PT - JOURNAL ARTICLE
AU - Pybus, Oliver G.
AU - Rambaut, Andrew
AU - Harvey, Paul H.
TI - An Integrated Framework for the Inference of Viral Population History From Reconstructed Genealogies
DP - 2000 Jul 01
TA - Genetics
PG - 1429--1437
VI - 155
IP - 3
4099 - http://www.genetics.org/content/155/3/1429.short
4100 - http://www.genetics.org/content/155/3/1429.full
SO - Genetics2000 Jul 01; 155
AB - 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.