Genetic Variation and Population Structure in Native Americans

The Wellcome Trust Sanger Institute, United Kingdom
PLoS Genetics (Impact Factor: 7.53). 12/2007; 3(11):e185. DOI: 10.1371/journal.pgen.0030185
Source: PubMed

ABSTRACT We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians--signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.

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Available from: Maria-Luiza Petzl-Erler, Sep 26, 2015
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    • "In populations with a high level of genetic homogeneity (Ache have one of the lowest levels of genetic heterozygosity in the world; Lewis 2010; Wang et al. 2007), partible paternity may grant women greater leverage in choosing different fathers for successive children. If women indeed benefit from genetic diversity of offspring, co-fathers should be less likely to be close relatives of one another. "
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    ABSTRACT: Hypotheses on the benefits of the practice of partible paternity are tested using demographic data for Ache foragers of Paraguay. Partible paternity refers to the institution of multiple males considered to contribute to the conception of a single offspring. Analyses focus on patterns of primary and secondary co-fatherhood among men, genealogical relationships between co-fathers, and relation between band co-residence and co-fatherhood. Results indicate that men who had more secondary fatherhood also had more primary fatherhood; cofathers are more closely related, on average, than men who are not co-fathers; and co-fathers were also more likely to reside together than men who were not co-fathers, even after controlling for relatedness. Results are most consistent with women choosing co- fathers of offspring in ways that maximize likelihood and amount of investment (multiple investors hypothesis) and men competing for more mates with at least partially affiliative outcomes (mate competition and male alliance hypotheses).
    Current Anthropology 10/2014; 55(5):647-653. DOI:10.1086/678324 · 2.93 Impact Factor
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    • "The inclusion of an individual in a group excluded that individual from being part of any other population. • Genetic markers such as blood group systems: ABO (O for Amerindians and B for the Afro-Caribbeans), rhesus, MNS, P, Kell, Kidd, Duffy, Diego, and Lewis; plasmatic protein systems (albumin, transferrin , haptoglobin, and ceruloplasmin) (Barrantes et al., 1990; Bieber, Bieber, Rodewald, & Barrantes, 1996); single nucleotide polymorphisms (SNPs) (Herrmann et al., 2002); microsatellites (Wang et al., 2007); mitochondrial DNA (Santos et al., 1994) and chromosome Y (Ruiz- Narváez et al., 2005). "
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    ABSTRACT: CYP2D6 differences have already been demonstrated within Latin American populations by the CEIBA.FP Consortium of the Ibero-American Network of Pharmacogenetics (RIBEF, as per the acronym in Spanish). However, within the population of Costa Rica, no research has been conducted until now, even though this population has a trihybrid component ancestry that represents an interesting condition. Thus, the present study was aimed to determine the frequency of Ultra-rapid Metabolizers (UMs) and Poor Metabolizers (PMs) in a Costa Rican population, as well as to determine whether there are differences in the CYP2D6-predicted phenotype frequencies among three Costa Rican groups with different ethnic backgrounds. Additionally, these frequencies of PMs and UMs obtained were compared with Ibero-American populations published data. Finally, we also aimed to describe allele frequencies among different Costa Rican ethnic groups. This research has been undertaken within the framework of the RIBEF CEIBA Consortium studies on Latin American populations. A total of 385 individuals were included in the study: 139 mestizos, 197 Amerindians, and 49 Afro-Caribbeans. CYP2D6 genotypes were determined by XL-PCR and Real-Time PCR. The CYP2D6 variant alleles and *41 were also determined. For the entire Costa Rican population, the frequency of PMs and UMs was 6% and 6.5%, respectively. The percentage of UMs in the mestizo population was higher than in the Amerindian population. CYP2D6 UMs vary from 3.6% to 10.1% and PMs from 1.4% to 10.2% among three Costa Rican groups. The highest frequencies of UMs (10.1%) and PMs (10.2%) were found in the mestizo and Amerindian populations, respectively. In conclusion, the frequencies of UMs and PMs for CYP2D6 varied widely across the mestizo, Amerindian and Afro-Caribbean Costa Rican populations. Future research in this population should be oriented to identify new CYP2D6 variants through sequencing methods, as well as to determine CYP2D6 phenotype, in order to establish the phenotype-genotype relation. Finally, further studies involving genetic markers of ancestry are needed in the Costa Rican population. Rev. Biol. Trop. 62 (4): 1659-1671. Epub 2014 December 01.
    Revista de biologia tropical 07/2014; 62(4):1659-1671. DOI:10.15517/rbt.v62i4.12916 · 0.52 Impact Factor
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    • "These so-called ‘founder lineages’ have been used to describe the demographic history of Native American populations and to shed light on the timing of the entry into and spread throughout the Americas [4]–[6]. The fact that the mtDNAs of all human populations native to the Americas can be assigned to one of the founder lineages pertains to stochastic events that would have affected the initial colonizers of the Americas [7]. The low genetic variation found in modern Native American groups is believed to be due to either population bottlenecks or genetic drift [8], [9]. "
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    ABSTRACT: Phylogeographic studies have described a reduced genetic diversity in Native American populations, indicative of one or more bottleneck events during the peopling and prehistory of the Americas. Classical sequencing approaches targeting the mitochondrial diversity have reported the presence of five major haplogroups, namely A, B, C, D and X, whereas the advent of complete mitochondrial genome sequencing has recently refined the number of founder lineages within the given diversity to 15 sub-haplogroups. We developed and optimized a SNaPshot assay to study the mitochondrial diversity in pre-Columbian Native American populations by simultaneous typing of 26 single nucleotide polymorphisms (SNPs) characterising Native American sub-haplogroups. Our assay proved to be highly sensitive with respect to starting concentrations of target DNA and could be applied successfully to a range of ancient human skeletal material from South America from various time periods. The AmericaPlex26 is a powerful assay with enhanced phylogenetic resolution that allows time- and cost-efficient mitochondrial DNA sub-typing from valuable ancient specimens. It can be applied in addition or alternative to standard sequencing of the D-loop region in forensics, ancestry testing, and population studies, or where full-resolution mitochondrial genome sequencing is not feasible.
    PLoS ONE 03/2014; 9(3):e93292. DOI:10.1371/journal.pone.0093292 · 3.23 Impact Factor
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