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Allele frequency spectra in structured populations: Novel-allele probabilities under the labelled coalescent.

Publication ,  Journal Article
Uyenoyama, MK; Takebayashi, N; Kumagai, S
Published in: Theoretical population biology
June 2020

We address the effect of population structure on key properties of the Ewens sampling formula. We use our previously-introduced inductive method for determining exact allele frequency spectrum (AFS) probabilities under the infinite-allele model of mutation and population structure for samples of arbitrary size. Fundamental to the sampling distribution is the novel-allele probability, the probability that given the pattern of variation in the present sample, the next gene sampled belongs to an as-yet-unobserved allelic class. Unlike the case for panmictic populations, the novel-allele probability depends on the AFS of the present sample. We derive a recursion that directly provides the marginal novel-allele probability across AFSs, obviating the need first to determine the probability of each AFS. Our explorations suggest that the marginal novel-allele probability tends to be greater for initial samples comprising fewer alleles and for sampling configurations in which the next-observed gene derives from a deme different from that of the majority of the present sample. Comparison to the efficient importance sampling proposals developed by De Iorio and Griffiths and colleagues indicates that their approximation for the novel-allele probability generally agrees with the true marginal, although it may tend to overestimate the marginal in cases in which the novel-allele probability is high and migration rates are low.

Duke Scholars

Published In

Theoretical population biology

DOI

EISSN

1096-0325

ISSN

0040-5809

Publication Date

June 2020

Volume

133

Start / End Page

130 / 140

Related Subject Headings

  • Probability
  • Mutation
  • Models, Genetic
  • Genetics, Population
  • Gene Frequency
  • Evolutionary Biology
  • Alleles
  • 4901 Applied mathematics
  • 3104 Evolutionary biology
  • 3103 Ecology
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Uyenoyama, M. K., Takebayashi, N., & Kumagai, S. (2020). Allele frequency spectra in structured populations: Novel-allele probabilities under the labelled coalescent. Theoretical Population Biology, 133, 130–140. https://doi.org/10.1016/j.tpb.2020.01.002
Uyenoyama, Marcy K., Naoki Takebayashi, and Seiji Kumagai. “Allele frequency spectra in structured populations: Novel-allele probabilities under the labelled coalescent.Theoretical Population Biology 133 (June 2020): 130–40. https://doi.org/10.1016/j.tpb.2020.01.002.
Uyenoyama MK, Takebayashi N, Kumagai S. Allele frequency spectra in structured populations: Novel-allele probabilities under the labelled coalescent. Theoretical population biology. 2020 Jun;133:130–40.
Uyenoyama, Marcy K., et al. “Allele frequency spectra in structured populations: Novel-allele probabilities under the labelled coalescent.Theoretical Population Biology, vol. 133, June 2020, pp. 130–40. Epmc, doi:10.1016/j.tpb.2020.01.002.
Uyenoyama MK, Takebayashi N, Kumagai S. Allele frequency spectra in structured populations: Novel-allele probabilities under the labelled coalescent. Theoretical population biology. 2020 Jun;133:130–140.
Journal cover image

Published In

Theoretical population biology

DOI

EISSN

1096-0325

ISSN

0040-5809

Publication Date

June 2020

Volume

133

Start / End Page

130 / 140

Related Subject Headings

  • Probability
  • Mutation
  • Models, Genetic
  • Genetics, Population
  • Gene Frequency
  • Evolutionary Biology
  • Alleles
  • 4901 Applied mathematics
  • 3104 Evolutionary biology
  • 3103 Ecology