The evolution and population genetics of the ALDH2 locus: random genetic drift, selection, and low levels of recombination.
The catalytic deficiency of human aldehyde dehydrogenase 2 (ALDH2) is caused by a nucleotide substitution (G1510A; Glu487Lys) in exon 12 of the ALDH2 locus. This SNP, and four non-coding SNPs, including one in the promoter, span 40 kb of ALDH2; these and one downstream STRP have been tested in 37 worldwide populations. Only four major SNP-defined haplotypes account for almost all chromosomes in all populations. A fifth haplotype harbours the functional variant and is only found in East Asians. Though the SNPs showed virtually no historic recombination, LD values are quite variable because of varying haplotype frequencies, demonstrating that LD is a statistical abstraction and not a fundamental aspect of the genome, and is not a function solely of recombination. Among populations, different sets of tagging SNPs, sometimes not overlapping, can be required to identify the common haplotypes. Thus, solely because haplotype frequencies vary, there is no common minimum set of tagging SNPs globally applicable. The Fst values of the promoter region SNP and the functional SNP were about two S.D. above the mean for a reference distribution of 117 autosomal biallelic markers. These high Fst values may indicate selection has operated at these or very tightly linked sites.
Oota
Hiroki
H
Department of Genetics, Yale University School of Medicine, 333 Cedar Street, PO Box 208005, New Haven, CT 06520-8005, USA.
Pakstis
Andrew J
AJ
Bonne-Tamir
Batsheva
B
Goldman
David
D
Grigorenko
Elena
E
Kajuna
Sylvester L B
SL
Karoma
Nganyirwa J
NJ
Kungulilo
Selemani
S
Lu
Ru-Band
RB
Odunsi
Kunle
K
Okonofua
Friday
F
Zhukova
Olga V
OV
Kidd
Judith R
JR
Kidd
Kenneth K
KK
D000444:Aldehyde Dehydrogenase / Q000235:genetics*; D000071396:Aldehyde Dehydrogenase, Mitochondrial; D000483:Alleles; D000818:Animals; D019143:Evolution, Molecular; D005787:Gene Frequency; D040961:Genetic Drift; D005838:Genotype; D006239:Haplotypes; D015186:Hominidae / Q000235:genetics; D006801:Humans; D015810:Linkage Disequilibrium; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D012641:Selection, Genetic; D020080:Tandem Repeat Sequences
C096127:ALDH2 protein, human; D000444:Aldehyde Dehydrogenase; D000071396:Aldehyde Dehydrogenase, Mitochondrial