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Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I, Patterson N, Reich D. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci Data 2024; 11:182. [PMID: 38341426 PMCID: PMC10858950 DOI: 10.1038/s41597-024-03031-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.
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Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- BIOMICs Research Group, University of the Basque Country, 01006, Vitoria-Gasteiz, Spain
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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Arencibia V, Muñoz M, Crespo CM, Russo MG, Vera P, Lia VV, García Guraieb S, Goñi RA, Avena S, Puebla A, Dejean CB. Novel B2 mitogenomes from Continental southern Patagonia's Late Holocene: New insights into the peopling of the Southern Cone. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023. [PMID: 37548135 DOI: 10.1002/ajpa.24822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/23/2023] [Accepted: 07/09/2023] [Indexed: 08/08/2023]
Abstract
OBJECTIVES The main aim of this study is to discuss the migratory processes and peopling dynamics that shaped the genetic variability of populations during the settlement of the Southern Cone, through the analysis of complete mitogenomes of individuals from southern Patagonia. MATERIALS AND METHODS Complete mitogenomes were sequenced through massively parallel sequencing from two late Holocene individuals (SAC 1-1-3 and SAC 1-1-4) buried in the same chenque at Salitroso Lake Basin (Santa Cruz province, Argentina). To evaluate matrilineal phylogenetic affinities with other haplotypes, maximum likelihood and Bayesian phylogenetic reconstructions were performed, as well as a haplotype median-joining network. RESULTS The mitogenomes were assigned to haplogroups B2 and B2b, exhibiting an average depth of 54X and 89X (≥1X coverage of 98.6% and 100%), and a high number of nucleotide differences among them. The phylogenetic analyses showed a relatively close relationship between the haplotype found in SAC 1-1-4 and those retrieved from a Middle Holocene individual from Laguna Chica (Buenos Aires province), and from a group of individuals from the Peruvian coast. For the SAC 1-1-3, no clear affiliations to any other haplotype were established. DISCUSSION The large divergence between the haplotypes presented in this study suggests either a highly variable founder gene pool, or a later enrichment by frequent biological contact with other populations. Our results underline the persistence of genetic signals related to the first waves of peopling in South America, suggesting that the regional settlement of the southern end of the continent has been much more complex than initially thought.
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Affiliation(s)
- Valeria Arencibia
- Equipo de Antropología Biológica, CCNAA, Universidad Maimónides, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marianne Muñoz
- Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
- Instituto de Biotecnología-IABIMO (CONICET), Unidad de Genómica, Nodo CATG, Buenos Aires, Argentina
| | - Cristian M Crespo
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales (ICPA), Universidad Nacional de Tierra del Fuego, Ushuaia, Tierra del Fuego, Argentina
| | - M Gabriela Russo
- Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Grupo de Investigación en Biología Evolutiva (GIBE), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Pablo Vera
- Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
- Instituto de Biotecnología-IABIMO (CONICET), Unidad de Genómica, Nodo CATG, Buenos Aires, Argentina
| | - Verónica V Lia
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Solana García Guraieb
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto Nacional de Antropología y Pensamiento Latinoamericano (INAPL), Buenos Aires, Argentina
- Facultad de Filosofía y Letras, Departamento de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rafael A Goñi
- Instituto Nacional de Antropología y Pensamiento Latinoamericano (INAPL), Buenos Aires, Argentina
- Facultad de Filosofía y Letras, Departamento de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sergio Avena
- Equipo de Antropología Biológica, CCNAA, Universidad Maimónides, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Filosofía y Letras, Departamento de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Andrea Puebla
- Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
- Instituto de Biotecnología-IABIMO (CONICET), Unidad de Genómica, Nodo CATG, Buenos Aires, Argentina
| | - Cristina B Dejean
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Facultad de Filosofía y Letras, Departamento de Ciencias Antropológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Filosofía y Letras, Instituto de Ciencias Antropológicas, Sección Antropología Biológica, Universidad de Buenos Aires, Buenos Aires, Argentina
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Dalal V, Pasupuleti N, Chaubey G, Rai N, Shinde V. Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide. Genes (Basel) 2023; 14:479. [PMID: 36833406 PMCID: PMC9956214 DOI: 10.3390/genes14020479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.
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Affiliation(s)
- Vasundhra Dalal
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | | | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Niraj Rai
- Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, Lucknow 226007, Uttar Pradesh, India
| | - Vasant Shinde
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
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Campelo dos Santos AL, Owings A, Sullasi HSL, Gokcumen O, DeGiorgio M, Lindo J. Genomic evidence for ancient human migration routes along South America's Atlantic coast. Proc Biol Sci 2022; 289:20221078. [PMID: 36322514 PMCID: PMC9629774 DOI: 10.1098/rspb.2022.1078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
An increasing body of archaeological and genomic evidence has hinted at a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level.
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Affiliation(s)
- Andre Luiz Campelo dos Santos
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA,Department of Archaeology, Federal University of Pernambuco, Recife, Pernambuco 50670-901, Brazil
| | - Amanda Owings
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | | | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
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