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Supplemental Information

Map of Collection Sites in Japan

Map of collection sites in Japan with the number of samples from each location: carrion crows = orange; jungle crows = green.

DOI: 10.7287/peerj.preprints.621v2/supp-1

MHC IIB exon 2 amino acid alignment

. MHC IIB exon 2 (246 bp) amino acid alignment of common alleles (occurring in ≥ 4 birds) of three species of crows (Coma: Corvus macrorhynchos, Coco: C. corone, Cobr: C. brachyrhynchos) with three other species of Passeriformes (Apco: Aphelocoma coerulescens, Getr: Geothlypis trichas, Tumi: Turdus migratorius) and one representative of Falconiformes (Fati: Falco tinnunculus). Accession numbers for crows are [TBA]. Accession numbers for other species are listed after label.

DOI: 10.7287/peerj.preprints.621v2/supp-2

NJ Trees of MHC IIB Using Wu-Kabot Plot Sites

Neighbor joining trees (Jukes Cantor, 500 bootstrap replicates) of all MHC IIB variants in this study using a 246 bp fragment of exon 2. Branches with bootstrap support are indicated: light red ≥ 50%; dark red ≥ 70. Coco (orange) = carrion crow; Cobr (blue) = American crow; Coma (green) = jungle crow. Fig. S3A: Tree constructed by comparing non-synonymous substitutions/ nonsynonymous site from codon positions identified as variable from a Wu-Kabot Plot (11 codons). Red shading indicates supported interspecific clades. Fig. S3B: Tree constructed by comparing synonymous substitutions/synonymous site at remaining (non-Wu-Kabot) sites (71 codons). Blue shading indicates supported interspecific clades.

DOI: 10.7287/peerj.preprints.621v2/supp-3

NJ Trees of MHC IIB Using Human HLA PBR

Neighbor joining trees (Jukes Cantor, 500 bootstrap replicates) of all MHC IIB variants in this study using a 246 bp fragment of exon 2. Branches with bootstrap support are indicated: light red ≥ 50%; dark red ≥ 70. Coco (orange) = carrion crow; Cobr (blue) = American crow; Coma (green) = jungle crow. Fig. S4A: Tree constructed by comparing non-synonymous substitutions/ nonsynonymous site from codon positions identified as the peptide binding region (PBR) in HLA (Brown et al. 1993) (22 codons). Red shading indicates supported interspecific clades. Fig. S3B: Tree constructed by comparing synonymous substitutions/synonymous site at remaining (non-PBR) sites (60 codons). Blue shading indicates supported interspecific clades.

DOI: 10.7287/peerj.preprints.621v2/supp-4

Additional Information

Competing Interests

Isao Nishiumi is an employee of the National Museum of Nature and Science, Tsukuba, Japan.

Author Contributions

John A Eimes conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Andrea K Townsend analyzed the data, wrote the paper, reviewed drafts of the paper.

Irem Sepil performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, reviewed drafts of the paper.

Isao Nishiumi performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Yoko Satta analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Animal Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

For American crow only: This work was performed under protocols approved by the Institutional Animal Care and Use Committee of the University of California, Davis (Permit Number: 16897). All work was conducted on the private property of the University of California, Davis. No protected species were sampled. Carrion and jungle crow samples were from museums collections.

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

For American crow only: This work was performed under protocols approved by the Institutional Animal Care and Use Committee of the University of California, Davis (Permit Number: 16897).

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

NCBI Genbank Accession numbers: TBA;

MHC IIB: TBA;

Crow mtDNA: KM246294-308;

Crow nuclear intronic: KM246309-23;

Data Deposition

The following information was supplied regarding the deposition of related data:

Figshare: http://dx.doi.org/10.6084/m9.figshare.1236628

Funding

This work was supported by Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Sports, Science and Technology of Japan (22133007) to YS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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