What genetic data are available for each bird

List of genetic data obtained for individuals in each of 94 nests. Columns are Year (year of nesting attempt: 2010 or 2013), Nest # (burrow number, unique within year but not between years), Adult Female Band # (leg band # of breeding female), Adult Male Band # (leg band # of breeding male), and then a series of Yes/No columns reporting whether genetic data are available for parents and for nestlings at MHC genes and at microsatellite loci

Permutation Model - simulation core

The permutation of the phylogeny was conducted with a set of scripts written and run in 4th Dimension (4D Inc., San Jose, CA). This second script is the simulation core. It makes N number of trial records composed of randomized distribution of alleles in the phylogenetic framework

Permutation Model - calculate within an individual

The permutation of the phylogeny was conducted with a set of scripts written and run in 4th Dimension (4D Inc., San Jose, CA). This fourth script looks up pairwise distances between alleles and then calculates the average distance between 4 alleles within an individual

MHC genotypes without Copy Number Variation

MHC genotypes of 188 adults + 22 chicks assuming no Copy Number Variation, in a table of 211 rows x 9 columns. Genotypes were determined from Illumina sequencing based on an assumption of no Copy Number Variation as described in Supporting Information lines 104-127. First row is header, and each remaining row corresponds to one bird. Columns are Year (year of nesting attempt: 2010 or 2013), Nest # (burrow number, unique within year but not between years), Age (Adult or Chick), Sex (determined by PCR), CWS Bird Band #, Ocle-DAB1*allele1, Ocle-DAB1*allele2, Ocle-DAB2*allele1, and Ocle-DAB2*allele2

MHC allele sequences

24 MHC Class II B alleles found at Ocle-DAB1 and Ocle-DAB2 in this sample of 188 adults and 22 nestlings. Each allele is trimmed to exon 2 and is described with a DNA sequence, an amino acid translation, and a GenBank accession number. Four alleles have an in-frame 3-bp deletion; this is indicated by '---' in the DNA sequence, but the gap is closed in the amino acid sequence

MHC genotypes when allowing Copy Number Variation

MHC genotypes of 188 adults + 22 chicks allowing Copy Number Variation, in a table of 211 rows x 12 columns. Genotypes were determined from Illumina sequencing based on an algorithm that permits Copy Number Variation as described in Supporting Information lines 129-145. First row is header, and each remaining row corresponds to one bird. Columns are Year (year of nesting attempt: 2010 or 2013), Nest # (burrow number, unique within year but not between years), Age (Adult or Chick), Sex (determined by PCR), CWS Bird Band #, Ocle-DAB1*allele1, Ocle-DAB1*allele2, Ocle-DAB1*allele3, Ocle-DAB2*allele1, and Ocle-DAB2*allele2, Ocle-DAB2*allele3, and Ocle-DAB2*allele4

Permutation Model - set up arrays

The permutation of the phylogeny was conducted with a set of scripts written and run in 4th Dimension (4D Inc., San Jose, CA). This first script takes the imported data in Individuals, Distances, Alleles and puts them into arrays

Permutation Model - rare case simulation

The permutation of the phylogeny was conducted with a set of scripts written and run in 4th Dimension (4D Inc., San Jose, CA). This third script is the same as , but modified to handle the rarity of very low or high monophyly

Permutation Model - calculate means across individuals

The permutation of the phylogeny was conducted with a set of scripts written and run in 4th Dimension (4D Inc., San Jose, CA). Once the trials are made, this fifth and final script calculates the mean of mean distances between alleles within individuals in population

Microsatellite genotypes

Genotypes of 188 adults and 34 nestlings at 15 microsatellite loci. File is in GenePop format. The file has 3 introductory rows: 1) metadata, 2) 15 locus names, 3) 'POP'. Next is a table of 222 rows x 16 tab-delimited columns. The first column of the table is the identity of the bird. Adults are identified by the last 5 digits of their Canadian Wildlife Service metal leg band. Nestlings were too young to band and thus are identified by their nest number and the suffix -Chk (for 'Chick'). The remaining 15 columns are microsatellite genotypes at 15 loci, with the loci ordered according to the names in the second row of the file. Genotypes are 6 digits: two 3-digit numbers, each corresponding to the size (in base pairs) of an allele. Missing genotypes are represented by a single zero