Data from: Birdsong signals individual diversity at the major histocompatibility complex

Slade JWG, Watson MJ, MacDougall-Shackleton EA

Date Published: October 17, 2017

DOI: https://doi.org/10.5061/dryad.8g1bb

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Title Dryad1_PCRandSeqconditions
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Description PCR and sequencing conditions for song sparrow MHC class IIß
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Title Dryad2_FigS1_MHCalleletree
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Description Figure S1. Phylogeny of MHC class IIß amino acid alleles amplified from 32 male song sparrows. Evolutionary history was inferred using the maximum likelihood method based on the WAG amino acid substitution model. The tree with the highest likelihood is shown. The percentage of replicate trees in which the associated alleles cluster together in the bootstrap test (500 replicates) is shown at each node. The tree is drawn to scale, with branch lengths corresponding to number of substitutions per site. The analysis involved 186 amino acid sequences (SOSP-DAB*#). Each vertical red line indicates a superallele (SA) composed of multiple similar sequences, and each black arrow indicates a single sequence that belonged to its own SA.
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Title Dryad3_Rcode
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Description Annotated R code used in data analysis.
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Title Dryad4_MHC_composition_table
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Description MHC composition table for 32 male song sparrows. Each row corresponds to an individual bird, and each column corresponds to a unique amino acid sequence at MHC IIß (allele). Presence or absence of each allele in each individual’s genotype is denoted by 1 or 0, respectively. Alleles are listed here as X1, X2, … and correspond to sequences SOSP-DAB*1, SOSP-DAB*2, … on Figure S1 and on GenBank.
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Title Dryad5_MHC_composition_table_with_IDs
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Description MHC composition table for 32 male song sparrows, including individual identifiers. Each row corresponds to an individual bird, and each column corresponds to a unique amino acid sequence at MHC IIß (“allele”). Presence or absence of each allele in each individual’s genotype is denoted by 1 or 0, respectively. Alleles are listed here as X1, X2, … and correspond to sequences SOSP-DAB*1, SOSP-DAB*2, … on Figure S1 and on GenBank.
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Title Dryad6_MHC_AA_sequences
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Description Amino acid sequences for 32 male song sparrows genotyped at MHC IIß (FASTA format).
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Title Dryad7_MHC_AA_tree
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Description Newick tree topography for amino acid alleles characterized at MHC IIß. Evolutionary history was inferred as described in Figure S1 (file Dryad2).
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Title Dryad8_song_unifrac_matrix
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Description Matrix of UniFrac distances calculated for all pairwise combinations of 32 male song sparrows genotyped at MHC IIß.
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Title Dryad9_MHC_UniFrac_Matrix
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Description Matrix of UniFrac distances calculated for all pairwise combinations of 32 male song sparrows genotyped at MHC IIß. This file is identical to file Dryad8 except that it includes individual identity along the top row.
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Title Dryad10_syllable_jaccard_SIMILARITY_index
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Description Matrix of Jaccard similarity based on syllable sharing, calculated for all pairwise combinations of 32 male song sparrows. A = syllables produced by individual A but not B; B = syllables produced by individual B but not A; C = syllables common to both individuals; D = difference in repertoire size (number of syllables) between individuals A and B.
Download Dryad10_syllable_jaccard_SIMILARITY_index.xlsx (110.7 Kb)
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Title Dryad11_syllable_Jaccard_Dissimilarity
Downloaded 1 time
Description Pairwise matrix of Jaccard DISSIMILARITY, calculated as 1-Jaccard similarity, for all pairwise combinations of 32 male song sparrows.
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Title Dryad12_MHC_SAs_and_Song_Data
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Description Number of MHC superalleles (SA) and song repertoire size (Song) for each of 32 male song sparrows.
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Title Dryad13_Suppl_ analysis
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Description Tables S1 and S2. Predictors of song sparrow song repertoire size, after excluding a potentially influential datapoint.
Download Dryad13_Suppl_ analysis.docx (69.25 Kb)
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When using this data, please cite the original publication:

Slade JWG, Watson MJ, MacDougall-Shackleton EA (2017) Birdsong signals individual diversity at the major histocompatibility complex. Biology Letters 13(11): 20170430. https://doi.org/10.1098/rsbl.2017.0430

Additionally, please cite the Dryad data package:

Slade JWG, Watson MJ, MacDougall-Shackleton EA (2017) Data from: Birdsong signals individual diversity at the major histocompatibility complex. Dryad Digital Repository. https://doi.org/10.5061/dryad.8g1bb
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