Immune genes are hotspots of convergent positive selection in birds

<p>Evolutionary theory predicts that genes encoding proteins involved in host-pathogen interactions will be subject to arms race dynamics, in which repeated adaptations and counter-adaptations will fix in both hosts and pathogens. In genomic sequence comparisons, this dynamic leads to a pattern of diversifying selection, detectable by an excess of amino acid substitutions fixed by natural selection (positive selection). Previous work in mammals and other groups has provided evidence that this process is important in the evolution of immune system proteins and proteins that interact with viruses. In this talk, we infer the history of selection on genes using comparative genomic methods, present new work on the evolution of the innate immune system in birds, and contrast patterns of selection seen in these species with mammals. Using alignments of orthologous protein-coding genes from 39 species of birds, we estimated parameters related to models of positive selection for 11,000 genes conserved across birds. We show that diversifying selection is particularly important in the evolution of pathways involved in the response to Influenza A and other pathogens, particularly viruses. By comparing these results to previous work in mammals, we then show that genes under selection in birds are enriched for genes that are also under selection in mammals. Finally, we demonstrate that sets of genes known to interact with viruses, bacteria, or Plasmodium are more likely to be under selection in both birds and mammals. These findings suggest that pathogens consistently target the same genes, and that these genes are hotspots of host-pathogen conflict over deep evolutionary time.</p

Additional file 13: of OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

Model selection table for models comprising different combinations of factors with a putative role in characterizing genes with and without annotated isoforms. (XLS 59 kb

Additional file 9: of OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

Protein alignment of the OG EOG6R4ZDK (hymenopteran histone H3). Clipped to include only residues shared between all genes. (TXT 13 kb

Additional file 11: of OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

Genes with more than 10 isoforms present in OGS2. (XLS 48 kb

Additional file 7: of OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

OGS2 genes whose ortholog groups are characterized by lineage-specific expansions or contractions. (XLS 3711 kb

Additional file 5: of OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

Chain files, GFF mapping and transcript status of OGS2 on Nvit_2.1 genome assembly. (XLS 17233 kb

Additional file 1: Figure S1. of OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

Expression values relative to gene structures for RNA-Seq (Reads) and genome tiling path microarrays (Tile) for species Nasonia (purple, this project), Drosophila (red, blue, [74]) and Daphnia (green, [107]). Annotated gene near-exon spans are scored per base for average expression scores from the data sets, and relative expression plotted with respect to gene transcript start (first exon), stop (last exon), and inner exon start, stop positions. Both methods (genome tiling and RNA-Seq) have abrupt expression strength changes at exon boundaries, on average, indicating their value in modeling gene structure positions. Expression scores are read-coverage for RNA-Seq, and log-normalized intensity for tiling array, as described in the Methods section. Figure S2. Gene modeling example with tile expression data, including gene evidence (upper tracks with tiling, introns, proteins), tiling TAR-exon to Exonerate models (middle), and gene predictions from tile TAR hints (lower), on genome map. The lower tracks have excessive false UTR spans attached to gene models, primarily due to tiling expression that lacks gene start/stop and intron splice joining signals. These false UTR spans are supported by expression evidence, but as a combination of alternate exons, separate gene loci, and non-coding expression. Intermediate tracks (Exonerate models) often match gene structures from other methods, but have a high proportion of unsupported exon extensions as for lower track. Figure S3. Gene join error example. A mistaken gene model from honey bee (tan, lower, LOC552483) is transferred to Nasonia in NCBI RefSeq models (dark orange, middle), merging a ribosomal protein (right) and Ankyrin repeat protein (left). EvidentialGene models (yellow, top) did not contain this mistake, due to the combination of RNA-Seq assemblies (purple, bottom) that are un-joined (but could be parts of one gene), the lack of intron joining evidence, and the orthology assessment metrics that distinguish gene joins from true complete genes. NCBI Refseq models for both Apis (new LOC102654426 and mRpL52 in NCBI Apis rel. 102) and Nasonia have been updated to correct this join error. Figure S4. Log counts of methylated and unmethylated genes in different classes of expression support. Grey bars indicate genes with no known methylation status. (ZIP 938 kb

Additional file 8: of OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

Protein evolutionary distances of OGS2.0 genes compared to ant and bee lineages, residuals distances after model fitting and fast/slow evolving categorization at the 5th and 20th quantile threshold. (XLS 2790 kb

Additional file 2: Table S1. of OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

Consensus in the location of the OGS2 gene set on the genome assemblies of sibling species Nasonia longicornis and N. giraulti, including recent, high identity paralogs. Almost all OGS2 genes are located on 2 sibling species draft assemblies [4], using GMAP [36] transcript mapping. Paralog locus consensus patterns are tabulated for inparalogs (sharing orthology to other species) and uniquepar (lacking strong homology to other species). Of the total paralog families, each with several genes, most paralogs are on different scaffolds for all species. The counts of tandem paralogs with different separations are indicated. Table S2. A set of 62 orthology groups found in Nasonia transcript assemblies that are poorly mapped onto the current genome, but should be considered as part of a complete Nasonia gene set. Table S3. A total of 75 orthology groups missing from Nasonia but found in 9 other insect genomes. Table S4. Histone genes present in OGS2.0 annotated with presence or absence of lineage-specific expansions. NA entries were not assigned to orthologous groups at the level of Hymenoptera. (ZIP 33 kb

Early origin of sweet perception in the songbird radiation

From savory to sweet Seeing a bird eat nectar from a flower is a common sight in our world. The ability to detect sugars, however, is not ancestral in the bird lineage, where most species were carnivorous. Toda et al. looked at receptors within the largest group of birds, the passerines or songbirds, and found that the emergence of sweet detection involved a single shift in a receptor for umami (see the Perspective by Barker). This ancient change facilitated sugar detection not just in nectar feeding birds, but also across the songbird group, and in a way that was different from, though convergent with, that in hummingbirds. Science , abf6505, this issue p. 226 ; see also abj6746, p. 154 <br