Data from: Gene duplication and divergence produce divergent MHC genotypes without disassortative mating

Dearborn DC, Gager AB, McArthur AG, Gilmour ME, Mandzhukova E, Mauck RA

Date Published: July 5, 2016

DOI: http://dx.doi.org/10.5061/dryad.j413n

 

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Title MHC allele sequences
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Description 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.
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Title What genetic data are available for each bird
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Description 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.
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Title Microsatellite genotypes
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Description 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.
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Title MHC genotypes without Copy Number Variation
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Description 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.
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Title MHC genotypes when allowing Copy Number Variation
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Description 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.
Download MHC_withCNV.csv (9.808 Kb)
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Title Microsoft Excel macro for mate choice randomization tests
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Description Randomization tests were used to test whether mean and variance in MHC similarity of actual mates were significantly different from random. These tests were run in Microsoft Excel using a macro to create 10,000 iterations of randomly pairing each of the 94 females with one male (without replacement), saving the average and variance of the MHC similarity between random mates for each iteration. This file is an example of one such Excel file -- in this case, the one that analyzes average p-distance between MHC alleles of mates using all 89 amino acids of exon 2, the results of which are shown in the graph in Figure S4a in Supplemental Information. Similar analyses were conducted for other metrics of MHC similarity and for microsatellite-based estimates of relatedness coefficients between mates. SEE ReadMe FILE FOR DETAILS OF FILE CONTENTS.
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Title Permutation Model - set up arrays
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Description 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.
Download DD_BS_Setup_Reference_Arrays.txt (1.281 Kb)
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Title Permutation Model - simulation core
Downloaded 5 times
Description 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.
Download DD_BS_DistributeAlleles.txt (4.275 Kb)
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Title Permutation Model - rare case simulation
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Description 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 <DD_BS_Distribute_Alleles.txt>, but modified to handle the rarity of very low or high monophyly.
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Title Permutation Model - calculate within an individual
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Description 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.
Download DD_Rtn_Mean_Dist.txt (1.06 Kb)
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Title Permutation Model - calculate means across individuals
Downloaded 2 times
Description 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.
Download DD_BS_Calc_means_from_trial.txt (3.198 Kb)
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When using this data, please cite the original publication:

Dearborn DC, Gager AB, McArthur AG, Gilmour ME, Mandzhukova E, Mauck RA (2016) Gene duplication and divergence produce divergent MHC genotypes without disassortative mating. Molecular Ecology 25(17): 4355–4367. http://dx.doi.org/10.1111/mec.13747

Additionally, please cite the Dryad data package:

Dearborn DC, Gager AB, McArthur AG, Gilmour ME, Mandzhukova E, Mauck RA (2016) Data from: Gene duplication and divergence produce divergent MHC genotypes without disassortative mating. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.j413n
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