Sub-Populations Within the Major European and African Derived Haplogroups R1b3 and E3a Are Differentiated by Previously Phylogenetically Undefined Y-SNPs

Biomolecular Sciences, Graduate Program in Chemistry, University of Central Florida, Orlando 32816-2366, USA.
Human Mutation (Impact Factor: 5.14). 01/2007; 28(1):97. DOI: 10.1002/humu.9469
Source: PubMed


Single nucleotide polymorphisms on the Y chromosome (Y-SNPs) have been widely used in the study of human migration patterns and evolution. Potential forensic applications of Y-SNPs include their use in predicting the ethnogeographic origin of the donor of a crime scene sample, or exclusion of suspects of sexual assaults (the evidence of which often comprises male/female mixtures and may involve multiple perpetrators), paternity testing, and identification of non- and half-siblings. In this study, we used a population of 118 African- and 125 European-Americans to evaluate 12 previously phylogenetically undefined Y-SNPs for their ability to further differentiate individuals who belong to the major African (E3a)- and European (R1b3, I)-derived haplogroups. Ten of these markers define seven new sub-clades (equivalent to E3a7a, E3a8, E3a8a, E3a8a1, R1b3h, R1b3i, and R1b3i1 using the Y Chromosome Consortium nomenclature) within haplogroups E and R. Interestingly, during the course of this study we evaluated M222, a sub-R1b3 marker rarely used, and found that this sub-haplogroup in effect defines the Y-STR Irish Modal Haplotype (IMH). The new bi-allelic markers described here are expected to find application in human evolutionary studies and forensic genetics.

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Available from: Lynn M Sims, Oct 05, 2015
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    • "obling and Tyler - Smith , 2003 ) , which is also distributed throughout West Asia , Central Asia and South Asia ( Chiaroni et al . , 2009 ) . Other studies have found that most African - Americans and European - Americans in the United States belong to one of the two main sub - haplogroups , which are E1b1a ( 58 – 62% ) and R1b ( 47 – 58 . 3% ) ( Sims et al . , 2007 ; Hammer et al . , 2006 ; Vallone and Butler , 2004 ) . The results from the Providencia and San Andrés paternal Y - STR lineages indicate a similar phenomenon of preserving their African and European ancestry , which is derived from the colonization and slavery processes that took place from 1730 to 1853 . This period also encompassed "
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    ABSTRACT: The Archipelago of San Andrés and Providencia is a Colombian Department in the western waters of the Caribbean Sea. Most of its inhabitants belong to the African-Colombian group known as raizal. This group has unique cultural traits that are derived from centuries of admixture of the primarily African slaves and European colonists. Currently, not much is known about the genetic profile of this population. Therefore, this study aimed to determine the Y-chromosome STR genetic structure and relationship to previously published reference populations. A total of 54 natives from the islands were selected based on the genealogical criterion of having three generations of ancestors born in the Archipelago. Seventeen Y-STRs were analyzed, supplemented by information on the first surname inherited. The genetic substructure hypothesis in the studied islands was tested, and no significant differences were found (p>0.05). Y-chromosome haplogroups were predicted, and E1b1a and R1b were the most commonly found haplogroups. They account for more than 80% of the sample. The E1b1a and R1ba haplogroups are common in the African and European populations, respectively. For comparative genetic analysis, genetic distances were calculated with respect to populations from the Caribbean, Colombia, Europe and Africa. We found greater similarity between the African and Caribbean populations. The surname analysis demonstrated that most of the time, the "raizales" with the same surname also shared the same Y-STR haplotype. This suggests that some kinship relationship exists between participants with the same surname, which was confirmed by the haplotype diversity levels found in the studied islands.
    Homo: internationale Zeitschrift fur die vergleichende Forschung am Menschen 01/2013; 64(1). DOI:10.1016/j.jchb.2012.11.006 · 0.96 Impact Factor
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    • "R1b1b1 lineages are also observed at commensurate levels in Bahamians (at an average frequency of 18.5%), US African Americans (Hammer et al., 2006; Sims et al., 2007), Afro-Ecuadorans (Gonzá lez-Andrade et al., 2007), and Barbadians (Harris et al., 2006). However, when downstream markers within this haplogroup are examined , the collections from Abaco and Long Island exhibit much higher levels of M405 derived chromosomes than US African Americans (Sims et al., 2007), a profile consistent with the European American population examined in the same study. The comparable distributions of the two most common haplogroups, E1b1a-M2 and R1b1b1-M269, in the Bahamian and other New World African populations, especially US African Americans (Table 3), may represent genetic signatures from similar ancestral sources and/or episodes of gene flow between the different countries within the region. "
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    ABSTRACT: Over the past 500 years, the Bahamas has been influenced by a wide array of settlers, some of whom have left marked genetic imprints throughout the archipelago. To assess the extent of each group's genetic contributions, high-resolution Y-chromosome analyses were performed, for the first time, to delineate the patriarchal ancestry of six islands in the Northwest (Abaco and Grand Bahama) and Central (Eleuthera, Exuma, Long Island, and New Providence) Bahamas and their genetic relationships with previously published reference populations. Our results reveal genetic signals emanating primarily from African and European sources, with the predominantly sub-Saharan African and Western European haplogroups E1b1a-M2 and R1b1b1-M269, respectively, accounting for greater than 75% of all Bahamian patrilineages. Surprisingly, we observe notable discrepancies among the six Bahamian populations in their distribution of these lineages, with E1b1a-M2 predominating Y-chromosomes in the collections from Abaco, Exuma, Eleuthera, Grand Bahama, and New Providence, whereas R1b1b1-M269 is found at elevated levels in the Long Island population. Substantial Y-STR haplotype variation within sub-haplogroups E1b1a7a-U174 and E1b1ba8-U175 (greater than any continental African collection) is also noted, possibly indicating genetic influences from a variety of West and Central African groups. Furthermore, differential European genetic contributions in each island (with the exception of Exuma) reflect settlement patterns of the British Loyalists subsequent to the American Revolution.
    American Journal of Physical Anthropology 12/2011; 146(4):594-608. DOI:10.1002/ajpa.21616 · 2.38 Impact Factor
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    • "Populations sampled are either native groups settled in the area where Bantu expansion is thought to have originated or in the regions located in the putative origin of the Western stream. The analysis of paternal lineages was based on recently discovered SNPs (Wilder et al. 2004a; Sims et al. 2007; Karafet et al. 2008), which make our level of resolution higher than in previous studies on the genetic legacy of Bantu expansion (Jobling et al. 2004; Beleza et al. 2005; Wood et al. 2005; Berniell-Lee et al. 2009). The availability of a large and tailored population dataset together with a more-in-depth dissection of genetic variation made it possible to perform an analysis of the relationships between genetic variation, geographical , and linguistic factors in the Bantu area. "
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    ABSTRACT: The current distribution of Bantu languages is commonly considered to be a consequence of a relatively recent population expansion (3-5kya) in Central Western Africa. While there is a substantial consensus regarding the centre of origin of Bantu languages (the Benue River Valley, between South East Nigeria and Western Cameroon), the identification of the area from where the population expansion actually started, the relation between the processes leading to the spread of languages and peoples and the relevance of local migratory events remain controversial. In order to shed new light on these aspects, we studied Y chromosome variation in a broad dataset of populations encompassing Nigeria, Cameroon, Gabon and Congo. Our results evidence an evolutionary scenario which is more complex than had been previously thought, pointing to a marked differentiation of Cameroonian populations from the rest of the dataset. In fact, in contrast with the current view of Bantu speakers as a homogeneous group of populations, we observed an unexpectedly high level of interpopulation genetic heterogeneity and highlighted previously undetected diversity for lineages associated with the diffusion of Bantu languages (E1b1a (M2) sub-branches). We also detected substantial differences in local demographic histories, which concord with the hypotheses regarding an early diffusion of Bantu languages into the forest area and a subsequent demographic expansion and migration towards eastern and western Africa.
    Molecular Ecology 07/2011; 20(13):2693-708. DOI:10.1111/j.1365-294X.2011.05130.x · 6.49 Impact Factor
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