Haplotype allelic classes for detecting ongoing positive selection

Julie Hussin,Damian Labuda,Philippe Nadeau,Jean-François Lefebvre

doi:10.1186/1471-2105-11-65

Abstract

BackgroundNatural selection eliminates detrimental and favors advantageous phenotypes. This process leaves characteristic signatures in underlying genomic segments that can be recognized through deviations in allelic or haplotypic frequency spectra. To provide an identifiable signature of recent positive selection that can be detected by comparison with the background distribution, we introduced a new way of looking at genomic polymorphisms: haplotype allelic classes.ResultsThe model combines segregating sites and haplotypic information in order to reveal useful data characteristics. We developed a summary statistic, Svd, to compare the distribution of the haplotypes carrying the selected allele with the distribution of the remaining ones. Coalescence simulations are used to study the distributions under standard population models assuming neutrality, demographic scenarios and selection models. To test, in practice, haplotype allelic class performance and the derived statistic in capturing deviation from neutrality due to positive selection, we analyzed haplotypic variation in detail in the locus of lactase persistence in the three HapMap Phase II populations.ConclusionsWe showed that the Svd statistic is less sensitive than other tests to confounding factors such as demography or recombination. Our approach succeeds in identifying candidate loci, such as the lactase-persistence locus, as targets of strong positive selection and provides a new tool complementary to other tests to study natural selection in genomic data.

Highlights

Natural selection eliminates detrimental and favors advantageous phenotypes
In order to combine information on alleles of single nucleotide polymorphisms (SNPs) with that of the resulting haplotypes, we propose to plot haplotype allelic classes (HACs) that group haplotypes of the same mutational distance from a predefined reference haplotype [13]
Svd is less efficient than iHS at false discovery rates (FDR) < 0.05 and its performance becomes comparable to D at even lower FDRs

Summary

Introduction

Natural selection eliminates detrimental and favors advantageous phenotypes. This process leaves characteristic signatures in underlying genomic segments that can be recognized through deviations in allelic or haplotypic frequency spectra. The increasing availability of such data led to the development of new statistical methods to detect signatures of natural selection along DNA sequences. As these techniques use and analyze DNA diversity in different ways, the overlap between the reported candidate loci under selection is relatively low [6]. In the context of human evolution, it is interesting to look for recent selection events resulting from local adaptations. These should have left signatures of incomplete selective sweeps in the human genome, where the

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