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Espitia Fajardo M, Rivera Franco N, Braga Y, Barreto G. New Y-SNPs in QM3 indigenous populations of Colombia. PLoS One 2023; 18:e0294516. [PMID: 38055663 PMCID: PMC10699635 DOI: 10.1371/journal.pone.0294516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/01/2023] [Indexed: 12/08/2023] Open
Abstract
In evolutionary studies of human populations based on the Y chromosome, the majority of Native Americans belong to the QM3 lineage. Therefore, to study the history of groups inhabiting northern South America, it is necessary to have a higher resolution of the tree. The objective of this work was to identify new SNPs of the QM3 lineage that would allow the evaluation of the phylogenetic relationships between Andean and Amazonian populations of Colombia. Sequences previously obtained from two Y chromosomes of Amazonian populations were used, from which 13 potential SNPs were selected and typed in 171 Amazonian samples from the Vaupés region and in 60 samples from the Pasto, Nasa, Embera, Arhuaco and Kogüi ethnic groups of the Andean region. In addition, the main SNPs/markers (L56, L54, M346, M848, Z780, CTS11780) defining autochthonous Q lineages were typed, along with others defined by different SNPs/markers as reported in the literature (CTS11357, SA05, Z19319, Z5915, and Z19384). It was found that all the new SNPs are present in the Amazonian samples and only 2 of them are shared with the Embera, Nasa and Pasto, but none with the Kogüi and Arhuaco from the northern Andes, in the Colombian Caribbean. Combining the 13 variants of the present study with 14 previously reported and using TMRCA, a new QM3 tree proposal is generated. This method makes it possible to increase the number of sublineages of QM3 with a higher resolution and to detect differences between the different populations of Vaupés in the Amazon, as in the case of the Kubeos and Pisamiras, the latter of which is in grave danger of extinction. These new sublineages are useful for microevolutionary studies of the Amerindian populations of South America.
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Affiliation(s)
- Marisol Espitia Fajardo
- Laboratory of Human Molecular Genetics, Biology Department, Universidad del Valle, Cali, Colombia
| | - Nelson Rivera Franco
- Laboratory of Human Molecular Genetics, Biology Department, Universidad del Valle, Cali, Colombia
| | - Yamid Braga
- Laboratory of Human Molecular Genetics, Biology Department, Universidad del Valle, Cali, Colombia
- Research Group in Biology, Languages and History, IMGB, Corpodihva, Mitú, Colombia
| | - Guillermo Barreto
- Laboratory of Human Molecular Genetics, Biology Department, Universidad del Valle, Cali, Colombia
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Joerin-Luque IA, Augusto DG, Calonga-Solís V, de Almeida RC, Lopes CVG, Petzl-Erler ML, Beltrame MH. Uniparental markers reveal new insights on subcontinental ancestry and sex-biased admixture in Brazil. Mol Genet Genomics 2022; 297:419-435. [DOI: 10.1007/s00438-022-01857-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
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3
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Azulay RSDS, Porto LC, Silva DA, Tavares MDG, Reis RMDF, Nascimento GC, Damianse SDSP, Rocha VCDC, Magalhães M, Rodrigues V, Carvalho PRVB, Faria MDS, Gomes MB. Genetic ancestry inferred from autosomal and Y chromosome markers and HLA genotypes in Type 1 Diabetes from an admixed Brazilian population. Sci Rep 2021; 11:14157. [PMID: 34239025 PMCID: PMC8266844 DOI: 10.1038/s41598-021-93691-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 06/29/2021] [Indexed: 12/19/2022] Open
Abstract
This study aimed to investigate the relationship between genetic ancestry inferred from autosomal and Y chromosome markers and HLA genotypes in patients with Type 1 Diabetes from an admixed Brazilian population. Inference of autosomal ancestry; HLA-DRB1, -DQA1 and -DQB1 typifications; and Y chromosome analysis were performed. European autosomal ancestry was about 50%, followed by approximately 25% of African and Native American. The European Y chromosome was predominant. The HLA-DRB1*03 and DRB1*04 alleles presented risk association with T1D. When the Y chromosome was European, DRB1*03 and DRB1*04 homozygote and DRB1*03/DRB1*04 heterozygote genotypes were the most frequent. The results suggest that individuals from Maranhão have a European origin as their major component; and are patrilineal with greater frequency from the R1b haplogroup. The predominance of the HLA-DRB1*03 and DRB1*04 alleles conferring greater risk in our population and being more frequently related to the ancestry of the European Y chromosome suggests that in our population, the risk of T1D can be transmitted by European ancestors of our process miscegenation. However, the Y sample sizes of Africans and Native Americans were small, and further research should be conducted with large mixed sample sizes to clarify this possible association.
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Affiliation(s)
- Rossana Santiago de Sousa Azulay
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA/EBSERH), Rua Barão de Itapary, 227, Centro, São Luís, Maranhão, 65020-070, Brazil.
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís, Brazil.
| | - Luís Cristóvão Porto
- Histocompatibility and Cryopreservation Laboratory (HLA), Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dayse Aparecida Silva
- DNA Diagnostic Laboratory (LDD), Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria da Glória Tavares
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA/EBSERH), Rua Barão de Itapary, 227, Centro, São Luís, Maranhão, 65020-070, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís, Brazil
| | | | - Gilvan Cortês Nascimento
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA/EBSERH), Rua Barão de Itapary, 227, Centro, São Luís, Maranhão, 65020-070, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís, Brazil
| | - Sabrina da Silva Pereira Damianse
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA/EBSERH), Rua Barão de Itapary, 227, Centro, São Luís, Maranhão, 65020-070, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís, Brazil
| | - Viviane Chaves de Carvalho Rocha
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA/EBSERH), Rua Barão de Itapary, 227, Centro, São Luís, Maranhão, 65020-070, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís, Brazil
| | - Marcelo Magalhães
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís, Brazil
- Clinical Research Center of the University Hospital of the Federal University of Maranhão (CEPEC - HUUFMA), São Luís, Brazil
| | - Vandilson Rodrigues
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís, Brazil
| | - Paulo Ricardo Vilas Boas Carvalho
- Histocompatibility and Cryopreservation Laboratory (HLA), Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Manuel Dos Santos Faria
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA/EBSERH), Rua Barão de Itapary, 227, Centro, São Luís, Maranhão, 65020-070, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís, Brazil
- Clinical Research Center of the University Hospital of the Federal University of Maranhão (CEPEC - HUUFMA), São Luís, Brazil
| | - Marília Brito Gomes
- Diabetes Unit, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
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Schaan AP, Gusmão L, Jannuzzi J, Modesto A, Amador M, Marques D, Rabenhorst SH, Montenegro R, Lopes T, Yoshioka FK, Pinto G, Santos S, Costa L, Silbiger V, Ribeiro-Dos-Santos Â. New insights on intercontinental origins of paternal lineages in Northeast Brazil. BMC Evol Biol 2020; 20:15. [PMID: 31996123 PMCID: PMC6990597 DOI: 10.1186/s12862-020-1579-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/09/2020] [Indexed: 12/29/2022] Open
Abstract
Background The current Brazilian population is the product of centuries of admixture between intercontinental founding groups. Although previous results have revealed a heterogeneous distribution of mitochondrial lineages in the Northeast region, the most targeted by foreign settlers during the sixteenth century, little is known about the paternal ancestry of this particular population. Considering historical records have documented a series of territorial invasions in the Northeast by various European populations, we aimed to characterize the male lineages found in Brazilian individuals in order to discover to what extent these migrations have influenced the present-day gene pool. Our approach consisted of employing four hierarchical multiplex assays for the investigation of 45 unique event polymorphisms in the non-recombining portion of the Y-chromosome of 280 unrelated men from several Northeast Brazilian states. Results Primary multiplex results allowed the identification of six major haplogroups, four of which were screened for downstream SNPs and enabled the observation of 19 additional lineages. Results reveal a majority of Western European haplogroups, among which R1b-S116* was the most common (63.9%), corroborating historical records of colonizations by Iberian populations. Nonetheless, FST genetic distances show similarities between Northeast Brazil and several other European populations, indicating multiple origins of settlers. Regarding Native American ancestry, our findings confirm a strong sexual bias against such haplogroups, which represented only 2.5% of individuals, highly contrasting previous results for maternal lineages. Furthermore, we document the presence of several Middle Eastern and African haplogroups, supporting a complex historical formation of this population and highlighting its uniqueness among other Brazilian regions. Conclusions We performed a comprehensive analysis of the major Y-chromosome lineages that form the most dynamic migratory region from the Brazilian colonial period. This evidence suggests that the ongoing entry of European, Middle Eastern, and African males in the Brazilian Northeast, since at least 500 years, was significantly responsible for the present-day genetic architecture of this population.
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Affiliation(s)
- Ana Paula Schaan
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Juliana Jannuzzi
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Antonio Modesto
- Center for Oncology Research, Federal University of Pará, Belém, PA, 66073-005, Brazil
| | - Marcos Amador
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil
| | - Diego Marques
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil
| | - Silvia Helena Rabenhorst
- Pathology and Legal Medicine Department, Federal University of Ceará, Fortaleza, CE, 60020-181, Brazil
| | - Raquel Montenegro
- Pathology and Legal Medicine Department, Federal University of Ceará, Fortaleza, CE, 60020-181, Brazil
| | - Thayson Lopes
- Genetics and Molecular Biology Laboratory, Federal University of Piauí, Parnaíba, PI, 64202-020, Brazil
| | - France Keiko Yoshioka
- Genetics and Molecular Biology Laboratory, Federal University of Piauí, Parnaíba, PI, 64202-020, Brazil
| | - Giovanny Pinto
- Genetics and Molecular Biology Laboratory, Federal University of Piauí, Parnaíba, PI, 64202-020, Brazil
| | - Sidney Santos
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil
| | - Lorenna Costa
- Clinical and Toxicological Analyses Department, Federal University of Rio Grande do Norte, Natal, RN, 59300-000, Brazil
| | - Vivian Silbiger
- Clinical and Toxicological Analyses Department, Federal University of Rio Grande do Norte, Natal, RN, 59300-000, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil. .,Center for Oncology Research, Federal University of Pará, Belém, PA, 66073-005, Brazil.
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Jannuzzi J, Ribeiro J, Alho C, de Oliveira Lázaro e Arão G, Cicarelli R, Simões Dutra Corrêa H, Ferreira S, Fridman C, Gomes V, Loiola S, da Mota MF, Ribeiro-dos-Santos Â, de Souza CA, de Sousa Azulay RS, Carvalho EF, Gusmão L. Male lineages in Brazilian populations and performance of haplogroup prediction tools. Forensic Sci Int Genet 2020; 44:102163. [DOI: 10.1016/j.fsigen.2019.102163] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/25/2019] [Accepted: 09/19/2019] [Indexed: 11/26/2022]
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Kimura L, Nunes K, Macedo-Souza LI, Rocha J, Meyer D, Mingroni-Netto RC. Inferring paternal history of rural African-derived Brazilian populations from Y chromosomes. Am J Hum Biol 2016; 29. [PMID: 27761960 DOI: 10.1002/ajhb.22930] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 08/20/2016] [Accepted: 09/27/2016] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Quilombo remnants are relics of communities founded by runaway or abandoned African slaves, but often with subsequent extensive and complex admixture patterns with European and Native Americans. We combine a genetic study of Y-chromosome markers with anthropological surveys in order to obtain a portrait of quilombo structure and history in the region that has the largest number of quilombo remnants in the state of São Paulo. METHODS Samples from 289 individuals from quilombo remnants were genotyped using a set of 17 microsatellites on the Y chromosome (AmpFlSTR-Yfiler). A subset of 82 samples was also genotyped using SNPs array (Axiom Human Origins-Affymetrix). We estimated haplotype and haplogroup frequencies, haplotype diversity and sharing, and pairwise genetic distances through FST and RST indexes. RESULTS We identified 95 Y chromosome haplotypes, classified into 15 haplogroups. About 63% are European, 32% are African, and 6% Native American. The most common were: R1b (European, 34.2%), E1b1a (African, 32.3%), J1 (European, 6.9%), and Q (Native American, 6.2%). Genetic differentiation among communities was low (FST = 0.0171; RST = 0.0161), and haplotype sharing was extensive. Genetic, genealogical and oral surveys allowed us to detect five main founder haplotypes, which explained a total of 27.7% of the Y chromosome lineages. CONCLUSIONS Our results showed a high European patrilineal genetic contribution among the founders of quilombos, high amounts of gene flow, and a recent common origin of these populations. Common haplotypes and genealogical data indicate the origin of quilombos from a few male individuals. Our study reinforces the importance of a dual approach, involving the analysis of both anthropological and genetic data.
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Affiliation(s)
- Lilian Kimura
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, CEP, 05508-090, Brazil
| | - Kelly Nunes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, CEP, 05508-090, Brazil
| | - Lúcia Inês Macedo-Souza
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, CEP, 05508-090, Brazil
| | - Jorge Rocha
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, s/n, Porto, 4169-007, Portugal
| | - Diogo Meyer
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, CEP, 05508-090, Brazil
| | - Regina Célia Mingroni-Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, CEP, 05508-090, Brazil
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7
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Resque R, Gusmão L, Geppert M, Roewer L, Palha T, Alvarez L, Ribeiro-dos-Santos Â, Santos S. Male Lineages in Brazil: Intercontinental Admixture and Stratification of the European Background. PLoS One 2016; 11:e0152573. [PMID: 27046235 PMCID: PMC4821637 DOI: 10.1371/journal.pone.0152573] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 03/16/2016] [Indexed: 12/27/2022] Open
Abstract
The non-recombining nature of the Y chromosome and the well-established phylogeny of Y-specific Single Nucleotide Polymorphisms (Y-SNPs) make them useful for defining haplogroups with high geographical specificity; therefore, they are more apt than the Y-STRs to detect population stratification in admixed populations from diverse continental origins. Different Y-SNP typing strategies have been described to address issues of population history and movements within geographic territories of interest. In this study, we investigated a set of 41 Y-SNPs in 1217 unrelated males from the five Brazilian geopolitical regions, aiming to disclose the genetic structure of male lineages in the country. A population comparison based on pairwise FST genetic distances did not reveal statistically significant differences in haplogroup frequency distributions among populations from the different regions. The genetic differences observed among regions were, however, consistent with the colonization history of the country. The sample from the Northern region presented the highest Native American ancestry (8.4%), whereas the more pronounced African contribution could be observed in the Northeastern population (15.1%). The Central-Western and Southern samples showed the higher European contributions (95.7% and 93.6%, respectively). The Southeastern region presented significant European (86.1%) and African (12.0%) contributions. The subtyping of the most frequent European lineage in Brazil (R1b1a-M269) allowed differences in the genetic European background of the five Brazilian regions to be investigated for the first time.
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Affiliation(s)
- Rafael Resque
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.,Laboratório de Toxicologia e Química Farmacêutica, Departamento de Ciências da Saúde e Biológicas, Universidade Federal do Amapá, Macapá, Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil.,IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Maria Geppert
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Teresinha Palha
- Laboratório de Genética Forense, Instituto de Criminalística, Centro de Perícias Científicas Renato Chaves, Belém, Pará, Brasil
| | - Luis Alvarez
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.,Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Brazil
| | - Sidney Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.,Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Brazil
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Rodrigues de Moura R, Coelho AVC, de Queiroz Balbino V, Crovella S, Brandão LAC. Meta-analysis of Brazilian genetic admixture and comparison with other Latin America countries. Am J Hum Biol 2015; 27:674-80. [DOI: 10.1002/ajhb.22714] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 01/22/2015] [Accepted: 02/11/2015] [Indexed: 01/13/2023] Open
Affiliation(s)
- Ronald Rodrigues de Moura
- Department of Genetics; Federal University of Pernambuco (UFPE); Recife Pernambuco Brazil
- Laboratory of Immunopatology Keizo Asami (LIKA/UFPE); Recife Pernambuco Brazil
| | - Antonio Victor Campos Coelho
- Department of Genetics; Federal University of Pernambuco (UFPE); Recife Pernambuco Brazil
- Laboratory of Immunopatology Keizo Asami (LIKA/UFPE); Recife Pernambuco Brazil
| | | | - Sergio Crovella
- Department of Genetics; Federal University of Pernambuco (UFPE); Recife Pernambuco Brazil
- Laboratory of Immunopatology Keizo Asami (LIKA/UFPE); Recife Pernambuco Brazil
| | - Lucas André Cavalcanti Brandão
- Laboratory of Immunopatology Keizo Asami (LIKA/UFPE); Recife Pernambuco Brazil
- Department of Pathology; Federal University of Pernambuco (UFPE); Recife Pernambuco Brazil
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9
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Rowold D, Garcia-Bertrand R, Calderon S, Rivera L, Benedico DP, Alfonso Sanchez MA, Chennakrishnaiah S, Varela M, Herrera RJ. At the southeast fringe of the Bantu expansion: genetic diversity and phylogenetic relationships to other sub-Saharan tribes. Meta Gene 2014; 2:670-85. [PMID: 25606451 PMCID: PMC4287857 DOI: 10.1016/j.mgene.2014.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 07/06/2014] [Accepted: 08/15/2014] [Indexed: 11/16/2022] Open
Abstract
Here, we present 12 loci paternal haplotypes (Y-STR profiles) against the backdrop of the Y-SNP marker system of Bantu males from the Maputo Province of Southeast Africa, a region believed to represent the southeastern fringe of the Bantu expansion. Our Maputo Bantu group was analyzed within the context of 27 geographically relevant reference populations in order to ascertain its genetic relationship to other Bantu and non Bantu (Pygmy, Khoisan and Nilotic) sub-equatorial tribes from West and East Africa. This study entails statistical pair wise comparisons and multidimensional scaling based on YSTR Rst distances, network analyses of Bantu (B2a-M150) and Pygmy (B2b-M112) lineages as well as an assessment of Y-SNP distribution patterns. Several notable findings include the following: 1) the Maputo Province Bantu exhibits a relatively close paternal affinity with both east and west Bantu tribes due to high proportion of Bantu Y chromosomal markers, 2) only traces of Khoisan (1.3%) and Pygmy (1.3%) markers persist in the Maputo Province Bantu gene pool, 3) the occurrence of R1a1a-M17/M198, a member of the Eurasian R1a-M420 branch in the population of the Maputo Province, may represent back migration events and/or recent admixture events, 4) the shared presence of E1b1b1-M35 in all Tanzanian tribes examined, including Bantu and non-Bantu groups, in conjunction with its nearly complete absence in the West African populations indicate that, in addition to a shared linguistic, cultural and genetic heritage, geography (e.g., east vs. west) may have impacted the paternal landscape of sub-Saharan Africa, 5) the admixture and assimilation processes of Bantu elements were both highly complex and region-specific. Maputo Bantus exhibit close affinities with other West and East African Bantus. Traces of Khoisan and Pygmy markers persist in the Maputo Province Bantus. R1a1a-M17/M198 in the Maputo Province may represent back or recent migration. Linguistic, cultural and genetic heritages are reflected in Maputo's gene pool. Admixture and assimilation processes of Bantu elements were region-specific.
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Affiliation(s)
- Diane Rowold
- Foundation for Applied Molecular Evolution, Gainesville, FL 32601, USA
| | - Ralph Garcia-Bertrand
- Biology Department, Colorado College, Colorado Springs, CO 80903, USA
- Corresponding author at: Biology Department, Colorado College, 14 East Cache La Poudre Street, Colorado Springs, CO 80903-3294, USA. Tel.: + 1 719 389 6402; fax: + 1 719 389 6940.
| | - Silvia Calderon
- College of Dentistry, New York University, New York, NY 10010, USA
| | - Luis Rivera
- College of Health Sciences, Florida International University, Miami, FL 33199, USA
| | | | - Miguel A. Alfonso Sanchez
- Departamento de Genética y Antropología Fısica, Facultad de Ciencia y Tecnología, Universidad del País Vasco, 48080 Bilbao, Bizkaia, Spain
| | | | - Mangela Varela
- Biology Department, Colorado College, Colorado Springs, CO 80903, USA
| | - Rene J. Herrera
- Biology Department, Colorado College, Colorado Springs, CO 80903, USA
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10
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Oliveira AM, Domingues PM, Gomes V, Amorim A, Jannuzzi J, de Carvalho EF, Gusmão L. Male lineage strata of Brazilian population disclosed by the simultaneous analysis of STRs and SNPs. Forensic Sci Int Genet 2014; 13:264-8. [PMID: 25259770 DOI: 10.1016/j.fsigen.2014.08.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/28/2014] [Accepted: 08/29/2014] [Indexed: 12/09/2022]
Abstract
Brazil has a large territory divided in five geographical regions harboring highly diverse populations that resulted from different degrees and modes of admixture between Native Americans, Europeans and Africans. In this study, a sample of 605 unrelated males was genotyped for 17 Y-STRs and 46 Y-SNPs aiming a deep characterization of the male gene pool of Rio de Janeiro and its comparison with other Brazilian populations. High values of Y-STR haplotype diversity (0.9999±0.0001) and Y-SNP haplogroup diversity (0.7589±0.0171) were observed. Population comparisons at both haplotype and haplogroup levels showed significant differences between Brazilian South Eastern and Northern populations that can be explained by differences in the proportion of African and Native American Y chromosomes. Statistical significant differences between admixed urban samples from the five regions of Brazil were not previously detected at haplotype level based on smaller size samples from South East, which emphasizes the importance of sample size to detected population stratification for an accurate interpretation of profile matches in kinship and forensic casework. Although not having an intra-population discrimination power as high as the Y-STRs, the Y-SNPs are more powerful to disclose differences in admixed populations. In this study, the combined analysis of these two types of markers proved to be a good strategy to predict population sub-structure, which should be taken into account when delineating forensic database strategies for Y chromosome haplotypes.
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Affiliation(s)
- Andréa M Oliveira
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Patricia M Domingues
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Verónica Gomes
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - António Amorim
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal; FCUP - Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Juliana Jannuzzi
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Elizeu F de Carvalho
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil; IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.
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Abstract
A general introduction to the origins and history of Latin American populations is followed by a systematic review of the data from molecular autosomal assessments of the ethnic/continental (European, African, Amerindian) ancestries for 24 Latin American countries or territories. The data surveyed are of varying quality but provide a general picture of the present constitution of these populations. A brief discussion about the applications of these results (admixture mapping) is also provided. Latin American populations can be viewed as natural experiments for the investigation of unique anthropological and epidemiological issues.
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Affiliation(s)
- Francisco Mauro Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Mónica Sans
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo, Uruguay
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Palha T, Ribeiro-Rodrigues E, Ribeiro-dos-Santos Â, Santos S. Fourteen short tandem repeat loci Y chromosome haplotypes: Genetic analysis in populations from northern Brazil. Forensic Sci Int Genet 2012; 6:413-8. [DOI: 10.1016/j.fsigen.2011.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 08/01/2011] [Accepted: 08/08/2011] [Indexed: 10/17/2022]
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