Alexander, D.H., Lange, K. (2011). Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics 12:246.
Alexander, D.H., Novembre, J. and Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research. 19: 1655–1664.
Al-Mamun, H.A., Clark, S.A., Kwan, P. and Gondro, C. (2015). Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep. Genetics Selection Evolution. 47(1): 1-14.
Ben Jemaa, S., Boussaha, M., Ben Mehdi, M., Lee, J.H. and Lee, S.H. (2015). Genome-wide insights into population structure and genetic history of tunisian local cattle using the illumina bovinesnp50 beadchip. BMC Genomics. 16: 67.7.
Bett, R.C., Okeyo, M.A., Malmfors, B., Johansson, K., Agaba, M., Kugonza, D.R., Bhuiyan, A.K.F.H., Mariante, A.S., Mujibi, F.D. and Philipsson, J. (2013). Cattle breeds: extinction or quasi-extant? Resources. 2(3): 335-357.
Bollongino, R., Burger, J., Powell, A., Mashkour, M., Vigne, J.D. and Thomas, MG. (2012). Modern taurine cattle descended from small number of Near-Eastern founders. Molecular Biology and Evolution. 29: 2101–2104.
Cornélis, D., Melletti, M., Korte, L., Ryan, S. J., Mirabile, M., Prin, T. and Prin, H.H.T. (2014). Ecology, Evolution and Behaviour of Wild Cattle. Implications for Conservation. Cambridge University Press Publication. Cambridge. UK. pp: 326-372.
Decker, J.E., McKay, S.D., Rolf, M.M., Kim, J., Molina Alcala, A., Sonstegard, T.S. and et al. ( 2014). Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genetics. 10: e1004254.
FAO. (2018). Food and agriculture and organization of the united nations. Retrieved from www.fao.org/home/en
history of French cattle from dense SNP data on 47 worldwide breeds. PloS one. 5(9), p.e13038.
Groeneveld, L.F., Lenstra, J.A., Eding, H., Toro, M.A., Scherf, B., Pilling, D. ET AL. (2010). Genetic diversity in farm animals: A review. Animal Genetics. 41: 6–31.
Hole, F. (2004). Neolithic Age in Iran. In: Encyclopaedia Iranica. onlineth ed. New York: Columbia University.
Jarrige, J.F. Mehrgarh Neolithic. In Proceedings of the International Seminar on the “First Farmers in Global Perspective”, Lucknow, India, 18–20 January 2006; pp. 135–154.
Jombart, T., Devillard, S. and Balloux, F. (2010). Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics.11: 1-15.
Karimi, K. (2017). Investigation of the Population Structure in Iranian Native Cattle using Discriminant Analysis of Principal Components. Research on Animal Production. 8 (17):184-193.
Karimi, K., Koshkoiyeh, A.E., Fozi, M.A., Porto-Neto, L.R. and Gondro, C. (2016a). Prioritization for conservation of Iranian native cattle breeds based on genome-wide SNP data. Conservation Genetics. 17(1): 77-89.
Karimi, K., Strucken, E. M., Moghaddar, N., Ferdosi, M. H., Esmailizadeh, A. and Gondro, C. (2016b). Local and global patterns of admixture and population structure in Iranian native cattle. BMC genetics. 17(1): 1-14.
Kijas, J.W., Ortiz, J.S., McCulloch, R., James, A., Brice, B., Swain, B. and et al. (2013). Genetic diversity and investigation of polledness in divergent goat populations using 52 088 SNPs. Animal Genetics. 44(3): 325-335.
Kukučková, V., Moravčíková, N., Ferenčaković, M., Simčič, M., Mészáros, G., Sölkner, J., Trakovická, A., Kadlečík, O., Curik, I. and Kasarda, R. (2017). Genomic characterization of Pinzgau cattle: genetic conservation and breeding perspectives. Conservation Genetics, 18(4): 893-910.
Mastrangelo, S., Sardina, M.T., Tolone, M., Di Gerlando, R., Sutera, A.M., Fontanesi, L. and Portolano, B. (2018). Genome-wide identification of runs of homozygosity islands and associated genes in local dairy cattle breeds. Animal. 12(12): 2480-2488.
Medugorac, I., Medugorac, A., Russ, I., Veit-Kensch, C.E., Taberlet, P., Luntz, B. ET AL. (2009). Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size. Molecular Ecology. 18: 3394–3410.
Nei, M. (1978) Estimation of average heterozygosity and genetic distance from small number of individuals. Genetics. 89: 583–90.
Papachristou, D., Koutsouli, P., Laliotis, G.P., Kunz, E., Upadhyay, M., Seichter, D., Russ, I., Gjoko, B., Kostaras, N., Bizelis, I. and Medugorac, I. (2020). Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations. Genetics Selection Evolution. 52(1): 1-23.
Pitt, D., Sevane, N., Nicolazzi, E.L., MacHugh, D.E., Park, S., Colli, L., Martinez, R., Bruford, M.W. and Orozco-terWengel, P. (2018). Domestication of cattle: Two or threeevents? Evolutionary applications, 12 (1), 123–136.
Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A. and Reich, D. (2006). Principal components analysis corrects for stratification in genome-wide association studies. Nature genetics. 38(8): 904-909.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A.R., Bender, D. and et al. (2007). PLINK: a toolset for whole-genome association and population-based linkage analysis. The American Journal of Human Genetics. 81: 559–575.
Qanbari, S., Pimentel, E.C.G., Tetens, J., Thaller, G., Lichtner, P., Sharifi, A.R. and Simianer, H., (2011). A genome‐wide scan for signatures of recent selection in Holstein cattle. Animal genetics. 41(4): 377-389.
R Core Team (2020) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna. Available at URL:
http://www.r-project.org/index.html
Reynolds, J., Weir, B.S. and Cockerham, C.C. (1983) Estimation of the coancestry coefficient basis for a short-term genetic distance. Genetics. 105: 767–779.
Ringner, M. (2008). What is principal component analysis? Nature Biotechnology. 26: 303-304.
Rothammer, S., Seichter, D., Förster, M. and Medugorac, I. (2013). A genome-wide scan for signatures of differential artificial selection in ten cattle breeds. BMC genomics. 14(1): 1-17.
Soma, P., Kotze, A., Grobler, J.P. and vanWyk, J.B. (2012). South African sheep breeds: population genetic structure and conservation implications. Small Ruminant Research. 103(2–3):112–119.
Upadhyay, M., Bortoluzzi, C., Barbato, M., Ajmonemarsan, P., Colli, L., Ginja, C. et al. (2019). Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome‐wide SNPs. Evolutionary applications. 12(5): 951-963.
Uzzaman, M.R., Zewdu Edea, M., Bhuiyan, S.A., Walker, J., Bhuiyan, A.K.F.H. and Kim, K. S. (2014). Genome-wide single nucleotide polymorphism analyses reveal genetic diversity and structure of wild and domestic cattle in Bangladesh. Asian-Australasian journal of animal sciences. 27(10): 1381.
Weir, B.S., and Cockerham, C.C. (1984). Estimating F-statistics for the analysis of population structure. Evolution. 1358-1370.
Wultsch, C., Waits, L.P. and Kelly, M.J. (2016). A comparative analysis of genetic diversity and structure in jaguars (Panthera onca), pumas (Puma concolor), and ocelots (Leopardus pardalis) in fragmented landscapes of a critical Mesoamerican linkage zone. PloS one. 11(3).
Zeder, M.A., Emshwiller, E., Smith, B.D. and Bradley, D.G. (2006). Documenting domestication: the intersection of genetics and archaeology. TRENDS in Genetics. 22(3): 139-155.
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