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

D. Garrigan, P. W. Hedrick

Research output: Contribution to journalArticle

42 Citations (Scopus)

Abstract

Twelve MHC class I exon 2 sequences were uncovered in a sample from the endangered Sacramento River winter-run Chinook salmon in the central valley of California. Phylogenetic analysis of the 12 sequences indicates that the alleles descend from two of six major allelic lineages found among four Pacific salmon species. Nine of the 12 alleles belong to an allelic lineage that began diversifying 8 million years ago, just prior to the estimated time of Chinook speciation. The most recent common ancestor of all 12 winter-run alleles is estimated to be 15 million years ago, approximately 5 million years before the radiation of the Pacific salmon species. The average nonsynonymous distance among the peptide binding-region codons of exon 2 for the 12 alleles is significantly higher than the average synonymous distance in these codons. We estimate the symmetrical overdominant selection coefficient against homozygotes for this exon to be 0.038. Thus, strong positive and balancing selection has maintained functional diversity in the peptide-binding region of the exon over millions of years and this variation has not yet been substantially eliminated by increased genetic drift due to the recent dramatic decline in abundance of this Chinook salmon population.

Original languageEnglish (US)
Pages (from-to)483-489
Number of pages7
JournalImmunogenetics
Volume53
Issue number6
DOIs
StatePublished - 2001

Fingerprint

Salmon
Exons
Alleles
Codon
Genetic Drift
Peptides
Homozygote
Rivers
Sequence Analysis
Radiation
Population

Keywords

  • Chinook salmon
  • Major histocompatibility complex
  • Polymorphism
  • Positive selection
  • Substitution rate
  • Trans-species evolution

ASJC Scopus subject areas

  • Immunology
  • Genetics

Cite this

Class I MHC polymorphism and evolution in endangered California Chinook and other Pacific salmon. / Garrigan, D.; Hedrick, P. W.

In: Immunogenetics, Vol. 53, No. 6, 2001, p. 483-489.

Research output: Contribution to journalArticle

Garrigan, D. ; Hedrick, P. W. / Class I MHC polymorphism and evolution in endangered California Chinook and other Pacific salmon. In: Immunogenetics. 2001 ; Vol. 53, No. 6. pp. 483-489.
@article{b1d9a8e173a44bb6ad4f7c712ab090d2,
title = "Class I MHC polymorphism and evolution in endangered California Chinook and other Pacific salmon",
abstract = "Twelve MHC class I exon 2 sequences were uncovered in a sample from the endangered Sacramento River winter-run Chinook salmon in the central valley of California. Phylogenetic analysis of the 12 sequences indicates that the alleles descend from two of six major allelic lineages found among four Pacific salmon species. Nine of the 12 alleles belong to an allelic lineage that began diversifying 8 million years ago, just prior to the estimated time of Chinook speciation. The most recent common ancestor of all 12 winter-run alleles is estimated to be 15 million years ago, approximately 5 million years before the radiation of the Pacific salmon species. The average nonsynonymous distance among the peptide binding-region codons of exon 2 for the 12 alleles is significantly higher than the average synonymous distance in these codons. We estimate the symmetrical overdominant selection coefficient against homozygotes for this exon to be 0.038. Thus, strong positive and balancing selection has maintained functional diversity in the peptide-binding region of the exon over millions of years and this variation has not yet been substantially eliminated by increased genetic drift due to the recent dramatic decline in abundance of this Chinook salmon population.",
keywords = "Chinook salmon, Major histocompatibility complex, Polymorphism, Positive selection, Substitution rate, Trans-species evolution",
author = "D. Garrigan and Hedrick, {P. W.}",
year = "2001",
doi = "10.1007/s002510100352",
language = "English (US)",
volume = "53",
pages = "483--489",
journal = "Immunogenetics",
issn = "0093-7711",
publisher = "Springer Verlag",
number = "6",

}

TY - JOUR

T1 - Class I MHC polymorphism and evolution in endangered California Chinook and other Pacific salmon

AU - Garrigan, D.

AU - Hedrick, P. W.

PY - 2001

Y1 - 2001

N2 - Twelve MHC class I exon 2 sequences were uncovered in a sample from the endangered Sacramento River winter-run Chinook salmon in the central valley of California. Phylogenetic analysis of the 12 sequences indicates that the alleles descend from two of six major allelic lineages found among four Pacific salmon species. Nine of the 12 alleles belong to an allelic lineage that began diversifying 8 million years ago, just prior to the estimated time of Chinook speciation. The most recent common ancestor of all 12 winter-run alleles is estimated to be 15 million years ago, approximately 5 million years before the radiation of the Pacific salmon species. The average nonsynonymous distance among the peptide binding-region codons of exon 2 for the 12 alleles is significantly higher than the average synonymous distance in these codons. We estimate the symmetrical overdominant selection coefficient against homozygotes for this exon to be 0.038. Thus, strong positive and balancing selection has maintained functional diversity in the peptide-binding region of the exon over millions of years and this variation has not yet been substantially eliminated by increased genetic drift due to the recent dramatic decline in abundance of this Chinook salmon population.

AB - Twelve MHC class I exon 2 sequences were uncovered in a sample from the endangered Sacramento River winter-run Chinook salmon in the central valley of California. Phylogenetic analysis of the 12 sequences indicates that the alleles descend from two of six major allelic lineages found among four Pacific salmon species. Nine of the 12 alleles belong to an allelic lineage that began diversifying 8 million years ago, just prior to the estimated time of Chinook speciation. The most recent common ancestor of all 12 winter-run alleles is estimated to be 15 million years ago, approximately 5 million years before the radiation of the Pacific salmon species. The average nonsynonymous distance among the peptide binding-region codons of exon 2 for the 12 alleles is significantly higher than the average synonymous distance in these codons. We estimate the symmetrical overdominant selection coefficient against homozygotes for this exon to be 0.038. Thus, strong positive and balancing selection has maintained functional diversity in the peptide-binding region of the exon over millions of years and this variation has not yet been substantially eliminated by increased genetic drift due to the recent dramatic decline in abundance of this Chinook salmon population.

KW - Chinook salmon

KW - Major histocompatibility complex

KW - Polymorphism

KW - Positive selection

KW - Substitution rate

KW - Trans-species evolution

UR - http://www.scopus.com/inward/record.url?scp=0034802015&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0034802015&partnerID=8YFLogxK

U2 - 10.1007/s002510100352

DO - 10.1007/s002510100352

M3 - Article

C2 - 11685459

AN - SCOPUS:0034802015

VL - 53

SP - 483

EP - 489

JO - Immunogenetics

JF - Immunogenetics

SN - 0093-7711

IS - 6

ER -