期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 32, 期 1, 页码 258-267出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msu286
关键词
BLAST; gene age; phylogenetic dating
资金
- U.S. National Institutes of Health (NIH) [R01GM103232]
- NIH training grant in genome sciences [T32HG000040]
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [T32HG000040] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM103232] Funding Source: NIH RePORTER
Phylostratigraphy is a method for dating the evolutionary emergence of a gene or gene family by identifying its homologs across the tree of life, typically by using BLAST searches. Applying this method to all genes in a species, or genomic phylostratigraphy, allows investigation of genome-wide patterns in new gene origination at different evolutionary times and thus has been extensively used. However, gene age estimation depends on the challenging task of detecting distant homologs via sequence similarity, which is expected to have differential accuracies for different genes. Here, we evaluate the accuracy of phylostratigraphy by realistic computer simulation with parameters estimated from genomic data, and investigate the impact of its error on findings of genome evolution. We show that 1) phylostratigraphy substantially underestimates gene age for a considerable fraction of genes, 2) the error is especially serious when the protein evolves rapidly, is short, and/or its most conserved block of sites is small, and 3) these errors create spurious nonuniform distributions of various gene properties among age groups, many of which cannot be predicted a priori. Given the high likelihood that conclusions about gene age are faulty, we advocate the use of realistic simulation to determine if observations from phylostratigraphy are explainable, at least qualitatively, by a nullmodel of biased measurement, and in all cases, critical evaluation of results.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据