Abstract
Annual Review of Genetics
Vol. 39:
197-218
(Volume publication date December 2005)
(doi:10.1146/annurev.genet.39.073003.112420)
First published online as a Review in Advance on August 31, 2005MOLECULAR SIGNATURES OF NATURAL SELECTION Rasmus NielsenCenter for Bioinformatics and Department of Evolutionary Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark; email: rasmus@binf.ku.dk Abstract There is an increasing interest in detecting genes, or genomic regions, that have been targeted by natural selection. The interest stems from a basic desire to learn more about evolutionary processes in humans and other organisms, and from the realization that inferences regarding selection may provide important functional information. This review provides a nonmathematical description of the issues involved in detecting selection from DNA sequences and SNP data and is intended for readers who are not familiar with population genetic theory. Particular attention is placed on issues relating to the analysis of large-scale genomic data sets. Acronyms dN: number of nonsynonymous mutations per nonsynonymous site dN/dS ratio: the rate ratio of nonsynonymous to synonymous substitutions ds: number of synonymous mutations per synonymous site LD: linkage disequilibrium PRF: Poisson random field SNP: single nucleotide polymorphism Terms and Definitions Balancing selection: selection that increases variability within a population Frequency spectrum: the allelic sample distribution in independent nucleotide sites Negative selection: selection acting upon new deleterious mutation Neutral mutation: a mutation that does not affect the fitness of individuals who carry it in either heterozygous or homozygous condition Neutrality test: a statistical test of a model which assumes all mutations are either neutral or strongly deleterious Positive selection: selection acting upon new advantageous mutations Selective sweep: the process by which a new advantageous mutation eliminates or reduces variation in linked neutral sites as it increases in frequency in the population Most recent citing papers (via CrossRef)The genomic legacy from the extinct
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