11 research outputs found
Eggshell data, including pigment concentrations and bacteria community composition
Eggshell data, including pigment concentrations and bacteria community compositio
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
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
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
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 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