Recurrent mutation in the ancestry of a rare variant.
Ewens sampling formula
coalescent theory
human SNPs
recurrent mutation
Journal
Genetics
ISSN: 1943-2631
Titre abrégé: Genetics
Pays: United States
ID NLM: 0374636
Informations de publication
Date de publication:
06 Jul 2023
06 Jul 2023
Historique:
received:
30
01
2023
accepted:
08
03
2023
medline:
10
7
2023
pubmed:
27
3
2023
entrez:
26
3
2023
Statut:
ppublish
Résumé
Recurrent mutation produces multiple copies of the same allele which may be co-segregating in a population. Yet, most analyses of allele-frequency or site-frequency spectra assume that all observed copies of an allele trace back to a single mutation. We develop a sampling theory for the number of latent mutations in the ancestry of a rare variant, specifically a variant observed in relatively small count in a large sample. Our results follow from the statistical independence of low-count mutations, which we show to hold for the standard neutral coalescent or diffusion model of population genetics as well as for more general coalescent trees. For populations of constant size, these counts are distributed like the number of alleles in the Ewens sampling formula. We develop a Poisson sampling model for populations of varying size and illustrate it using new results for site-frequency spectra in an exponentially growing population. We apply our model to a large data set of human SNPs and use it to explain dramatic differences in site-frequency spectra across the range of mutation rates in the human genome.
Identifiants
pubmed: 36967220
pii: 7086184
doi: 10.1093/genetics/iyad049
pmc: PMC10324944
pii:
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NHGRI NIH HHS
ID : R01 HG010372
Pays : United States
Organisme : NIH HHS
ID : R35-GM127131
Pays : United States
Commentaires et corrections
Type : ErratumIn
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.
Déclaration de conflit d'intérêts
Conflicts of interest The authors declare no conflicts of interest.
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