2016.

, H5N1 highly pathogenic avian influenza: Timeline of major events, 2014.

E. Hoffmann, J. Stech, Y. Guan, R. G. Webster, and D. R. Perez, Universal primer set for the full-length amplification of all influenza A viruses, Arch Virol, vol.146, pp.2275-2289, 2001.

S. Yamada, Y. Suzuki, T. Suzuki, M. Q. Le, C. A. Nidom et al., Haemagglutinin mutations responsible for the binding of H5N1 influenza A viruses to human-type receptors, Nature, vol.444, pp.378-382, 2006.

D. J. Tang, Y. M. Lam, Y. L. Siu, C. H. Lam, S. L. Chu et al., A single residue substitution in the receptor-binding domain of H5N1 hemagglutinin is critical for packaging into pseudotyped lentiviral particles, PLoS One, vol.7, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-00750639

M. Naughtin, J. C. Dyason, S. Mardy, S. Sorn, M. Von-itzstein et al., Neuraminidase inhibitor sensitivity and receptor-binding specificity of Cambodian clade 1 highly pathogenic H5N1 influenza virus, Antimicrob Agents Chemother, vol.55, 2004.

Y. Gao, Y. Zhang, K. Shinya, G. Deng, Y. Jiang et al., Identification of amino acids in HA and PB2 critical for the transmission of H5N1 avian influenza viruses in a mammalian host, PLOS Pathog, vol.5, 2009.

K. Shinya, S. Hamm, M. Hatta, H. Ito, T. Ito et al., PB2 amino acid at position 627 affects replicative efficiency, but not cell tropism, 2004.

, Hong Kong H5N1 influenza A viruses in mice, Virology, vol.320, pp.258-266

M. M. Naguib, J. Kinne, H. Chen, K. H. Chan, S. Joseph et al., Outbreaks of highly pathogenic avian influenza H5N1 clade 2.3.2.1c in hunting falcons and kept wild birds in Dubai implicate intercontinental virus spread, J Gen Virol, vol.96, pp.3212-3222, 2015.

, BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research

, Highly Pathogenic Avian Influenza H5N1 Clade 2.3.2.1c Virus in Lebanon, 2016.

B. Author-;-ali-el-romeh, A. Zecchin, E. Fusaro, B. E. Ibrahim, J. E. Bazzal et al., , vol.61, pp.271-273

, BioOne provides a sustainable online platform for over 170 journals and books published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Web site, and all posted and associated content indicates your acceptance of BioOne's Terms of Use, available at www.bioone.org/page/terms_of_use. Usage of BioOne content is strictly limited to personal, educational, and non-commercial use. Commercial inquiries or rights and permissions requests should be directed to the individual publisher as copyright holder. Case ReportHighly Pathogenic Avian, BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and environmental sciences, 2016.

A. E. Romeh, . Bianca-zecchin, A. Bd, E. Fusaro, . Ibrahim et al., Jdeidet El-Metin Fanar, Lebanon Received, vol.10, pp.90-1965, 2016.

, Our whole-genome sequencing analysis revealed that the Lebanese H5N1 virus belongs to genetic clade 2.3.2.1c and clusters with viruses from, Europe and West Africa, 2016.

. Resumen, Reporte de caso-Virus de la influenza aviar altamente patógena H5N1 Clado 2.3.2.1c en el Líbano, p.2016

, Se presenta el análisis filogenético del primer brote del virus de influenza aviar altamente patógena H5N1 detectado en avicultura en el Líbano en abril del 2016. El análisis de secuenciación de todo el genoma reveló que el virus H5N1 libanés pertenece al clado genético 2.3.2.1c y se agrupó con virus de Europa y ´ Africa Occidental. Key words: influenza A virus

, USA) technology, as described by Fusaro et al. of the eight gene segments of A/chicken/Lebanon/ 16vir-2783-20/2016 were submitted to GISAID under the accession numbers EPI774540 (HA gene), CA, vol.888808, p.888812

, NA gene), EPI888818 (MP gene), and EPI888820 (NS gene)

, Avian influenza: Iraq (WA) poultry, HPAI H5N1, spread. ProMed, 2016.

P. Murcia, G. Massi, L. Zamperin, S. Bonfanti, G. Marangon et al.,

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New algorithms and methods to estimate maximumlikelihood phylogenies: assessing the performance of PhyML 3.0, Syst. Biol, vol.59, pp.307-321, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

M. Naughtin, J. C. Dyason, S. Mardy, S. Sorn, M. Von-itzstein et al., Neuraminidase inhibitor sensitivity and receptor-binding specificity of Cambodian clade 1 highly pathogenic H5N1 influenza virus, Antimicrob. Agents Chemother, vol.55, issue.5, pp.2004-2010, 2011.

M. B. Pearce, C. Pappas, K. M. Gustin, C. T. Davis, M. J. Pantin-jackwood et al., , vol.502, pp.114-122, 2017.

G. J. Smith and R. O. Donis, World Health Organization/World 2a, 2.2.1, and 2.3.4 during 2013-2014. Influenza Other Respir, Viruses, vol.9, issue.5, pp.271-276, 2015.

L. Tassoni, A. Fusaro, A. Milani, P. Lemey, J. A. Awuni et al.,

O. Sedor, A. N. Dogbey, C. Commey, T. Meseko, G. L. Joannis et al., Genetically different highly pathogenic avian influenza A(H5N1) viruses in West Africa, Emerging Infect. Dis, vol.22, issue.12, pp.2132-2136, 2015.

Z. Y. Yang, C. J. Wei, W. P. Kong, L. Wu, L. Xu et al., animal-health-in-the-world/update-on-avian-influenza/2015/ 11. World Organization for Animal Health, WHO. Assessment of risk associated with influenza A(H5N8) virus, WHO, vol.317, pp.1825-1828, 2013.

R. S. Bennett, A. K. Gresko, B. R. Murphy, and S. S. Whitehead, Tahyna virus genetics, infectivity, and immunogenicity in mice and monkeys, Virol. J, vol.8, p.135, 2011.

N. Gibbens, Schmallenberg virus: a novel viral disease in northern Europe, Vet. Rec, vol.170, issue.2, p.58, 2012.

B. Hoffmann, M. Scheuch, D. Höper, R. Jungblut, M. Holsteg et al., Novel orthobunyavirus in cattle, vol.18, issue.3, pp.469-472, 2011.

K. M. Horne and D. L. Vanlandingham, Bunyavirus-Vector Interactions, Viruses, vol.6, issue.11, pp.4373-4397, 2014.

H. Jöst, A. Bialonski, D. Maus, V. Sambri, M. Eiden et al., Isolation of Usutu virus in Germany, Am. J. Trop. Med. Hyg, vol.85, issue.3, pp.551-553, 2011.

K. Lievaart-peterson, S. J. Luttikholt, R. Van-den-brom, and P. Vellema, Schmallenberg virus infection in small ruminants-First review of the situation and prospects in Northern Europe, Small Ruminant Res, vol.106, issue.2-3, pp.71-76, 2012.

K. Lievaart-peterson, S. Luttikholt, K. Peperkamp, R. Van-den-brom, and P. Vellema, Schmallenberg disease in sheep or goats: Past, present and future, Vet. Microbiol, vol.181, pp.147-153, 2015.

E. Méroc, N. De-regge, F. Riocreux, A. B. Caij, . Van-den et al., Distribution of Schmallenberg Virus and Seroprevalence in Belgian Sheep and Goats, Ministry of agriculture. 2009. The Agriculture in, vol.61, p.64, 2008.

W. J. Rogan and B. Gladen, Estimating prevalence from the result of a screening test, Am. J. Epidemiol, vol.107, issue.1, pp.71-76, 1978.

C. Sailleau, C. Boogaerts, A. Meyrueix, E. Laloy, E. Bréard et al., Schmallenberg virus infection in dogs, Emerg. Infect. Dis, vol.19, issue.11, pp.1896-1898, 2012.

R. Tarlinton, J. Daly, S. Dunham, and J. Kydd, The challenge of Schmallenberg virus emergence in Europe, Vet. J, vol.194, issue.1, pp.10-18, 2012.

W. P. Taylor and P. S. Mellor, The distribution of Akabane virus in the Middle East, Epidemiol. Infect, vol.113, issue.1, pp.175-185, 1994.