Towards Consensus Gene Ages.
Correctly estimating the age of a gene or gene family is important for a variety of fields, including molecular evolution, comparative genomics, and phylogenetics, and increasingly for systems biology and disease genetics. However, most studies use only a point estimate of a gene's age, neglecting the substantial uncertainty involved in this estimation. Here, we characterize this uncertainty by investigating the effect of algorithm choice on gene-age inference and calculate consensus gene ages with attendant error distributions for a variety of model eukaryotes. We use 13 orthology inference algorithms to create gene-age datasets and then characterize the error around each age-call on a per-gene and per-algorithm basis. Systematic error was found to be a large factor in estimating gene age, suggesting that simple consensus algorithms are not enough to give a reliable point estimate. We also found that different sources of error can affect downstream analyses, such as gene ontology enrichment. Our consensus gene-age datasets, with associated error terms, are made fully available at so that researchers can propagate this uncertainty through their analyses (geneages.org).
Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin Center for Computational Biology and Bioinformatics, University of Texas at Austin bliebeskind@austin.utexas.edu.
Benjamin J
BJ
Liebeskind
Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin.
Claire D
CD
McWhite
Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin.
Edward M
EM
Marcotte
D000465:Algorithms; D019143:Evolution, Molecular; D005796:Genes; D023281:Genomics; D006801:Humans; D005810:Multigene Family / Q000235:genetics*; D010802:Phylogeny
LECA; LUCA; ortholog; phylostratigraphy