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COMPUTER PROGRAMS: onesamp: a program to estimate effective population size using approximate Bayesian computation.

David A Tallmon1, Ally Koyuk, Gordon Luikart

  • 1Biology Program, University of Alaska Southeast, 11120 Glacier Highway, Juneau, AK 99801, USA, Division of Biological Sciences, DBS/HS 104, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA, School of Animal and Microbial Sciences, University of Reading, Whiteknights, Reading RG6 6AJ, UK.

Molecular Ecology Resources
|May 19, 2011
PubMed
Summary
This summary is machine-generated.

Estimating effective population size from genetic data is challenging. A new program, onesamp, uses approximate Bayesian computation for more precise estimations from microsatellite genotypes.

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Area of Science:

  • Population Genetics
  • Computational Biology
  • Conservation Genetics

Background:

  • Estimating effective population size (Ne) from a single sample of genetic markers is crucial for understanding population dynamics but is often imprecise or biased.
  • Existing methods for Ne estimation from one sample of genotypes face limitations in accuracy and reliability.

Purpose of the Study:

  • To develop a user-friendly, web-based program for estimating effective population size (Ne) from a single sample of microsatellite genotypes.
  • To address the challenges of imprecision and bias in current Ne estimation methods.

Main Methods:

  • Developed 'onesamp', a web-based program utilizing approximate Bayesian computation (ABC).
  • The program requires microsatellite genotype data and key sampling/biological parameters as input.
  • Employs ABC to infer Ne and its 95% credible limits.

Main Results:

  • onesamp provides an estimate of effective population size (Ne) with associated 95% credible limits.
  • Demonstrated the program's utility with a case study on a reintroduced ibex (Capra ibex) population.
  • The method offers improved precision and reduced bias compared to traditional estimators.

Conclusions:

  • onesamp offers a robust and accessible tool for estimating effective population size from single-sample microsatellite data.
  • The application of approximate Bayesian computation enhances the reliability of Ne estimates in population genetics.
  • This tool can aid conservation efforts by providing more accurate insights into population structure and viability.