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

Shultz, Allison J, Harvard University

Sackton, Timothy, Harvard University

Sackton, Timothy B, Harvard University

Published Jan 09, 2019 on Dryad. https://doi.org/10.5061/dryad.kt24554

Cite this dataset

Shultz, Allison J; Sackton, Timothy; Sackton, Timothy B (2019). Data from: Immune genes are hotspots of shared positive selection across birds and mammals [Dataset]. Dryad. https://doi.org/10.5061/dryad.kt24554

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.

Usage notes

Alignments used for comparative genomics

Multiple species alignment for each HOG. NCBI gene IDs for HOGs can be found in R_data_and_scripts/02_output_annotated_data/raw_results_sptrees_all_annotations.csv from zipped R_data_and_scripts file.

comparative_genomics_hog_alignments.zip

R Scripts and Data Files

All selection scan and differential expression results (PAML results, HyPhy results, Sleuth results), and all scripts for subsequent analyses. There are seven modules that include and R script, directory with any necessary input data, and directory with any output files. The scripts do the following: 1. process all PAML and HyPhy output into analysis-ready formats. 2. Annotate all HOGs with NCBI and Ensembl gene IDs. 3. General dataset statistic calculations 4. Bird KEGG pathway enrichment analyses. 5. Comparisons of bird and mammal selection scan results 6. Clustering and analysis of bird aBS-REL results. 7. Transcriptome analyses for both birds and mammals.

R_data_and_scripts.zip