Mapping selection within Drosophila melanogaster embryo's anatomy

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DOI

  • Irepan Salvador-Martínez, Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
  • ,
  • Marta Coronado-Zamora, Genomics, Bioinformatics and Evolution. Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
  • ,
  • David Castellano
  • ,
  • Antonio Barbadilla, Genomics, Bioinformatics and Evolution. Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
  • ,
  • Isaac Salazar-Ciudad, Genomics, Bioinformatics and Evolution. Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.

We present a survey of selection across Drosophila melanogaster embryonic anatomy. Our approach integrates genomic variation, spatial gene expression patterns and development, with the aim of mapping adaptation over the entire embryo's anatomy. Our adaptation map is based on analyzing spatial gene expression information for 5,969 genes (from text-based annotations of in situ hybridization data directly from the BDGP database, Tomancak et al. 2007) and the polymorphism and divergence in these genes (from the project DGRP, Mackay et al. 2012).The proportion of non-synonymous substitutions that are adaptive, neutral or slightly deleterious are estimated for the set of genes expressed in each embryonic anatomical structure using the DFE-alpha method (Eyre-Walker and Keightley 2009),. This method is a robust derivative of the McDonald and Kreitman test (McDonald and Kreitman 1991). We also explore whether different anatomical structures differ in the phylogenetic age, codon usage or expression bias of the genes they express and whether genes expressed in many anatomical structures show more adaptive substitutions than other genes.We found that: (i) most of the digestive system and ectoderm-derived structures are under selective constraint, (ii) the germ line and some specific mesoderm-derived structures show high rates of adaptive substitution and (iii) the genes that are expressed in a small number of anatomical structures show higher expression bias, lower phylogenetic ages and less constraint.

Original languageEnglish
JournalMolecular Biology and Evolution
Volume35
Issue1
Pages (from-to)66-79
ISSN0737-4038
DOIs
Publication statusPublished - 1 Jan 2018

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  • Journal Article

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