<b>Dataset and R code for: Inbreeding does not reduce major histocompatibility complex diversity in the banded mongoose</b>

This repository includes R code and data necessary to reproduce manuscript results and figures. The code has been written by Jamie Winternitz (jcwinternitz-at-gmail.com) and Nadine Schubert (nadine.schubert-at-uni-bielefeld.de).The R code '<b>MHC_supertype_characterization.R</b>' includes supertype characterization analyses and produces components of Figure 1 &amp; 2 and S2. It requires the following data:'MHCIex2_AA_alignment_classical.fasta''MHCIex3_AA_alignment_classical.fasta''MHCIIex2_AA_alignment_classical.fasta''Banded mongoose genotypes MHCIex2.csv''Banded mongoose genotypes MHCIex3.csv''Banded mongoose genotypes MHCIIDRBex2.csv'The R code '<b>alignment_plots.R</b>' produces Figures 1 &amp; 2 and requires the following data:'MHC-Iex2 supertype assignment classical.csv''MHC-Iex3 supertype assignment classical.csv''MHC-IIex2 supertype assignment classical.csv''MHCI_Ex2_classical_meerkat_HLA_proteins_residues_35-110_new.csv''MHCI_Ex3_classical_meerkat_HLA_proteins_residues_122-198_new.csv''MHCII_Ex2_classical only_meerkat_HLA_proteins_residues_50-115_new.csv''PBS_MHC-I_exon2_Mm_x.csv''PBS_MHC-I_exon3_Mm_x.csv''PBS_DRBII-exon2_Mm_x.csv'The R code '<b>allele_frequency_plots.R</b>' produces Figure 3 and requires the following data:'MHCI_Ex2_frequencies.csv''MHCI_Ex3_frequencies.csv''MHCII_DRBexon2_frequencies.csv'The R code '<b>pairwise_linkage_MHC.R</b>' includes the pairwise-linkage disequilibrium analysis and produces Figure 4. It requires the following data:'Banded mongoose genotypes MHCIex2.csv''Banded mongoose genotypes MHCIex3.csv''Banded mongoose genotypes MHCIIDRBex2.csv'The R code '<b>phylogenetic_trees.R</b>' includes the phylogenetic tree analysis and produces Figure 5. It requires the following data:'Species tip dated.nex''species_tree.csv''Supplementary_Data_2.csv''MHCI.contree.newick''Supplementary_Data_3.csv''MHCII.contree.newick'The R code '<b>phylogenetic_regression.R</b>' includes the phylogenetic mixed model analysis and produces Figure 6 &amp; Figure S4. It requires the following data:'Supplementary_Data_1.csv''tree-pruner-tree.nex'The R code '<b>accumulation_curve.R</b>' produces Figure S3. It requires the following data:'sequences for accumulation curve - MHCIex2.csv''sequences for accumulation curve - MHCIex3.csv''sequences for accumulation curve - MHCII.csv'For questions or reproduction of results, please refer to the manuscript or contact the authors.