Trends in Ecology & Evolution
The utility of single nucleotide polymorphisms in inferences of population history
Section snippets
Application of SNPs in studies of population history
It is only recently that a conceptual framework for the population genetic analysis of SNPs, founded appropriately on coalescent theory, has been developed 9, 11. Perhaps the most important nuance to SNP analysis is the need to correct for the ascertainment bias [33] that arises as a by-product of how the SNPs are identified and/or screened [11]. Before starting a SNP study of population history, the researcher must make two decisions that will determine the necessary ascertainment correction.
Mutation pattern
Unlike microsatellites, which have mutation rates per generation of the order of 10−4, SNPs have relatively low mutation rates (10−8–10−9). Multiple mutations at a single site are thus unlikely, and so most SNPs are bi-allelic, a quality that facilitates high-throughput genotyping and minimizes recurrent substitutions at a single site that would confound the population history. The restriction to four character states might make SNPs less informative than microsatellites for parentage analyses
Recombination
A complication of an approach that assays variation at many loci across the genome is that recombination cannot be ignored, as it is in mitochondrial and human Y chromosome studies. Recombination influences both the interpretation and the sampling strategy of SNP variation. Nachman [46] has reviewed the dramatic effects of recombination on the level of SNP variation in humans, in which SNP variation is low in regions of low recombination, and high in regions of high recombination. The same
Conclusion
SNPs have the potential to place historical demography and speciation studies on a common molecular framework, one that is easily comparable to the decades of mtDNA work already undertaken [77]. Their simplicity, ease of modeling and sheer abundance will make them powerful contributors to the new era of using multiple biparentally inherited, potentially recombining loci to infer population histories. The challenge for evolutionary biologists will be to harness and assay variation at large
Acknowledgements
For providing helpful comments, we thank A. Di Rienzo, M. Hare, H.L. Gibbs, B. Jennings, C. Moritz, M. Nachman, R. Nielsen, P. Palsbøll, M. Slatkin, J. Wakeley and two anonymous reviewers. We thank L. Knowles for providing us with a prepublication copy of her manuscript. Work on this article was made possible in part by support from National Science Foundation grants DBI-9974235 (to R.T.B.), DEB 0108249 (to S.V.E. and P.B.), DEB 0129487 (to S.V.E.) and DEB9815650 (to J. Felsenstein); and
Glossary
Glossary
- Ascertainment bias:
- bias introduced into an analysis because of arbitrary decisions made during data sampling. In SNP or microsatellite studies, ascertainment bias can arise if only the most variable loci are analysed or if only a small panel of individuals is used to discover variation.
- Coalescent theory:
- population genetic framework that allows one to calculate the probability of obtaining a given genealogical structure for many contemporary samples under many different population genetic models.
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