Annals of Human Genetics

An Asian–Native American paternal lineage identified by RPS4Y resequencing and by microsatellite haplotyping

A. W. BERGEN a1c1p1, C.-Y. WANG a1, J. TSAI a1, K. JEFFERSON a1, C. DEY a1, K. D. SMITH a2, S.-C. PARK a3, S.-J. TSAI a4 and D. GOLDMAN a1
a1 Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, Park 451, 12420 Parklawn Drive, Rockville, MD 20852 USA
a2 Kennedy Krieger Institute, Johns Hopkins University, Baltimore, MD 21205 USA
a3 Department of Biochemistry, College of Medicine, Seoul National University, Chongro-Ku, Seoul 110-799, Korea
a4 Taipei Blood Center, Taipei 100, Taiwan


Human paternal population history was studied in 9 populations [three Native American, three Asian, two Caucasian and one African-derived sample(s)] using sequence and short tandem repeat haplotype diversity within the non-pseudoautosegmal region of the Y chromosome. Complete coding and additional flanking sequences (949 base pairs) of the RPS4Y locus were determined in 59 individuals from three of the populations, revealing a nucleotide diversity of 0.0147%, consistent with previous estimates from Y chromosome resequencing studies. One RPS4Y sequence variant, 711C>T, was polymorphic in Asian and Native American populations, but not in African and Caucasian population samples. The RPS4Y 711C>T variant, a second unique sequence variant at DYS287 and nine Y chromosome short tandem repeat (YSTR) loci were used to analyze the evolution of Y chromosome lineages. Three unambiguous lineages were defined in Asian, Native American and Jamaican populations using sequence variants at RPS4Y and DYS287. These lineages were independently supported by the haplotypes defined solely by YSTR alleles, demonstrating the haplotypes constructed from YSTRs can evaluate population diversity, admixture and phylogeny.

(Received September 23 1998)
(Accepted February 7 1999)

c1 Corresponding author.
p1 Current address: Genetic Epidemiology Branch/DCEG/NCI, EPS 7110, 6120 Executive Boulevard, Rockville, MD 20852 USA. Tel: (301) 402-9529, Fax: (301) 402-4489. Email: