Cryptic MHC polymorphism revealed but not explained by selection on the class IIb peptide-binding region

Area of Science:

• Evolutionary genetics
• Immunogenetics
• Population genetics

Background:

• Major histocompatibility complex (MHC) genes exhibit extreme nucleotide and haplotype diversity, typically maintained by pathogen-driven balancing selection on the peptide-binding region (PBR).
• Recent studies indicate some populations have allele clusters with nearly identical proteins, questioning the functional basis for selection.
• Understanding the mechanisms maintaining nucleotide polymorphism with limited functional variation is crucial.

Purpose of the Study:

• To investigate the maintenance of nucleotide polymorphism in MHC class II DAB genes in wild guppy populations.
• To determine if nucleotide variation can persist with minimal functional divergence.
• To explore the role of gene conversion and extended sequencing in characterizing MHC variation.

Main Methods:

• Sequencing of an extended region (750-850 bp) of MHC class II DAB genes in four wild guppy populations (Poecilia reticulata).
• Analysis of gene conversion events and their impact on sequence homogenization.
• Microsatellite analysis for population demography reconstruction and simulations to test evolutionary models.

Main Results:

• Extended sequencing uncovered 40.9% more alleles than exon 2 alone, highlighting potential underestimation of variation.
• Evidence of gene conversion events homogenizing sequence variation, reducing apparent copy number variation (CNV).
• A cluster of 27 nearly identical sequences showed no signal of selection within the PBR; simulations indicated non-neutral behavior.

Conclusions:

• Selection may operate outside the PBR, potentially on linked immune genes or MHC-associated 'sheltered load'.
• Extended amplicon sizes are recommended for MHC studies to capture cryptic haplotype variation and CNV.
• This approach can help identify other MHC regions under selection beyond the PBR.