title: Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences.
abstract: A gene's duplication relaxes selection. Loss of duplicate, low-function DNA (fractionation) sometimes follows, mostly by deletion in plants, but mostly via the pseudogene pathway in fish and other clades with smaller population sizes. Subfunctionalization--the founding term of the Xfunctionalization lexicon--while not the general cause of differences in duplicate gene retention, becomes primary as the number of a gene's cis-regulatory sites increases. Balanced gene drive explains retention for the average gene. Both maintenance-of-balance and subfunctionalization drive gene content nonrandomly, and currently fall outside of our accepted Theory of Evolution. The 'typical' mutation encountered by a gene duplicate is not a neutral loss-of-function; dominant mutations (Muller's lexicon; these are not neutral) abound, and confound X functionalization terms like 'neofunctionalization'. Confusion of words may cause confusion of thought. As with many plants, fish tetraploidies provide a higher throughput surrogate-genetic method to infer function from human and other vertebrate ENCODE-like regulatory sites.
authors.affiliation: Department of Plant and Microbial Biology, Univ. California, Berkeley, CA 94720, United States. Electronic address: freeling@berkeley.edu.
authors.forename: Michael
authors.initials: M
authors.lastname: Freeling
authors.affiliation: Section of Plant Biology, Cornell University, Ithaca, NY 14853, United States.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Scanlon
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, United States.
authors.forename: John E
authors.initials: JE
authors.lastname: Fowler
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D010944:Plants