Class I MHC polymorphism and evolution in endangered California Chinook and other Pacific salmon

Area of Science:

• Population genetics
• Molecular evolution
• Immunogenetics

Background:

• The Sacramento River winter-run Chinook salmon (Oncorhynchus tschawytscha) is an endangered population facing significant genetic challenges.
• Major histocompatibility complex (MHC) genes are crucial for immune response and exhibit high diversity in vertebrates.
• Exon 2 of MHC class I genes encodes the peptide-binding region, a key area for immune recognition.

Purpose of the Study:

• To investigate the MHC class I exon 2 genetic diversity within the endangered Sacramento River winter-run Chinook salmon population.
• To understand the evolutionary history and selection pressures shaping this critical immune gene region.

Main Methods:

• Sequencing of twelve MHC class I exon 2 alleles from a winter-run Chinook salmon sample.
• Phylogenetic analysis to determine the evolutionary relationships of these alleles among Pacific salmon species.
• Analysis of synonymous and nonsynonymous distances to infer selection pressures.

Main Results:

• Twelve MHC class I exon 2 sequences were identified, descending from two of six major allelic lineages found in Pacific salmon.
• Nine alleles belong to a lineage diversifying 8 million years ago, predating Chinook speciation.
• High nonsynonymous distance in the peptide-binding region suggests strong balancing selection (selection coefficient = 0.038) maintaining functional diversity.

Conclusions:

• Ancient balancing selection has preserved functional diversity in the MHC class I exon 2 peptide-binding region over millions of years.
• This genetic variation persists despite recent population declines and increased genetic drift in the endangered winter-run Chinook salmon.
• The findings highlight the long-term evolutionary forces maintaining immune gene diversity in salmonids.