DOI: 10.6084/m9.figshare.c.3818065_d1
title: Additional file 1: Table S1. of Retention of functional variation despite extreme genomic erosion: MHC allelic repertoires in the Lynx genus

description: Nucleotide sequence alignment of the second exon of MHC class I alleles observed in Lynx. Numbers indicate the nucleotide positions inferred from human MHC class I loci (Bjorkman et al. 1987; Bjorkman & Parham 1990). Dots indicate identity to allele Lypa_MHCI*10/Lyly_MHCI*10, which is used as reference. Table S2. Nucleotide sequence alignment of the second exon of MHC class II-DRB alleles observed in Lynx. Alleles are aligned to Lypa_DRB*1/Lyly_DRB*1/Lyca_DRB*1/Lyru_DRB*1. Numbers indicate the nucleotide positions of exon 2 inferred from the human sequence (Brown et al. 1993). Dots indicate identity to the top sequence. Table S3. Lynx MHCI pseudogenization signatures. For each allele we show whether it contains insertion and/or deletions (along with the inserted base and its position), whether it shows an Open Reading Frame (ORF), and if it was considered as a pseudogene in this study. Table S4. Integrative MHCI positive and negative selection tests. dN-dS ratios for codon showing signals of selection in any of the test performed (SLAC, FEL, REL, and FURBAR) are reported along with their significance values (either p-value or Bayes factor), whether they were significant for each test (+) or not (−), and if they were considered in this study (Yes/No), with those considered also shaded in light blue. Table S5 Amino acid sequence alignment of the second exon of MHC class I alleles observed in Lynx. Alleles are aligned to Lypa_DRB*10/Lyly_DRB*10. Numbers indicate the amino acid positions and asterisks putative ABS inferred from human MHC class I loci (Bjorkman et al. 1987; Bjorkman & Parham 1990). Dots indicate identity to the top sequence. The amino acids inferred to be under positive or negative selection are marked with a + or a – sign, respectively. Table S6. Integrative MHCII-DRB positive and negative selection tests. dN-dS ratios for codon showing signals of selection in any of the test performed (SLAC, FEL, REL, and FURBAR) are reported along with their significance values (either p-value or Bayes factor), whether they were significant for each test (+) or not (−), and if they were considered in this study (Yes/No), with those considered also shaded in light blue. Table S7. Amino acid sequence alignment of the second exon of MHC class II-DRB alleles observed in lynxes. Alleles are aligned to Lypa_DRB*1/Lyly_DRB*1/Lyca_DRB*1/Lyru_DRB*1. Numbers indicate the amino acid positions and asterisks putative ABS inferred from human MHC class I loci (Brown et al. 1993). Dots indicate identity to the top sequence. The amino acids inferred to be under positive or negative selection are marked with a + or a – sign, respectively. Table S8. Unique MHCI nucleotide alleles found across Felidae. Each Felidae allele were collapsed into unique nucleotide sequences and the instances of identical sequences being shared by different species were identified. For each shared sequence we show an identification number (Seq), the number of species in which it appears (#Species), the acromin of such species (Species), whether it is present in any Lynx species (Lynx), whether it is shared by any Lynx species and one non-Lynx species (Lynx_Other), the number of alleles collapsed (#Alleles), and the alleles names (Alleles names). Table S9. Unique MHCI amino acid alleles found across Felidae. Each Felidae allele were collapsed into unique amino acids sequences and the instances of identical sequences being shared by different species were identified. For each shared sequence we show an identification number (Seq), the number of species in which it appears (#Species), the acromin of such species (Species), whether it is present in any Lynx species (Lynx), whether it is shared by any Lynx species and one non-Lynx species (Lynx_Other), the number of alleles collapsed (#Alleles), and the alleles names (Alleles names). Table S10. Felidae MHCI supertype definition based on hierarchical clustering. Each Felidae allele was clustered following a pocket based approach that considered only ABS. For each allele we show its name (Allele) and the supertype it was assigned to within the Felidae analysis(Supertype). Lynx alleles are shown in bold. For each supertype we report whether it contains at least one Lynx allele, and if so we indicate the supertype cluster they correspond to in Fig. 3a (Supertype present in Lynx genus) and whether this was exclusive to Lynx or shared with other felid species (Supertype shared with other felids). Table S11. Unique MHCII-DRB nucleotide alleles found across Felidae. Each Felidae allele were collapsed into unique nucleotide sequences and the instances of identical sequences being shared by different species were identified. For each shared sequence we show an identification number (Seq), the number of species in which it appears (#Species), the acromin of such species (Species), whether it is present in any Lynx species (Lynx), whether it is shared by any Lynx species and one non-Lynx species (Lynx_Other), the number of alleles collapsed (#Alleles), and the alleles names (Alleles names). Table S12. Unique MHCII-DRB amino acid alleles found across Felidae. Each Felidae allele were collapsed into unique amino acids sequences and the instances of identical sequences being shared by different species were identified. For each shared sequence we show an identification number (Seq), the number of species in which it appears (#Species), the acromin of such species (Species), whether it is present in any Lynx species (Lynx), whether it is shared by any Lynx species and one non-Lynx species (Lynx_Other), the number of alleles collapsed (#Alleles), and the alleles names (Alleles names). Table S13. Felidae MHCII-DRB supertype definition based on hierarchical clustering. Each Felidae allele was clustered following a pocket based approach that consireded only ABS. For each allele we show its name (Allele), the supertype it was assigned to (Supertype). Lynx alleles are shown in bold. For each supertype we report whether it contains at least one Lynx allele, and if so we indicate the supertype cluster they correspond to in Fig. 3a (Supertype present in Lynx genus) and whether this was exclusive to Lynx or shared with other felid species (Supertype shared with other felids). (XLS 350 kb)