title: Estimation of Gene Insertion/Deletion Rates with Missing Data.
abstract: Lateral gene transfer is an important mechanism for evolution among bacteria. Here, genome-wide gene insertion and deletion rates are modeled in a maximum-likelihood framework with the additional flexibility of modeling potential missing data. The performance of the models is illustrated using simulations and a data set on gene family phyletic patterns from Gardnerella vaginalis that includes an ancient taxon. A novel application involving pseudogenization/genome reduction magnitudes is also illustrated, using gene family data from Mycobacterium spp. Finally, an R package called indelmiss is available from the Comprehensive R Archive Network at https://cran.r-project.org/package=indelmiss, with support documentation and examples.
authors: Departments of Biology and Mathematics and Statistics, McMaster University, Hamilton, Ontario L8S-4L8, Canada.
authors: Utkarsh J
authors: UJ
authors: Dang
authors: MYcroarray, Ann Arbor, Michigan 48105.
authors: Alison M
authors: AM
authors: Devault
authors: Departments of Medicine and Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53705.
authors: Tatum D
authors: TD
authors: Mortimer
authors: Departments of Medicine and Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53705.
authors: Caitlin S
authors: CS
authors: Pepperell
authors: Department of Anthropology, McMaster University, Hamilton, Ontario L8S-4K1, Canada.
authors: Hendrik N
authors: HN
authors: Poinar
authors: Department of Biology, McMaster University, Hamilton, Ontario L8S-4K1, Canada golding@mcmaster.ca.
authors: G Brian
authors: GB
authors: Golding
mesh_terms: D003627:Data Interpretation, Statistical; D019143:Evolution, Molecular; D006194:Gardnerella vaginalis / Q000235:genetics; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D016680:Genome, Bacterial; D054643:INDEL Mutation / Q000235:genetics*; D016254:Mutagenesis, Insertional / Q000235:genetics; D059645:Mutation Rate; D009161:Mycobacterium / Q000235:genetics
keywords: gene insertion/deletion; indel rates; maximum likelihood; unobserved data