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      Patterns of Positive Selection in Seven Ant Genomes

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          Abstract

          The evolution of ants is marked by remarkable adaptations that allowed the development of very complex social systems. To identify how ant-specific adaptations are associated with patterns of molecular evolution, we searched for signs of positive selection on amino-acid changes in proteins. We identified 24 functional categories of genes which were enriched for positively selected genes in the ant lineage. We also reanalyzed genome-wide data sets in bees and flies with the same methodology to check whether positive selection was specific to ants or also present in other insects. Notably, genes implicated in immunity were enriched for positively selected genes in the three lineages, ruling out the hypothesis that the evolution of hygienic behaviors in social insects caused a major relaxation of selective pressure on immune genes. Our scan also indicated that genes implicated in neurogenesis and olfaction started to undergo increased positive selection before the evolution of sociality in Hymenoptera. Finally, the comparison between these three lineages allowed us to pinpoint molecular evolution patterns that were specific to the ant lineage. In particular, there was ant-specific recurrent positive selection on genes with mitochondrial functions, suggesting that mitochondrial activity was improved during the evolution of this lineage. This might have been an important step toward the evolution of extreme lifespan that is a hallmark of ants.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            Gene Ontology: tool for the unification of biology

            Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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              Evolution of genes and genomes on the Drosophila phylogeny.

              Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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                Author and article information

                Journal
                Mol Biol Evol
                Mol. Biol. Evol
                molbev
                molbiolevol
                Molecular Biology and Evolution
                Oxford University Press
                0737-4038
                1537-1719
                July 2014
                29 April 2014
                29 April 2014
                : 31
                : 7
                : 1661-1685
                Affiliations
                1Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
                2SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
                3Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
                4CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
                Author notes

                Present address: Department of Human Genetics, University of Chicago, Chicago, IL

                §Present address: Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel

                *Corresponding author: E-mail: julien.roux@ 123456unil.ch .

                Associate editor: Tal Pupko

                Article
                msu141
                10.1093/molbev/msu141
                4069625
                24782441
                33ef50e1-0a00-47fb-a894-e9531534ffc1
                © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Page count
                Pages: 25
                Categories
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                Molecular biology
                comparative genomics,sociality,dn/ds,aging,lifespan,immunity,neurogenesis,olfactory receptors,metabolism,hymenoptera,bees,drosophila

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