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Parolin ML, Real LE, Martinazzo LB, Basso NG. Population genetic analyses of the Powerplex ® Fusion kit in a cosmopolitan sample of Chubut Province (Patagonia Argentina). Forensic Sci Int Genet 2015; 19:221-222. [DOI: 10.1016/j.fsigen.2015.07.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 10/23/2022]
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Valente C, Alvarez L, Marks SJ, Lopez-Parra AM, Parson W, Oosthuizen O, Oosthuizen E, Amorim A, Capelli C, Arroyo-Pardo E, Gusmão L, Prata MJ. Exploring the relationship between lifestyles, diets and genetic adaptations in humans. BMC Genet 2015; 16:55. [PMID: 26018448 PMCID: PMC4445807 DOI: 10.1186/s12863-015-0212-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 04/30/2015] [Indexed: 12/05/2022] Open
Abstract
Background One of the most important dietary shifts underwent by human populations began to occur in the Neolithic, during which new modes of subsistence emerged and new nutrients were introduced in diets. This change might have worked as a selective pressure over the metabolic pathways involved in the breakdown of substances extracted from food. Here we applied a candidate gene approach to investigate whether in populations with different modes of subsistence, diet-related genetic adaptations could be identified in the genes AGXT, PLRP2, MTRR, NAT2 and CYP3A5. Results At CYP3A5, strong signatures of positive selection were detected, though not connected to any dietary variable, but instead to an environmental factor associated with the Tropic of Cancer. Suggestive signals of adaptions that could indeed be connected with differences in dietary habits of populations were only found for PLRP2 and NAT2. Contrarily, the demographic history of human populations seemed enough to explain patterns of diversity at AGXT and MTRR, once both conformed the evolutionary expectations under selective neutrality. Conclusions Accumulated evidence indicates that CYP3A5 has been under adaptive evolution during the history of human populations. PLRP2 and NAT2 also appear to have been modelled by some selective constrains, although clear support for that did not resist to a genome wide perspective. It is still necessary to clarify which were the biological mechanisms and the environmental factors involved as well as their interactions, to understand the nature and strength of the selective pressures that contributed to shape current patterns of genetic diversity at those loci. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0212-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cristina Valente
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal. .,Faculty of Sciences, University of Porto, Porto, Portugal.
| | - Luis Alvarez
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.
| | - Sarah J Marks
- Department of Zoology, University of Oxford, Oxford, UK.
| | - Ana M Lopez-Parra
- Departamento de Toxicología y Legislación Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain.
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria. .,Penn State Eberly College of Science, University Park, Pennsylvania, USA.
| | | | | | - António Amorim
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal. .,Faculty of Sciences, University of Porto, Porto, Portugal.
| | | | - Eduardo Arroyo-Pardo
- Departamento de Toxicología y Legislación Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain.
| | - Leonor Gusmão
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal. .,DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil.
| | - Maria J Prata
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal. .,Faculty of Sciences, University of Porto, Porto, Portugal.
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Muñoz A, Albeza MV, Acreche N, Castro JA, Ramon MM, Picornell A. Allele frequencies of 15 STRs in the Calchaqui Valleys population (North-Western Argentina). Forensic Sci Int Genet 2011; 6:e58-60. [PMID: 21641291 DOI: 10.1016/j.fsigen.2011.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 05/05/2011] [Accepted: 05/07/2011] [Indexed: 10/18/2022]
Abstract
Allele frequencies for 15 short tandem repeat (STR) loci were obtained from a sample of 110 individuals from the Calchaqui Valleys population (North-Western Argentina). The combined power of exclusion and combined power of discriminating for the 15 tested STR loci were 0.999964 and 0.9999999999999998, respectively. Matching probability was 1 in 4.58 × 10(15). Therefore, it may be concluded that the set of 15 STRs included in the AmpF STR Identifiler kit, represents a powerful tool for forensic applications, paternity testing and population genetics studies in the Calchaqui Valleys population.
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Barbosa AAL, Sousa SMB, Abé-Sandes K, Alonso CA, Schneider V, Costa DC, Cavalli IJ, Azevêdo EES. Microsatellite studies on an isolated population of African descent in the Brazilian state of Bahia. Genet Mol Biol 2006. [DOI: 10.1590/s1415-47572006000100004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | - Kiyoko Abé-Sandes
- Universidade Estadual do Sudoeste da Bahia, Brazil; Universidade de São Paulo, Brazil
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Alves S, Rocha J, Amorim A, Prata MJ. Tracing the origin of the most common thiopurine methyltransferase (TPMT) variants: preliminary data from the patterns of haplotypic association with two CA repeats. Ann Hum Genet 2005; 68:313-23. [PMID: 15225157 DOI: 10.1046/j.1529-8817.2004.00104.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Thiopurine methyltransferase (TPMT) is an essential enzyme for normal metabolism of thiopurine drugs. In humans TPMT activity is largely dependent upon genetic variation at the TPMT locus, with TPMT*3A and TPMT*3C being the most frequent mutant alleles associated with reduced activity. TPMT*3C is a widespread allele reaching the highest frequencies in Africans, whereas TPMT*3A is virtually restricted to Caucasian descendent populations. To estimate the time of origin of these two alleles, we analyzed the levels of diversity at two CA repeats flanking the TPMT gene. In accordance to its pattern of geographical distribution, the study of the decay in linkage disequilibrium over time indicated that TPMT*3A was the younger allele. The estimated age was 5700 years, which coincides with the Neolithic, a period characterized by major population expansion that could have been responsible for the spread of TPMT*3A from its place of origin, maybe a western Eurasian population. TPMT*3C was found to have arisen earlier, roughly 14000 years ago, which could explain the worldwide dispersal of TPMT*3C.
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Fernandes AT, Velosa R, Jesus J, Carracedo A, Brehm A. Genetic differentiation of the Cabo Verde archipelago population analysed by STR polymorphisms. Ann Hum Genet 2003; 67:340-7. [PMID: 12914568 DOI: 10.1046/j.1469-1809.2003.00029.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Allele frequencies for 17 STR loci were analyzed in a sample of unrelated males from the Cabo Verde Archipelago. The samples were gathered in such a way that the origin of the subjects was perfectly identified, and they could be included in one of the leeward or windward groups of islands. This study reveals that there are significant differences between both groups of islands, and between Cabo Verdeans and other populations from sub-Sahara Africa including the Guineans, the most probable source population for Cabo Verdeans. This study confirms mtDNA data and, together with HLA and Y chromosome data already published, shows that the Cabo Verde population is sub-structured and atypical, diverging substantially from mainland sub-Saharan populations. Overall these differences are most probably due to admixture between sub-Saharan slaves brought into the islands and other settlers of European origin. In the absence of a clear indication of a different ethnic composition of the first sub-Saharan settlers of Cabo Verde, the differentiation exhibited in both groups of islands can be most probably be attributed to genetic drift.
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Affiliation(s)
- A T Fernandes
- Human Genetics Laboratory, Centre of Macaronesian Studies, University of Madeira, Penteada, 9000 Funchal, Portugal
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Tofanelli S, Boschi I, Bertoneri S, Coia V, Taglioli L, Franceschi MG, Destro-Bisol G, Pascali V, Paoli G. Variation at 16 STR loci in Rwandans (Hutu) and implications on profile frequency estimation in Bantu-speakers. Int J Legal Med 2003; 117:121-6. [PMID: 12690511 DOI: 10.1007/s00414-002-0349-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2002] [Accepted: 10/23/2002] [Indexed: 11/29/2022]
Abstract
A data set of 16 autosomal STRs (the 13 CODIS loci plus HumCD4, HumFES, HumF13A1) was obtained in a sample of 52 unrelated Hutus from Rwanda. Genotypes at all loci met Hardy-Weinberg expectations with the exception of HumCSF1PO. No significant evidence of association across alleles at independent loci was obtained. Statistical parameters demonstrated the forensic usefulness of the analysed systems (combined PE=0.9999996, combined PD=1:2.27 x 10(18)). Pairwise comparisons showed that the Hutu gene pool differs substantially from that of other Bantu-speaking populations suggesting the use of ethnic-specific population databases in forensic casework analysis. The introduction of a non-negligible bias was confirmed by calculating the differences between multiple-locus profile frequencies of western and eastern Bantoids using local and non-local reference databases.
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Affiliation(s)
- Sergio Tofanelli
- Department of Ethology, Ecology and Evolution, Anthropology Unit, University of Pisa, Via S. Maria 55, 56126, Pisa, Italy.
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Gonçalves R, Jesus J, Fernandes AT, Brehm A. Genetic profile of a multi-ethnic population from Guiné-Bissau (west African coast) using the new PowerPlex 16 System kit. Forensic Sci Int 2002; 129:78-80. [PMID: 12231003 DOI: 10.1016/s0379-0738(02)00204-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Allele and haplotype frequencies of 15 chromosome STR loci included in the kit PowerPlex16 System from Promega, were determined in a sample of unrelated males from Guiné-Bissau, a country from the west African coast. All individuals were subjected to an interview in order to make sure that their ancestors belonged to the same ethnic group. This way we intended to look for possible inter-ethnic differences. PowerPlex 16 includes STRs not studied before in any multi-ethnic population. The kit includes two new allele markers (Penta D and Penta E), which are very useful either in forensics or population genetic studies. The Guinean population presents significant differences when compared with other African populations.
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Affiliation(s)
- Rita Gonçalves
- Human Genetics Laboratory, Center of Macaronesian Studies, University of Madeira, Penteada, 9000, Funchal, Portugal
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