Year: 2011
Type: article
Abstract: Rate heterogeneity among lineages is a common feature of molecular evolution, and it has long impeded our ability to accurately estimate the age of evolutionary divergence events. The development of relaxed molecular clocks, which model variable substitution rates among lineages, was intended to rectify this problem. Major subtypes of pandemic HIV-1 group M are thought to exemplify closely related lineages with different substitution rates. Here, we report that inferring the time of most recent common ancestor of all these subtypes in a single phylogeny under a single (relaxed) molecular clock produces significantly different dates for many of the subtypes than does analysis of each subtype on its own. We explore various methods to ameliorate this problem. We conclude that current molecular dating methods are inadequate for dealing with this type of substitution rate variation in HIV-1. Through simulation, we show that heterotachy causes root ages to be overestimated.
Source: Molecular Biology and Evolution
Institution: University of California San Diego
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: bronze
Awards: Modeling HIV Escape from Neutralizing Antibody Respones, G1781340182, G1812340134, G2132829350, BIOMATHEMATICAL ANALYSIS OF VIRAL DYNAMICS AND EVOLUTION, Identifying Selection Pressures on Viral Genomes, G2344635089, Primary Infection Resource Consortium (PIRC), Biomathematical Analysis of Viral Dynamics and Evolution, G473273920, BIOMATHEMATICAL ANALYSIS OF VIRAL DYNAMICS AND EVOLUTION, G5918387183, Southern California Primary Infection Program, Determinants of HIV Transmission, HyPhy: comprehensive, fast, and user-friendly software for evolutionary analysis, G9000031394, G9000062723, G9000096674, San Diego Center for AIDS Research (SD CFAR), HOPE Training Grant
OpenAlex ID: W2117681388