Ancient trans-species polymorphism at the Major Histocompatibility Complex in primates
- Department of Biology, Stanford University, United States
- Department of Genetics, Stanford University, United States
Figures
Figure 1 with 2 supplements
The MHC region in humans (HLA).
(A) Each point at top represents the location of a gene. The different types of HLA genes are distinguished by different colors, shown in the key at left. The 19 functional HLA genes are labeled with their name (omitting their ‘HLA’ prefix due to space constraints). Gray points represent non-HLA genes and pseudogenes in the region. The black line shows nucleotide diversity (Nei and Li’s π) across the region, while the pink horizontal line shows the genome-wide average nucleotide diversity () (Sachidanandam et al., 2001). (B) Nucleotide diversity around classical Class I gene HLA-A, with exon structure shown. (C) Nucleotide diversity around classical Class II gene HLA-DRB1, with exon structure shown. (D) Species tree showing the phylogenetic relationships among selected primates from this study (Kuderna et al., 2023). The colors of the icons are consistent with colors used throughout the paper to distinguish species. The pink vertical dashed lines indicate split times of the new-world monkeys (NWM) from the apes/old-world monkeys (OWM) (39 MYA), OWM from the apes (31 MYA), and the lesser apes (gibbons) from the great apes (23 MYA).
Figure 1—figure supplement 1
Nucleotide diversity in the human HLA region.
Nucleotide diversity (Nei and Li’s π) around each HLA gene is shown in black, while the pink horizontal line shows the genome-wide average nucleotide diversity () (Sachidanandam et al., 2001). The genes are shown in order along the genome (from top left to bottom right), but the x-axis is repeatedly broken in order to zoom in on detail around each gene. The genes are colored according to their type, with key shown at bottom right. For the functional genes (and some pseudogenes), the exon structure is shown by boxes; other pseudogenes are not annotated with this level of detail.
Figure 1—figure supplement 2
Species key.
On the left-hand side is the species tree relating the species used in this study (Kuderna et al., 2023; Foley et al., 2023). Each species/tip is labeled with a unique color and 4-letter abbreviation, which is composed of the first two letters of the genus name and first two letters of the species name. The common name and Latin name for each species is shown on the right-hand side. Plecturocebus moloch is listed in the IPD-MHC database under its old name, Callicebus moloch, and uses a different abbreviation (Camo) in that resource. Similarly, Leontocebus fuscicolis was formerly known as Saguinus fuscicollis (Safu) in the IPD-MHC database. There appears to be some debate as to whether the pygmy marmoset should be placed in the Callithrix or Cebuella genus, but we have used the name Cebuella pygmaea (Cepy) in accordance with a recent primate study (Kuderna et al., 2023). This species is known as Callithrix pygmaea (Capy) in IPD-MHC. OWM, Old-World Monkeys; NWM, New World Monkeys; Str., Strepsirrhini; Gli., Glires; Lau., Laurasiatheria; Atl., Atlantogenata.
Figure 2 with 16 supplements
BEAST2 allele summary trees using sequences from exon 2.
(A) MHC-C, (B) MHC-DQB1, and (C) MHC-DOA. Each tip represents an allele, with color and four-letter abbreviation representing the species (see Figure 1—figure supplement 2 for full species key). The species label is followed by the allele name (see Appendix 1 for more details on nomenclature) or RefSeq accession number. For simplicity, monophyletic groups of similar alleles are collapsed with a triangle and labeled with their one-field allele name. The color/abbreviation key (center) also depicts the species tree (Kuderna et al., 2023). Human alleles (HLA; red) are bolded for emphasis. Dashed outgroup branches are scaled by a factor of to clarify tree structure within the clade of interest. The smaller inset tree in panel B highlights the relationships between two human allele groups (red) and two OWM allele groups (green). The indicated human and OWM lineages coalesce more recently between groups than within each group. Pri., primate backbone sequences; Mam., mammal outgroup sequences.
Figure 2—figure supplement 1
MHC-A-related group BEAST2 tree for exon 2 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; > 100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 2—figure supplement 2
MHC-B-related group BEAST2 tree for exon 2 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1Appendix 1for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; > 100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 2—figure supplement 3
MHC-C-related group BEAST2 tree for exon 2 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 2—figure supplement 4
MHC-E-related group BEAST2 tree for exon 2 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 2—figure supplement 5
MHC-F-related group BEAST2 tree for exon 2 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 2—figure supplement 6
MHC-G-related group BEAST2 tree for exon 2 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 2—figure supplement 7
MHC-DRA-related group BEAST2 tree for exon 2 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 2—figure supplement 8
MHC-DQA-related group BEAST2 tree for exon 2 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 2—figure supplement 9
MHC-DPA-related group BEAST2 tree for exon 2 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 2—figure supplement 10
MHC-DMA-related group BEAST2 tree for exon 2 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 2—figure supplement 11
MHC-DOA-related group BEAST2 tree for exon 2 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 2—figure supplement 12
MHC-DRB-related group BEAST2 tree for exon 2 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 2—figure supplement 13
MHC-DQB-related group BEAST2 tree for exon 2 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 2—figure supplement 14
MHC-DPB-related group BEAST2 tree for exon 2 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 2—figure supplement 15
MHC-DMB-related group BEAST2 tree for exon 2 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 2—figure supplement 16
MHC-DOB-related group BEAST2 tree for exon 2 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 3 with 14 supplements
Strong support for TSP at Class I genes MHC-B and -C.
Bayes factors computed over the set of BEAST trees indicate deep TSP. Different species comparisons are listed on the y-axis, and different gene regions are listed on the x-axis. Each table entry is colored and labeled with the maximum Bayes factor among all tested quartets of alleles belonging to that category. High Bayes factors (orange) indicate support for TSP among the given species for that gene region, while low Bayes factors (teal) indicate that alleles assort according to the species tree, as expected. Bayes factors above 100 are considered decisive. Tan values show poor support for either hypothesis, while white boxes indicate that there are not enough alleles in that category with which to calculate Bayes factors. MHC-A is not present in the NWMs, and MHC-C was not present before the human-orangutan ancestor, so it is not possible to calculate Bayes factors for these species comparisons.
Figure 3—figure supplement 1
MHC-A-related group BEAST2 tree for exon 3 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 3—figure supplement 2
MHC-A-related group BEAST2 tree for exon 4 (non-PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 3—figure supplement 3
MHC-B-related group BEAST2 tree for exon 3 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 3—figure supplement 4
MHC-B-related group BEAST2 tree for exon 4 (non-PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 3—figure supplement 5
MHC-C-related group BEAST2 tree for exon 3 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 3—figure supplement 6
MHC-C-related group BEAST2 tree for exon 4 (non-PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 3—figure supplement 7
MHC-E-related group BEAST2 tree for exon 3 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 3—figure supplement 8
MHC-E-related group BEAST2 tree for exon 4 (non-PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 3—figure supplement 9
MHC-F-related group BEAST2 tree for exon 3 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 3—figure supplement 10
MHC-F-related group BEAST2 tree for exon 4 (non-PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 3—figure supplement 11
MHC-G-related group BEAST2 tree for exon 3 (PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 3—figure supplement 12
MHC-G-related group BEAST2 tree for exon 4 (non-PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 3—figure supplement 13
TSP among old-world monkey groups for the Class I genes.
Different species comparisons are listed on the y-axis, and different gene regions are listed on the x-axis. Each table entry is colored and labeled with the maximum Bayes factor among all tested quartets of alleles belonging to that category. High Bayes factors (orange) indicate support for TSP among the given species for that gene region, while low Bayes factors (teal) indicate that alleles assort according to the species tree, as expected. Bayes factors above 100 are considered decisive. Tan values show poor support for either hypothesis, while white boxes indicate that there are not enough alleles in that category with which to calculate Bayes factors. MHC-C was not present before the human-orangutan ancestor, so it is not possible to calculate Bayes factors for MHC-C for these species comparisons.
Figure 3—figure supplement 14
TSP among new-world monkey groups for the Class I genes.
Different species comparisons are listed on the y-axis, and different gene regions are listed on the x-axis. Each table entry is colored and labeled with the maximum Bayes factor among all tested quartets of alleles belonging to that category. High Bayes factors (orange) indicate support for TSP among the given species for that gene region, while low Bayes factors (teal) indicate that alleles assort according to the species tree, as expected. Bayes factors above 100 are considered decisive. Tan values show poor support for either hypothesis, while white boxes indicate that there are not enough alleles in that category with which to calculate Bayes factors. MHC-C was not present before the human-orangutan ancestor, and MHC-A is not present in the NWM, so it is not possible to calculate Bayes factors for these genes.
Figure 4 with 12 supplements
Strong support for TSP at the classical Class II genes.
Bayes factors computed over the set of BEAST trees indicate deep TSP. Different species comparisons are listed on the y-axis, and different gene regions are listed on the x-axis. Each table entry is colored and labeled with the maximum Bayes factor among all tested quartets of alleles belonging to that category. High Bayes factors (orange) indicate support for TSP among the given species for that gene region, while low Bayes factors (teal) indicate that alleles assort according to the species tree, as expected. Bayes factors above 100 are considered decisive. Tan values show poor support for either hypothesis, while white boxes indicate that there are not enough alleles in that category with which to calculate Bayes factors.
Figure 4—figure supplement 1
MHC-DRA-related group BEAST2 tree for exon 3 (non-PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 4—figure supplement 2
MHC-DQA-related group BEAST2 tree for exon 3 (non-PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 4—figure supplement 3
MHC-DPA-related group BEAST2 tree for exon 3 (non-PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 4—figure supplement 4
MHC-DMA-related group BEAST2 tree for exon 3 (non-PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 4—figure supplement 5
MHC-DOA-related group BEAST2 tree for exon 3 (non-PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 4—figure supplement 6
MHC-DRB-related group BEAST2 tree for exon 3 (non-PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 4—figure supplement 7
MHC-DQB-related group BEAST2 tree for exon 3 (non-PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 4—figure supplement 8
MHC-DPB-related group BEAST2 tree for exon 3 (non-PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 4—figure supplement 9
MHC-DMB-related group BEAST2 tree for exon 3 (non-PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 4—figure supplement 10
MHC-DOB-related group BEAST2 tree for exon 3 (non-PBR-encoding).
In the tree, each tip represents a sequence (see Appendix 1 for more details on nomenclature), with the colored rectangle and four-letter abbreviation indicating the species (see Figure 1—figure supplement 2 for full species key). Following the rectangle, tips are labeled with the sequence name; sequences which have been assigned to loci are colored according to the gene group, while unassigned sequences are written in gray. Dashed branches are shortened to 10% of their length to expand detail in the rest of the tree. The left-hand side shows example Bayes factors we calculated from the set of posterior trees; the tree tips correspond to the rows of the grid. Each panel represents a type of comparison (labeled at top) and each column represents one of the top 5 highest-Bayes-factor comparisons (exact value at bottom; >100 indicates strong evidence for TSP). The four colored blocks in each column include two red blocks (human sequences) that were tested against two sequences from other species (see Materials and methods; Bayes factors). Grayed-out rows correspond to sequences that were not considered for Bayes factors, either because they belong to a non-orthologous gene or backbone sequence (and thus not relevant to compare with the human gene in question), or because they may have been involved in a gene conversion event in this exon (according to GENECONV or from the literature).
Figure 4—figure supplement 11
TSP among old-world monkey groups for the Class II genes.
Different species comparisons are listed on the y-axis, and different gene regions are listed on the x-axis. Each table entry is colored and labeled with the maximum Bayes factor among all tested quartets of alleles belonging to that category. High Bayes factors (orange) indicate support for TSP among the given species for that gene region, while low Bayes factors (teal) indicate that alleles assort according to the species tree, as expected. Bayes factors above 100 are considered decisive. Tan values show poor support for either hypothesis, while white boxes indicate that there are not enough alleles in that category with which to calculate Bayes factors.
Figure 4—figure supplement 12
TSP among new-world monkey groups for the Class II genes.
Different species comparisons are listed on the y-axis, and different gene regions are listed on the x-axis. Each table entry is colored and labeled with the maximum Bayes factor among all tested quartets of alleles belonging to that category. High Bayes factors (orange) indicate support for TSP among the given species for that gene region, while low Bayes factors (teal) indicate that alleles assort according to the species tree, as expected. Bayes factors above 100 are considered decisive. Tan values show poor support for either hypothesis, while white boxes indicate that there are not enough alleles in that category with which to calculate Bayes factors. There is not enough data in each category to compute Bayes factors for these groups for MHC-DPA1, -DMA, -DMB, -DOA, and -DOB.
Figure 5 with 5 supplements
Rapidly-evolving sites in the Class I genes.
(A) Rapidly-evolving sites are primarily located in exons 2 and 3. Here, the exons are concatenated such that the cumulative position along the coding region is on the x-axis. The dashed orange lines denote exon boundaries. The three genes are aligned such that the same vertical position indicates an evolutionarily equivalent site. The y-axis shows the substitution rate at each site, expressed as a fold change (the base-2 logarithm of each site’s evolutionary rate divided by the mean rate among mostly-gap sites in each alignment; see Materials and methods). (B) Rapidly-evolving sites are located in each protein’s peptide-binding pocket. Structures are Protein Data Bank (Berman et al., 2000) 4BCE (Teze et al., 2014) for HLA-B, 4NT6 (Choo et al., 2014) for HLA-C, and 7P4B (Walters et al., 2022) for HLA-E, with images created in PyMOL (Schrödinger, LLC, 2021). Substitution rates for each amino acid are computed as the mean substitution rate of the three sites composing the codon. Orange indicates rapidly-evolving amino acids, while teal indicates conserved amino acids. (C) Rapidly-evolving amino acids are significantly closer to the peptide than conserved amino acids. The y-axis shows the BEAST2 substitution rate and the x axis shows the minimum distance to the bound peptide, measured in PyMOL (Schrödinger, LLC, 2021). Each point is an amino acid, and distances are averaged over several structures (see Table 5). The orange line is a linear regression of substitution rate on minimum distance, with slope and p-value annotated on each panel.
Figure 5—figure supplement 1
Rapidly-evolving sites in the Class I genes.
Rapidly-evolving sites are primarily located in exons 2 and 3. Here, the exons are concatenated such that the cumulative position along the coding region is on the x-axis. The dashed orange lines denote exon boundaries and the exon numbers are labeled in the top panel. The genes are aligned such that the same vertical position indicates an evolutionarily equivalent site. The y-axis shows the substitution rate at each site, expressed as a fold change (the base-2 logarithm of each site’s evolutionary rate divided by the mean rate among mostly-gap sites in each alignment; see Materials and methods).
Figure 5—figure supplement 2
Proportions of rapidly-evolving sites for Class I.
Sites were binned into slowly-evolving (≤-1), rapidly-evolving (>1), or baseline (>-1 but ≤1) categories. We then calculated proportions of these categories for exon 2, exon 3, exon 4, and the ’other’ exons (not exons 2, 3, or 4). These bins are all approximately the same size, ∼270 bp. For each gene and exon, we tested the difference in the proportion of rapidly-evolving sites between that exon and the ‘other’ exons group (two-sample z-test for equality of proportions with continuity correction). Significant tests (Bonferroni corrected; p<0.05/3) are marked with an asterisk.
Figure 5—figure supplement 3
Rapidly-evolving sites on Class I protein structures.
Structures are Protein Data Bank (Berman et al., 2000) 6 J1W (Zhu et al., 2019) for HLA-A, 3BVN (Kumar et al., 2009) for HLA-B, 4NT6 (Choo et al., 2014) for HLA-C, 7P4B (Walters et al., 2022) for HLA-E, 5IUE (Dulberger et al., 2017) for HLA-F, and 3KYN (Walpole et al., 2010) for HLA-G, with images created in PyMOL (Schrödinger, LLC, 2021). Substitution rates for each amino acid are computed as the mean substitution rate of the three sites composing the codon. Orange indicates rapidly-evolving amino acids, while teal indicates conserved amino acids.
Figure 5—figure supplement 4
Evolutionary rate is related to the distance to peptide.
The y-axis shows the BEAST2 substitution rate, expressed as a fold change (the base-2 logarithm of each site’s evolutionary rate divided by the mean rate among mostly-gap sites in each alignment; see Materials and methods). The x-axis shows the minimum distance to the bound peptide, measured in PyMOL (Schrödinger, LLC, 2021). Each point is an amino acid, and distances are averaged over several structures (see Table 5). The orange line is a linear regression of substitution rate on minimum distance, with slope and p-value annotated on each panel. Amino acids with a fold change greater than 1.5 are labeled.
Figure 5—figure supplement 5
Class I rapidly-evolving sites by binned distance to peptide.
Nucleotide sites were divided into those whose corresponding amino acids contact the peptide (<4Å) versus do not contact the peptide (≥4Å), shown on the x-axis. This distance has been used previously to define plausible peptide-contacting residues (Nielsen et al., 2007). The y-axis shows the substitution rate at each site, expressed as a fold change (the base-2 logarithm of each site’s evolutionary rate divided by the mean rate among mostly-gap sites in each alignment; see Materials and methods). For each gene, the groups are compared using a Wilcoxon test, with p-value displayed at the top of each panel.
Figure 6 with 7 supplements
Rapidly-evolving sites in the Class II genes.
(A) Rapidly-evolving sites are primarily located in exon 2. Here, the exons are concatenated such that the cumulative position along the coding region is on the x-axis. The dashed orange lines denote exon boundaries. The α genes (top two plots) are aligned such that the same vertical position indicates an evolutionarily equivalent site; the same is true for the β genes (bottom two plots). The y-axis shows the substitution rate at each site, expressed as a fold change (the base-2 logarithm of each site’s evolutionary rate divided by the mean rate among mostly-gap sites in each alignment; see Materials and methods). (B) Rapidly-evolving sites are located in each protein’s peptide-binding pocket. Structures are Protein Data Bank (Berman et al., 2000) 5JLZ (Gerstner et al., 2016) for HLA-DR and 2NNA (Henderson et al., 2007) for HLA-DQ, with images created in PyMOL (Schrödinger, LLC, 2021). Substitution rates for each amino acid are computed as the mean substitution rate of the three sites composing the codon. Orange indicates rapidly-evolving amino acids, while teal indicates conserved amino acids. (C) Rapidly-evolving amino acids are significantly closer to the peptide than conserved amino acids. The y-axis shows the BEAST2 substitution rate and the x axis shows the minimum distance to the bound peptide, measured in PyMOL (Schrödinger, LLC, 2021). Each point is an amino acid, and distances are averaged over several structures (see Table 5). The orange line is a linear regression of substitution rate on minimum distance, with slope and p-value annotated on each panel.
Figure 6—figure supplement 1
Rapidly-evolving sites in the Class IIA genes.
Rapidly-evolving sites are primarily located in exon 2. Here, the exons are concatenated such that the cumulative position along the coding region is on the x-axis. The dashed orange lines denote exon boundaries and the exon numbers are labeled in the top panel. The genes are aligned such that the same vertical position indicates an evolutionarily equivalent site. The y-axis shows the substitution rate at each site, expressed as a fold change (the base-2 logarithm of each site’s evolutionary rate divided by the mean rate among mostly-gap sites in each alignment; see Materials and methods).
Figure 6—figure supplement 2
Proportions of rapidly-evolving sites for Class IIA.
Sites were binned into slowly-evolving (≤-1), rapidly-evolving (>1), or baseline (>-1 but ≤1) categories. We then calculated proportions of these categories for exon 2, exon 3, and the ‘other’ exons (not exons 2 or 3). These bins are all approximately the same size, ∼270bp. For each gene and exon, we tested the difference in the proportion of rapidly-evolving sites between that exon and the ‘other’ exons group (two-sample z-test for equality of proportions with continuity correction). Significant tests (Bonferroni corrected; p<0.05/2) are marked with an asterisk.
Figure 6—figure supplement 3
Rapidly-evolving sites in the Class IIB genes.
Rapidly-evolving sites are primarily located in exon 2. Here, the exons are concatenated such that the cumulative position along the coding region is on the x-axis. The dashed orange lines denote exon boundaries and the exon numbers are labeled in the top panel. The genes are aligned such that the same vertical position indicates an evolutionarily equivalent site. The y-axis shows the substitution rate at each site, expressed as a fold change (the base-2 logarithm of each site’s evolutionary rate divided by the mean rate among mostly-gap sites in each alignment; see Materials and methods).
Figure 6—figure supplement 4
Proportions of rapidly-evolving sites for Class IIB.
Sites were binned into slowly-evolving (≤-1), rapidly-evolving (>1), or baseline (>-1 but ≤1) categories. We then calculated proportions of these categories for exon 2, exon 3, and the ‘other’ exons (not exons 2 or 3). These bins are all approximately the same size, ∼270 bp. For each gene and exon, we tested the difference in the proportion of rapidly-evolving sites between that exon and the ‘other’ exons group (two-sample z-test for equality of proportions with continuity correction). Significant tests (Bonferroni corrected; p<0.05/2) are marked with an asterisk.
Figure 6—figure supplement 5
Rapidly-evolving sites on Class II protein structures.
Structures are Protein Data Bank (Berman et al., 2000) 5JLZ (Gerstner et al., 2016) for HLA-DR, 2NNA (Henderson et al., 2007) for HLA-DQ, 7 T2A (Ciacchi et al., 2023) for HLA-DP, 2BC4 (Nicholson et al., 2006) for HLA-DM, and 4I0P (Guce et al., 2013) for HLA-DO, with images created in PyMOL (Schrödinger, LLC, 2021). Substitution rates for each amino acid are computed as the mean substitution rate of the three sites composing the codon. Orange indicates rapidly-evolving amino acids, while teal indicates conserved amino acids.
Figure 6—figure supplement 6
Class II rapidly-evolving sites by binned distance to peptide.
Nucleotide sites were divided into those whose corresponding amino acids contact the peptide (<4Å) versus do not contact the peptide (≥4Å), shown on the x-axis. This distance has been used previously to define plausible peptide-contacting residues (Nielsen et al., 2007). The y-axis shows the substitution rate at each site, expressed as a fold change (the base-2 logarithm of each site’s evolutionary rate divided by the mean rate among mostly-gap sites in each alignment; see Materials and methods). For each gene, the groups are compared using a Wilcoxon test, with p-value displayed at the top of each panel. MHC-DM and -DO are not shown because they do not bind peptides.
Figure 6—figure supplement 7
Number of associations per amino acid as a function of evolutionary rate.
The x-axis shows the substitution rate at each site, expressed as a fold change (the base-2 logarithm of each site’s evolutionary rate divided by the mean rate among mostly-gap sites in each alignment; see Materials and methods). The y-axis shows the number of unique associations for each amino acid, including diseases, TCR phenotypes, and protein expression levels. Only genes with associations are shown; at the time of publishing, there were no amino acid associations meeting our criteria for MHC-E, -F, -G, -DRA, -DMA, -DMB, -DOA, or -DOB. For each gene, a regression line is shown in orange, with slope and p-value displayed at the top of each panel. The amino acids with the greatest number of associations within each gene are also labeled.
Figure 7
Possible unrooted trees of 4 alleles.
There is one tree where the human alleles are monophyletic, and two trees where they are non-monophyletic.
Appendix 1—figure 1
MHC allele nomenclature.
(A) Human HLA alleles are named in a standard fashion, with the gene name followed by four colon-separated fields. The first field indicates a broad-scale allele group which sometimes corresponds to a serological antigen. The second field denotes a specific HLA protein. The third field indicates synonymous changes to the nucleotide sequence in the coding region, while the fourth field is used to distinguish alleles with differences in the noncoding regions. If an allele’s expression has been characterized, an informative suffix is sometimes added (Robinson et al., 2024; Marsh et al., 2010). (B) Researchers have applied the same format to non-human alleles, with some key differences. Instead of ‘HLA’, a prefix which concatenates the first two letters of the genus name with the first two letters of the species name is used, except in certain cases where the species’ MHC system was named long ago. Paralogs can be distinguished using numbers, but sequences unassigned to a particular locus or paralog might incorporate a ‘W’ in the gene name. Use of expression tags varies, with some being added to the end of the gene name instead of the end of the entire allele name. Pseudogenes can be denoted with gene name suffixes, gene names themselves, expression suffixes, or not at all. For both human and non-human alleles, the lack of an expression suffix does not imply normal expression (de Groot et al., 2020). SLA: Swine Leukocyte Antigen; Chsa: Chlorocebus sabaeus—green monkey; Lero: Leontopithecus rosalia—golden lion tamarin; Mamu: Macaca mulatta—rhesus macaque; Aotr: Aotus trivirgatus—three-striped night monkey; Popy: Pongo pygmaeus—Bornean orangutan; Ceat: Cercocebus atys—sooty mangabey; Sala: Saguinus labiatus—white-lipped tamarin; Gogo: Gorilla gorilla—Western gorilla; Rano: Rattus norvegicus—brown rat; Patr: Pan troglodytes—chimpanzee; Papa: Pan paniscus—bonobo.
Tables
Table 1
Rapidly-evolving amino acids in MHC-B and their trait and disease associations.
Shown here are all amino acid positions in the MHC-B group evolving at more than twice the baseline rate (fold change ≥ 1). Many corresponding positions in human HLA-B have associations with autoimmune or infectious diseases, biomarkers, or TCR phenotypes. Disease associations were collected from a literature search of HLA fine-mapping studies with over 1000 cases (see Materials and methods).
| Amino Acid Position | Evol. Rate Fold Change | Distance to Peptide (Å) | Associations |
|---|---|---|---|
| 156 | 3.42 | 3.55 | Chronic Hepatitis C (Hirata et al., 2019), HIV Set Point Viral Load (Luo et al., 2021), Asthma (Sakaue et al., 2021), Eosinophil Count (Sakaue et al., 2021), Hypothyroidism (Sakaue et al., 2021), Pediatric Asthma (Sakaue et al., 2021), Systolic Blood Pressure (Sakaue et al., 2021), Total Protein (Sakaue et al., 2021), TCR β Interaction Probability >50% (Sharon et al., 2016), Plasma Protein Levels of ADAM8, AGER, ASPSCR1, B2M, CCL16, CCL28, CCL4, CD200R1, CD5L, CDSN, CX3CL1, FCRL5, IGF2R, IL12A, IL12B, IL5RA, MICB, NUCB2, PDCD1, RARRES2, SFTPD, SIGLEC6, SNX2, TIMD4, TNFRSF4, TNR, TYRP1 (Krishna et al., 2024) |
| 95 | 3.10 | 3.82 | KLRF1 Plasma Protein Level (Krishna et al., 2024) |
| 114 | 3.08 | 4.80 | Rheumatoid Arthritis (Sakaue et al., 2021), Plasma Protein Levels of AIF1, CD1C, DDR1, IL15, LILRB2, MICB (Krishna et al., 2024) |
| 116 | 2.84 | 3.44 | Eosinophil Count (Hirata et al., 2019), HIV Control (McLaren et al., 2012), Angina (Sakaue et al., 2021), Allergic Rhinitis (Waage et al., 2018), Psoriasis (Zhou et al., 2016), Plasma Protein Levels of ADAM15, APOM, BTN2A1, CD1C, CFB, CXCL11, CXCL9, FLT4, GNLY, KLRF1, LILRB1, MICB, PLXDC2, TNF, TNFRSF13C, TNXB (Krishna et al., 2024) |
| 70 | 2.64 | 3.71 | Platelet (Sakaue et al., 2021), Plasma Protein Levels of CD8A, GZMA, MICB, NRP2 (Krishna et al., 2024) |
| 97 | 2.37 | 4.29 | Ankylosing Spondylitis (Butler-Laporte et al., 2023), HIV Set Point Viral Load (Luo et al., 2021), HIV Control (McLaren et al., 2012), Adult Height (Sakaue et al., 2021), Alkaline Phosphatase (Sakaue et al., 2021), Body Weight (Sakaue et al., 2021), C-reactive Protein (Sakaue et al., 2021), IgA Nephritis (Sakaue et al., 2021), Mean Arterial Pressure (Sakaue et al., 2021), Mean Corpuscular Hemoglobin (Sakaue et al., 2021), Pneumonia (Tian et al., 2017), Tonsillectomy (Tian et al., 2017), Plasma Protein Levels of ADGRE2, BTN3A2, CCL21, CCL3, CD1C, CD8A, CDSN, CPVL, DXO, EBI3, EFCAB14, HBEGF, HCG22, IL12A, IL12B, LILRB2, LRP1, LRPAP1, LTB, LY75, MANF, MANSC1, MICB, OSCAR, PLA2G10, PRTN3, SIGLEC10, STAB2, TEK, TNFSF13, ZNRD2 (Krishna et al., 2024) |
| 24 | 2.35 | 4.68 | Hepatic Cancer (Sakaue et al., 2021), Plasma Protein Levels of ADAM15, CXCL10, FCRL6, GZMB, MICB, TNFSF8 (Krishna et al., 2024) |
| 163 | 2.23 | 4.13 | Lung Cancer (Squamous Cell Carcinoma) (Ferreiro-Iglesias et al., 2018), Alanine Aminotransferase (Sakaue et al., 2021), TCR Expression (TRAV38-1) (Sharon et al., 2016), TCR Interaction Probability >50% (Sharon et al., 2016), Plasma Protein Levels of DDR1, GZMA, LILRB1, MICB, NPTX1, SEPTIN3, TEK, WFDC2 (Krishna et al., 2024) |
| 67 | 1.96 | 3.72 | Graves’ Disease (Hirata et al., 2019), HIV Set Point Viral Load (Luo et al., 2021), Asthma (Sakaue et al., 2021), Psoriasis (Stuart et al., 2022), Plasma Protein Levels of AMBP, C2, CD160, CD28, CD48, CFB, FCRL1, FCRL6, FRZB, GP1BB, LILRB1, LTA, LY96, NID1, SIGLEC9, SORT1, THBD, TNFRSF4, TNFSF13B, TNXB, TP53BP1, VCAM1 (Krishna et al., 2024) |
| 152 | 1.96 | 3.53 | JIA (Oligoarthritis/RF-negative Polyarthritis) (Hinks et al., 2017), Plasma Protein Levels of LTBR, MICB, PLXNA4, RARRES2 (Krishna et al., 2024) |
| 63 | 1.71 | 2.94 | HIV Control (McLaren et al., 2012), Skin Cancer (Sakaue et al., 2021), B2M Plasma Protein Level (Krishna et al., 2024) |
| 99 | 1.70 | 3.00 | Plasma Protein Levels of APOM, CRTAM, DXO, IL15, MICB, OSCAR (Krishna et al., 2024) |
| 66 | 1.58 | 3.41 | TNFSF11 Plasma Protein Level (Krishna et al., 2024) |
| 69 | 1.56 | 4.69 | Parkinson’s Disease (Naito et al., 2021) |
| 74 | 1.31 | 4.30 | Chronic Sinusitis (Sakaue et al., 2021) |
| 62 | 1.29 | 3.89 | PGLYRP1 Plasma Protein Level (Krishna et al., 2024) |
| 138 | 1.26 | 9.18 | |
| 9 | 1.20 | 3.36 | Primary Biliary Cholangitis (Darlay et al., 2018), Systemic Lupus Erythematosus (Molineros et al., 2019), Rheumatoid Arthritis (Raychaudhuri et al., 2012), Hyperthyroidism (Sakaue et al., 2021), Monocyte Count (Sakaue et al., 2021), Serum Creatinine (Sakaue et al., 2021), Psoriasis (Zhou et al., 2016), Plasma Protein Levels of CD1C, CX3CL1, IL12B, LIPF, LTA, MICB, PDCD1, RGMA, SGSH, SLAMF7, TNFRSF8 (Krishna et al., 2024) |
| 81 | 1.03 | 4.04 |
-
Table 1—source data 1
Rapidly-evolving amino acids and their trait and disease associations for all studied genes.
For each gene group, the rapidly-evolving amino acid positions (substitution rate 𝑙𝑜𝑔2 fold change >1) are listed alongside their disease and trait associations. group: gene group; position: amino acid position; evol_rate: substitution rate 𝑙𝑜𝑔2 fold change; min_dist: minimum distance to peptide (Å); disease_assoc: list of disease, trait, and other associations, with citations.
- https://cdn.elifesciences.org/articles/103547/elife-103547-table1-data1-v1.txt
Table 2
Data summary for Class I.
Each row represents a species, and each column represents a gene group. Each cell lists the number of alleles included for each gene represented by that gene group. Bolded entries are ‘backbone’ sequences that are included in every group.
| Clade | Species Group | Species | Latin Name | Pref. | MHC-A Group | MHC-B Group | MHC-C Group | MHC-E Group | MHC-F Group | MHC-G Group |
|---|---|---|---|---|---|---|---|---|---|---|
| Ape | Human | Human | Homo sapiens | Hosa | 63 –A, 1 –A, 4 –H, 1 –H, 2 –Y, 1 –B, 1 –L, 1 –C, 1 –E, 1 –F, 1 –G, 1 –J, 1 –K, 1 –V, 1 –W | 1 –A, 1 –H, 91 –B, 1 –B, 1 –L, 1 –C, 1 –E, 1 –F, 1 –G, 1 –J, 1 –K, 1 –V, 1 –W | 1 –A, 1 –H, 1 –B, 1 –L, 90 –C, 1 –C, 1 –E, 1 –F, 1 –G, 1 –J, 1 –K, 1 –V, 1 –W | 1 –A, 1 –H, 1 –B, 1 –L, 1 –C, 15 –E, 1 –E, 1 –F, 1 –G, 1 –J, 1 –K, 1 –V, 1 –W | 1 –A, 1 –H, 1 –B, 1 –L, 1 –C, 1 –E, 10 –F, 1 –F, 1 –G, 1 –J, 1 –K, 1 –V, 1 –W | 1 –A, 1 –H, 1 –B, 1 –L, 1 –C, 1 –E, 1 –F, 17 –G, 1 –G, 1 –J, 1 –K, 1 –V, 1 –W |
| Chimpanzee | Bonobo | Pan paniscus | Papa | 10 –A, 1 –H | 26 –B | 11 –C | 1 –E | 1 –F | 2 –G | |
| Chimpanzee | Pan troglodytes | Patr | 30 –A, 3 –A/AL/OKO, 1 –H | 48 –B | 28 –C | 2 –E | 3 –F | 1 –G | ||
| Gorilla | Eastern gorilla | Gorilla beringei | Gobe | 1 –A/AL/OKO | 1 –B | 1 –C | ||||
| Western gorilla | Gorilla gorilla | Gogo | 4 –A, 4 –A/AL/OKO, 1 –H, 3 –Y | 10 –B, 3 –B | 8 –C | 2 –E | 3 –F | 2 –G | ||
| Orangutan | Sumatran orangutan | Pongo abelii | Poab | 5 –A/AL/OKO, 1 –H | 12 –B | 2 –C | 1 –E | 1 –F | 1 –G | |
| Bornean orangutan | Pongo pygmaeus | Popy | 12 –A/AL/OKO, 1 –H, 7 -Ap | 20 –B | 5 –C | 1 –E | 1 –F | |||
| Gibbon | Lar gibbon | Hylobates lar | Hyla | 2 –A | 1 –B | |||||
| Silvery gibbon | Hylobates moloch | Hymo | 1 –A | 1 unknown | 1 –E | 1 –F | ||||
| Northern white-cheeked gibbon | Nomascus leucogenys | Nole | 1 –A | 2 unknown | 1 –E | 1 –F | ||||
| OWM | Baboon | Olive baboon | Papio anubis | Paan | 1 –A, 1 –AG | 1 –B | 1 –E | 3 –F | 1 –AG | |
| Hamadryas baboon | Papio hamadryas | Paha | 2 –B | |||||||
| Yellow baboon | Papio cynocephalus | Pacy | 1 –E | |||||||
| Gelada | Gelada | Theropithecus gelada | Thge | 1 –A, 1 –AG | 1 –E | 1 –F | 1 –G | |||
| Mangabey | Sooty mangabey | Cercocebus atys | Ceat | 3 –A, 1 –AG | 1 –B, 1 –I | 5 –E | 5 –F | |||
| Drill | Drill | Mandrillus leucophaeus | Male | 1 –E | 1 –F | 2 –G | ||||
| Macaque | Crab-eating macaque | Macaca fascicularis | Mafa | 1 –L, 1 –V, 1 –W, 1 –A8 | 1 –B, 1 –L, 1 –V, 1 –W | 1 –L, 1 –V, 1 –W | 1 –L, 17 –E, 1 –V, 1 –W | 1 –L, 24 –F, 1 –V, 1 –W | 1 –L, 9 –G, 1 –V, 1 –W | |
| Rhesus macaque | Macaca mulatta | Mamu | 8 –A, 1 –A, 5 –AG, 1 –AG, 1 –B, 1 –I, 1 –E, 1 –F, 1 –G, 1 –J, 1 –K | 1 –A, 1 –AG, 9 –B, 1 –B, 1 –I, 1 –E, 1 –F, 1 –G, 1 –J, 1 –K | 1 –A, 1 –AG, 1 –B, 1 –I, 1 –E, 1 –F, 1 –G, 1 –J, 1 –K | 1 –A, 1 –AG, 1 –B, 1 –I, 30 –E, 1 –E, 1 –F, 1 –G, 1 –J, 1 –K | 1 –A, 1 –AG, 1 –B, 1 –I, 1 –E, 18–F, 1 –F, 1 –G, 1 –J, 1 –K | 1 –A, 5 –AG, 1 –AG, 1 –B, 1 –I, 1 –E, 1 –F, 4 –G, 1 –G, 1 –J, 1 –K | ||
| Stump-tailed macaque | Macaca arctoides | Maar | 1 –B | |||||||
| Assam macaque | Macaca assamensis | Maas | 1 –B | |||||||
| Northern pig-tailed macaque | Macaca leonina | Malo | 1 –B | |||||||
| Southern pig-tailed macaque | Macaca nemestrina | Mane | 2 –B | 10 –E | 7 –F | |||||
| Tibetan macaque | Macaca thibetana | Math | 1 –B | 1 –E | 1 –F | 1 –G | ||||
| Grivet | Grivet | Chlorocebus aethiops | Chae | 2 –G | ||||||
| Vervet Monkey | Vervet monkey | Chlorocebus pygerythrus | Chpy | 2 –B | ||||||
| Green Monkey | Green monkey | Chlorocebus sabaeus | Chsa | 1 –A, 1 –AG, 1 –A8 | 1 –B | 5 –E | 1 –F | 1 –AG | ||
| Guenon | Blue monkey | Cercopithecus mitis | Cemi | 2 –B | ||||||
| Colobus | Angola colobus | Colobus angolensis | Coan | 1 –AG | 2 –E | 1 –F | ||||
| Ugandan red colobus | Piliocolobus tephrosceles | Pite | 1 –E | 1 –F | 1 –G | |||||
| Langur | Francois’ langur | Trachypithecus francoisi | Trfr | 1 –A, 1 –AG | 1 –E | 1 –F | 1 –G | |||
| Snub-Nosed Monkey | Golden snub-nosed monkey | Rhinopithecus roxellana | Rhro | 1 –A, 1 –AG | 1 –E | 1 –G | ||||
| Black-and-white snub-nosed monkey | Rhinopithecus bieti | Rhbi | 1 –E | |||||||
| NWM | Tamarin | Cotton-top tamarin | Saguinus oedipus | Saoe | 1 –E | 4 –F | 9 –G, 1 –PS, 3 –N1/3/4 | |||
| Brown-mantled tamarin | Leontocebus fuscicollis | Lefu | 5 –G | |||||||
| Golden lion tamarin | Leontopithecus rosalia | Lero | 2 –G | |||||||
| White-lipped tamarin | Saguinus labiatus | Sala | 9 –G | |||||||
| Marmoset | Common marmoset | Callithrix jacchus | Caja | 1 –B, 1 –E, 1 –F, 1 –G | 8 –B, 1 –B, 1 –E, 1 –F, 1 –G | 1 –B, 1 –E, 1 –F, 1 –G | 1 –B, 2 –E, 1 –E, 1 –F, 1 –G | 1 –B, 1 –E, 17 –F, 1 –F, 1 –G | 1 –B, 1 –E, 1 –F, 76 –G, 1 –G, 1 –PS | |
| Night Monkey | Three-striped night monkey | Aotus trivirgatus | Aotr | 1 –E | 3 –G, 1 –PS | |||||
| Gray-bellied night monkey | Aotus lemurinus | Aole | 5 –F | |||||||
| Nancy Ma’s night monkey | Aotus nancymaae | Aona | 3 –F | 1 –B, 7 –G | ||||||
| Capuchin | Panamanian white-faced capuchin | Cebus imitator | Ceim | 1 –E | 1 –F | 6 –G, 1 unknown | ||||
| Tufted capuchin | Sapajus apella | Saap | 1 –E | 1 –F | 4 –G, 2 unknown | |||||
| Squirrel Monkey | Black-capped squirrel monkey | Saimiri boliviensis | Sabo | 3 –E | 2 –F | 1 –B, 3 –G, 1 unknown | ||||
| Common squirrel monkey | Saimiri sciureus | Sasc | 1 –G | |||||||
| Spider Monkey | White-bellied spider monkey | Ateles belzebuth | Atbe | 1 –B | 1 –E | 3 –G | ||||
| Black-headed spider monkey | Ateles fusciceps | Atfu | 1 –B | 2 –E | 9 –G | |||||
| Saki | White-faced saki | Pithecia pithecia | Pipi | 1 –B | 1 –E | 4 –G | ||||
| Tarsier | Tarsier | Philippine tarsier | Carlito syrichta | Casy | 1 unknown | 1 unknown | 1 unknown | 1 unknown | 1 unknown | 1 unknown |
| Strepsirrhini | Lemur | Ring-tailed lemur | Lemur catta | Leca | 1 unknown | 1 unknown | 1 unknown | 1 unknown | 1 unknown | 1 unknown |
Table 3
Data summary for Class IIA.
Each row represents a species, and each column represents a gene group. Each cell lists the number of alleles included for each gene represented by that gene group. Bolded entries are ‘backbone’ sequences that are included in every group.
| Clade | Species Group | Species | Latin Name | Pref. | MHC-DPA Group | MHC-DQA Group | MHC-DRA Group | MHC-DMA Group | MHC-DOA Group |
|---|---|---|---|---|---|---|---|---|---|
| Ape | Human | Human | Homo sapiens | Hosa | 22 –DPA, 2 –DPA, 2 –DQA, 1 –DRA, 1 –DMA, 1 –DOA | 2 –DPA, 22 –DQA, 2 –DQA, 1 –DRA, 1 –DMA, 1 –DOA | 2 –DPA, 2 –DQA, 4–DRA, 1 –DRA, 1 –DMA, 1 –DOA | 2 –DPA, 2 –DQA, 1 –DRA, 8–DMA, 1 –DMA, 1 –DOA | 2 –DPA, 2 –DQA, 1 –DRA, 1 –DMA, 14–DOA, 1–DOA |
| Chimpanzee | Bonobo | Pan paniscus | Papa | 1 –DPA | 2 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | |
| Chimpanzee | Pan troglodytes | Patr | 5 –DPA | 6 –DQA | 3 –DRA | 1 –DMA | 1 –DOA | ||
| Gorilla | Western gorilla | Gorilla gorilla | Gogo | 3 –DPA | 10 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | |
| Orangutan | Sumatran orangutan | Pongo abelii | Poab | 4 –DPA | 6 –DQA | 4 –DRA | 1 –DMA | 1 –DOA | |
| Bornean orangutan | Pongo pygmaeus | Popy | 4 –DPA | 4 –DQA | 2 –DRA | ||||
| Gibbon | Silvery gibbon | Hylobates moloch | Hymo | 1 –DPA | 3 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | |
| Northern white-cheeked gibbon | Nomascus leucogenys | Nole | 1 –DPA | 2 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | ||
| Lar gibbon | Hylobates lar | Hyla | 6 –DQA | ||||||
| OWM | Baboon | Olive baboon | Papio anubis | Paan | 13 –DPA | 8 –DQA | 3 –DRA | 1 –DMA | 1 –DOA |
| Hamadryas baboon | Papio hamadryas | Paha | 1 –DPA | 3 –DQA | |||||
| Yellow baboon | Papio cynocephalus | Pacy | 7 –DQA | ||||||
| Guinea baboon | Papio papio | Papp | 4 –DQA | ||||||
| Gelada | Gelada | Theropithecus gelada | Thge | 2 –DPA | 3 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | |
| Mangabey | Sooty mangabey | Cercocebus atys | Ceat | 2 –DPA | 2 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | |
| Black crested mangabey | Lophocebus aterrimus | Loat | 1 –DQA | ||||||
| Drill | Drill | Mandrillus leucophaeus | Male | 1 –DPA | 2 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | |
| Macaque | Crab-eating macaque | Macaca fascicularis | Mafa | 30 –DPA, 1 –DMA, 1 –DOA | 11 –DQA, 1 –DMA, 1 –DOA | 16 –DRA, 1 –DMA, 1 –DOA | 7 –DMA, 1 –DMA, 1 –DOA | 1 –DMA, 6 –DOA, 1 –DOA | |
| Northern pig-tailed macaque | Macaca leonina | Malo | 6 –DPA | 8 –DQA | 5 –DRA | 2 –DMA | 7 –DOA | ||
| Rhesus macaque | Macaca mulatta | Mamu | 22 –DPA, 1 –DPA, 2 –DQA, 1 –DRA | 1 –DPA, 9 –DQA, 2 –DQA, 1 –DRA | 1 –DPA, 2 –DQA, 12 –DRA, 1 –DRA | 1 –DPA, 2 –DQA, 1 –DRA, 4 –DMA | 1 –DPA, 2 –DQA, 1 –DRA, 1 –DOA | ||
| Southern pig-tailed macaque | Macaca nemestrina | Mane | 14 –DPA | 10 –DQA | 11 –DRA | 1 –DMA | 1 –DOA | ||
| Tibetan macaque | Macaca thibetana | Math | 7 –DPA | 1 –DQA | 1 –DRA | 10 –DMA | |||
| Stump-tailed macaque | Macaca arctoides | Maar | 1 –DPA | 2 –DQA | |||||
| Grivet | Grivet | Chlorocebus aethiops | Chae | 6 –DQA | |||||
| Green Monkey | Green monkey | Chlorocebus sabaeus | Chsa | 5 –DPA | 2 –DQA | 1 –DRA | 1 –DOA | ||
| Guenon | Blue monkey | Cercopithecus mitis | Cemi | 5 –DQA | |||||
| De Brazza’s monkey | Cercopithecus neglectus | Cene | 2 –DQA | ||||||
| Colobus | Angola colobus | Colobus angolensis | Coan | 2 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | ||
| Ugandan red colobus | Piliocolobus tephrosceles | Pite | 1 –DPA | 1 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | ||
| Mantled guereza | Colobus guereza | Cogu | 1 –DQA | ||||||
| Langur | Francois’ langur | Trachypithecus francoisi | Trfr | 1 –DPA | 1 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | |
| Snub-Nosed Monkey | Black-and-white snub-nosed monkey | Rhinopithecus bieti | Rhbi | 1 –DRA | 1 –DMA | 1 –DOA | |||
| Golden snub-nosed monkey | Rhinopithecus roxellana | Rhro | 1 –DPA | 1 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | ||
| NWM | Tamarin | Cotton-top tamarin | Saguinus oedipus | Saoe | 4 –DQA | ||||
| Marmoset | Common marmoset | Callithrix jacchus | Caja | 1 –DPA, 2 –DQA, 1 –DMA, 1 –DOA | 1 –DPA, 6 –DQA, 2 –DQA, 1 –DMA, 1 –DOA | 1 –DPA, 2 –DQA, 1 –DRA, 1 –DMA, 1 –DOA | 1 –DPA, 2 –DQA, 1 –DMA, 1 –DOA | 1 –DPA, 2 –DQA, 1 –DMA, 1 –DOA | |
| Night Monkey | Nancy Ma’s night monkey | Aotus nancymaae | Aona | 1 –DPA, 1 –DRA | 6 –DQA, 1 –DRA | 2 –DRA, 1 –DRA | 1 –DRA, 1 –DMA | 1 –DRA, 1 –DOA | |
| Gray-bellied night monkey | Aotus lemurinus | Aole | 3 –DQA | ||||||
| Spix’s night monkey | Aotus vociferans | Aovo | 3 –DRA | ||||||
| Capuchin | Panamanian white-faced capuchin | Cebus imitator | Ceim | 1 –DPA | 3 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | |
| Tufted capuchin | Sapajus apella | Saap | 1 –DPA | 3 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | ||
| Squirrel Monkey | Black-capped squirrel monkey | Saimiri boliviensis | Sabo | 2 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | ||
| Common squirrel monkey | Saimiri sciureus | Sasc | 3 –DPA | ||||||
| Tarsier | Tarsier | Philippine tarsier | Carlito syrichta | Casy | 3 –DPA | 2 –DQA | 1 –DRA | 1 –DMA | 1 –DOA |
| Strepsirrhini | Lemur | Ring-tailed lemur | Lemur catta | Leca | 1 –DPA, 1 –DQA, 1 –DRA, 1 –DMA, 1 –DOA | 1 –DPA, 1 –DQA, 1 –DRA, 1 –DMA, 1 –DOA | 1 –DPA, 1 –DQA, 1 –DRA, 1 –DMA, 1 –DOA | 1 –DPA, 1 –DQA, 1 –DRA, 1 –DMA, 1 –DOA | 1 –DPA, 1 –DQA, 1 –DRA, 1 –DMA, 1 –DOA |
| Gray mouse lemur | Microcebus murinus | Mimu | 1 –DPA | 1 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | ||
| Loris | Sunda slow loris | Nycticebus coucang | Nyco | 1 –DPA | 2 –DRA | 1 –DMA | 1 –DOA | ||
| Galago | Northern greater galago | Otolemur garnettii | Otga | 1 –DPA | 1 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | |
| Sifaka | Coquerel’s sifaka | Propithecus coquereli | Prco | 2 –DPA | 1 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | |
| Flying Lemur | Flying Lemur | Sunda flying lemur | Galeopterus variegatus | Gava | 2 –DPA | 1 –DRA | 1 –DMA | 1 –DOA | |
| Tree Shrew | Tree Shrew | Chinese tree shrew | Tupaia chinensis | Tuch | 4 –DPA | 1 –DQA | 1 –DRA | 1 –DMA | 1 –DOA |
| Glires | Rodent | Groundhog | Marmota monax | Mamo | 1 –DPA, 1 –DPA | 1 –DPA | 1 –DPA, 1 –DRA | 1 –DPA, 1 –DMA | 1 –DPA, 1 –DOA |
| Brown rat | Rattus norvegicus | Rano | 1 –DQA, 1 –DRA, 1 –DMA, 1 –DOA | 2 –DQA, 1 –DQA, 1 –DRA, 1 –DMA, 1 –DOA | 1 –DQA, 2 –DRA, 1 –DRA, 1 –DMA, 1 –DOA | 1 –DQA, 1 –DRA, 1 –DMA, 1 –DOA | 1 –DQA, 1 –DRA, 1 –DMA, 1–DOA, 1–DOA | ||
| Pika | Plateau pika | Ochotona curzoniae | Occu | 2 –DPA | 2 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | |
| American pika | Ochotona princeps | Ocpr | 2 –DPA | 1 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | ||
| Laurasiatheria | Artiodactyla | Bactrian camel | Camelus bactrianus | Caba | 1 –DPA | 1 –DQA | 1 –DMA | 1 –DOA | |
| Wild boar | Sus scrofa | SLA | 1 –DQA, 1 –DRA, 1 –DMA, 1 –DOA | 1 –DQA, 1 –DQA, 1 –DRA, 1 –DMA, 1 –DOA | 1 –DQA, 3 –DRA, 1 –DRA, 1 –DMA, 1 –DOA | 1 –DQA, 1 –DRA, 4 –DMA, 1 –DMA, 1 –DOA | 1 –DQA, 1 –DRA, 1 –DMA, 1 –DOA, 1 –DOA | ||
| Even-toed ungulates | Bos sp. | BoLA | 2 –DQA | ||||||
| Domestic yak | Bos grunniens | Bogr | 2 –DQA | ||||||
| Water buffalo | Bubalus bubalis | Bubu | 2 –DQA | ||||||
| Sheep | Ovis aries | Ovar | 4 –DQA | 3 –DRA | |||||
| Dromedary camel | Camelus dromedarius | Cadr | 1 –DRA | ||||||
| Bighorn sheep | Ovis canadensis | Ovca | 3 –DRA | ||||||
| Ferungulata | Sea otter | Enhydra lutris | Enlu | 1 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | ||
| Cat | Felis catus | Feca | 1 –DRA | 1 –DMA | 1 –DOA | ||||
| Sunda pangolin | Manis javanica | Maja | 1 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | |||
| Cougar | Puma concolor | Puco | 1 –DPA | 1 –DMA | 1 –DOA | ||||
| Jaguarundi | Puma yagouaroundi | Puya | 1 –DPA | 1 –DRA | 1 –DMA | 1 –DOA | |||
| Steller sea lion | Eumetopias jubatus | Euju | 1 –DPA | 1 –DQA | |||||
| Horse | Equus caballus | Eqca | 5 –DQA | 3 –DRA | |||||
| Bat | Big brown bat | Eptesicus fuscus | Epfu | 1 –DPA | 2 –DQA | 1 –DRA | 1 –DMA | ||
| Kuhl’s pipistrelle | Pipistrellus kuhlii | Piku | 1 –DPA | 1 –DQA | 1 –DRA | 1 –DMA | |||
| Large flying fox | Pteropus vampyrus | Ptva | 2 –DQA | 1 –DRA | 1 –DOA | ||||
| Mole | Star-nosed mole | Condylura cristata | Cocr | 3 –DQA | 1 –DOA | ||||
| Atlantogenata | Xenarthra | Linnaeus’s two-toed sloth | Choloepus didactylus | Chdi | 1 –DPA | 1 –DQA | 1 –DRA | 1 –DMA | 1 –DOA |
| Nine-banded armadillo | Dasypus novemcinctus | Dano | 1 –DPA | 2 –DQA | 1 –DRA | 1 –DMA | 1 –DOA | ||
| Afrotheria | Cape golden mole | Chrysochloris asiatica | Chas | 1 –DPA | 1 –DRA | 1 –DMA | 1 –DOA | ||
| Cape elephant shrew | Elephantulus edwardii | Eled | 1 –DPA | 1 –DPA, 1 –DQA | 1 –DPA, 1 –DRA | 1 –DPA, 1 –DMA | 1 –DPA, 1 –DOA | ||
| Aardvark | Orycteropus afer | Oraf | 1 –DPA | 1 –DQA | 1 –DMA | 1 –DOA | |||
| West Indian manatee | Trichechus manatus | Trma | 2 –DPA | 1 –DQA | 1 –DRA | 1 –DMA | |||
| Lesser hedgehog tenrec | Echinops telfairi | Ecte | 1 –DRA | 1 –DOA |
Table 4
Data summary for Class IIB.
Each row represents a species, and each column represents a gene group. Each cell lists the number of alleles included for each gene represented by that gene group. Bolded entries are ‘backbone’ sequences that are included in every group.
| Clade | Species Group | Species | Latin Name | Pref. | MHC-DPB Group | MHC-DQB Group | MHC-DRB Group | MHC-DMB Group | MHC-DOB Group |
|---|---|---|---|---|---|---|---|---|---|
| Ape | Human | Human | Homo sapiens | Hosa | 74 –DPB, 2 –DPB, 2 –DQB, 9 –DRB, 1 –DMB, 1 –DOB | 2 –DPB, 24 –DQB, 2 –DQB, 9 –DRB, 1 –DMB, 1 –DOB | 2 –DPB, 2 –DQB, 46 –DRB, 9 –DRB, 1 –DMB, 1 –DOB | 2 –DPB, 2 –DQB, 9 –DRB, 6 –DMB, 1 –DMB, 1 –DOB | 2 –DPB, 2 –DQB, 9 –DRB, 1 –DMB, 14 –DOB, 1 –DOB |
| Chimpanzee | Bonobo | Pan paniscus | Papa | 8 –DPB | 2 –DQB | 5 –DRB | 2 –DMB | 1 –DOB | |
| Chimpanzee | Pan troglodytes | Patr | 6 –DPB | 9 –DQB | 17 –DRB | 2 –DMB | 2 –DOB | ||
| Gorilla | Western gorilla | Gorilla gorilla | Gogo | 5 –DPB | 10 –DQB | 7 –DRB | 2 –DMB | 1 –DOB | |
| Orangutan | Sumatran orangutan | Pongo abelii | Poab | 5 –DPB | 6 –DQB | 7 –DRB | 1 –DMB | 1 –DOB | |
| Bornean orangutan | Pongo pygmaeus | Popy | 5 –DPB | 3 –DQB | 7 –DRB | 3 –DMB | |||
| Gibbon | Silvery gibbon | Hylobates moloch | Hymo | 1 –DPB | 2 –DQB | 5 –DRB | 1 –DMB | 1 –DOB | |
| Northern white-cheeked gibbon | Nomascus leucogenys | Nole | 1 –DPB | 2 –DQB | 1 –DMB | 1 –DOB | |||
| Lar gibbon | Hylobates lar | Hyla | 4 –DQB | ||||||
| OWM | Baboon | Olive baboon | Papio anubis | Paan | 5 –DPB | 5 –DQB | 11 –DRB | 1 –DMB | |
| Hamadryas baboon | Papio hamadryas | Paha | 3 –DQB | 1 –DRB | |||||
| Chacma baboon | Papio ursinus | Paur | 8 –DRB | ||||||
| Gelada | Gelada | Theropithecus gelada | Thge | 2 –DPB | 1 –DQB | 3 –DRB | 1 –DMB | 1 –DOB | |
| Mangabey | Sooty mangabey | Cercocebus atys | Ceat | 3 –DPB | 2 –DQB | 1 –DRB | 1 –DMB | 1 –DOB | |
| Drill | Drill | Mandrillus leucophaeus | Male | 1 –DPB | 1 –DRB | 1 –DMB | 1 –DOB | ||
| Mandrill | Mandrill | Mandrillus sphinx | Masp | 10 –DRB | |||||
| Macaque | Crab-eating macaque | Macaca fascicularis | Mafa | 7 –DPB, 2 –DRB, 1 –DMB, 1 –DOB | 5 –DQB, 2 –DRB, 1 –DMB, 1 –DOB | 6 –DRB, 2 –DRB, 1 –DMB, 1 –DOB | 2 –DRB, 4 –DMB, 1 –DMB, 1 –DOB | 2 –DRB, 1 –DMB, 6 –DOB, 1 –DOB | |
| Northern pig-tailed macaque | Macaca leonina | Malo | 5 –DPB | 5 –DQB | 3 –DRB | 2 –DMB | 3 –DOB | ||
| Rhesus macaque | Macaca mulatta | Mamu | 5 –DPB, 2 –DPB, 1 –DQB, 4 –DRB | 2 –DPB, 4 –DQB, 1 –DQB, 4 –DRB | 2 –DPB, 1 –DQB, 10 –DRB, 4 –DRB | 2 –DPB, 1 –DQB, 4 –DRB, 5 –DMB | 2 –DPB, 1 –DQB, 4 –DRB, 1 –DOB | ||
| Southern pig-tailed macaque | Macaca nemestrina | Mane | 5 –DPB | 5 –DQB | 6 –DRB | 1 –DMB | 1 –DOB | ||
| Tibetan macaque | Macaca thibetana | Math | 13 –DPB | 6 –DQB | 1 –DRB | 1 –DMB | 1 –DOB | ||
| Stump-tailed macaque | Macaca arctoides | Maar | 5 –DQB | 2 –DRB | |||||
| Japanese macaque | Macaca fuscata | Mafu | 3 –DRB | ||||||
| Lion-tailed macaque | Macaca silenus | Masi | 3 –DRB | ||||||
| Grivet | Grivet | Chlorocebus aethiops | Chae | 3 –DQB | 6 –DRB | ||||
| Green Monkey | Green monkey | Chlorocebus sabaeus | Chsa | 3 –DPB | 4 –DQB | 7 –DRB | 1 –DMB | 1 –DOB | |
| Colobus | Angola colobus | Colobus angolensis | Coan | 2 –DPB | 2 –DQB | 1 –DMB | 1 –DOB | ||
| Ugandan red colobus | Piliocolobus tephrosceles | Pite | 1 –DPB | 1 –DQB | 3 –DRB | 1 –DMB | 1 –DOB | ||
| Langur | Francois’ langur | Trachypithecus francoisi | Trfr | 2 –DPB | 1 –DQB | 3 –DRB | 1 –DMB | 1 –DOB | |
| Gray langur | Semnopithecus entellus | Seen | 1 –DPB | ||||||
| Snub-Nosed Monkey | Black-and-white snub-nosed monkey | Rhinopithecus bieti | Rhbi | 1 –DMB | 1 –DOB | ||||
| Golden snub-nosed monkey | Rhinopithecus roxellana | Rhro | 1 –DPB | 1 –DQB | 2 –DRB | 1 –DMB | 1 –DOB | ||
| NWM | Tamarin | Cotton-top tamarin | Saguinus oedipus | Saoe | 3 –DPB | 4 –DQB | 8 –DRB | ||
| White-lipped tamarin | Saguinus labiatus | Sala | 3 –DRB | ||||||
| Marmoset | Common marmoset | Callithrix jacchus | Caja | 1 –DPB, 1 –DPB, 2 –DQB, 1 –DRB, 1 –DMB, 1 –DOB | 1 –DPB, 3 –DQB, 2 –DQB, 1 –DRB, 1 –DMB, 1 –DOB | 1 –DPB, 2 –DQB, 3 –DRB, 1 –DRB, 1 –DMB, 1 –DOB | 1 –DPB, 2 –DQB, 1 –DRB, 1 –DMB, 1 –DOB | 1 –DPB, 2 –DQB, 1 –DRB, 1 –DMB, 1 –DOB | |
| Night Monkey | Nancy Ma’s night monkey | Aotus nancymaae | Aona | 4 –DPB | 3 –DQB | 6 –DRB | 1 –DMB | 1 –DOB | |
| Gray-bellied night monkey | Aotus lemurinus | Aole | 3 –DPB | 1 –DQB | |||||
| Azara’s night monkey | Aotus azarae | Aoaz | 2 –DRB | ||||||
| Black-headed night monkey | Aotus nigriceps | Aoni | 3 –DRB | ||||||
| Three-striped night monkey | Aotus trivirgatus | Aotr | 3 –DRB | ||||||
| Spix’s night monkey | Aotus vociferans | Aovo | 3 –DRB | ||||||
| Capuchin | Panamanian white-faced capuchin | Cebus imitator | Ceim | 1 –DPB | 3 –DQB | 1 –DRB | 1 –DMB | 1 –DOB | |
| Tufted capuchin | Sapajus apella | Saap | 1 –DPB | 4 –DQB | 3 –DRB | 1 –DMB | |||
| Squirrel Monkey | Black-capped squirrel monkey | Saimiri boliviensis | Sabo | 1 –DPB | 3 –DQB | 1 –DMB | 1 –DOB | ||
| Common squirrel monkey | Saimiri sciureus | Sasc | 2 –DRB | ||||||
| Spider Monkey | White-bellied spider monkey | Ateles belzebuth | Atbe | 2 –DRB | |||||
| Howler Monkey | Guatemalan black howler | Alouatta pitta | Alpi | 2 –DRB | |||||
| Saki | White-faced saki | Pithecia pithecia | Pipi | 3 –DRB | |||||
| Tarsier | Tarsier | Philippine tarsier | Carlito syrichta | Casy | 2 –DPB | 1 –DQB | 2 –DRB | 1 –DMB | 1 –DOB |
| Strepsirrhini | Lemur | Ring-tailed lemur | Lemur catta | Leca | 1 –DPB, 1 –DPB, 1 –DQB, 1 –DRB, 1 –DMB, 1 –DOB | 1 –DPB, 1 –DQB, 1 –DRB, 1 –DMB, 1 –DOB | 1 –DPB, 1 –DQB, 1 –DRB, 1 –DMB, 1 –DOB | 1 –DPB, 1 –DQB, 1 –DRB, 1 –DMB, 1 –DOB | 1 –DPB, 1 –DQB, 1 –DRB, 1 –DMB, 1 –DOB |
| Gray mouse lemur | Microcebus murinus | Mimu | 1 –DPB | 3 –DQB | 2 –DRB | 1 –DMB | 1 –DOB | ||
| Loris | Sunda slow loris | Nycticebus coucang | Nyco | 1 –DPB | |||||
| Galago | Northern greater galago | Otolemur garnettii | Otga | 1 –DPB | 1 –DQB | 1 –DRB | 1 –DMB | 1 –DOB | |
| Sifaka | Coquerel’s sifaka | Propithecus coquereli | Prco | 1 –DPB | 1 –DQB | 1 –DMB | 1 –DOB | ||
| Flying Lemur | Flying Lemur | Sunda flying lemur | Galeopterus variegatus | Gava | 2 –DPB | 2 –DRB | 1 –DMB | 1 –DOB | |
| Tree Shrew | Tree Shrew | Chinese tree shrew | Tupaia chinensis | Tuch | 1 –DPB | 1 –DMB | 1 –DOB | ||
| Glires | Rodent | Groundhog | Marmota monax | Mamo | 1 –DPB, 1 –DPB | 1 –DPB | 1 –DPB | 1 –DPB, 1–DMB | 1 –DPB |
| Brown rat | Rattus norvegicus | Rano | 1 –DQB, 1 –DRB, 1 –DMB, 1 –DOB | 2 –DQB, 1 –DQB, 1 –DRB, 1 –DMB, 1 –DOB | 1 –DQB, 3 –DRB, 1 –DRB, 1 –DMB, 1 –DOB | 1 –DQB, 1 –DRB, 1 –DMB, 1 –DMB, 1 –DOB | 1 –DQB, 1 –DRB, 1 –DMB, 1 –DOB | ||
| Pika | American pika | Ochotona princeps | Ocpr | 1 –DQB | 1 –DRB | 1 –DMB | |||
| Plateau pika | Ochotona curzoniae | Occu | 1 –DPB | 2 –DQB | 1 –DOB | ||||
| Laurasiatheria | Artiodactyla | Bactrian camel | Camelus bactrianus | Caba | 1 –DMB | 1 –DOB | |||
| Dromedary camel | Camelus dromedarius | Cadr | 1 –DPB | 1 –DPB | 1 –DPB | 1 –DPB | 1 –DPB | ||
| Wild boar | Sus scrofa | SLA | 1 –DQB, 1 –DRB, 1 –DMB, 1 –DOB | 2 –DQB, 1 –DQB, 1 –DRB, 1 –DMB, 1 –DOB | 1 –DQB, 4 –DRB, 1 –DRB, 1 –DMB, 1 –DOB | 1 –DQB, 1 –DRB, 1 –DMB, 1 –DOB | 1 –DQB, 1 –DRB, 1 –DMB, 2 –DOB, 1 –DOB | ||
| Even-toed ungulates | Bos sp. | BoLA | 1 –DQB | 2 –DRB | |||||
| Water buffalo | Bubalus bubalis | Bubu | 1 –DQB | ||||||
| Wild Bactrian camel | Camelus ferus | Cafe | 1 –DQB | ||||||
| Sheep | Ovis aries | Ovar | 6 –DQB | 1 –DRB | |||||
| Goat | Capra hircus | Cahi | 2 –DRB | ||||||
| Bighorn sheep | Ovis canadensis | Ovca | 1 –DRB | ||||||
| Ferungulata | Horse | Equus caballus | Eqca | 6 –DQB | 3 –DRB | 5 –DMB | 3 –DOB | ||
| Sunda pangolin | Manis javanica | Maja | 1 –DMB | 1 –DOB | |||||
| Cougar | Puma concolor | Puco | 1 –DPB | 1 –DMB | |||||
| Jaguarundi | Puma yagouaroundi | Puya | 1 –DMB | ||||||
| Northern elephant seal | Mirounga angustirostris | Mian | 1 –DRB | 1 –DOB | |||||
| Sea otter | Enhydra lutris | Enlu | 1 –DPB | 1 –DQB | |||||
| Steller sea lion | Eumetopias jubatus | Euju | 1 –DQB | ||||||
| Bat | Big brown bat | Eptesicus fuscus | Epfu | 2 –DQB | 1 –DRB | 1 –DMB | |||
| Large flying fox | Pteropus vampyrus | Ptva | 1 –DQB | 1 –DOB | |||||
| Kuhl’s pipistrelle | Pipistrellus kuhlii | Piku | 1 –DPB | 1 –DQB | |||||
| Mole | Star-nosed mole | Condylura cristata | Cocr | 2 –DQB | 1 –DRB | 1 –DMB | 1 –DOB | ||
| Atlantogenata | Xenarthra | Linnaeus’s two-toed sloth | Choloepus didactylus | Chdi | 2 –DPB | 1 –DQB | 1 –DMB | 1 –DOB | |
| Nine-banded armadillo | Dasypus novemcinctus | Dano | 1 –DPB | ||||||
| Afrotheria | Aardvark | Orycteropus afer | Oraf | 1 –DQB | 1 –DOB | ||||
| Cape elephant shrew | Elephantulus edwardii | Eled | 1 –DPB | ||||||
| West Indian manatee | Trichechus manatus | Trma | 1 –DPB | ||||||
| Lesser hedgehog tenrec | Echinops telfairi | Ecte | 1 –DRB |
Table 5
Structures used to calculate distances to peptide.
This table lists the Protein Data Bank (Berman et al., 2000) structure codes and references for all structures used to calculate peptide distances.
Additional files
-
MDAR checklist
- https://cdn.elifesciences.org/articles/103547/elife-103547-mdarchecklist1-v1.pdf
-
Source code 1
This zip file contains all xml files we used to run BEAST2 with SubstBMA on each gene group/exon alignment.
- https://cdn.elifesciences.org/articles/103547/elife-103547-code1-v1.zip
-
Supplementary file 1
This zip file contains lists of IPD database allele names or RefSeq accession numbers for the sequences we analyzed in each gene group.
- https://cdn.elifesciences.org/articles/103547/elife-103547-supp1-v1.zip
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Ancient trans-species polymorphism at the Major Histocompatibility Complex in primates
eLife 14:RP103547.
https://doi.org/10.7554/eLife.103547.3
