December 18, 2005

Y-chromosome haplogroups in US populations

A new comprehensive study of US Y-chromosomal haplogroups is published in Forensic Science International. US populations, with the exception of Native Americans, are usually neglected by researchers, because they have very little to offer in the reconstruction of ancient population movements which are the focus of many papers.

For the US population as a whole:
The most common haplogroup is R-M269 (37.8%), which is found in all of the ethnic groups. This haplogroup predominates in Western European populations [23]. E-P1, the second most frequent haplogroup in the U.S. (17.7%), is the most common haplogroup in West African populations [24]. It is found at high frequencies in our AA samples, and at lower frequencies in HA samples from the Eastern U.S. (Fig. 1). Three haplogroups that originate in Northern and Western European populations include I-P30 (6.1%), the third most common haplogroup in our U.S. sample, I-P19 (2.8%) and I-P37 (1.6%). Haplogroups that likely originate in Eastern and Southern European populations are also present in our U.S. database, including R-M17 (3.4%), E-M78 (2.4%), G-P15 (2.4%), and J-M172 (1.5%). The fourth and fifth most frequent haplogroups in our database, Q-P36 (5.9%) and Q-M3 (5.8%), along with C-P39 (1.5%), are founding Native-American Y chromosomes [30]. These haplogroups are frequent in our NA and HA samples, and are found at low frequency in our AA, EA, and SA samples. Asian-derived chromosomes, primarily in haplogroups O and N, are extremely rare in all but our SA sample.

MDS plot showing some of the differences between states:

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Forensic Science International (advance access)

Population structure of Y chromosome SNP haplogroups in the United States and forensic implications for constructing Y chromosome STR databases

Michael F. Hammer et al.


A set of 61 Y chromosome single-nucleotide-polymorphisms (Y-SNPs) is typed in a sample of 2517 individuals from 38 populations to infer the geographic origins of Y chromosomes in the United States and to test for paternal admixture among African-, European-, Hispanic-, Asian-, and Native-Americans. All of the samples were previously typed with the 11 core U.S. Y chromosome short tandem repeats (Y-STRs) recommended by SWGDAM, which revealed high levels of among ethnic group variation and low levels of among-population-within-ethnic-group variation. Admixture estimates vary greatly among populations and ethnic groups. The frequencies of non-European (3.4%) and non-Asian (4.5%) Y chromosomes are generally low in European–American and Asian–American populations, respectively. The frequencies of European Y chromosomes in Native-American populations range widely (i.e., 7–89%) and follow a West to East gradient, whereas they are relatively consistent in African–American populations (26.4 ± 8.9%) from different locations. The European (77.8 ± 9.3%) and Native-American (13.7 ± 7.4%) components of the Hispanic paternal gene pool are also relatively constant among geographic regions; however, the African contribution is much higher in the Northeast (10.5 ± 6.4%) than in the Southwest (1.5 ± 0.9%) or Midwest (0%). To test for the effects of inter-ethnic admixture on the structure of Y-STR diversity in the U.S., we perform subtraction analyses in which Y chromosomes inferred to be admixed by Y-SNP analysis are removed from the database and pairwise population differentiation tests are implemented on the remaining Y-STR haplotypes. Results show that low levels of heterogeneity previously observed between pairs of Hispanic-American populations disappear when African-derived chromosomes are removed from the analysis. This is not the case for an unusual sample of European–Americans from New York City when its African-derived chromosomes are removed, or for Native-American populations when European-derived chromosomes are removed. We infer that both inter-ethnic admixture and population structure in ancestral source populations may contribute to fine scale Y-STR heterogeneity within U.S. ethnic groups.


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