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Zuckerman MK, Marklein KE, Austin RM, Hofman CA. Exercises in ethically engaged work in biological anthropology. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024:e25015. [PMID: 39177071 DOI: 10.1002/ajpa.25015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 07/10/2024] [Accepted: 07/31/2024] [Indexed: 08/24/2024]
Abstract
An ethical paradigm shift currently taking place within biological anthropology is pushing scholars to envisage and develop paths toward more ethical futures. Drawing from case studies in our own teaching, research, and fieldwork experience, we reflect on the complex, diverse, and dynamic nature of ethical considerations in our field. We discuss the acquisition and institutional narrative of a human osteological teaching collection at the University of Louisville as an embodiment of structural apathy turned structural violence, and the need for professional guidance in the potential retirement of deceased individuals from our classrooms. In documented collections (i.e., the Robert J. Terry Collection), we share our process and scholarly reemphasis of the humanity of a deceased individual through contextualized analysis (i.e., osteobiography and archival history) and postmortem agentive acts. Lastly, we present an archeological site in the U.S. Virgin Islands, which poses ethical concerns as biocultural bioarcheologists and archeologists attempt to negotiate the possible wishes of the deceased with the cultural value of reconstructing the community's otherwise undocumented past, all amidst the immediate threat of anthropogenic climate change. We offer these exercises and discussion in ethically engaged projects transparently and with an overarching admission that none are models for replication. Rather, at various stages in our careers and engagement with ethics, we acknowledge that progress is worthwhile, albeit challenging, and that proceeding forward collectively as biological anthropologists should be deliberate, reflexive, and compassionate for deceased individuals and their descendant communities, as well as among and between colleagues.
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Affiliation(s)
- Molly K Zuckerman
- Department of Anthropology and Middle Eastern Cultures and Cobb Institute of Archaeology, Mississippi State University, Mississippi State, Mississippi, USA
- The Department of Anthropology, National Museum of Natural History, Washington, District of Columbia, USA
| | - Kathryn E Marklein
- Department of Anthropology and the Center for Archaeological and Cultural Heritage, University of Louisville, Louisville, Kentucky, USA
| | | | - Courtney A Hofman
- The Department of Anthropology, National Museum of Natural History, Washington, District of Columbia, USA
- Laboratories of Molecular Anthropology and Microbiome Research and the Department of Anthropology, University of Oklahoma, Norman, Oklahoma, USA
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2
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Fort J, Pérez-Losada J. Interbreeding between farmers and hunter-gatherers along the inland and Mediterranean routes of Neolithic spread in Europe. Nat Commun 2024; 15:7032. [PMID: 39147743 PMCID: PMC11327347 DOI: 10.1038/s41467-024-51335-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 08/05/2024] [Indexed: 08/17/2024] Open
Abstract
The Neolithic (i.e., farming and stockbreeding) spread from the Near East across Europe since about 9000 years before the common era (BCE) until about 4000 yr BCE. It followed two main routes, namely a sea route along the northern Mediterranean coast and an inland one across the Balkans and central Europe. It is known that the dispersive behavior of farmers depended on geography, with longer movements along the Mediterranean coast than along the inland route. In sharp contrast, here we show that for both routes the percentage of farmers who interbred with hunter-gatherers and/or acculturated one of them was strikingly the same (about 3.6%). Therefore, whereas the dispersive behavior depended on the proximity to the Mediterranean sea, the interaction behavior (incorporation of hunter-gatherers) did not depend on geographical constraints but only on the transition in the subsistence economy (from hunting and gathering to farming) and its associated way of life. These conclusions are reached by analyzing the clines of haplogroup K, which was virtually absent in hunter-gatherers and the most frequent mitochondrial haplogroup in early farmers. Similarly, the most frequent Y-chromosome Neolithic haplogroup (G2a) displays an inland cline that agrees with the percentage of interbreeding reported above.
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Affiliation(s)
- Joaquim Fort
- Complex Systems Laboratory, Universitat de Girona, C/ Maria Aurèlia Capmany 61, 17003, Girona, Catalonia, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 3, 08010, Barcelona, Catalonia, Spain.
| | - Joaquim Pérez-Losada
- Complex Systems Laboratory, Universitat de Girona, C/ Maria Aurèlia Capmany 61, 17003, Girona, Catalonia, Spain
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3
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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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4
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De Jesus O. Degenerative Cervical Disc Herniation: Prevalence of Affected Cervical Level in a Hispanic Population in Puerto Rico. World Neurosurg 2024; 181:e776-e779. [PMID: 37914080 DOI: 10.1016/j.wneu.2023.10.125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND In the literature, degenerative cervical disc herniation is considered to occur more frequently at the C5-C6 and C6-C7 levels. This study aimed to evaluate the operated cervical level prevalence among patients with degenerative cervical disc herniation in a Hispanic Puerto Rico population. METHODS The University of Puerto Rico Neurosurgery database was used to identify patients who underwent anterior cervical discectomy for degenerative cervical disc herniation during a 15-year period from January 1, 2006 until December 31, 2020. Operated cervical levels for each patient were analyzed. RESULTS During the study period, 409 patients were operated on for degenerative cervical disc herniation. Two hundred-eight patients (50.8%) had disc herniations at more than 1 cervical level for 663 treated levels. The most prevalent cervical levels in this Hispanic population were C5-C6 (34.8%) and C4-C5 (28.1%). The C6-C7 level was involved in 18.9% of the operated levels, and the C3-C4 level in 17.3%. The C7-T1 level was involved in only 0.6% of the operated levels, and the C2-3 level in 0.3%. The cohort included 51.3% of men and 48.7% of women, with a men-to-women ratio of 1.05:1. The median age of females was 56.5 (range 26-82) and 59.0 (range 31-85) for males. Operated cervical discs were most common between the ages of 48 and 66 years for either sex. CONCLUSIONS In a Hispanic Puerto Rico population, the most prevalent operated degenerative cervical disc levels were C5-C6 and C4-C5.
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Affiliation(s)
- Orlando De Jesus
- Department of Surgery, Section of Neurosurgery, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico, USA.
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Honap TP, Monroe CR, Johnson SJ, Jacobson DK, Abin CA, Austin RM, Sandberg P, Levine M, Sankaranarayanan K, Lewis CM. Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:542-556. [PMID: 37002784 DOI: 10.1002/ajpa.24735] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
OBJECTIVES Limited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre-contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA. MATERIALS AND METHODS Skeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250-1450 CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase-treated double-stranded DNA libraries were shotgun-sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted. RESULTS Paleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such as Tannerella forsythia and Treponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 and T. forsythia revealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre-contact Native Americans and were distinct from European and/or post-contact American strains. DISCUSSION We present the largest oral metagenome dataset from a pre-contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre-contact Americas.
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Affiliation(s)
- Tanvi P Honap
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Cara R Monroe
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
- Center for the Ethics of Indigenous Genomics Research (CEIGR), University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Sarah J Johnson
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - David K Jacobson
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Christopher A Abin
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Rita M Austin
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Paul Sandberg
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Marc Levine
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
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6
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Winful T, McCormack K, Mueller E, Chen L, Clemente MR, Torres JB. Exploring the legacy of African and Indigenous Caribbean admixture in Puerto Rico. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:194-209. [PMID: 37525538 DOI: 10.1002/ajpa.24814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 05/23/2023] [Accepted: 06/23/2023] [Indexed: 08/02/2023]
Abstract
OBJECTIVES From an anthropological genetic perspective, little is known about the ethnogenesis of African descendants in Puerto Rico. Furthermore, historical interactions between Indigenous Caribbean and African descendant peoples that may be reflected in the ancestry of contemporary populations are understudied. Given this dearth of genetic research and the precedence for Afro-Indigenous interactions documented by historical, archeological, and other lines of evidence, we sought to assess the biogeographic origins of African descendant Puerto Ricans and to query the potential for Indigenous ancestry within this community. MATERIALS AND METHODS Saliva samples were collected from 58 self-identified African descendant Puerto Ricans residing in Puerto Rico. We sequenced whole mitochondrial genomes and genotyped Y chromosome haplogroups for each male individual (n = 25). Summary statistics, comparative analyses, and network analysis were used to assess diversity and variation in haplogroup distribution between the sample and comparative populations. RESULTS As indicated by mitochondrial haplogroups, 66% had African, 5% had European, and 29% had Indigenous American matrilines. Along the Y chromosome, 52% had African, 28% had Western European, 16% had Eurasian, and, notably, 4% had Indigenous American patrilines. Both mitochondrial and Y chromosome haplogroup frequencies were significantly different from several comparative populations. DISCUSSION Biogeographic origins are consistent with historical accounts of African, Indigenous American, and European ancestry. However, this first report of Indigenous American paternal ancestry in Puerto Rico suggests distinctive features within African descendant communities on the island. Future studies expanding sampling and incorporating higher resolution genetic markers are necessary to more fully understand African descendant history in Puerto Rico.
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Affiliation(s)
- Taiye Winful
- Department of Anthropology, Genetic Anthropology and Biocultural Studies Laboratory, Vanderbilt University, Nashville, Tennessee, USA
| | - Katie McCormack
- Department of Anthropology, Genetic Anthropology and Biocultural Studies Laboratory, Vanderbilt University, Nashville, Tennessee, USA
| | - Elsa Mueller
- Department of Anthropology, Genetic Anthropology and Biocultural Studies Laboratory, Vanderbilt University, Nashville, Tennessee, USA
| | - Lijuan Chen
- Department of Anthropology, Genetic Anthropology and Biocultural Studies Laboratory, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Jada Benn Torres
- Department of Anthropology, Genetic Anthropology and Biocultural Studies Laboratory, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee, USA
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Sandoval JR, Revollo S, Cuellar C, Lacerda DR, Jota MS, Fujita R, Santos FR. Genetic portrait of the Amazonian communities of Peru and Bolivia: The legacy of the Takanan-speaking people. Ann Hum Genet 2023; 87:210-221. [PMID: 37161738 DOI: 10.1111/ahg.12510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023]
Abstract
During the colonial period in South America, many autochthonous populations were affected by relocation by European missionary reductions and other factors that impacted and reconfigured their genetic makeup. Presently, the descendants of some "reduced" and other isolated groups are distributed in the Amazonian areas of Peru, Bolivia, and Brazil, and among them, speakers of Takanan and Panoan languages. Based on linguistics, these peoples should be closely related, but so far no DNA comparison studies have been conducted to corroborate a genetic relationship. To clarify these questions, we used a set of 15 short tandem repeats of the non-recombining part of the Y-chromosome (Y-STRs) and mitochondrial DNA (mtDNA) control region sequence data. Paternal line comparisons showed the Takanan-speaking peoples from Peru and Bolivia descended from recent common ancestors; one group was related to Arawakan, Jivaroan, and Cocama and the other to Panoan speakers, consistent with linguistics. Also, a genetic affinity for maternal lines was observed between some Takanan speakers and individuals who spoke different Amazonian languages. Our results supported a shared ancestry of Takanan, Panoan, Cocama, and Jivaroan-speaking communities who appeared to be related to each other and came likely from an early Arawak expansion in the western Amazonia of South America.
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Affiliation(s)
- José R Sandoval
- Centro de Genética y Biología Molecular (CGBM), Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, Perú
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Daniela R Lacerda
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marilza S Jota
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ricardo Fujita
- Centro de Genética y Biología Molecular (CGBM), Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, Perú
| | - Fabricio R Santos
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Villa-Islas V, Izarraras-Gomez A, Larena M, Campos EMP, Sandoval-Velasco M, Rodríguez-Rodríguez JE, Bravo-Lopez M, Moguel B, Fregel R, Garfias-Morales E, Medina Tretmanis J, Velázquez-Ramírez DA, Herrera-Muñóz A, Sandoval K, Nieves-Colón MA, Zepeda García Moreno G, Villanea FA, Medina EFV, Aguayo-Haro R, Valdiosera C, Ioannidis AG, Moreno-Estrada A, Jay F, Huerta-Sanchez E, Moreno-Mayar JV, Sánchez-Quinto F, Ávila-Arcos MC. Demographic history and genetic structure in pre-Hispanic Central Mexico. Science 2023; 380:eadd6142. [PMID: 37167382 DOI: 10.1126/science.add6142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Aridoamerica and Mesoamerica are two distinct cultural areas in northern and central Mexico, respectively, that hosted numerous pre-Hispanic civilizations between 2500 BCE and 1521 CE. The division between these regions shifted southward because of severe droughts ~1100 years ago, which allegedly drove a population replacement in central Mexico by Aridoamerican peoples. In this study, we present shotgun genome-wide data from 12 individuals and 27 mitochondrial genomes from eight pre-Hispanic archaeological sites across Mexico, including two at the shifting border of Aridoamerica and Mesoamerica. We find population continuity that spans the climate change episode and a broad preservation of the genetic structure across present-day Mexico for the past 2300 years. Lastly, we identify a contribution to pre-Hispanic populations of northern and central Mexico from two ancient unsampled "ghost" populations.
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Affiliation(s)
- Viridiana Villa-Islas
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Alan Izarraras-Gomez
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Maximilian Larena
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Cuidad de México, Mexico
| | | | - Miriam Bravo-Lopez
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | - Barbara Moguel
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
- Centro de Geociencias, UNAM Juriquilla, Juriquilla, Querétaro, México
| | - Rosa Fregel
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Ernesto Garfias-Morales
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
| | | | | | | | - Karla Sandoval
- Equity and Gender Office of the Centre for Research and Advanced Studies (CODIGO-C), CINVESTAV, Mexico City, Mexico
| | - Maria A Nieves-Colón
- Unit of Advanced Genomics, National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
- Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | | | - Fernando A Villanea
- Department of Anthropology, University of Colorado Boulder, Boulder, CO, USA
| | | | | | - Cristina Valdiosera
- Departamento de Historia, Geografía y Comunicaciones, Universidad de Burgos, Burgos, Spain
- Department of History and Archaeology, La Trobe University, Melbourne, Australia
| | - Alexander G Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Andrés Moreno-Estrada
- Unit of Advanced Genomics, National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Flora Jay
- Laboratoire Interdisciplinaire des Sciences du Numérique, Université Paris-Saclay, CNRS, INRIA, 91400 Orsay, France
| | | | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México (UNAM), Querétaro, México
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Abstract
The ethics of the scientific study of Ancestors has long been debated by archaeologists, bioanthropologists, and, more recently, ancient DNA (aDNA) researchers. This article responds to the article "Ethics of DNA research on human remains: five globally applicable guidelines" published in 2021 in Nature by a large group of aDNA researchers and collaborators. We argue that these guidelines do not sufficiently consider the interests of community stakeholders, including descendant communities and communities with potential, but yet unestablished, ties to Ancestors. We focus on three main areas of concern with the guidelines. First is the false separation of "scientific" and "community" concerns and the consistent privileging of researcher perspectives over those of community members. Second, the commitment of the guidelines' authors to open data ignores the principles and practice of Indigenous Data Sovereignty. Further, the authors argue that involving community members in decisions about publication and data sharing is unethical. We argue that excluding community perspectives on "ethical" grounds is convenient for researchers, but it is not, in fact, ethical. Third, we stress the risks of not consulting communities that have established or potential ties to Ancestors, using two recent examples from the literature. Ancient DNA researchers cannot focus on the lowest common denominator of research practice, the bare minimum that is legally necessary. Instead, they should be leading multidisciplinary efforts to create processes to ensure communities from all regions of the globe are identified and engaged in research that affects them. This will often present challenges, but we see these challenges as part of the research, rather than a distraction from the scientific endeavor. If a research team does not have the capacity to meaningfully engage communities, questions must be asked about the value and benefit of their research.
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10
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Nieves-Colón MA. Anthropological genetic insights on Caribbean population history. Evol Anthropol 2022; 31:118-137. [PMID: 35060661 DOI: 10.1002/evan.21935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 06/18/2021] [Accepted: 12/15/2021] [Indexed: 11/09/2022]
Abstract
As the last American region settled by humans, yet the first to experience European colonization, the Caribbean islands have a complex history characterized by continuous migration, admixture, and demographic change. In the last 20 years, genetics research has transformed our understanding of Caribbean population history and revisited major debates in Caribbean anthropology, such as those surrounding the first peopling of the Antilles and the relationship between ancient Indigenous communities and present-day islanders. Genetics studies have also contributed novel perspectives for understanding pivotal events in Caribbean post-contact history such as European colonization, the Atlantic Slave Trade, and the Asian Indenture system. Here, I discuss the last 20 years of Caribbean genetics research and emphasize the importance of integrating genetics with interdisciplinary historic, archaeological, and anthropological approaches. Such interdisciplinary research is essential for investigating the dynamic history of the Caribbean and characterizing its impact on the biocultural diversity of present-day Caribbean peoples.
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Affiliation(s)
- Maria A Nieves-Colón
- Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
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11
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Mohammed RS, Turner G, Fowler K, Pateman M, Nieves-Colón MA, Fanovich L, Cooke SB, Dávalos LM, Fitzpatrick SM, Giovas CM, Stokowski M, Wrean AA, Kemp M, LeFebvre MJ, Mychajliw AM. Colonial legacies influence biodiversity lessons: how past trade routes and power dynamics shape present-day scientific research and professional opportunities for Caribbean scientists. Am Nat 2022; 200:140-155. [DOI: 10.1086/720154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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12
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South-to-north migration preceded the advent of intensive farming in the Maya region. Nat Commun 2022; 13:1530. [PMID: 35318319 PMCID: PMC8940966 DOI: 10.1038/s41467-022-29158-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 02/25/2022] [Indexed: 11/16/2022] Open
Abstract
The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of the ancestry of all later individuals. This new ancestry derived from a source related to present-day Chibchan speakers living from Costa Rica to Colombia. Its arrival corresponds to the first clear evidence for forest clearing and maize horticulture in what later became the Maya region. The genetic prehistory of central America has not been well explored. Here, the authors find evidence from ancient DNA from twenty individuals who lived in Belize 9,600 to 3,700 years ago of a migration from the south that coincided with the first evidence for forest clearing and the spread of maize horticulture.
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13
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Argüelles JM, Fuentes A, Yáñez B. Analyzing asymmetries and praxis in aDNA research: A bioanthropological critique. AMERICAN ANTHROPOLOGIST 2022. [DOI: 10.1111/aman.13692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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14
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Pedersen MW, Antunes C, De Cahsan B, Moreno-Mayar JV, Sikora M, Vinner L, Mann D, Klimov PB, Black S, Michieli CT, Braig HR, Perotti MA. Ancient human genomes and environmental DNA from the cement attaching 2,000 year-old head lice nits. Mol Biol Evol 2021; 39:6481551. [PMID: 34963129 PMCID: PMC8829908 DOI: 10.1093/molbev/msab351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Over the past few decades, there has been a growing demand for genome analysis of ancient human remains. Destructive sampling is increasingly difficult to obtain for ethical reasons, and standard methods of breaking the skull to access the petrous bone or sampling remaining teeth are often forbidden for curatorial reasons. However, most ancient humans carried head lice and their eggs abound in historical hair specimens. Here we show that host DNA is protected by the cement that glues head lice nits to the hair of ancient Argentinian mummies, 1,500–2,000 years old. The genetic affinities deciphered from genome-wide analyses of this DNA inform that this population migrated from north-west Amazonia to the Andes of central-west Argentina; a result confirmed using the mitochondria of the host lice. The cement preserves ancient environmental DNA of the skin, including the earliest recorded case of Merkel cell polyomavirus. We found that the percentage of human DNA obtained from nit cement equals human DNA obtained from the tooth, yield 2-fold compared with a petrous bone, and 4-fold to a bloodmeal of adult lice a millennium younger. In metric studies of sheaths, the length of the cement negatively correlates with the age of the specimens, whereas hair linear distance between nit and scalp informs about the environmental conditions at the time before death. Ectoparasitic lice sheaths can offer an alternative, nondestructive source of high-quality ancient DNA from a variety of host taxa where bones and teeth are not available and reveal complementary details of their history.
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Affiliation(s)
- Mikkel W Pedersen
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Catia Antunes
- Ecology and Evolutionary Biology Section, School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Binia De Cahsan
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Martin Sikora
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Lasse Vinner
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Darren Mann
- Oxford University Museum of Natural History, Oxford, United Kingdom
| | - Pavel B Klimov
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom.,Department of Ecology and Evolutionary Biology, University of Michigan, Museum of Zoology, Ann Arbor, USA
| | - Stuart Black
- Department of Geography and Environmental Science, Wager Building, University of Reading, Reading, United Kingdom
| | - Catalina Teresa Michieli
- Instituto de Investigaciones Arqueológicas y Museo "Prof. Mariano Gambier", Universidad Nacional de San Juan, San Juan, Argentina
| | - Henk R Braig
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom.,Institute and Museum of Natural Sciences, Faculty of Exact, Physical and Natural Sciences, National University of San Juan, San Juan, Argentina
| | - M Alejandra Perotti
- Ecology and Evolutionary Biology Section, School of Biological Sciences, University of Reading, Reading, United Kingdom
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15
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Razali RM, Rodriguez-Flores J, Ghorbani M, Naeem H, Aamer W, Aliyev E, Jubran A, Clark AG, Fakhro KA, Mokrab Y. Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes. Nat Commun 2021; 12:5929. [PMID: 34642339 PMCID: PMC8511259 DOI: 10.1038/s41467-021-25287-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/02/2021] [Indexed: 12/15/2022] Open
Abstract
Arab populations are largely understudied, notably their genetic structure and history. Here we present an in-depth analysis of 6,218 whole genomes from Qatar, revealing extensive diversity as well as genetic ancestries representing the main founding Arab genealogical lineages of Qahtanite (Peninsular Arabs) and Adnanite (General Arabs and West Eurasian Arabs). We find that Peninsular Arabs are the closest relatives of ancient hunter-gatherers and Neolithic farmers from the Levant, and that founder Arab populations experienced multiple splitting events 12–20 kya, consistent with the aridification of Arabia and farming in the Levant, giving rise to settler and nomadic communities. In terms of recent genetic flow, we show that these ancestries contributed significantly to European, South Asian as well as South American populations, likely as a result of Islamic expansion over the past 1400 years. Notably, we characterize a large cohort of men with the ChrY J1a2b haplogroup (n = 1,491), identifying 29 unique sub-haplogroups. Finally, we leverage genotype novelty to build a reference panel of 12,432 haplotypes, demonstrating improved genotype imputation for both rare and common alleles in Arabs and the wider Middle East. Arab populations are relatively understudied, especially their genetic architecture and historical relationship with early founders of the ancient Near East. Here, the authors examine 6,218 Qatari whole genomes, revealing insights on migration, population history and genetic structure of populations across the Middle Eastern region.
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Affiliation(s)
| | | | | | - Haroon Naeem
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Waleed Aamer
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Ali Jubran
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, New York, NY, USA
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar. .,Weill Cornell Medicine-Qatar, Doha, Qatar. .,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
| | - Younes Mokrab
- Department of Human Genetics, Sidra Medicine, Doha, Qatar. .,Weill Cornell Medicine-Qatar, Doha, Qatar. .,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
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16
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Roca-Rada X, Politis G, Messineo PG, Scheifler N, Scabuzzo C, González M, Harkins KM, Reich D, Souilmi Y, Teixeira JC, Llamas B, Fehren-Schmitz L. Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America. iScience 2021; 24:102553. [PMID: 34142055 PMCID: PMC8188552 DOI: 10.1016/j.isci.2021.102553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/26/2021] [Accepted: 05/14/2021] [Indexed: 01/02/2023] Open
Abstract
The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes-7 of which are novel-from human skeletal remains from 3 Early to Late Holocene archaeological sites. The Pampas present a distinctive genetic makeup compared to other Middle to Late Holocene pre-Columbian SCSA populations. We also report the earliest individuals carrying SCSA-specific mitochondrial haplogroups D1j and D1g from Early and Middle Holocene, respectively. Using these deep calibration time points in Bayesian phylogenetic reconstructions, we suggest that the first settlers of the Pampas were part of a single and rapid dispersal ∼15,600 years ago. Finally, we propose that present-day genetic differences between the Pampas and the rest of the SCSA are due to founder effects, genetic drift, and a partial population replacement ∼9,000 years ago.
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Affiliation(s)
- Xavier Roca-Rada
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Gustavo Politis
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Pablo G. Messineo
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría, Buenos Aires, Argentina
| | - Nahuel Scheifler
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría, Buenos Aires, Argentina
| | - Clara Scabuzzo
- CICYTTP-CONICET, Provincia de Entre Ríos-UADER-División Arqueología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata. Dr. Materi y España (3105), Diamante, Entre Ríos Argentina
| | - Mariela González
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría, Buenos Aires, Argentina
| | - Kelly M. Harkins
- UCSC Paleogenomics Department of Anthropology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics Department of Anthropology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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17
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Fernandes DM, Sirak KA, Ringbauer H, Sedig J, Rohland N, Cheronet O, Mah M, Mallick S, Olalde I, Culleton BJ, Adamski N, Bernardos R, Bravo G, Broomandkhoshbacht N, Callan K, Candilio F, Demetz L, Carlson KSD, Eccles L, Freilich S, George RJ, Lawson AM, Mandl K, Marzaioli F, McCool WC, Oppenheimer J, Özdogan KT, Schattke C, Schmidt R, Stewardson K, Terrasi F, Zalzala F, Antúnez CA, Canosa EV, Colten R, Cucina A, Genchi F, Kraan C, La Pastina F, Lucci M, Maggiolo MV, Marcheco-Teruel B, Maria CT, Martínez C, París I, Pateman M, Simms TM, Sivoli CG, Vilar M, Kennett DJ, Keegan WF, Coppa A, Lipson M, Pinhasi R, Reich D. A genetic history of the pre-contact Caribbean. Nature 2021; 590:103-110. [PMID: 33361817 PMCID: PMC7864882 DOI: 10.1038/s41586-020-03053-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 11/10/2020] [Indexed: 12/27/2022]
Abstract
Humans settled the Caribbean about 6,000 years ago, and ceramic use and intensified agriculture mark a shift from the Archaic to the Ceramic Age at around 2,500 years ago1-3. Here we report genome-wide data from 174 ancient individuals from The Bahamas, Haiti and the Dominican Republic (collectively, Hispaniola), Puerto Rico, Curaçao and Venezuela, which we co-analysed with 89 previously published ancient individuals. Stone-tool-using Caribbean people, who first entered the Caribbean during the Archaic Age, derive from a deeply divergent population that is closest to Central and northern South American individuals; contrary to previous work4, we find no support for ancestry contributed by a population related to North American individuals. Archaic-related lineages were >98% replaced by a genetically homogeneous ceramic-using population related to speakers of languages in the Arawak family from northeast South America; these people moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools that reflect small effective population sizes, which we estimate to be a minimum of 500-1,500 and a maximum of 1,530-8,150 individuals on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the individuals who we analysed lived. Census sizes are unlikely to be more than tenfold larger than effective population sizes, so previous pan-Caribbean estimates of hundreds of thousands of people are too large5,6. Confirming a small and interconnected Ceramic Age population7, we detect 19 pairs of cross-island cousins, close relatives buried around 75 km apart in Hispaniola and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically differentiated groups from the mainland, but instead reflected interactions within an interconnected Caribbean world1,8.
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Affiliation(s)
- Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Kendra A Sirak
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Harald Ringbauer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Jakob Sedig
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Brendan J Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Guillermo Bravo
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Department of Legal Medicine, Toxicology and Physical Anthropology, University of Granada, Granada, Spain
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Anthropology, University of California, Santa Cruz, CA, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Francesca Candilio
- Superintendency of Archaeology, Fine Arts and Landscape for the city of Cagliari and the provinces of Oristano and South Sardinia, Cagliari, Italy
| | - Lea Demetz
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | | | - Laurie Eccles
- Department of Anthropology, The Pennsylvania State University, University Park, PA, USA
| | - Suzanne Freilich
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Richard J George
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Fabio Marzaioli
- Department of Mathematics and Physics, Campania University 'Luigi Vanvitelli', Caserta, Italy
| | - Weston C McCool
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Kadir T Özdogan
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Constanze Schattke
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Ryan Schmidt
- CIBIO-InBIO, University of Porto, Vairão, Portugal
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Filippo Terrasi
- Department of Mathematics and Physics, Campania University 'Luigi Vanvitelli', Caserta, Italy
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | | | - Roger Colten
- Peabody Museum of Natural History, Yale University, New Haven, CT, USA
| | - Andrea Cucina
- Facultad de Ciencias Antropológicas, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Francesco Genchi
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Claudia Kraan
- National Archaeological-Anthropological Memory Management (NAAM), Willemstad, Curaçao
| | | | - Michaela Lucci
- DANTE Laboratory of Diet and Ancient Technology, Sapienza University of Rome, Rome, Italy
| | | | | | | | | | - Ingeborg París
- Instituto de Investigaciones Bioantropológicas y Arqueológicas, Universidad de Los Andes, Mérida, Venezuela
| | - Michael Pateman
- Turks and Caicos National Museum Foundation, Cockburn Town, Turks and Caicos Islands
- AEX Bahamas Maritime Museum, Freeport, Bahamas
| | - Tanya M Simms
- Department of Biology, University of The Bahamas, Nassau, Bahamas
| | - Carlos Garcia Sivoli
- Instituto de Investigaciones Bioantropológicas y Arqueológicas, Universidad de Los Andes, Mérida, Venezuela
| | - Miguel Vilar
- National Geographic Society, Washington, DC, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - William F Keegan
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Alfredo Coppa
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy.
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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18
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Roca-Rada X, Souilmi Y, Teixeira JC, Llamas B. Ancient DNA Studies in Pre-Columbian Mesoamerica. Genes (Basel) 2020; 11:E1346. [PMID: 33202852 PMCID: PMC7696771 DOI: 10.3390/genes11111346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/04/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
Mesoamerica is a historically and culturally defined geographic area comprising current central and south Mexico, Belize, Guatemala, El Salvador, and border regions of Honduras, western Nicaragua, and northwestern Costa Rica. The permanent settling of Mesoamerica was accompanied by the development of agriculture and pottery manufacturing (2500 BCE-150 CE), which led to the rise of several cultures connected by commerce and farming. Hence, Mesoamericans probably carried an invaluable genetic diversity partly lost during the Spanish conquest and the subsequent colonial period. Mesoamerican ancient DNA (aDNA) research has mainly focused on the study of mitochondrial DNA in the Basin of Mexico and the Yucatán Peninsula and its nearby territories, particularly during the Postclassic period (900-1519 CE). Despite limitations associated with the poor preservation of samples in tropical areas, recent methodological improvements pave the way for a deeper analysis of Mesoamerica. Here, we review how aDNA research has helped discern population dynamics patterns in the pre-Columbian Mesoamerican context, how it supports archaeological, linguistic, and anthropological conclusions, and finally, how it offers new working hypotheses.
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Affiliation(s)
- Xavier Roca-Rada
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (Y.S.); (J.C.T.)
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (Y.S.); (J.C.T.)
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (Y.S.); (J.C.T.)
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (Y.S.); (J.C.T.)
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
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19
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D’Atanasio E, Trionfetti F, Bonito M, Sellitto D, Coppa A, Berti A, Trombetta B, Cruciani F. Y Haplogroup Diversity of the Dominican Republic: Reconstructing the Effect of the European Colonization and the Trans-Atlantic Slave Trades. Genome Biol Evol 2020; 12:1579-1590. [PMID: 32835369 PMCID: PMC7523727 DOI: 10.1093/gbe/evaa176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2020] [Indexed: 12/12/2022] Open
Abstract
The Dominican Republic is one of the two countries on the Hispaniola island, which is part of the Antilles. Hispaniola was affected by the European colonization and massive deportation of African slaves since the XVI century and these events heavily shaped the genetic composition of the present-day population. To shed light about the effect of the European rules, we analyzed 92 single nucleotide polymorphisms on the Y chromosome in 182 Dominican individuals from three different locations. The Dominican Y haplogroup composition was characterized by an excess of northern African/European lineages (59%), followed by the African clades (38%), whereas the Native-American lineages were rare (3%). The comparison with the mitochondrial DNA variability, dominated by African clades, revealed a sex-biased admixture pattern, in line with the colonial society dominated by European men. When other Caribbean and non-Caribbean former colonies were also considered, we noted a difference between territories under a Spanish rule (like the Dominican Republic) and British/French rule, with the former characterized by an excess of European Y lineages reflecting the more permissive Iberian legislation about mixed people and slavery. Finally, we analyzed the distribution in Africa of the Dominican lineages with a putative African origin, mainly focusing on central and western Africa, which were the main sources of African slaves. We found that most (83%) of the African lineages observed in Santo Domingo have a central African ancestry, suggesting that most of the slaves were deported from regions.
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Affiliation(s)
- Eugenia D’Atanasio
- Istituto di Biologia e Patologia Molecolari, CNR, Roma, Italy
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Flavia Trionfetti
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Maria Bonito
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | | | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Andrea Berti
- Reparto CC Investigazioni Scientifiche di Roma, Sezione di Biologia, Rome, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Fulvio Cruciani
- Istituto di Biologia e Patologia Molecolari, CNR, Roma, Italy
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, Italy
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Nägele K, Posth C, Iraeta Orbegozo M, Chinique de Armas Y, Hernández Godoy ST, González Herrera UM, Nieves-Colón MA, Sandoval-Velasco M, Mylopotamitaki D, Radzeviciute R, Laffoon J, Pestle WJ, Ramos-Madrigal J, Lamnidis TC, Schaffer WC, Carr RS, Day JS, Arredondo Antúnez C, Rangel Rivero A, Martínez-Fuentes AJ, Crespo-Torres E, Roksandic I, Stone AC, Lalueza-Fox C, Hoogland M, Roksandic M, Hofman CL, Krause J, Schroeder H. Genomic insights into the early peopling of the Caribbean. Science 2020; 369:456-460. [PMID: 32499399 DOI: 10.1126/science.aba8697] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/18/2020] [Indexed: 12/31/2022]
Abstract
The Caribbean was one of the last regions of the Americas to be settled by humans, but where they came from and how and when they reached the islands remain unclear. We generated genome-wide data for 93 ancient Caribbean islanders dating between 3200 and 400 calibrated years before the present and found evidence of at least three separate dispersals into the region, including two early dispersals into the Western Caribbean, one of which seems connected to radiation events in North America. This was followed by a later expansion from South America. We also detected genetic differences between the early settlers and the newcomers from South America, with almost no evidence of admixture. Our results add to our understanding of the initial peopling of the Caribbean and the movements of Archaic Age peoples in the Americas.
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Affiliation(s)
- Kathrin Nägele
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Jena, Germany.,Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Miren Iraeta Orbegozo
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Silvia Teresita Hernández Godoy
- Grupo de Investigación y Desarrollo, Dirección Provincial de Cultura, Matanzas, Cuba.,Universidad de Matanzas, Matanzas, Cuba
| | | | - Maria A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Marcela Sandoval-Velasco
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dorothea Mylopotamitaki
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rita Radzeviciute
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Jason Laffoon
- Faculty of Archaeology, Leiden University, Leiden, Netherlands
| | | | - Jazmin Ramos-Madrigal
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - William C Schaffer
- Liberal Arts Department, Phoenix College, Phoenix, AZ, USA.,Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA
| | - Robert S Carr
- Archaeological and Historical Conservancy Inc., Davie, FL, USA
| | - Jane S Day
- Research Atlantica Inc., Boca Raton, FL, USA
| | | | - Armando Rangel Rivero
- Museo Antropológico Montané, Facultad de Biología, Universidad de La Habana, Havana, Cuba
| | | | - Edwin Crespo-Torres
- Departamento de Sociología y Antropología, Universidad de Puerto Rico Rio Piedras, San Juan, Puerto Rico
| | - Ivan Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, Spanish National Research Council (CSIC)-Universitat Pompeu Fabra, Barcelona, Spain
| | - Menno Hoogland
- Faculty of Archaeology, Leiden University, Leiden, Netherlands.,Royal Netherlands Institute of Southeast Asian and Caribbean Studies, Leiden, Netherlands
| | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada
| | - Corinne L Hofman
- Faculty of Archaeology, Leiden University, Leiden, Netherlands.,Royal Netherlands Institute of Southeast Asian and Caribbean Studies, Leiden, Netherlands
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Hannes Schroeder
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Faculty of Archaeology, Leiden University, Leiden, Netherlands
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Kemp ME, Mychajliw AM, Wadman J, Goldberg A. 7000 years of turnover: historical contingency and human niche construction shape the Caribbean's Anthropocene biota. Proc Biol Sci 2020; 287:20200447. [PMID: 32429803 PMCID: PMC7287370 DOI: 10.1098/rspb.2020.0447] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The human-mediated movement of species across biogeographic boundaries-whether intentional or accidental-is dramatically reshaping the modern world. Yet humans have been reshaping ecosystems and translocating species for millennia, and acknowledging the deeper roots of these phenomena is important for contextualizing present-day biodiversity loss, ecosystem functioning and management needs. Here, we present the first database of terrestrial vertebrate species introductions spanning the entire anthropogenic history of a system: the Caribbean. We employ this approximately 7000-year dataset to assess the roles of historical contingency and priority effects in shaping present-day community structure and conservation outcomes, finding that serial human colonization events contributed to habitat modifications and species extinctions that shaped the trajectories of subsequent species introductions by other human groups. We contextualized spatial and temporal patterns of species introductions within cultural practices and population histories of Indigenous, colonial and modern human societies, and show that the taxonomic and biogeographic diversity of introduced species reflects diversifying reasons for species introductions through time. Recognition of the complex social and economic structures across the 7000-year human history of the Caribbean provides the necessary context for interpreting the formation of an Anthropocene biota.
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Affiliation(s)
- Melissa E Kemp
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Alexis M Mychajliw
- La Brea Tar Pits and Museum, 5801 Wilshire Blvd, Los Angeles, CA 90036, USA.,Institute of Low Temperature Science, Hokkaido University, Kita-19 Nishi-8 Kita-ku, Sapporo 060-0819, Japan.,Laboratories of Molecular Anthropology and Microbiome Research, 101 David L. Boren Blvd, Norman, OK 73019, USA
| | - Jenna Wadman
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
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22
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Ross AH, Keegan WF, Pateman MP, Young CB. Faces Divulge the Origins of Caribbean Prehistoric Inhabitants. Sci Rep 2020; 10:147. [PMID: 31924849 PMCID: PMC6954214 DOI: 10.1038/s41598-019-56929-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022] Open
Abstract
The origins of the first peoples to colonize the Caribbean Islands have been the subject of intense debate for over 30 years. Competing hypotheses have identified five separate migrations from the mainland with a separate debate concerning the colonization of The Bahamas. Significant differences in the facial morphology of the pre-Columbian inhabitants of Hispaniola and Cuba led to the present study of Lucayan skulls from The Bahamas. The goal was to determine which group the native Lucayans more closely resembled to resolve this long-standing dispute. The results indicate that they are related to groups from Hispaniola and Jamaica and not to Cuban inhabitants. This study clarified the larger picture of Caribbean migrations and supports evidence for a Carib invasion of the Greater Antilles around AD 800.
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Affiliation(s)
- Ann H Ross
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
- Research Associate, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA.
| | - William F Keegan
- Curator of Caribbean Archaeology, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Michael P Pateman
- Director, Turks & Caicos National Museum, Grand Turk, Turks & Caicos Islands, Turks, USA
| | - Colleen B Young
- Department of Anthropology, University of Missouri, Columbia, MO, 65203, USA
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