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      Immune genes are hotspots of shared positive selection across birds and mammals

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          Abstract

          Consistent patterns of positive selection in functionally similar genes can suggest a common selective pressure across a group of species. We use alignments of orthologous protein-coding genes from 39 species of birds to estimate parameters related to positive selection for 11,000 genes conserved across birds. We show that functional pathways related to the immune system, recombination, lipid metabolism, and phototransduction are enriched for positively selected genes. By comparing our results with mammalian data, we find a significant enrichment for positively selected genes shared between taxa, and that these shared selected genes are enriched for viral immune pathways. Using pathogen-challenge transcriptome data, we show that genes up-regulated in response to pathogens are also enriched for positively selected genes. Together, our results suggest that pathogens, particularly viruses, consistently target the same genes across divergent clades, and that these genes are hotspots of host-pathogen conflict over deep evolutionary time.

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

          Yoav Benjamini, Yosef Hochberg (1995)
          Article 0 comments Cited 25157 times – based on 0 reviews     Review now
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            Mobile elements: drivers of genome evolution.

            Haig H. Kazazian (2004)
            Mobile elements within genomes have driven genome evolution in diverse ways. Particularly in plants and mammals, retrotransposons have accumulated to constitute a large fraction of the genome and have shaped both genes and the entire genome. Although the host can often control their numbers, massive expansions of retrotransposons have been tolerated during evolution. Now mobile elements are becoming useful tools for learning more about genome evolution and gene function.
            Article 0 comments Cited 633 times – based on 0 reviews     Review now
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              Interferons and viruses: an interplay between induction, signalling, antiviral responses and virus countermeasures.

              Richard E. Randall, Stephen Goodbourn (2008)
              The interferon (IFN) system is an extremely powerful antiviral response that is capable of controlling most, if not all, virus infections in the absence of adaptive immunity. However, viruses can still replicate and cause disease in vivo, because they have some strategy for at least partially circumventing the IFN response. We reviewed this topic in 2000 [Goodbourn, S., Didcock, L. & Randall, R. E. (2000). J Gen Virol 81, 2341-2364] but, since then, a great deal has been discovered about the molecular mechanisms of the IFN response and how different viruses circumvent it. This information is of fundamental interest, but may also have practical application in the design and manufacture of attenuated virus vaccines and the development of novel antiviral drugs. In the first part of this review, we describe how viruses activate the IFN system, how IFNs induce transcription of their target genes and the mechanism of action of IFN-induced proteins with antiviral action. In the second part, we describe how viruses circumvent the IFN response. Here, we reflect upon possible consequences for both the virus and host of the different strategies that viruses have evolved and discuss whether certain viruses have exploited the IFN response to modulate their life cycle (e.g. to establish and maintain persistent/latent infections), whether perturbation of the IFN response by persistent infections can lead to chronic disease, and the importance of the IFN system as a species barrier to virus infections. Lastly, we briefly describe applied aspects that arise from an increase in our knowledge in this area, including vaccine design and manufacture, the development of novel antiviral drugs and the use of IFN-sensitive oncolytic viruses in the treatment of cancer.
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                Author and article information

                Contributors
                Allison J Shultz:
                ORCID: https://orcid.org/0000-0002-2089-4086
                Timothy B Sackton:
                ORCID: http://orcid.org/0000-0003-1673-9216
                Christian R Landry: Role: Reviewing Editor
                Diethard Tautz: Role: Senior Editor
                Journal
                Journal ID (nlm-ta): eLife
                Journal ID (iso-abbrev): Elife
                Journal ID (publisher-id): eLife
                Title: eLife
                Publisher: eLife Sciences Publications, Ltd
                ISSN (Electronic): 2050-084X
                Publication date (Electronic, pub): 08 January 2019
                Publication date Collection: 2019
                Volume: 8
                Electronic Location Identifier: e41815
                Affiliations
                [1 ]deptInformatics Group Harvard University CambridgeUnited States
                [2 ]deptDepartment of Organismic and Evolutionary Biology Harvard University CambridgeUnited States
                [3 ]deptMuseum of Comparative Zoology Harvard University CambridgeUnited States
                Université Laval Canada
                Max-Planck Institute for Evolutionary Biology Germany
                Université Laval Canada
                Author notes
                [†]

                Natural History Museum of Los Angeles County, Los Angeles, United States.

                Author information
                https://orcid.org/0000-0002-2089-4086
                http://orcid.org/0000-0003-1673-9216
                Article
                Publisher ID: 41815
                DOI: 10.7554/eLife.41815
                PMC ID: 6338464
                PubMed ID: 30620335
                SO-VID: b97a2855-5b6d-48ec-afda-89153ce8c557
                Copyright © © 2019, Shultz and Sackton
                License:

                This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

                History
                Date received : 06 September 2018
                Date accepted : 08 January 2019
                Funding
                The authors declare that there was no external funding received for this work.
                Categories
                Subject: Research Article
                Subject: Evolutionary Biology
                Subject: Genetics and Genomics
                Custom metadata
                Author impact statement Pathogens, particularly viruses, target the same genes over deep evolutionary time, resulting in shared signatures of positive selection and transcriptional responses at the same genes.

                ScienceOpen disciplines: Life sciences
                Keywords: birds,host-pathogen co-evolution,comparative genomics,comparative transcriptomics,viruses,mammals,chicken,other
                Data availability:
                ScienceOpen disciplines: Life sciences
                Keywords: birds, host-pathogen co-evolution, comparative genomics, comparative transcriptomics, viruses, mammals, chicken, other

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