Blog
About

  • Record: found
  • Abstract: found
  • Article: not found

Bayesian coalescent inference of past population dynamics from molecular sequences.

Molecular Biology and Evolution

Animals, Bayes Theorem, Bison, genetics, DNA, Mitochondrial, Egypt, epidemiology, Evolution, Molecular, Genetics, Population, Hepacivirus, Time Factors, pathogenicity, Hepatitis C, transmission, Humans, Markov Chains, Models, Genetic, Monte Carlo Method, Population Density, Population Dynamics, Algorithms

Read this article at

ScienceOpenPublisherPubMed
Bookmark
      There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

      Abstract

      We introduce the Bayesian skyline plot, a new method for estimating past population dynamics through time from a sample of molecular sequences without dependence on a prespecified parametric model of demographic history. We describe a Markov chain Monte Carlo sampling procedure that efficiently samples a variant of the generalized skyline plot, given sequence data, and combines these plots to generate a posterior distribution of effective population size through time. We apply the Bayesian skyline plot to simulated data sets and show that it correctly reconstructs demographic history under canonical scenarios. Finally, we compare the Bayesian skyline plot model to previous coalescent approaches by analyzing two real data sets (hepatitis C virus in Egypt and mitochondrial DNA of Beringian bison) that have been previously investigated using alternative coalescent methods. In the bison analysis, we detect a severe but previously unrecognized bottleneck, estimated to have occurred 10,000 radiocarbon years ago, which coincides with both the earliest undisputed record of large numbers of humans in Alaska and the megafaunal extinctions in North America at the beginning of the Holocene.

      Related collections

      Author and article information

      Journal
      15703244
      10.1093/molbev/msi103

      Comments

      Comment on this article