D1S80 Single-Locus Discrimination Among African Populations

Abstract

The highly polymorphic D1S80 locus has no known genetic function. However, this variable number of tandem repeats (VNTR) locus has been highly valuable in forensic identification. In this study we report the allele and genotype frequencies of five African populations (Benin, Cameroon, Egypt, Kenya, and Rwanda), which can be used as databases to help characterize populations and identify individuals. The allele frequencies were used to infer genetic associations through phylogenetic, principal component, and G test statistical analyses. Compliance with Hardy-Weinberg equilibrium expectations was determined as were F ST estimates, theta p values, and power of discrimination assessment for each population. Our analyses of 28 additional populations demonstrate that the D1S80 locus alone can be used to discriminate geographic and ethnic groups. We have generated databases useful for human identification and phylogenetic studies. The D1S80 locus is found in the telomeric region of the p arm of chromosome 1 at position 1p36-p35. Since it was first characterized (Nakamura et al. 1988), the D1S80 locus has been widely used in phylogenetic studies, forensic analysis, and paternity testing. It has been described as the most characterized amplified fragment length polymorphism (AmpliFLP) locus (Budowle et al. 1996). The D1S80 marker locus has a variable number of tandem repeats (VNTR) of a 16-nucleotide unit and shows a high degree of polymorphism. The observed heterozygosity for this locus has been reported to be as high as 87.6% (Budowle et al. 1997; Duncan 1996). A previous study has shown that the D1S80 locus alone allows for the discrimination of geographic and ethnic groups (Duncan et al. 1996). The patterns of genetic variation in African populations are multifaceted and complex. Interactions between the Arab world and African civilizations in North, East, and West Africa as well as the Bantu expansion, which changed the demographic and language map of central and southern Africa, are partially responsible for the genetic diversity of these groups (Holden 2002

Minisatellite DNA Markers in Population Studies

“…Subsequently, taking into account the extensive data available on the D1S80 polymorphism among African populations, we compared the D1S80 allele patterns of Russians and Yakuts with our African samples. Although our African DNAs were collected from students who presumably came from all over sub-Saharan Africa, the final distribution of D1S80 allele frequencies observed did not differ significantly from the spectra described for African populations in general (Herrera et al, 2004).…”

“…The authors presented the spectra of D1S80 allele frequencies and, using the method of factor correspondence analysis, revealed clear-cut distinctions between European, Asian, Afro-American, American Indian, and Indian ethnic groups. Subsequently, the D1S80 polymorphism was analyzed in 33 world populations with a focus on the variability of the marker in sub-Saharan African populations (aboriginals of Africa) and a population of Arabian origin (the population of Egypt) (Herrera et al, 2004). As the differentiation of ethnic groups based on D1S80 data provided a very good description of the peculiarities of the groups, which were demonstrated previously via the analysis of biochemical markers, and conforms with the geographical locations of the populations with the peculiarities of their origin, the authors drew a conclusion allowing the applicability of only one marker, D1S80, to the study of the phylogenetic interrelationships of populations (Herrera et al, 2004).…”

“…Some D1S80 alleles occur quite frequently, e.g., the total frequency of allele variants with 18 and 24 repeats is as high as 70% (Das & Mastana, 2003, Herrera et al, 2004, Walsh & Eckhoff , 2007. The first major allele, which contains 18 repeat units, occurs in 5.5-9% of sub-Saharan African populations, in 15-21% of Asian populations, and in 13-35% of European populations.…”

“…The first major allele, which contains 18 repeat units, occurs in 5.5-9% of sub-Saharan African populations, in 15-21% of Asian populations, and in 13-35% of European populations. The second major allele (24 repeats) has a frequency of 26-45% in Europeans, 6-29% in sub-Saharan Africans, and 17-24% in Asians (Das & Mastana, 2003;Duncan et al, 1996-97;Budowle et al, 1991Budowle et al, , 1995Herrera et al, 2004;Sajantila et al, 1992).…”

The Peopling of the Bahamas: A Phylogeographical Perspective

“…Historical accounts for the West Indies indicate extensive gene flow from continental Africa during the period of the Transatlantic slave trade in addition to varying degrees of genetic input from European, Asian, and/or other sources Herrera et al, 2004;Benn-Torres et al, 2008 and Jamaica, respectively], but this disparity should be tempered considering the unequal distribution of loci within the two categories. The New World Africans also exhibit the highest intra-population variance level of any group examined (Table 5).…”