Dataset and R code for: Inbreeding does not reduce major histocompatibility complex diversity in the banded mongoose
Year: 2025
Type: article
Abstract: 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 'MHC_supertype_characterization.R' includes supertype characterization analyses and produces components of Figure 1 & 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 'alignment_plots.R' produces Figures 1 & 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 'allele_frequency_plots.R' produces Figure 3 and requires the following data:'MHCI_Ex2_frequencies.csv''MHCI_Ex3_frequencies.csv''MHCII_DRBexon2_frequencies.csv'The R code 'pairwise_linkage_MHC.R' 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 'phylogenetic_trees.R' 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 'phylogenetic_regression.R' includes the phylogenetic mixed model analysis and produces Figure 6 & Figure S4. It requires the following data:'Supplementary_Data_1.csv''tree-pruner-tree.nex'The R code 'accumulation_curve.R' 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.
Source: Figshare
Author: Winternitz, Jamie
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
Funder: Deutsche Forschungsgemeinschaft
Awards: TRR 212: Eine neue Synthese zur Individualisation für die Verhaltensforschung, Ökologie und Evolution: Nischenwahl, Nischenkonformität, Nischenkonstruktion (NC3), Einflüsse von Nischenwahl auf ParasitWirt Beziehungen beim Mäusebussard, Genetisch determinierte soziale Kommunikation in einem ingezüchteten, in Gruppen lebenden wilden Säugetier
OpenAlex ID: W7086780467
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