Mitochondrial ancestry from complete mitogenomes highlights a lack of characterization of indigenous haplogroups in Brazilian Amazon population
Abstract Mitochondrial genome is an essential resource to investigate the dispersion and diversification of human populations. However, the lack of genomic data from non-European ancestry hinders demographic, anthropologic and genetic studies. Indigenous people from the Brazilian Amazon are especial...
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Nature Portfolio
2025-05-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-025-08126-4 |
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| author | Felipe Gouvea de Souza Gustavo Barra Matos Camille Sena Santos Tatiane Piedade Souza Angélica Rita Gobbo Patrícia Fagundes da Costa Claudio Guedes Salgado Gracivane Lopes Eufraseo André Vitor de Souza Fernandes Bruno Lopes Santos-Lobato Sidney Santos Giovanna C. Cavalcante André M. Ribeiro dos Santos Gilderlanio S. de Araújo Ândrea Ribeiro- dos-Santos |
| author_facet | Felipe Gouvea de Souza Gustavo Barra Matos Camille Sena Santos Tatiane Piedade Souza Angélica Rita Gobbo Patrícia Fagundes da Costa Claudio Guedes Salgado Gracivane Lopes Eufraseo André Vitor de Souza Fernandes Bruno Lopes Santos-Lobato Sidney Santos Giovanna C. Cavalcante André M. Ribeiro dos Santos Gilderlanio S. de Araújo Ândrea Ribeiro- dos-Santos |
| author_sort | Felipe Gouvea de Souza |
| collection | DOAJ |
| description | Abstract Mitochondrial genome is an essential resource to investigate the dispersion and diversification of human populations. However, the lack of genomic data from non-European ancestry hinders demographic, anthropologic and genetic studies. Indigenous people from the Brazilian Amazon are especially underrepresented among large genetic datasets, despite their significative contribution to the Brazilian genetic pool. We investigated 157 mitochondrial genomes from the Brazilian Amazon using bioinformatics tools for ancestry inference and phylogenetics. Results were compared with 2578 global mitogenomes to assess haplogroup frequencies and genetic distances. Thirteen macrohaplogroups were identified from investigated samples, including Indigenous, European and African ancestries. Despite being prominent in our sample, Indigenous haplogroup assignment confidence by prediction tools was lower and many samples lacked key-defining variants, suggesting misassignment due to low representation in reference datasets. We also identified potential new groups sharing specific variants. Thus, underrepresentation of Indigenous haplogroups contributes to phylogenetic inconsistencies and needs future investigations. |
| format | Article |
| id | doaj-art-54ff0583bb4e4e69b04294a9e80141ca |
| institution | OA Journals |
| issn | 2399-3642 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj-art-54ff0583bb4e4e69b04294a9e80141ca2025-08-20T02:00:09ZengNature PortfolioCommunications Biology2399-36422025-05-01811910.1038/s42003-025-08126-4Mitochondrial ancestry from complete mitogenomes highlights a lack of characterization of indigenous haplogroups in Brazilian Amazon populationFelipe Gouvea de Souza0Gustavo Barra Matos1Camille Sena Santos2Tatiane Piedade Souza3Angélica Rita Gobbo4Patrícia Fagundes da Costa5Claudio Guedes Salgado6Gracivane Lopes Eufraseo7André Vitor de Souza Fernandes8Bruno Lopes Santos-Lobato9Sidney Santos10Giovanna C. Cavalcante11André M. Ribeiro dos Santos12Gilderlanio S. de Araújo13Ândrea Ribeiro- dos-Santos14Laboratory of Human and Medical Genetics (LGHM), Institute of Biological Sciences, Federal University of Pará (UFPA)Laboratory of Human and Medical Genetics (LGHM), Institute of Biological Sciences, Federal University of Pará (UFPA)Laboratory of Human and Medical Genetics (LGHM), Institute of Biological Sciences, Federal University of Pará (UFPA)Laboratory of Human and Medical Genetics (LGHM), Institute of Biological Sciences, Federal University of Pará (UFPA)Laboratory of Dermato-Immunology (LDI), Institute of Biological Sciences, Federal University of Pará (UFPA)Laboratory of Dermato-Immunology (LDI), Institute of Biological Sciences, Federal University of Pará (UFPA)Laboratory of Dermato-Immunology (LDI), Institute of Biological Sciences, Federal University of Pará (UFPA)Laboratory of Experimental Neurology (LaNEx), Federal University of Pará (UFPA)Laboratory of Experimental Neurology (LaNEx), Federal University of Pará (UFPA)Laboratory of Experimental Neurology (LaNEx), Federal University of Pará (UFPA)Laboratory of Human and Medical Genetics (LGHM), Institute of Biological Sciences, Federal University of Pará (UFPA)Laboratory of Human and Medical Genetics (LGHM), Institute of Biological Sciences, Federal University of Pará (UFPA)Laboratory of Human and Medical Genetics (LGHM), Institute of Biological Sciences, Federal University of Pará (UFPA)Laboratory of Human and Medical Genetics (LGHM), Institute of Biological Sciences, Federal University of Pará (UFPA)Laboratory of Human and Medical Genetics (LGHM), Institute of Biological Sciences, Federal University of Pará (UFPA)Abstract Mitochondrial genome is an essential resource to investigate the dispersion and diversification of human populations. However, the lack of genomic data from non-European ancestry hinders demographic, anthropologic and genetic studies. Indigenous people from the Brazilian Amazon are especially underrepresented among large genetic datasets, despite their significative contribution to the Brazilian genetic pool. We investigated 157 mitochondrial genomes from the Brazilian Amazon using bioinformatics tools for ancestry inference and phylogenetics. Results were compared with 2578 global mitogenomes to assess haplogroup frequencies and genetic distances. Thirteen macrohaplogroups were identified from investigated samples, including Indigenous, European and African ancestries. Despite being prominent in our sample, Indigenous haplogroup assignment confidence by prediction tools was lower and many samples lacked key-defining variants, suggesting misassignment due to low representation in reference datasets. We also identified potential new groups sharing specific variants. Thus, underrepresentation of Indigenous haplogroups contributes to phylogenetic inconsistencies and needs future investigations.https://doi.org/10.1038/s42003-025-08126-4 |
| spellingShingle | Felipe Gouvea de Souza Gustavo Barra Matos Camille Sena Santos Tatiane Piedade Souza Angélica Rita Gobbo Patrícia Fagundes da Costa Claudio Guedes Salgado Gracivane Lopes Eufraseo André Vitor de Souza Fernandes Bruno Lopes Santos-Lobato Sidney Santos Giovanna C. Cavalcante André M. Ribeiro dos Santos Gilderlanio S. de Araújo Ândrea Ribeiro- dos-Santos Mitochondrial ancestry from complete mitogenomes highlights a lack of characterization of indigenous haplogroups in Brazilian Amazon population Communications Biology |
| title | Mitochondrial ancestry from complete mitogenomes highlights a lack of characterization of indigenous haplogroups in Brazilian Amazon population |
| title_full | Mitochondrial ancestry from complete mitogenomes highlights a lack of characterization of indigenous haplogroups in Brazilian Amazon population |
| title_fullStr | Mitochondrial ancestry from complete mitogenomes highlights a lack of characterization of indigenous haplogroups in Brazilian Amazon population |
| title_full_unstemmed | Mitochondrial ancestry from complete mitogenomes highlights a lack of characterization of indigenous haplogroups in Brazilian Amazon population |
| title_short | Mitochondrial ancestry from complete mitogenomes highlights a lack of characterization of indigenous haplogroups in Brazilian Amazon population |
| title_sort | mitochondrial ancestry from complete mitogenomes highlights a lack of characterization of indigenous haplogroups in brazilian amazon population |
| url | https://doi.org/10.1038/s42003-025-08126-4 |
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