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DNA footprints of livestock domestication and evolutionary history

Published online by Cambridge University Press:  06 January 2011

P. Ajmone-Marsan
P. Ajmone-Marsan*
Affiliation:
Institute of Zootechnics and Biodiversity and Ancient DNA Research Centre, Università Cattolica del S. Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy
*
†E-mail: [email protected]
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Abstract

The observation of animal and plant breeding greatly influenced Darwin's thought. During the maturation of his theory of evolution, he realised that anthropogenic selection was the driving force shaping domestic animal phenotypes to meet human needs. A concept that was transferred to natural species after the reading of Malthus’ book on the struggle for existence. After the definition of his theory, Darwin continuously searched in domestic plant and animals confirmation of his hypotheses on the transmission of traits and evolution of species. He also observed that some morphological and physiological traits were shared among unrelated domestic animal species but were absent in the wild ancestors. The Russian scientist Dmitri Belyaev proved that these traits emerged as a consequence of domestication by recording their appearance in silver fox selected for tame behaviour, an experiment that is ongoing since about 50 years. Nowadays, genomic technologies allow scientists to explore the molecular basis of these traits and to reconstruct the evolutionary history of domestic animals. The availability of high-density single nucleotide polymorphisms panels permits the detection of signatures left by natural and artificial selection along the genome of domestic animals. The analysis of genomic and mitochondrial DNA contributes substantial information for the identification of sites of primary domestication, Neolithic routes of world colonisation and later voyages linked to human migration events. The understanding of all changes occurring following domestication and anthropogenic selection may help in understanding natural selection and molecular evolution occurring in all living organisms.

Keywords

Darwinanimal breedinggenomicsselection signature
Type
Full Paper
Information
Advances in Animal Biosciences , Volume 1 , Issue 3: Darwin Symposium: EAAP Annual Meeting Barcelona, Spain – Tuesday 25th August 2009 , 06 January 2011 , pp. 538 - 545
Copyright
Copyright © The Animal Consortium 2010

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References

Achilli, A, Olivieri, A, Pellecchia, M, Uboldi, C, Colli, L, Al-Zahery, N, Accetturo, M, Pala, M, Kashani, BH, Perego, UA, Battaglia, V, Fornarino, S, Kalamati, J, Houshmand, M, Negrini, R, Semino, O, Richards, M, Macaulay, V, Ferretti, L, Bandelt, HJ, Ajmone-Marsan, P, Torroni, A 2008. Mitochondrial genomes of extinct aurochs survive in domestic cattle. Current Biology 18, 157–158.CrossRefGoogle ScholarPubMed
Anderung, C, Bouwman, A, Persson, P, Carretero, JM, Ortega, AI, Elburg, R, Smith, C, Arsuaga, JL, Ellegren, H, Götherström, A 2005. Prehistoric contacts over the Straits of Gibraltar indicated by genetic analysis of Iberian Bronze Age cattle. Proceedings of the National Academy of Science USA 102, 8431–8435.CrossRefGoogle ScholarPubMed
Bae, JS, Cheong, HS, Kim, LH, Namgung, S, Park, TJ, Chun, JY, Kim, JY, Pasaje, CF, Lee, JS, Shin, HD 2010. Identification of copy number variations and common deletion polymorphisms in cattle. BMC Genomics 11, 232.CrossRefGoogle ScholarPubMed
Barendse, W, Harrison, BE, Bunch, RJ, Thomas, MB, Turner, LB 2009. Genome wide signatures of positive selection: the comparison of independent samples and the identification of regions associated to traits. BMC Genomics 10, 178.CrossRefGoogle ScholarPubMed
Beja-Pereira, A, Caramelli, D, Lalueza-Fox, C, Vernesi, C, Ferrand, N, Casoli, A, Goyache, F, Royo, LJ, Conti, S, Lari, M, Martini, A, Ouragh, L, Magid, A, Atash, A, Zsolnai, A, Boscato, P, Triantaphylidis, C, Ploumi, K, Sineo, L, Mallegni, F, Taberlet, P, Erhardt, G, Sampietro, L, Bertranpetit, J, Barbujani, G, Luikart, G, Bertorelle, G 2006. The origin of European cattle, evidence from modern and ancient DNA. Proceedings of the National Academy of Science USA 103, 8113–8118.CrossRefGoogle ScholarPubMed
Belyaev, DK 1979. Destabilizing selection as a factor in domestication. Journal of Heredity 70, 301–308.CrossRefGoogle ScholarPubMed
Bollongino, R, Edwards, CJ, Alt, KW, Burger, J, Bradley, DG 2006. Early history of European domestic cattle as revealed by ancient DNA. Biology Letters 2, 155–159.CrossRefGoogle ScholarPubMed
Bovine HapMap Consortium, Gibbs, RA, Taylor, JF, Van Tassell, CP, Barendse, W, Eversole, KA, Gill, CA, Green, RD, Hamernik, DL, Kappes, SM, Lien, S, Matukumalli, LK, McEwan, JC, Nazareth, LV, Schnabel, RD, Weinstock, GM, Wheeler, DA, Ajmone-Marsan, P, Boettcher, PJ, Caetano, AR, Garcia, JF, Hanotte, O, Mariani, P, Skow, LC, Sonstegard, TS, Williams, JL, Diallo, B, Hailemariam, L, Martinez, ML, Morris, CA, Silva, LO, Spelman, RJ, Mulatu, W, Zhao, K, Abbey, CA, Agaba, M, Araujo, FR, Bunch, RJ, Burton, J, Gorni, C, Olivier, H, Harrison, BE, Luff, B, Machado, MA, Mwakaya, J, Plastow, G, Sim, W, Smith, T, Thomas, MB, Valentini, A, Williams, P, Womack, J, Woolliams, JA, Liu, Y, Qin, X, Worley, KC, Gao, C, Jiang, H, Moore, SS, Ren, Y, Song, XZ, Bustamante, CD, Hernandez, RD, Muzny, DM, Patil, S, San Lucas, A, Fu, Q, Kent, MP, Vega, R, Matukumalli, A, McWilliam, S, Sclep, G, Bryc, K, Choi, J, Gao, H, Grefenstette, JJ, Murdoch, B, Stella, A, Villa-Angulo, R, Wright, M, Aerts, J, Jann, O, Negrini, R, Goddard, ME, Hayes, BJ, Bradley, DG, Barbosa da Silva, M, Lau, LP, Liu, GE, Lynn, DJ, Panzitta, F, Dodds, KG 2009. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324, 528–532.Google ScholarPubMed
Bradley, DG, MacHugh, DE, Cunningham, P, Loftus, R 1996. Mitochondrial diversity and the origins of African and European cattle. Proceedings of the National Academy of Science USA 93, 5131–5135.CrossRefGoogle ScholarPubMed
Bradley, DG, Magee, DA 2006. Genetics and origins of domestic cattle. In Documenting domestication. New genetic and archaeological paradigms (ed. MA Zeder, DG Bradley, E Emshwiller and BD Smith). University of California Press, Berkeley.Google Scholar
Cymbron, T, Loftus, RT, Malheiro, MI, Bradley, DG 1999. Mitochondrial sequence variation suggests an African influence in Portuguese cattle. Proceedings of the Royal Society Biological Science 266, 597–603.CrossRefGoogle ScholarPubMed
Darwin, CR 1859. On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. First edition. John Murray, London.CrossRefGoogle Scholar
Darwin, CR 1868. The variation of animals and plants under domestication, vol. 2, First edition. John Murray, London.Google Scholar
Darwin, CR 1887. The life and letters of Charles Darwin including an autobiographical chapter. (ed. F Darwin) vol. 3. John Murray, London.Google Scholar
Denbow, J 1990. Congo to Kalahari: data and hypotheses about the political economy of the western stream of the Early Iron Age. African Archaeological Reviews 8, 139–175.CrossRefGoogle Scholar
Dessinioti, C, Stratigos, AJ, Rigopoulos, D, Katsambas, AD 2009. A review of genetic disorders of hypopigmentation: lessons learned from the biology of melanocytes. Experimental Dermatology 18, 741–749.CrossRefGoogle ScholarPubMed
Ennis, S 2007. Linkage disequilibrium as a tool for detecting signatures of natural selection. Methods in Molecular Biology 376, 59–70.CrossRefGoogle ScholarPubMed
FAO 2007. The state of the world's animal genetic resources for food and agriculture. FAO, Rome.Google Scholar
Ganesan, A, Nolan, L, Crabb, SJ, Packham, G 2009. Epigenetic therapy: histone acetylation, DNA methylation and anti-cancer drug discovery. Current Cancer Drug Targets 9, 963–981.CrossRefGoogle ScholarPubMed
Georges, M, Coppieters, W, Charlier, C 2007. Polymorphic miRNA-mediated gene regulation: contribution to phenotypic variation and disease. Current Opinions in Genetics and Development 17, 166–176.CrossRefGoogle ScholarPubMed
Giuffra, E, Törnsten, A, Marklund, S, Bongcam-Rudloff, E, Chardon, P, Kijas, JMH, Anderson, SI, Archibald, AL, Andersson, L 2002. A large duplication associated with dominant white color in pigs originated by homologous recombination between LINE elements flanking KIT. Mammalian Genome 13, 569–577.CrossRefGoogle ScholarPubMed
Glessner, JT, Wang, K, Cai, G, Korvatska, O, Kim, CE, Wood, S, Zhang, H, Estes, A, Brune, CW, Bradfield, JP, Imielinski, M, Frackelton, EC, Reichert, J, Crawford, EL, Munson, J, Sleiman, PM, Chiavacci, R, Annaiah, K, Thomas, K, Hou, C, Glaberson, W, Flory, J, Otieno, F, Garris, M, Soorya, L, Klei, L, Piven, J, Meyer, KJ, Anagnostou, E, Sakurai, T, Game, RM, Rudd, DS, Zurawiecki, D, McDougle, CJ, Davis, LK, Miller, J, Posey, DJ, Michaels, S, Kolevzon, A, Silverman, JM, Bernier, R, Levy, SE, Schultz, RT, Dawson, G, Owley, T, McMahon, WM, Wassink, TH, Sweeney, JA, Nurnberger, JI, Coon, H, Sutcliffe, JS, Minshew, NJ, Grant, SF, Bucan, M, Cook, EH, Buxbaum, JD, Devlin, B, Schellenberg, GD, Hakonarson, H 2009. Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature 459, 569–573.CrossRefGoogle ScholarPubMed
Goldammer, T, Brunner, RM, Schwerin, M 1997. Comparative analysis of Y chromosome structure in Bos taurus and Bos indicus by FISH using region-specific, microdissected, and locus-specific DNA probes. Cytogenetics and Cell Genetics 77, 238–241.CrossRefGoogle ScholarPubMed
Hanotte, O, Bradley, DG, Ochieng, JW, Verjee, Y, Hill, EW, Rege, JE 2002. African pastoralism: gentic imprints of origins and migrations. Science 296, 336–339.CrossRefGoogle Scholar
Hoei-Hansen, CE, Kraggerud, SM, Abeler, VM, Kaern, J, Rajpert-De Meyts, E, Lothe, RA 2007. Ovarian dysgerminomas are characterised by frequent KIT mutations and abundant expression of pluripotency markers. Molecular Cancer 2, 6–12.Google Scholar
Hayes, BJ, Lien, S, Nilsen, H, Olsen, HG, Berg, P, Maceachern, S, Potter, S, Meuwissen, TH 2008. The origin of selection signatures on bovine chromosome 6. Animal Genetics 39, 105–111.CrossRefGoogle ScholarPubMed
Helmer, D, Gourichon, L, Monchot, H, Peters, J, Segui, MS 2005. Identifying early domestic cattle from pre-pottery Neolithic sites on the Middle Eurphrates using sexual dimorphism. In The first steps of animal domestication. New archaeological approaches (ed. JD Vigne, J Peters and D Helmer). Oxbow Books, Oxford.Google Scholar
Hiendleder, S, Lewalski, H, Janke, A 2007. Complete mitochondrial genomes of Bos taurus and Bos indicus provide new insights into intra-species variation, taxonomy and domestication. Cytogenetics and Genome Research 120, 150–156.CrossRefGoogle Scholar
Hutt, KJ, McLaughlin, EA, Holland, MK 2006. Kit ligand and c-Kit have diverse roles during mammalian oogenesis and folliculogenesis. Molecular Human Reproduction 12, 61–69.CrossRefGoogle ScholarPubMed
Lai, SJ, Liu, YP, Liu, YX, Lia, XW, Yao, YG 2006. Genetic diversity and origin of Chinese cattle revealed by mtDNA D-loop sequence variation. Molecular Phylogenetics and Evolution 38, 146–154.CrossRefGoogle ScholarPubMed
Loftus, RT, MacHugh, DE, Bradley, DG, Sharp, PM, Cunningham, P 1994. Evidence for two independent domestications of cattle. Proceedings of the National Academy of Science USA 91, 2757–2761.CrossRefGoogle ScholarPubMed
Malthus, TR 1798. An essay on the principle of population. Oxford World's Classics Reprint.Google Scholar
Mannen, H, Kohno, M, Nagata, Y, Tsuji, S, Bradley, DG, Yeo, JS, Nyamsamba, D, Zagdsuren, Y, Yokohama, M, Nomura, K, Amanf, T 2004. Independent mitochondrial origin and historical genetic differentiation in North Eastern Asian cattle. Molecular Phylogenetics and Evolution 32, 539–544.CrossRefGoogle ScholarPubMed
Meadow, A 1993. Animal domestication in the Middle East: a revised view from the Eastern margin. In Harappar Civilization (ed. G Possehl). Oxford and IBH, New Dehli.Google Scholar
Medjugorac, I, Kustermann, W, Lazar, P, Russ, I, Pirchner, F 1994. Marker-derived phylogeny of European cattle supports demic expansion of agriculture. Animal Genetics (suppl. 1), 19–27.CrossRefGoogle ScholarPubMed
Miretti, MM, Dunner, S, Naves, M, Contel, EP, Ferro, JA 2000. Predominant African-derived mtDNA in Caribbean and Brazilian Creole cattle is also found in Spanish cattle (Bos taurus). Journal of Heredity 95, 450–453.CrossRefGoogle Scholar
Mona, S, Catalano, G, Lari, M, Larson, G, Boscato, P, Casoli, A, Sineo, L, Di Patti, C, Pecchioli, E, Caramelli, D, Bertorelle, G 2010. Population dynamic of the extinct European aurochs: genetic evidence of a north-south differentiation pattern and no evidence of post-glacial expansion. BMC Evolutionary Biology 10, 83.CrossRefGoogle ScholarPubMed
Payne, WJA, Hodges, J 1997. Tropical cattle, origins, breeds and breeding policies. Blackwell Science Ltd, Oxford.Google Scholar
Pellecchia, M, Negrini, R, Colli, L, Patrini, M, Milanesi, E, Achilli, A, Bertorelle, G, Cavalli-Sforza, LL, Piazza, A, Torroni, A, Ajmone-Marsan, P 2007. The mystery of Etruscan origins, novel clues from Bos taurus mitochondrial DNA. Proceedings of the Royal Society Biological Science 274, 1175–1179.CrossRefGoogle ScholarPubMed
Rubin, CJ, Zody, MC, Eriksson, J, Meadows, JR, Sherwood, E, Webster, MT, Jiang, L, Ingman, M, Sharpe, T, Ka, S, Hallböök, F, Besnier, F, Carlborg, O, Bed'hom, B, Tixier-Boichard, M, Jensen, P, Siegel, P, Lindblad-Toh, K, Andersson, L 2010. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464, 587–591.CrossRefGoogle ScholarPubMed
Stella, A, Ajmone-Marsan, P, Lazzari, B, Boettcher, P 2010. Identification of selection signatures in cattle breeds selected for dairy production. Genetics (in press).CrossRefGoogle ScholarPubMed
Troy, CS, MacHugh, DE, Bailey, JF, Magee, DA, Loftus, RT, Cunningham, P, Chamberlain, AT, Sykes, BC, Bradley, DG 2001. Genetic evidence for Near-Eastern origins of European cattle. Nature 410, 1088–1091.CrossRefGoogle ScholarPubMed
Trut, L, Oskina, I, Kharlamova, A 2009. Animal evolution during domestication: the domesticated fox as a model. BioEssays 31, 349–360.CrossRefGoogle ScholarPubMed
Weaver, JR, Susiarjo, M, Bartolomei, MS 2009. Imprinting and epigenetic changes in the early embryo. Mammalian Genome 20, 532–543.CrossRefGoogle ScholarPubMed
Wilner, E 2006. Darwin's artificial selection as an experiment. Studies in History and Philosophy of Biological and Biomedical Sciences 37, 26–40.CrossRefGoogle ScholarPubMed
Xia, Q, Guo, Y, Zhang, Z, Li, D, Xuan, Z, Li, Z, Dai, F, Li, Y, Cheng, D, Li, R, Cheng, T, Jiang, T, Becquet, C, Xu, X, Liu, C, Zha, X, Fan, W, Lin, Y, Shen, Y, Jiang, L, Jensen, J, Hellmann, I, Tang, S, Zhao, P, Xu, H, Yu, C, Zhang, G, Li, J, Cao, J, Liu, S, He, N, Zhou, Y, Liu, H, Zhao, J, Ye, C, Du, Z, Pan, G, Zhao, A, Shao, H, Zeng, W, Wu, P, Li, C, Pan, M, Li, J, Yin, X, Li, D, Wang, J, Zheng, H, Wang, W, Zhang, X, Li, S, Yang, H, Lu, C, Nielsen, R, Zhou, Z, Wang, J, Xiang, Z, Wang, J 2009. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 326, 433–436.CrossRefGoogle ScholarPubMed