Correlated evolution of oxidative physiology and MHC-based immunosurveillance in birds
Data files
May 02, 2024 version files 669.38 KB
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Minias_et_al_sequence_DATA.fasta
634.22 KB
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Minias_et_al_species_DATA.xlsx
27.20 KB
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Minias_et_al_tree_DATA.phy
3.05 KB
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README.md
4.90 KB
Abstract
Maintenance and activation of the immune system incurs costs, not only in terms of substrates and energy, but also via collateral oxidative damage to host cells or tissues during immune response. So far, associations between immune function and oxidative damage have been primarily investigated at intra-specific scales. Here, we hypothesized that pathogen-driven selection should favour evolution of effective immunosurveillance mechanisms (e.g. Major Histocompatibility Complex, MHC) and antioxidant defences to mitigate oxidative damage resulting from immune function. Using phylogenetically-informed comparative approaches, we provided evidence for correlated evolution of host oxidative physiology and MHC-based immunosurveillance in birds. Species selected for more robust MHC-based immunosurveillance (higher gene copy numbers and allele diversity) showed stronger antioxidant defences, although selection for MHC diversity still showed a positive evolutionary association with oxidative damage to lipids. Our results indicate that historical pathogen-driven selection for highly duplicated and diverse MHC could have promoted the evolution of efficient antioxidant mechanisms, but these evolutionary solutions may be insufficient to keep oxidative stress at bounds. Although the precise nature of mechanistic links between the MHC and oxidative stress remains unclear, our study suggests that a general evolutionary investment in immune function may require co-adaptations at the level of host oxidative metabolism.
Description of the data and file structure
Minias_et_al_species_DATA.xlsx file contains species-specific data used in the phylogenetically-informed comparative analyses of oxidative physiology and Major Histocompatibility (MHC) genes.
MHC_gene_copy_number spreadsheet contains data used for the analyses of MHC gene copy number variation (n = 50 species), including information on:
- Species
- TAS_mean - mean total antioxidant status
- TAS_corrected_UA - total antioxidant status corrected for variation in uric acid (best linear unbiased estimate)
- TAS_corrected_year - total antioxidant status corrected for between-year variation (best linear unbiased estimate)
- TAS_n - sample size for total antioxidant status (number of individuals measured)
- UA_mean - mean uric acid
- UA_corrected_year - uric acid corrected for between-year variation (best linear unbiased estimate)
- UA_n - sample size for uric acid (number of individuals measured)
- tGSH_mean - mean total glutathione
- tGSH_n - sample size for total glutathione (number of individuals measured)
- MDA_mean - mean malondialdehyde
- MDA_n - sample size for malondialdehyde (number of individuals measured)
- ROMs_mean - mean reactive oxygen metabolites
- ROMs_n - sample size for reactive oxygen metabolites (number of individuals measured)
- MHC_copy_number - mean number of functional MHC-I/MHC-II genes
- MHC_copy_number_log - log z-transformed number of functional MHC-I/MHC-II genes
- Body_mass (g)
- Clutch_size (number of eggs)
- Residual_lifespan - residual of maximum lifespan (years) against source of data (wild-living vs. captivity), sampling effort, and body mass
- Diet
Selection_for_MHC-I_diversity spreadsheet contains data used for the analyses of selection for MHC-I diversity (n = 28 species), including information on:
- Species
- TAS_mean - mean total antioxidant status
- TAS_corrected_UA - total antioxidant status corrected for variation in uric acid (best linear unbiased estimate)
- TAS_corrected_year - total antioxidant status corrected for between-year variation (best linear unbiased estimate)
- TAS_n - sample size for total antioxidant status (number of individuals measured)
- UA_mean - mean uric acid
- UA_corrected_year - uric acid corrected for between-year variation (best linear unbiased estimate)
- UA_n - sample size for uric acid (number of individuals measured)
- tGSH_mean - mean total glutathione
- tGSH_n - sample size for total glutathione (number of individuals measured)
- MDA_mean - mean malondialdehyde
- MDA_corrected_TAS - malondialdehyde corrected for variation in total antioxidant status (best linear unbiased estimate)
- MDA_corrected_UA - malondialdehyde corrected for variation in uric acid (best linear unbiased estimate)
- MDA_corrected_year - malondialdehyde corrected for between-year variation (best linear unbiased estimate)
- MDA_n - sample size for malondialdehyde (number of individuals measured)
- ROMs_mean - mean reactive oxygen metabolites
- ROMs_n - sample size for reactive oxygen metabolites (number of individuals measured)
- Residual_dN_human_PBR - residuals of dN_human_PBR against dS_human_PBR
- dN_human_PBR - non-synonymous nucleotide substitution rate across human peptide-binding residues (PBR) at the MHC-I exon 3
- dS_human_PBR - synonymous nucleotide substitution rate across human peptide-binding residues (PBR) at the MHC-I exon 3
- Residual_dN_bird_PSS - residuals of dN_bird_PSS against dS_bird_PSS
- dN_bird_PSS - non-synonymous nucleotide substitution rate across 20 most positively selected sites (PSS) at the MHC-I exon 3
- dS_bird_PSS - synonymous nucleotide substitution rate across 20 most positively selected sites (PSS) at the MHC-I exon 3
- Body_mass (g)
- Clutch_size (number of eggs)
- Residual_lifespan - residual of maximum lifespan (years) against source of data (wild-living vs. captivity), sampling effort, and body mass
- Diet
Minias_et_al_sequence_DATA.fasta file contains sequence data (n = 1777 sequences) used to quantify non-synonymous (dN) and synonymous (dS) nucleotide substitution rates at the MHC-I (n = 28 species).
All sequences were retrieved from GenBank NCBI database. GenBank number and species are provided for each sequence.
Minias_et_al_tree_DATA.phy file contains consensus phylogenetic tree (n = 50 species) generated across a random sample of 1000 alternative trees retrieved from the BirdTree webserver (http://www.birdtree.org).
Sharing/Access information
Not applicable
Code/Software
Minias_et_al_code.txt file contains R code used for the phylogenetically-informed comparative analyses of oxidative physiology and Major Histocompatibility (MHC) genes.