Çiftlik Hayvanlarında Seleksiyon İzlerinin Tanımlanmasında Kullanılan Kavram ve Yaklaşımlar

Year 2024, , 63 - 82, 30.06.2024

Mustafa Karabaş , Onur Yılmaz

https://doi.org/10.51970/jasp.1390270

Abstract

İnsanlar ve yabani hayvan popülasyonları arasındaki etkileşimler çeşitli evcilleştirme süreçlerine yol açmıştır. Bu etkileşimler, insanlarla aynı çevreye uyum sağlama yeteneği yüksek olan yabani hayvan türlerinde evrim mekanizmalarının işleyişini değiştirmiştir. Bu evcilleştirme süreçleri, yabani hayvan türlerinde morfolojik, davranışsal ve üretim özellikleri odaklı bazı genotipik ve fenotipik değişikliklere neden olarak günümüzde çiftlik hayvanı ırklarının oluşumunu sağlamıştır. Bu süreçler boyunca genom üzerinde seleksiyona maruz kalmış bölgelerin tespit edilmesi, ilgili özelliklerle ilişkili genlerin tanımlanmasında faydalı olabilmektedir. Son yıllarda moleküler genetik teknikler ve biyoinformatik alanındaki gelişmeler, bu süreçlerin çiftlik hayvanları genomunda neden olduğu kalıtsal genetik değişikliklerin bıraktığı seleksiyon izlerini tespit edebilme imkanı sağlamıştır. Sunulan bu derlemede, çiftlik hayvanlarında seleksiyon izleri ve seleksiyon izlerinin tespit edilmesinde kullanılan yöntemler tartışılmıştır.

Keywords

Evcilleştirme, Pozitif seleksiyon, Sseçici sürükleme, Evrim

Concepts and Approaches Used in identifying Selection Signatures in Farm Animals

Abstract

Interactions between humans and wild animal populations have led to various processes of domestication. These interactions have altered the functioning of evolutionary mechanisms in wild animal species that are highly adaptable to the same environment as humans. These domestication processes caused genotypic and phenotypic changes, specifically in the morphological, behavioral, and production characteristics of wild animal species. These changes ultimately led to the development of the farm animal breeds that we see today. Identifying regions on the genome that have undergone selection during these processes can be useful for identifying genes associated with relevant traits. In recent years, advancements in molecular genetic techniques and bioinformatics have provided the opportunity to identify the selection signatures left by heritable genetic changes caused by these processes in the genomes of farm animals. In this review, selection signatures in farm animals, the methods used to detect these signatures, and the problems encountered are discussed in detail.

Keywords

Domestication, Positive selection, Selective sweep, Evolution

References

• Almeida, O.A.C., Moreira, G.C.M., Rezende, F.M., Boschiero, C., Peixoto, J.D., Ibelli, A.M.G., Ledur, M.C., de Novais, F.J. and Coutinho, L.L., 2019. Identification of selection signatures involved in performance traits in a paternal broiler line. Bmc Genomics 20.
• Alter, S.G., 2007. Darwin's artificial selection analogy and the generic character of "Phyletic" evolution. History and Philosophy of the Life Sciences 29, 57-81.
• Bamshad, M. and Wooding, S.P., 2003. Signatures of natural selection in the human genome. Nature Reviews Genetics 4, 99-111A.
• Beichman, A.C., Phung, T.N. and Lohmueller, K.E., 2017. Comparison of single genome and allele frequency data reveals discordant demographic histories. G3:Genes, Genomes, Genetics 7, 3605-3620.
• Biswas, S. and Akey, J.M., 2006. Genomic insights into positive selection. Trends in Genetics 22, 437-446.
• Bomba, L., Nicolazzi, E.L., Milanesi, M., Negrini, R., Mancini, G., Biscarini, F., Stella, A., Valentini, A. and Ajmone-Marsan, P., 2015. Relative extended haplotype homozygosity signals across breeds reveal dairy and beef specific signatures of selection. Genetics Selection Evolution 47.
• Bonhomme, M., Chevalet, C., Servin, B., Boitard, S., Abdallah, J., Blott, S. and SanCristobal, M., 2010. Detecting Selection in Population Trees: The Lewontin and Krakauer Test Extended. Genetics 186, 241-U406.
• Cadzow, M., Boocock, J., Nguyen, H.T., Wilcox, P., Merriman, T.R. and Black, M.A., 2014. A bioinformatics workflow for detecting signatures of selection in genomic data. Frontiers in Genetics 5.
• Charlesworth, B. and Charlesworth, D., 2018. Neutral variation in the context of selection. Molecular Biology and Evolution 35, 1359-1361.
• Chen, C.H., Chuang, T.J., Liao, B.Y. and Chen, F.C., 2009. Scanning for the Signatures of Positive Selection for Human-Specific Insertions and Deletions. Genome Biology and Evolution 1, 415-419.
• Cheruiyot, E.K., Bett, R.C., Amimo, J.O., Zhang, Y., Mrode, R. and Mujibi, F.D.N., 2018. Signatures of selection in admixed dairy cattle in Tanzania. Frontiers in Genetics 9.
• Comeron, J.M., 2014. Background selection as baseline for nucleotide variation across the genome. Plos Genetics 10.
• Cui, F.S. and Yuan, B., 2018. Fixation probability of a beneficial mutation conferring decreased generation time in changing environments. Bmc Systems Biology 12.
• Cutter, A.D. and Payseur, B.A., 2013. Genomic signatures of selection at linked sites: unifying the disparity among species. Nature Reviews Genetics 14, 262-274.
• Denamur, E. and Matic, I., 2006. Evolution of mutation rates in bacteria. Molecular Microbiology 60, 820-827.
• Desai, M.M. and Fisher, D.S., 2007. Beneficial mutation-selection balance and the effect of linkage on positive selection. Genetics 176, 1759-1798.
• Diamond, J., 2002. Evolution, consequences and future of plant and animal domestication. Nature 418, 700-707.
• Fariello, M.I., Boitard, S., Naya, H., SanCristobal, M. and Servin, B., 2013. Detecting Signatures of Selection Through Haplotype Differentiation Among Hierarchically Structured Populations. Genetics 193, 929-+.
• Fariello, M.I., Servin, B., Tosser-Klopp, G., Rupp, R., Moreno, C., San Cristobal, M., Boitard, S. and Consortium, I.S.G., 2014. Selection Signatures in Worldwide Sheep Populations. Plos One 9.
• Fay, J.C. and Wu, C.I., 2000. Hitchhiking under positive Darwinian selection. Genetics 155, 1405-1413.
• Fernández, M.E., Goszczynski, D.E., Lirón, J.P., Villegas-Castagnasso, E.E., Carino, M.H., Ripoli, M.V., Rogberg-Muñoz, A., Posik, D.M., Peral-García, P. and Giovambattista, G., 2013. Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd. Genetics and Molecular Biology 36, 185-191.
• Fijarczyk, A. and Babik, W., 2015. Detecting balancing selection in genomes: limits and prospects. Molecular Ecology 24, 3529-3545.
• Foulkes, W.D. and Real, F.X., 2013. Many mosaic mutations. Current oncology 20, 85-87.
• Frantz, L.A.F., Bradley, D.G., Larson, G. and Orlando, L., 2020. Animal domestication in the era of ancient genomics. Nature Reviews Genetics 21, 449-460.
• Fu, Y.X. and Li, W.H., 1993. Statistical tests of neutrality of mutations. Genetics 133, 693-709.
• Gorssen, W., Meyermans, R., Janssens, S. and Buys, N., 2021. A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species. Genetics Selection Evolution 53.
• Gouveia, J.J.D., Paiva, S.R., McManus, C.M., Caetano, A.R., Kijas, J.W., Facó, O., Azevedo, H.C., de Araujo, A.M., de Souza, C.J., Yamagishi, M.E.B., Carneiro, P.L.S., Lôbo, R.N.B., de Oliveira, S.M.P. and da Silva, M.V.G.B., 2017. Genome-wide search for signatures of selection in three major Brazilian locally adapted sheep breeds. Livestock Science 197, 36-45.
• Griffith, S.C., Owens, I.P. and Burke, T., 1999. Environmental determination of a sexually selected trait. Nature 400, 358-360.
• Gurgul, A., Jasielczuk, I., Ropka-Molik, K., Semik-Gurgul, E., Pawlina-Tyszko, K., Szmatola, T., Szyndler-Nedza, M., Bugno-Poniewierska, M., Blicharski, T., Szulc, K., Skrzypczak, E. and Krupinski, J., 2018. A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland. Bmc Genetics 19.
• Gurgul, A., Jasielczuk, I., Szmatola, T., Sosin-Bzducha, E., Majewska, A. and Litwinczuk, Z., 2020. Divergent selection signatures of phenotypic and production traits among conserved and commercial cattle breeds. Livestock Science 239.
• Hedrick, P.W., 2015. Heterozygote Advantage:The Effect of Artificial Selection in Livestock and Pets. Journal of Heredity 106, 141-154.
• Hermisson, J. and Pennings, P.S., 2017. Soft sweeps and beyond: understanding the patterns and probabilities of selection footprints under rapid adaptation. Methods in Ecology and Evolution 8, 700-716.
• Jung, H., Kim, H.S., Kim, J.Y., Sun, J.M., Ahn, J.S., Ahn, M.J., Park, K., Esteller, M., Lee, S.H. and Choi, J.K., 2019. DNA methylation loss promotes immune evasion of tumours with high mutation and copy number load. Nature Communications 10.
• Kaplan, N.L., Hudson, R.R. and Langley, C.H., 1989. The hitchhiking effect revisited. Genetics 123, 887-899.
• Khan, M.M.H., Rafii, M.Y., Ramlee, S.I., Jusoh, M., Al Mamun, M. and Halidu, J., 2021. DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut [L.] Verdc.) accessions using ISSR markers system. Scientific Reports 11, 14527.
• Kim, E.S., Cole, J.B., Huson, H., Wiggans, G.R., Van Tassell, C.P., Crooker, B.A., Liu, G., Da, Y. and Sonstegard, T.S., 2013. Effect of artificial selection on runs of homozygosity in US Holstein cattle. Plos One 8.
• Kim, Y. and Stephan, W., 2002. Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160, 765-777.
• Korneliussen, T.S., Moltke, I., Albrechtsen, A. and Nielsen, R., 2013. Calculation of Tajima's and other neutrality test statistics from low depth next-generation sequencing data. Bmc Bioinformatics 14.
• Kosiol, C. and Anisimova, M., 2019. Selection acting on genomes. Evolutionary Genomics, 2 Edition 1910, 373-397.
• Kreitman, M., 2000. Methods to detect selection in populations with applications to the human. Annual Review of Genomics and Human Genetics 1, 539-559.
• Kreitman, M. and Di Rienzo, A., 2004. Balancing claims for balancing selection. Trends in Genetics 20, 300-304.
• Kristofich, J., Morgenthaler, A.B., Kinney, W.R., Ebmeier, C.C., Snyder, D.J., Old, W.M., Cooper, V.S. and Copley, S.D., 2018. Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme. Plos Genetics 14.
• Laan, M. and Paabo, S., 1997. Demographic history and linkage disequilibrium in human populations. Nature Genetics 17, 435-438.
• Lachance, J. and Tishkoff, S.A., 2013. SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it. Bioessays 35, 780-786.
• Larson, G. and Fuller, D.Q., 2014. The evolution of animal domestication. Annual Review of Ecology, Evolution, and Systematics, Vol 45 45, 115-136.
• Lebeuf-Taylor, E., McCloskey, N., Bailey, S.F., Hinz, A. and Kassen, R., 2019. The distribution of fitness effects among synonymous mutations in a gene under directional selection. Elife 8.
• Lewontin, R.C. and Krakauer, J., 1973. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74, 175-195.
• Lye, Z.N. and Purugganan, M.D., 2019. Copy number variation in domestication. Trends in Plant Science 24, 352-365.
• Marsden, C.D., Ortega-Del Vecchyo, D., O'Brien, D.P., Taylor, J.F., Ramirez, O., Vilà, C., Marques-Bonet, T., Schnabel, R.D., Wayne, R.K. and Lohmueller, K.E., 2016. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs. Proceedings of the National Academy of Sciences of the United States of America 113, 152-157.
• McDougall, P.T., Réale, D., Sol, D. and Reader, S.M., 2006. Wildlife conservation and animal temperament:: causes and consequences of evolutionary change for captive, reintroduced, and wild populations. Animal Conservation 9, 39-48.
• McQuillan, R., Leutenegger, A.L., Abdel-Rahman, R., Franklin, C.S., Pericic, M., Barac-Lauc, L., Smolej-Narancic, N., Janicijevic, B., Polasek, O., Tenesa, A., MacLeod, A.K., Farrington, S.M., Rudan, P., Hayward, C., Vitart, V., Rudan, I., Wild, S.H., Dunlop, M.G., Wright, A.F., Campbell, H. and Wilson, J.F., 2008. Runs of homozygosity in European populations. American Journal of Human Genetics 83, 658-658.
• Mendivil, R.O. and Ferrier, D.E., 2012. Mechanisms of gene duplication and translocation and progress towards understanding their relative contributions to animal genome evolution. International Journal of Evolutionary Biology, 846421.
• Mérot, C., Llaurens, V., Normandeau, E., Bernatchez, L. and Wellenreuther, M., 2020. Balancing selection via life-history trade-offs maintains an inversion polymorphism in a seaweed fly. Nature Communications 11.
• Mignon-Grasteau, S., Boissy, A., Bouix, J., Faure, J.M., Fisher, A.D., Hinch, G.N., Jensen, P., Le Neindre, P., Mormède, P., Prunet, P., Vandeputte, M. and Beaumont, C., 2005. Genetics of adaptation and domestication in livestock. Livestock Production Science 93, 3-14.
• Moradian, H., Koshkoiyeh, A.E., Mohammadabadi, M. and Fozi, M.A., 2020. Whole genome detection of recent selection signatures in Sarabi cattle: a unique Iranian taurine breed. Genes & Genomics 42, 203-215.
• Nielsen, R., 2001. Statistical tests of selective neutrality in the age of genomics. Heredity 86, 641-647.
• Nielsen, R., 2005. Molecular signatures of natural selection. Annual Review of Genetics 39, 197-218.
• Oleksyk, T.K., Smith, M.W. and O'Brien, S.J., 2010. Genome-wide scans for footprints of natural selection. Philosophical Transactions of the Royal Society B-Biological Sciences 365, 185-205.
• Parmley, J.L. and Hurst, L.D., 2007. How do synonymous mutations affect fitness? Bioessays 29, 515-519.
• Pritchard, J.K., Pickrell, J.K. and Coop, G., 2010. The genetics of human adaptation: hard Sweeps, soft Sweeps, and polygenic adaptation. Current Biology 20, R208-R215.
• Pruvost, M., Bellone, R., Benecke, N., Sandoval-Castellanos, E., Cieslak, M., Kuznetsova, T., Morales-Muñiz, A., O'Connor, T., Reissmann, M., Hofreiter, M. and Ludwig, A., 2011. Genotypes of predomestic horses match phenotypes painted in Paleolithic works of cave art. Proceedings of the National Academy of Sciences of the United States of America 108, 18626-18630.
• Purfield, D.C., Berry, D.P., McParland, S. and Bradley, D.G., 2012. Runs of homozygosity and population history in cattle. Bmc Genetics 13.
• Purfield, D.C., McParland, S., Wall, E. and Berry, D.P., 2017. The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds. Plos One 12.
• Qanbari, S., Gianola, D., Hayes, B., Schenkel, F., Miller, S., Moore, S., Thaller, G. and Simianer, H., 2011. Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. Bmc Genomics 12.
• Qanbari, S. and Simianer, H., 2014. Mapping signatures of positive selection in the genome of livestock. Livestock Science 166, 133-143.
• Randhawa, I.A.S., Khatkar, M.S., Thomson, P.C. and Raadsma, H.W., 2014. Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep. Bmc Genetics 15.
• Rubin, C.J., Zody, M.C., Eriksson, J., Meadows, J.R.S., Sherwood, E., Webster, M.T., Jiang, L., Ingman, M., Sharpe, T., Ka, S., Hallböök, F., Besnier, F., Carlborg, Ö., Bed'hom, B., Tixier-Boichard, M., Jensen, P., Siegel, P., Lindblad-Toh, K. and Andersson, L., 2010. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464, 587-U145.
• Sabeti, P.C., Reich, D.E., Higgins, J.M., Levine, H.Z.P., Richter, D.J., Schaffner, S.F., Gabriel, S.B., Platko, J.V., Patterson, N.J., McDonald, G.J., Ackerman, H.C., Campbell, S.J., Altshuler, D., Cooper, R., Kwiatkowski, D., Ward, R. and Lander, E.S., 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832-837.
• Sabeti, P.C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X.H., Byrne, E.H., McCarroll, S.A., Gaudet, R., Schaffner, S.F., Lander, E.S. and Consortium, I.H., 2007. Genome-wide detection and characterization of positive selection in human populations. Nature 449, 913-U12.
• Saravanan, K.A., Panigrahi, M., Kumar, H., Bhushan, B., Dutt, T. and Mishra, B.P., 2020. Selection signatures in livestock genome: A review of concepts, approaches and applications. Livestock Science 241.
• Scally, A., 2016. Mutation rates and the evolution of germline structure. Philosophical Transactions of the Royal Society B-Biological Sciences 371.
• Simonsen, K.L., Churchill, G.A. and Aquadro, C.F., 1995. Properties of Statistical Tests of Neutrality for DNA Polymorphism Data. Genetics 141, 413-429.
• Slatkin, M., 2008. Linkage disequilibrium - understanding the evolutionary past and mapping the medical future. Nature Reviews Genetics 9, 477-485.
• Spurgin, L.G. and Richardson, D.S., 2010. How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings. Proceedings of the Royal Society B: Biological Sciences 277, 979-988.
• Stephan, W., 2010. Genetic hitchhiking versus background selection: the controversy and its implications. Philosophical Transactions of the Royal Society B-Biological Sciences 365, 1245-1253.
• Stephan, W., 2019. Selective sweeps. Genetics 211, 5-13.
• Tajima, F., 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105, 437-460.
• Tajima, F., 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595.
• Tang, K., Thornton, K.R. and Stoneking, M., 2007. A new approach for using genome scans to detect recent positive selection in the human genome. Plos Biology 5, 1587-1602.
• Teletchea, F., 2019. Animal domestication: A brief overview, IntechOpen.
• Tijjani, A., Utsunomiya, Y.T., Ezekwe, A.G., Nashiru, O. and Hanotte, O., 2019. Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle. Frontiers in Genetics 10.
• Uspenskaya, N.Y., Akopov, S.B., Snezhkov, E.V. and Sverdlov, E.D., 2019. The Rate of Human Germline MutationsVariable Factor of Evolution and Diseases. Russian Journal of Genetics 55, 523-534.
• Van Eenennaam, A.L. and Young, A.E., 2018. Genetic improvement of food animals: past and future, in: Birner, R. (Ed.), Encyclopedia of Food Security and Sustainability. Elsevier, Amsterdam.
• Vitti, J.J., Grossman, S.R. and Sabeti, P.C., 2013. Detecting Natural Selection in Genomic Data. Annual Review of Genetics, Vol 47 47, 97-120.
• Voight, B.F., Kudaravalli, S., Wen, X.Q. and Pritchard, J.K., 2006. A map of recent positive selection in the human genome. Plos Biology 4, 446-458.
• Vy, H.M.T. and Kim, Y., 2015. A Composite-Likelihood Method for Detecting Incomplete Selective Sweep from Population Genomic Data. Genetics 200, 633-+.
• Watterson, G., 1975. On the number of segregating sites in genetical models without recombination. Theoretical Population Biology 7, 256-276.
• Watterson, G., 1977. Heterosis or neutrality? Genetics 85, 789-814.
• Watterson, G., 1978. The homozygosity test of neutrality. Genetics 88, 405-417.
• Weigand, H. and Leese, F., 2018. Detecting signatures of positive selection in non-model species using genomic data. Zoological Journal of the Linnean Society 184, 528-583.
• Whitehead, A. and Crawford, D.L., 2006. Variation within and among species in gene expression: raw material for evolution. Molecular Ecology 15, 1197-1211.
• Wright, S., 1949. The genetical structure of populations. Annals of Eugenics 15, 323-354.
• Yamamoto, S., Humle, T. and Tanaka, M., 2013. Basis for cumulative cultural evolution in chimpanzees: social learning of a more efficient tool-use technique. Plos One 8.
• Zeder, M.A., 2012. Pathways to animal domestication. Biodiversity in Agriculture: Domestication, Evolution, and Sustainability, 227-259.
• Zeng, K., Fu, Y.X., Shi, S. and Wu, C.I., 2006. Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics 174, 1431-1439.
• Zeng, K., Shi, S. and Wu, C.I., 2007. Compound tests for the detection of hitchhiking under positive selection. Molecular Biology and Evolution 24, 1898-1908.
• Zhang, Q.Q., Guldbrandtsen, B., Bosse, M., Lund, M.S. and Sahana, G., 2015a. Runs of homozygosity and distribution of functional variants in the cattle genome. Bmc Genomics 16.
• Zhang, Q.R., Tyler-Smith, C. and Long, Q., 2015b. An extended Tajima's D neutrality test incorporating SNP calling and imputation uncertainties. Statistics and Its Interface 8, 447-456.
• Zhao, F.P., McParland, S., Kearney, F., Du, L.X. and Berry, D.P., 2015. Detection of selection signatures in dairy and beef cattle using high-density genomic information. Genetics Selection Evolution 47.
• Zohary, D., Tchernov, E. and Horwitz, L.K., 1998. The role of unconscious selection in the domestication of sheep and goats. Journal of Zoology 245, 129-135.