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The Use of Intraallelic Variability for Testing Neutrality and Estimating Population Growth Rate

Slatkin, Montgomery, Bertorelle, Giorgio·2001·Genetics
DOI 10.1093/genetics/158.2.865
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Abstract

To better understand the forces affecting individual alleles, we introduce a method for finding the joint distribution of the frequency of a neutral allele and the extent of variability at closely linked marker loci (the intraallelic variability). We model three types of intraallelic variability: (a) the number of nonrecombinants at a linked biallelic marker locus, (b) the length of a conserved haplotype, and (c) the number of mutations at a linked marker locus. If the population growth rate is known, the joint distribution provides the basis for a test of neutrality by testing whether the observed level of intraallelic variability is consistent with the observed allele frequency. If the population growth rate is unknown but neutrality can be assumed, the joint distribution provides the likelihood of the growth rate and leads to a maximum-likelihood estimate. We apply the method to data from published data sets for four loci in humans. We conclude that the Δ32 allele at CCR5 and a disease-associated allele at MLH1 arose recently and have been subject to strong selection. Alleles at PAH appear to be neutral and we estimate the recent growth rate of the European population to be ∼0.027 per generation with a support interval of (0.017-0.037). Four of the relatively common alleles at CFTR also appear to be neutral but ΔF508 appears to be significantly advantageous to heterozygous carriers.

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Cited by

Metadata

Authors
Slatkin, M., & Bertorelle, G.
Affiliations
  • Department of Integrative Biology, University of California, Berkeley, California 94720-3140
  • Sezione di Biologia Evolutiva, Dipartimento di Biologia, Universitá di Ferrara, 44100 Ferrara, Italy
Venue
Genetics
Publisher
Oxford University Press (OUP)
Published
2001-06-01
Volume
158
Issue
2
Pages
865-874
ISSN
1943-2631
DOI
10.1093/genetics/158.2.865
Cited by
44
References
2
Language
en
Licence
academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)

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