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

  1. Allison J Shultz  Is a corresponding author
  2. Timothy Sackton  Is a corresponding author
  1. Harvard University, United States

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.

Data availability

All data generated and analyzed during this study, including all source data for all figures are included in the manuscript, supporting files, Dryad repository (doi:10.5061/dryad.kt24554). All alignments used to perform analyses of PAML and HyPhy results are also available in the Dryad repository. Computing scripts for all analyses are available here: https://github.com/ajshultz/avian-immunity.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Allison J Shultz

    FAS Informatics, Harvard University, Cambridge, United States
    For correspondence
    allisonjshultz@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2089-4086
  2. Timothy Sackton

    FAS Informatics, Harvard University, Cambridge, United States
    For correspondence
    tsackton@g.harvard.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1673-9216

Funding

The authors declare that there was no external funding received for this work.

Reviewing Editor

  1. Christian R Landry, Université Laval, Canada

Publication history

  1. Received: September 6, 2018
  2. Accepted: January 8, 2019
  3. Accepted Manuscript published: January 8, 2019 (version 1)
  4. Version of Record published: January 18, 2019 (version 2)

Copyright

© 2019, Shultz & Sackton

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

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  1. Allison J Shultz
  2. Timothy Sackton
(2019)
Immune genes are hotspots of shared positive selection across birds and mammals
eLife 8:e41815.
https://doi.org/10.7554/eLife.41815

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