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The origin of the contribution of uniparental heritage were analyzed in 615 samples of individuals proceeding from 13 towns classified according to historic differences in their emergence and development as African-derived, European-derived, and admixed/urban. Mitochondrial and Y-chromosome haplogroups were identified by PCR-restriction fragment length polymorphism. The results were compared with previous estimates of admixture made with autosomal markers and with historic aspects. The results show a predominantly indigenous genetic contribution through the female, being more prevalent in urban populations; the African contribution, although dispersed, presents a larger concentration in the African-derived towns, whereas the European contribution is limited to populations with this origin, reflecting isolation and the conservation of the distribution pattern of genes of the Colonial era. With regard to admixture through males, it is almost exclusively of European origin, whereas the African contribution is basically concentrated in the African-derived towns, and the Amerindian lineages are almost nonexistent. The genome of paternal heredity, as opposed to the autosomal and the mitochondrial, shows a homogeneous pattern of admixture that is independent of the origin of the population studied, suggesting that European genes have been introduced into the Venezuelan population through male immigrations, whereas the indigenous contribution has been preserved in the Venezuelan genetic pool through the women. These results provide evidence of the heterogeneity in the genetic origin of the Venezuelan population, which should be taken into account in forensic and epidemiologic genetic studies.
Bitter taste is one of the most important senses alerting humans to noxious foods. In gatherer communities, sensitivity to bitterness is presumably advantageous because of various noxious plants. TAS2R16 is the gene coding the taste receptor molecules for some of the most common toxins in plants. A previous study of this gene indicated selection has increased the frequency of a derived allele in this gene that arose before the human expansion out of Africa. We have applied a different methodology for detecting selection, the Long Range Haplotype (LRH) analysis, to TAS2R16 in a larger sampling of populations from around the world. The haplotype with the derived alleles at both the functional polymorphism and a polymorphism in the regulatory region of TAS2R16 showed evidence for recent positive selection in most of the Eurasian populations, though the highest selection signal occurs in Mbuti Pygmies, an African hunter-gatherer group. In Eurasia, only populations of Mesopotamia and the southeast coast of China have no signals of selection. The evidence of recent selection found in most Eurasian populations differs from the geographic pattern seen in the earlier study of selection. One can speculate that the difference may result from a gathering lifestyle extending into the most recent 10,000 yrs and the need to recognize newly encountered bitter natural toxins as populations expanded into new environments and the biota changes with the ending of the most recent ice age. Alternatively, the promoter region variant may be a marker for altered function beyond what the derived amino acid allele conferred.
The aim of the present study is to document the evolution of the lactase persistence trait in Central Asia, a geographical area that is thought to have been a region of long-term pastoralism. Several ethnic groups co-exist in this area: Indo-Iranian speakers who are traditionally agriculturist (Tajik) and Turkic speakers who used to be nomadic herders (Kazakh, Karakalpak, Kyrgyz, Turkmen). It was recently demonstrated that horse milking practice existed in the Botai culture of Kazakhstan as early as 5,500 BP (Outram et al. 2009). However, the frequency of the lactase persistence trait and its genetic basis in Central Asian populations remain largely unknown. We propose here the first genotype-phenotype study of lactase persistence in Central Asia based on 183 individuals, as well as the estimation of the time of expansion of the lactase-persistence associated polymorphism. Our results show a remarkable genetic-phenotypic correlation, with the causal polymorphism being the same than in Europe (-13.910C>T, rs4988235). The lactase persistence trait is at low frequency in these populations: between 25% and 32% in the Kazakh population (traditionally herders), according to phenotype used, and between 11% and 30% in the Tajiko-Uzbek population (agriculturalists). The difference in lactase persistence between populations, even if small, is significant when using individuals concordant for both excretion of breath hydrogen and the lactose tolerance blood glucose test phenotypes (P = 0.018, 25% for Kazakh vs. 11% for Tajiko-Uzbeks), and the difference in frequency of the -13.910*T allele is almost significant (P = 0.06, 30% for Kazakhs vs. 19% for Tajiko-Uzbeks). Using the surrounding haplotype, we estimate a date of expansion of the T allele around 6,000–12,000 yrs ago, which is consistent with archaeological records for the emergence of agropastoralism and pastoralism in Central Asia.
Population surname structure in northeastern Italy municipalities, in which small Slovenian-speaking groups are present, are compared with neighboring populations of both Italian and Slovenian nationality. In the early 20th century those municipalities were part of the Italian territory and underwent a massive Italianization process that led to the mutation of the original Slovenian surnames into a derived Italian form. In order to track surname relationships among the examined communities, two different similarity analyses were performed: the first using the surnames as they are recorded in the Italian and Slovenian official telephone directories, and the second restoring the Italianized Slovenian surnames to their original form and then recalculating the populations' similarity. Both comparisons evidence a separation that depends on nationality, which is less marked after restoring surnames to their original form. Geographical elements, older historical events, and socioeconomic traits allow interpretation of these results.
The Austroasiatic linguistic family disputes its origin between two geographically distant regions of Asia, India, and Southeast Asia, respectively. As genetic studies based on classical and gender-specific genetic markers provided contradictory results to this debate thus far, we investigated the HLA diversity (HLA-A, -B, and -DRB1 loci) of an Austroasiatic Munda population from Northeast India and its relationships with other populations from India and Southeast Asia. Because molecular methods currently used to test HLA markers often provide ambiguous results due to the high complexity of this polymorphism, we applied two different techniques (reverse PCR-SSO typing on microbeads arrays based on Luminex technology, and PCR-SSP typing) to type the samples. After validating the resulting frequency distributions through the original statistical method described in our companion article (Nunes et al. 2011), we compared the HLA genetic profile of the sampled Munda to those of other Asiatic populations, among which Dravidian and Indo-European-speakers from India and populations from East and Southeast Asia speaking languages belonging to different linguistic families.
We showed that the Munda from Northeast India exhibit a peculiar genetic profile with a reduced level of HLA diversity compared to surrounding Indian populations. They also exhibit less diversity than Southeast Asian populations except at locus DRB1. Several analyses using genetic distances indicate that the Munda are much more closely related to populations from the Indian subcontinent than to Southeast Asian populations speaking languages of the same Austroasiatic linguistic family. On the other hand, they do not share a closer relationship with Dravidians compared with Indo-Europeans, thus arguing against the idea that the Munda share a common and ancient Indian origin with Dravidians. Our results do not favor either a scenario where the Munda would be representative of an ancestral Austroasiatic population giving rise to an eastward Austroasiatic expansion to Southeast Asia. Rather, their peculiar genetic profile is better explained by a decrease in genetic diversity through genetic drift from an ancestral population having a genetic profile similar to present-day Austroasiatic populations from Southeast Asia (thus suggesting a possible southeastern origin), followed by intensive gene flow with neighboring Indian populations. This conclusion is in agreement with archaeological and linguistic information. The history of the Austroasiatic family represents a fascinating example where complex interactions among culturally distinct human populations occurred in the past.
The development of molecular typing techniques applied to the study of population genetic diversity originates data with increasing precision but at the cost of some ambiguities. As distinct techniques may produce distinct kinds of ambiguities, a crucial issue is to assess the differences between frequency distributions estimated from data produced by alternative techniques for the same sample. To that aim, we developed a resampling scheme that allows evaluating, by statistical means, the significance of the difference between two frequency distributions. The same approach is then shown to be applicable to test selective neutrality when only sample frequencies are known. The use of these original methods is presented here through an application to the genetic study of a Munda human population sample, where three different HLA loci were typed using two different molecular methods (reverse PCR-SSO typing on microbeads arrays based on Luminex technology and PCR-SSP typing), as described in details in the companion article by Riccio et al. [The Austroasiatic Munda population from India and its enigmatic origin: An HLA diversity study. Hum. Biol. 38:405–435 (2011)]. The differences between the frequency estimates of the two typing techniques were found to be smaller than those resulting from sampling. Overall, we show that using a resampling scheme in validating frequency estimates is effective when alternative frequency estimates are available. Moreover, resampling appears to be the unique way to test selective neutrality when only frequency data are available to describe the genetic structure of populations.