Primate microRNAs miR-220 and miR-492 lie within processed pseudogenes.
ABSTRACT MicroRNAs (miRNAs) are a new and abundant class of small, noncoding RNAs. To date, the evolutionary history of most of these loci appears to be marked by duplication and divergence. The ultimate origin of miRNAs remains an open question. A survey of the genomic context of more than 300 human miRNA loci revealed that two primate-specific miRNAs, miR-220 and miR-492, each lie within a processed pseudogene. In silico and in vitro examinations of these two loci suggest that this is a rare phenomenon requiring the juxtaposition of a specific combination of factors. Thus it appears that, while processed pseudogenes are good candidates for miRNA incubators, it is unlikely that more than a very small percentage of new miRNAs arise this way.
Full-textDOI: · Available from: Eric J Devor, May 28, 2015
SourceAvailable from: cdn.intechopen.com
Deep Metazoan Phylogeny: the Backbone of the Tree of Life - New Insights from Analyses of Molecules, Morphology, and Theory of Data Analysis, 02/2014: chapter 15; Walter de Gruyter., ISBN: 9783110277524
[Show abstract] [Hide abstract]
ABSTRACT: Recent improvements of tools for inference of phylogenies from molecular data could not impede that tree topologies estimated from different data sets are often mutually incompatible (see e.g. recent discussions about placement of Porifera in the metazoan tree). There are obviously causes of error that remain undetected. Fundamental discrepancies between molecular phylogenies and morphological data (see e.g. Wägele and Kück, this book) nourish major doubts concerning the reliability of established methods. A series of simulations with a 11-taxon setup designed to study conditions (branch length ratios, among site variation, alignment lengths) that are prone to long branch effects prove that three different classes of artefacts (Wägele and Mayer, 2007) can be discerned. Maximum likelihood inference is more successful if among site variation is considered with a mixed-distribution model, however reconstruction fails when differences in branch lengths are very large, especially in topologies with short stem-lineages. Long inner branches can lead to a systematic error with high support for the wrong tree caused by plesiomorphies even when long alignments and the correct model are used. Other errors are caused by signal erosion and by chance similarities. We present for a set of tree topologies the parameter ranges for which correct topologies can be obtained.Deep Metazoan Phylogeny: The Backbone of the Tree of Life, 1 edited by J.W. Wägele, T. Bartolomaeus, 02/2014: chapter Systematic errors in maximum-likelihood tree inference: pages 563-583; DeGruyter., ISBN: 9783110262636