An integrated framework for the inference of viral population history from reconstructed genealogies

O G Pybus, A Rambaut, P H Harvey

Research output: Contribution to journalArticlepeer-review

Abstract

We describe a unified set of methods for the inference of demographic history using genealogies reconstructed from gene sequence data. We introduce the skyline plot, a graphical, nonparametric estimate of demographic history. We discuss both maximum-likelihood parameter estimation and demographic hypothesis testing. Simulations are carried out to investigate the statistical properties of maximum-likelihood estimates of demographic parameters. The simulations reveal that (i) the performance of exponential growth model estimates is determined by a simple function of the true parameter values and (ii) under some conditions, estimates from reconstructed trees perform as well as estimates from perfect trees. We apply our methods to HIV-1 sequence data and find strong evidence that subtypes A and B have different demographic histories. We also provide the first (albeit tentative) genetic evidence for a recent decrease in the growth rate of subtype B.

Original languageEnglish
Pages (from-to)1429-1437
Number of pages9
JournalGenetics
Volume155
Issue number3
Publication statusPublished - Jul 2000

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