title: miRNAs: small genes with big potential in metazoan phylogenetics.
abstract: microRNAs (miRNAs) are a key component of gene regulatory networks and have been implicated in the regulation of virtually every biological process found in multicellular eukaryotes. What makes them interesting from a phylogenetic perspective is the high conservation of primary sequence between taxa, their accrual in metazoan genomes through evolutionary time, and the rarity of secondary loss in most metazoan taxa. Despite these properties, the use of miRNAs as phylogenetic markers has not yet been discussed within a clear conceptual framework. Here we highlight five properties of miRNAs that underlie their utility in phylogenetics: 1) The processes of miRNA biogenesis enable the identification of novel miRNAs without prior knowledge of sequence; 2) The continuous addition of miRNA families to metazoan genomes through evolutionary time; 3) The low level of secondary gene loss in most metazoan taxa; 4) The low substitution rate in the mature miRNA sequence; and 5) The small probability of convergent evolution of two miRNAs. Phylogenetic analyses using both Bayesian and parsimony methods on a eumetazoan miRNA data set highlight the potential of miRNAs to become an invaluable new tool, especially when used as an additional line of evidence, to resolve previously intractable nodes within the tree of life.
authors.affiliation: Department of Biological Sciences, Dartmouth College, Hanover, NH.
authors.forename: James E
authors.initials: JE
authors.lastname: Tarver
authors.forename: Erik A
authors.initials: EA
authors.lastname: Sperling
authors.forename: Audrey
authors.initials: A
authors.lastname: Nailor
authors.forename: Alysha M
authors.initials: AM
authors.lastname: Heimberg
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Robinson
authors.forename: Benjamin L
authors.initials: BL
authors.lastname: King
authors.forename: Davide
authors.initials: D
authors.lastname: Pisani
authors.forename: Philip C J
authors.initials: PC
authors.lastname: Donoghue
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Peterson
mesh_terms: D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D017124:Conserved Sequence; D019143:Evolution, Molecular; D053263:Gene Regulatory Networks; D016678:Genome; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism*; D010802:Phylogeny; D064210:Secondary Metabolism / Q000235:genetics; D013045:Species Specificity
chemical_list: D035683:MicroRNAs
keywords: microRNA; phylogenetics; rare genomic character