Abstract
The emigration of humankind from Africa and the adoption of agriculture have meant that the selective pressures on humankind have changed in recent evolutionary times. A selective sweep occurs when a positive mutation spreads through a population. For example, a mutation that enables adults to digest lactase has spread through the Northern European population, although it is very rare in the African population. Since neutral alleles that are strongly linked to such a positive mutation also tend to spread through the population, these sweeps leave a signature, a valley of low genetic variation.This article reviews the development of statistical tests for the detection of selective sweeps using genomic data, particularly in the light of recent advances in genome mapping. It also points out directions for future research.
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Achaz, G. (2008). Testing for neutrality in samples with sequencing errors. Genetics, 179, 1409–1424.
Akey, J. M., Zhang, G., Zhang, K., Jin, L., & Shriver, M. D. (2002). Interrogating a high-density snp map for signatures of natural selection. Genome Research, 12, 1805–1814.
Avery, P. J., & Henderson, D. A. (1999). Detecting a changed segment in dna sequences. Applied Statistics, 48, 489–503.
Barnes, M. R. (2006). Navigating the hapmap. Briefings in Bioinformatics, 7, 211–224.
Cannings, C. (1974). The latent roots of certain markov chains arising in genetics: A new approach, i. haploid models. Advances in Applied Probability, 6, 260–290.
Carlson, C. S., Thomas, D. J., Eberle, M. A., Swanson, J. E., Livingston, R. J., Rieder, M. J., et al. (2005). Genomic regions exhibiting positive selection identified from dense genotype data. Genome Research, 15, 1553–1565.
Consortium, T. I. H. (2003). The international hapmap project. Nature, 426, 789–796.
Durrett, R., & Schweinsberg, J. (2004). Approximating selective sweeps. Theoretical Population Biology, 66, 129–138.
Fu, Y. X., & Li, W. H. (1992). Statistical test of neutrality of mutations. Genetics, 133, 693–709.
Hamblin, M. T., & Di Rienzo, A. (2000). Detection of the signature of natural selection in humans: Evidence from the duffy blood group locus. American Journal of Human Genetics, 66, 1669–1679.
Hein, J., Schierup, M., & Wiuf, C. (2004). Gene genealogies, variation and evolution: A primer in coalescent theory. Oxford, UK: Oxford University Press.
Hoggart, C. J., Chadeau-Hyam, M., Clark, T. G., Lampariello, R., Whittaker, J. C., De Iorio, M., et al. (2007). Sequence-level population simulations over large genomic regions. Genetics, 177, 1725–1731.
Hudson, R. R. (2002). Generating samples under a wright-fisher neutral model of genetic variation. Bioinformatics, 18, 337–338.
Husmeier, D., & McGuire, G. (2002). Detecting recombination with mcmc. Bioinformatics, 18, 345–353.
Innan, H., & Kim, Y. (2004). Pattern of polymorphism after strong artificial selection in a domestication event. Proceedings of the National Academy of Sciences, 101, 10667–10672.
Innan, H., & Kim, Y. (2008). Detection of local adaptation using the joint sampling of polymorphism data in the parental and derived population. Genetics, 179, 1713–1720.
Jensen, J. D., Kim, Y., DuMont, V. B., Aquadro, C. F., & Bustamante, C. D. (2005). Distinguishing between selective sweeps and demography using dna polymorphism data. Genetics, 170, 1401–1410.
Jensen, J. D., Thornton, K. R., & Aquadro, C. F. (2008). Inferring selection in partially sequenced regions. Molecular and Biological Evolution, 25, 438–446.
Jensen, J. D., Thornton, K. R., Bustamante, C. D., & Aquadro, C. F. (2007). On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations. Genetics, 176, 2371–2379.
Johnson, P. L. F., & Slatkin, M. (2006). Inference of population genetic parameters in metagenomics: A clean look at messy data. Genome Research, 16, 1320–1327.
Kim, Y., & Nielsen, R. (2004). Linkage disequilibrium as a signature of selective sweeps. Genetics, 167, 1513–1524.
Kim, Y., & Stepham, W. (2002). Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics, 160, 765–777.
Kimura, M. (1971). Theoretical foundation of population genetics at the molecular level. Theoretical Population Biology, 2, 174–208.
Kimura, R., Fujimoto, A., Tokunaga, K., & Ohashi, J. (2007). A practical genome scan for population-specific strong selective sweeps that have reached fixation. PLoS One, 2, e286.
Lewontin, R. C., & Krakauer, J. (1973). Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics, 74, 175–195.
Macpherson, J. M., González, J., Witten, D. M., Davis, J. C., Rosenberg, N. A., Hirsh, A. E., et al. (2008). Nonadaptive explanations for signatures of partial selective sweeps in drosophila. Molecular and Biological Evolution, 25, 1025–1042.
Maynard Smith, J., & Haigh, J. (1974). The hitchhiking effect of a favourable gene. Genetics, 23, 23–35.
McVean, G., Spencer, C. C. A., & Chaix, R. (2005). Perspectives on human genetic variation from hapmap project. PLoS Genetics, 1, e54.
Möller, D. A., Tenaillon, M. I., & Tiffin, P. (2007). Population structure and its effects on patterns of nucleotide polymorphism in teosinte. Genetics, 176, 1799–1809.
Neuhauser, C., & Krone, S. M. (1997). The genealogy of samples in models with selection. Genetics, 145, 519–534.
Nielsen, R., Hubisz, M. J., & Clark, A. G. (2004). Reconstituting the frequency spectrum of ascertained snp data. Genetics, 168, 2373–2382.
Nielsen, R., Williamson, S., Kim, Y., Hubisz, M. J., Clark, A. G., & Bustamante, C. (2005). Genomic scans for selective sweeps using snp data. Genome Research, 15, 1566–1575.
Padhukasahasram, B., Marjoram, P., Wall, J. D., Bustamante, C. D., & Nordborg, M. (2008). Exploring population genetic models with recombination using efficient forward-time simulations. Genetics, 178, 2417–2427.
Pan, J., & MacKenzie, G. (2003). On modelling mean-covariance structures in longitudinal studies. Biometrika, 90, 239–244.
Pfaffelhuber, P., Lehnert, A., & Stephan, W. (2008). Linkage disequilibrium under genetic hitchhiking in finite populations. Genetics, 179, 527–537.
Project, S. S. (2004). SeattleSNPs. NHLBI Program for Genomic Applications. Seattle, WA: SeattleSNPs. http://pga.gs.washington.edu
Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z., Richter, D. J., Schaffner, S. F., et al. (2002). Detecting recent positive selection in the human genome from haplotype structure. Nature, 419, 832–837.
Slatkin, M. (2000). A coalescent view of population structure. In R. S. Singh & C. B. Krimbas (Eds.), In evolutionary genetics. New York: Cambridge University Press.
Spencer, C. A., & Coop, G. (2004). Selsim: A program to simulate population genetic data under coalescent models. Bioinformatics, 20, 3673–3675.
Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by dna polymorphism. Genetics, 123, 585–595.
Teshima, K. M., Coop, G., & Przeworski, M. (2006). How reliable are empirical genomic scans for selective sweeps? Genome Research, 16, 702–712.
Voight, B. F., Kudaravalli, S., Wen, X., & Pritchard, J. K. (2006). A map of recent positive selection in the human genome using empirical scores. PLoS Biology, 4, e72.
Williamson, S. H., Hernandez, R., Fledel-Alon, A., Zhu, L., Nielsen, R., & Bustamante, C. D. (2005). Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proceedings of the National Academy of Sciences, 102, 7882–7887.
Yamasaki, M., Tenaillon, M. I., Bi, I. V., Schroeder, S. G., Sanchez-Villeda, H., Doebley, J. F., et al. (2005). A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell, 17, 2859–2872.
Zeng, K., Shi, S., & Wu, C. I. (2007). Compound tests for the detection of hitchhiking under positive selection. Molecular and Biological Evolution, 24, 1898–1908.
Acknowledgements
This work was carried out in the Department of Mathematics & Statistics at the University of Limerick, Ireland, and was supported by Science Foundation Ireland, Grant No. 07/MI/012 (BIO-SI project, www3.ul.ie/bio-si).
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Ramsey, D. (2014). Statistical Methods for Detecting Selective Sweeps. In: MacKenzie, G., Peng, D. (eds) Statistical Modelling in Biostatistics and Bioinformatics. Contributions to Statistics. Springer, Cham. https://doi.org/10.1007/978-3-319-04579-5_13
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DOI: https://doi.org/10.1007/978-3-319-04579-5_13
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