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Likelihoods from summary statistics: recent divergence between species.

Publication ,  Journal Article
Leman, SC; Chen, Y; Stajich, JE; Noor, MAF; Uyenoyama, MK
Published in: Genetics
November 2005

We describe an importance-sampling method for approximating likelihoods of population parameters based on multiple summary statistics. In this first application, we address the demographic history of closely related members of the Drosophila pseudoobscura group. We base the maximum-likelihood estimation of the time since speciation and the effective population sizes of the extant and ancestral populations on the pattern of nucleotide variation at DPS2002, a noncoding region tightly linked to a paracentric inversion that strongly contributes to reproductive isolation. Consideration of summary statistics rather than entire nucleotide sequences permits a compact description of the genealogy of the sample. We use importance sampling first to propose a genealogical and mutational history consistent with the observed array of summary statistics and then to correct the likelihood with the exact probability of the history determined from a system of recursions. Analysis of a subset of the data, for which recursive computation of the exact likelihood was feasible, indicated close agreement between the approximate and exact likelihoods. Our results for the complete data set also compare well with those obtained through Metropolis-Hastings sampling of fully resolved genealogies of entire nucleotide sequences.

Duke Scholars

Published In

Genetics

DOI

EISSN

1943-2631

ISSN

0016-6731

Publication Date

November 2005

Volume

171

Issue

3

Start / End Page

1419 / 1436

Related Subject Headings

  • Mutation
  • Monte Carlo Method
  • Models, Genetic
  • Markov Chains
  • Likelihood Functions
  • Genetics, Population
  • Genetic Speciation
  • Drosophila
  • Developmental Biology
  • Animals
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Leman, S. C., Chen, Y., Stajich, J. E., Noor, M. A. F., & Uyenoyama, M. K. (2005). Likelihoods from summary statistics: recent divergence between species. Genetics, 171(3), 1419–1436. https://doi.org/10.1534/genetics.104.040402
Leman, Scotland C., Yuguo Chen, Jason E. Stajich, Mohamed A. F. Noor, and Marcy K. Uyenoyama. “Likelihoods from summary statistics: recent divergence between species.Genetics 171, no. 3 (November 2005): 1419–36. https://doi.org/10.1534/genetics.104.040402.
Leman SC, Chen Y, Stajich JE, Noor MAF, Uyenoyama MK. Likelihoods from summary statistics: recent divergence between species. Genetics. 2005 Nov;171(3):1419–36.
Leman, Scotland C., et al. “Likelihoods from summary statistics: recent divergence between species.Genetics, vol. 171, no. 3, Nov. 2005, pp. 1419–36. Epmc, doi:10.1534/genetics.104.040402.
Leman SC, Chen Y, Stajich JE, Noor MAF, Uyenoyama MK. Likelihoods from summary statistics: recent divergence between species. Genetics. 2005 Nov;171(3):1419–1436.

Published In

Genetics

DOI

EISSN

1943-2631

ISSN

0016-6731

Publication Date

November 2005

Volume

171

Issue

3

Start / End Page

1419 / 1436

Related Subject Headings

  • Mutation
  • Monte Carlo Method
  • Models, Genetic
  • Markov Chains
  • Likelihood Functions
  • Genetics, Population
  • Genetic Speciation
  • Drosophila
  • Developmental Biology
  • Animals