Data from: Immunogenetic heterogeneity in a widespread ungulate: the European roe deer (Capreolus capreolus)

Quéméré E, Galan M, Cosson J, Klein F, Aulagnier S, Gilot-Fromont E, Merlet J, Hewison AJM, Charbonnel N

Date Published: June 25, 2015

DOI: http://dx.doi.org/10.5061/dryad.3vb7h

 

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Title Microsatellite data
Downloaded 6 times
Description Microsatellite genotypes of the three roe deer study populations (12 loci)
Download Roedeer_microsatellite_Genotypes_Quemereetal.txt (40.05 Kb)
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Title 454 sequencing of the MHC-Drb exon 2
Downloaded 5 times
Description Raw sequence 454 data + primers with MID barcodes. We used a modified version of the primers LA31 (5’- GATCCTCTCTCTGCAGCACATTTCCT-3’) and LA32 (5’-TTCGCGTCACCTCGCCGCTG-3’) initially designed for cattle (Sigurdardottir et al. 1991), with the addition of individual-specific MIDS (Multiplex Identifiers) and adaptors required for emPCR and 454 sequencing.
Download MHC-DRB_CaCapreolus_454_rawdata.zip (276.0 Mb)
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Title PAML4_CodeML_infiles
Downloaded 6 times
Description we estimated the non-synonymous/synonymous rate ratio (dN/dS) at each codon site using the Bayesian approach implemented in the CodeML program of the PAML4 package (Yang 2007) .
Download PAML4_CodeML_infiles.zip (9.765 Kb)
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Title Input files for DNAsp (Phased Haplotypes)
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Description This files contains the DNA sequences alignments (phased haplotypes) of each immunity-related genes (fasta format).
Download DNAsp_phased_input_fasta.zip (23.16 Kb)
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Title Alignment of (unique) haplotypes for each immunity-related genes
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Description This files contains the fasta alignment of (unique) haplotypes for each immunity-related gene.
Download unique_haplotypes_fasta_alignement.zip (8.38 Kb)
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Title Genotypic data for all individuals and immune loci
Downloaded 6 times
Description This file includes the genotypic data off all individuals for the 8 innate immune loci (21 SNPs genotyped using the KASPar technology) and the Mhc-Drb (sequences are available in genbank, accession numbers are in the supplementary material of the paper- Table S2)
Download Roedeer_Immunogenetics_Genotypicdata_Quem...al.txt (57.85 Kb)
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When using this data, please cite the original publication:

Quéméré E, Galan M, Cosson J, Klein F, Aulagnier S, Gilot-Fromont E, Merlet J, Bonhomme M, Hewison AJM, Charbonnel N (2015) Immunogenetic heterogeneity in a widespread ungulate: the European roe deer (Capreolus capreolus). Molecular Ecology 24(15): 3873–3887. http://dx.doi.org/10.1111/mec.13292

Additionally, please cite the Dryad data package:

Quéméré E, Galan M, Cosson J, Klein F, Aulagnier S, Gilot-Fromont E, Merlet J, Hewison AJM, Charbonnel N (2015) Data from: Immunogenetic heterogeneity in a widespread ungulate: the European roe deer (Capreolus capreolus). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.3vb7h
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