Statistical properties of the allelic mismatch distribution in neutrally evolving haploid populations

Research output: Contribution to journalArticleScientificpeer-review

Abstract

The pairwise mismatch distribution for molecular marker loci is a commonly used statistic in ecology to investigate historical population growth, selection and effects of demographical processes. Since the statistical properties of the stationary mismatch distribution are not yet well understood for complex models, we investigate its behavior under the neutral Wright-Fisher model with mutation, recombination, migration and local stochastic propagation of haplotypes corresponding to microepidemics in a host population. Under such circumstances the traditional analytical tools for deriving equilibrium distributions do not apply, making derivation of recursive expressions elusive. Using simulations we show that the mismatch distribution of a population typically exhibits a considerable level of stochasticity over generations unless the mutation rate is sufficiently high. The stationary mean mismatch distribution is a more stable summary but it may remain insensitive to changes in the model parameters, suggesting that additional complementary population summaries are needed for inference. We illustrate mismatch distribution dynamics using data on asymptomatic pediatric carriage of Streptococcus pneumoniae, indicating a thoroughly mixing population with rapid dynamics across local communities.
Original languageEnglish
JournalAmerican Naturalist
ISSN0003-0147
Publication statusSubmitted - 2016
MoE publication typeA1 Journal article-refereed

Fields of Science

  • 112 Statistics and probability
  • 1183 Plant biology, microbiology, virology

Cite this

@article{5a1979fb672241169f1567cbbeed3236,
title = "Statistical properties of the allelic mismatch distribution in neutrally evolving haploid populations",
abstract = "The pairwise mismatch distribution for molecular marker loci is a commonly used statistic in ecology to investigate historical population growth, selection and effects of demographical processes. Since the statistical properties of the stationary mismatch distribution are not yet well understood for complex models, we investigate its behavior under the neutral Wright-Fisher model with mutation, recombination, migration and local stochastic propagation of haplotypes corresponding to microepidemics in a host population. Under such circumstances the traditional analytical tools for deriving equilibrium distributions do not apply, making derivation of recursive expressions elusive. Using simulations we show that the mismatch distribution of a population typically exhibits a considerable level of stochasticity over generations unless the mutation rate is sufficiently high. The stationary mean mismatch distribution is a more stable summary but it may remain insensitive to changes in the model parameters, suggesting that additional complementary population summaries are needed for inference. We illustrate mismatch distribution dynamics using data on asymptomatic pediatric carriage of Streptococcus pneumoniae, indicating a thoroughly mixing population with rapid dynamics across local communities.",
keywords = "112 Statistics and probability, 1183 Plant biology, microbiology, virology",
author = "Mikhail Shubin and Numminen, {Suvi Elina} and Gutmann, {Urs Michael} and Hanage, {William P.} and Corander, {Jukka Ilmari}",
year = "2016",
language = "English",
journal = "American Naturalist",
issn = "0003-0147",
publisher = "The University of Chicago Press",

}

Statistical properties of the allelic mismatch distribution in neutrally evolving haploid populations. / Shubin, Mikhail; Numminen, Suvi Elina; Gutmann, Urs Michael; Hanage, William P.; Corander, Jukka Ilmari.

In: American Naturalist, 2016.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Statistical properties of the allelic mismatch distribution in neutrally evolving haploid populations

AU - Shubin, Mikhail

AU - Numminen, Suvi Elina

AU - Gutmann, Urs Michael

AU - Hanage, William P.

AU - Corander, Jukka Ilmari

PY - 2016

Y1 - 2016

N2 - The pairwise mismatch distribution for molecular marker loci is a commonly used statistic in ecology to investigate historical population growth, selection and effects of demographical processes. Since the statistical properties of the stationary mismatch distribution are not yet well understood for complex models, we investigate its behavior under the neutral Wright-Fisher model with mutation, recombination, migration and local stochastic propagation of haplotypes corresponding to microepidemics in a host population. Under such circumstances the traditional analytical tools for deriving equilibrium distributions do not apply, making derivation of recursive expressions elusive. Using simulations we show that the mismatch distribution of a population typically exhibits a considerable level of stochasticity over generations unless the mutation rate is sufficiently high. The stationary mean mismatch distribution is a more stable summary but it may remain insensitive to changes in the model parameters, suggesting that additional complementary population summaries are needed for inference. We illustrate mismatch distribution dynamics using data on asymptomatic pediatric carriage of Streptococcus pneumoniae, indicating a thoroughly mixing population with rapid dynamics across local communities.

AB - The pairwise mismatch distribution for molecular marker loci is a commonly used statistic in ecology to investigate historical population growth, selection and effects of demographical processes. Since the statistical properties of the stationary mismatch distribution are not yet well understood for complex models, we investigate its behavior under the neutral Wright-Fisher model with mutation, recombination, migration and local stochastic propagation of haplotypes corresponding to microepidemics in a host population. Under such circumstances the traditional analytical tools for deriving equilibrium distributions do not apply, making derivation of recursive expressions elusive. Using simulations we show that the mismatch distribution of a population typically exhibits a considerable level of stochasticity over generations unless the mutation rate is sufficiently high. The stationary mean mismatch distribution is a more stable summary but it may remain insensitive to changes in the model parameters, suggesting that additional complementary population summaries are needed for inference. We illustrate mismatch distribution dynamics using data on asymptomatic pediatric carriage of Streptococcus pneumoniae, indicating a thoroughly mixing population with rapid dynamics across local communities.

KW - 112 Statistics and probability

KW - 1183 Plant biology, microbiology, virology

M3 - Article

JO - American Naturalist

JF - American Naturalist

SN - 0003-0147

ER -