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Martin-Roy R, Thyrring J, Mata X, Bangsgaard P, Bennike O, Christiansen G, Funder S, Gotfredsen AB, Gregersen KM, Hansen CH, Ilsøe PC, Klassen L, Kristensen IK, Ravnholt GB, Marin F, Der Sarkissian C. Advancing responsible genomic analyses of ancient mollusc shells. PLoS One 2024; 19:e0302646. [PMID: 38709766 PMCID: PMC11073703 DOI: 10.1371/journal.pone.0302646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
The analysis of the DNA entrapped in ancient shells of molluscs has the potential to shed light on the evolution and ecology of this very diverse phylum. Ancient genomics could help reconstruct the responses of molluscs to past climate change, pollution, and human subsistence practices at unprecedented temporal resolutions. Applications are however still in their infancy, partly due to our limited knowledge of DNA preservation in calcium carbonate shells and the need for optimized methods for responsible genomic data generation. To improve ancient shell genomic analyses, we applied high-throughput DNA sequencing to 27 Mytilus mussel shells dated to ~111-6500 years Before Present, and investigated the impact, on DNA recovery, of shell imaging, DNA extraction protocols and shell sub-sampling strategies. First, we detected no quantitative or qualitative deleterious effect of micro-computed tomography for recording shell 3D morphological information prior to sub-sampling. Then, we showed that double-digestion and bleach treatment of shell powder prior to silica-based DNA extraction improves shell DNA recovery, also suggesting that DNA is protected in preservation niches within ancient shells. Finally, all layers that compose Mytilus shells, i.e., the nacreous (aragonite) and prismatic (calcite) carbonate layers, with or without the outer organic layer (periostracum) proved to be valuable DNA reservoirs, with aragonite appearing as the best substrate for genomic analyses. Our work contributes to the understanding of long-term molecular preservation in biominerals and we anticipate that resulting recommendations will be helpful for future efficient and responsible genomic analyses of ancient mollusc shells.
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Affiliation(s)
- Raphaël Martin-Roy
- Centre for Anthropobiology and Genomics of Toulouse, UMR5288, CNRS, University Paul Sabatier, Toulouse, France
| | - Jakob Thyrring
- Department of Ecoscience, Aarhus University, Aarhus, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Xavier Mata
- Centre for Anthropobiology and Genomics of Toulouse, UMR5288, CNRS, University Paul Sabatier, Toulouse, France
| | - Pernille Bangsgaard
- Globe Institute, Section for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Ole Bennike
- Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | | | - Svend Funder
- Globe Institute, Section for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Peter Carsten Ilsøe
- Globe Institute, Section for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Frédéric Marin
- Biogéosciences, UMR6282, CNRS-EPHE-uB, University of Burgundy, EPHE, Dijon, France
| | - Clio Der Sarkissian
- Centre for Anthropobiology and Genomics of Toulouse, UMR5288, CNRS, University Paul Sabatier, Toulouse, France
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Gancz AS, Wright SL, Weyrich LS. Ancient human dental calculus metadata collection and sampling strategies: Recommendations for best practices. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 183:e24871. [PMID: 37994571 DOI: 10.1002/ajpa.24871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/26/2023] [Accepted: 10/18/2023] [Indexed: 11/24/2023]
Abstract
OBJECTIVES Ancient human dental calculus is a unique, nonrenewable biological resource encapsulating key information about the diets, lifestyles, and health conditions of past individuals and populations. With compounding calls its destructive analysis, it is imperative to refine the ways in which the scientific community documents, samples, and analyzes dental calculus so as to maximize its utility to the public and scientific community. MATERIALS AND METHODS Our research team conducted an IRB-approved survey of dental calculus researchers with diverse academic backgrounds, research foci, and analytical specializations. RESULTS This survey reveals variation in how metadata is collected and utilized across different subdisciplines and highlights how these differences have profound implications for dental calculus research. Moreover, the survey suggests the need for more communication between those who excavate, curate, and analyze biomolecular data from dental calculus. DISCUSSION Challenges in cross-disciplinary communication limit researchers' ability to effectively utilize samples in rigorous and reproducible ways. Specifically, the lack of standardized skeletal and dental metadata recording and contamination avoidance procedures hinder downstream anthropological applications, as well as the pursuit of broader paleodemographic and paleoepidemiological inquiries that rely on more complete information about the individuals sampled. To provide a path forward toward more ethical and standardized dental calculus sampling and documentation approaches, we review the current methods by which skeletal and dental metadata are recorded. We also describe trends in sampling and contamination-control approaches. Finally, we use that information to suggest new guidelines for ancient dental calculus documentation and sampling strategies that will improve research practices in the future.
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Affiliation(s)
- Abigail S Gancz
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sterling L Wright
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Laura S Weyrich
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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3
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Orlando L. The history of the Coast Salish "woolly dogs". Science 2023; 382:1236-1237. [PMID: 38096278 DOI: 10.1126/science.adm6959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
DNA and traditional knowledge reveal the history of an extinct dog bred for its wool.
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Affiliation(s)
- Ludovic Orlando
- Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR5288, Université Paul Sabatier, Toulouse, France
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4
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Claw KG, Nashoba A. Indigenous diversity in Australia's DNA tapestry unlocked for genetic equity. Nature 2023; 624:536-537. [PMID: 38093045 DOI: 10.1038/d41586-023-03785-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
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Kralick AE, Canington SL, Eller AR, McGrath K. Specimens as individuals: Four interventions and recommendations for great ape skeletal collections research and curation. Evol Anthropol 2023; 32:336-355. [PMID: 37750542 DOI: 10.1002/evan.22002] [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: 04/30/2022] [Revised: 04/14/2023] [Accepted: 08/01/2023] [Indexed: 09/27/2023]
Abstract
Extensive discourse surrounds the ethics of human skeletal research and curation, but there has yet to be a similar discussion of the treatment of great ape skeletal remains, despite the clear interest in their ethical treatment when alive. Here we trace the history of apes who were killed and collected for natural history museums during the early 20th century and showcase how the guiding research questions of the colonial era continue to influence scholarship. We discuss best practices for improving industry and academic standards of research on, and the curation of, ape remains. The suggested interventions involve restoring individual identity and narrative to great apes while engaging with contextual reflexivity and decolonial theory. The resulting recommendations include contextualizing the individual, piecing individuals back together, challenging/questioning the captive-wild dichotomy, and collaborative international conversations. Our objective is to encourage a conversation regarding ethical and theoretical considerations in great ape skeletal remains research.
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Affiliation(s)
- Alexandra E Kralick
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephanie L Canington
- Center for Functional Anatomy and Evolution, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Basic and Translational Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrea R Eller
- Department of Anthropology, Smithsonian National Museum of Natural History, Washington, District of Columbia, USA
| | - Kate McGrath
- Department of Anthropology, SUNY Oneonta, Oneonta, New York, USA
- Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia, USA
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Houldcroft CJ, Underdown S. Infectious disease in the Pleistocene: Old friends or old foes? AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:513-531. [PMID: 38006200 DOI: 10.1002/ajpa.24737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 11/26/2023]
Abstract
The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.
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Affiliation(s)
| | - Simon Underdown
- Human Origins and Palaeoenvironmental Research Group, School of Social Sciences, Oxford Brookes University, Oxford, UK
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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Tamburrini C, Dahinten SL, Saihueque RRR, Ávila-Arcos MC, Parolin ML. Towards an ethical and legal framework in archeogenomics: A local case in the Atlantic coast of central Patagonia. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:161-176. [PMID: 37525572 DOI: 10.1002/ajpa.24821] [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: 10/17/2022] [Revised: 06/12/2023] [Accepted: 07/09/2023] [Indexed: 08/02/2023]
Abstract
Ethical discussions around ancient DNA (aDNA) research predate the technological breakthroughs that led to the accelerated generation of ancient genomic data, revealing a long-due need to address these aspects in the field. Given the diverse conflicts that genomics has raised towards the communities associated with the Non-living Human Ancestors under study, it has been suggested that the ethical and legal implications of genetically studying present-day and ancient human populations should be considered case-by-case. Nevertheless, the discussions have focused on US and European perspectives. To contribute from a local and Latin American position to the problem, we present the history of consensus and disagreement of the relationships between scientists and Indigenous communities of the Atlantic coast of the central Argentinian Patagonia. We describe how these relationships resulted in the approval of a groundbreaking provincial law that acknowledges the Indigenous community's right to be involved in decision-making concerning their Ancestors. In addition, we emphasize how these established relationships allowed the development of aDNA studies. With this background, we address the main ethical concerns of genomic studies of Ancestors identified in the reference literature and commit to applying some of the recommendations suggested in those ethical guidelines. Then, we reflect on possible negative consequences of ongoing research and propose some suggestions based on personal experiences that will contribute to moving the ethical field towards a more contextualized science with a local perspective.
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Affiliation(s)
- Camila Tamburrini
- Instituto de Diversidad y Evolución Austral (IDEAus, CCT CONICET-CENPAT), Puerto Madryn, Chubut, Argentina
| | - Silvia Lucrecia Dahinten
- Instituto de Diversidad y Evolución Austral (IDEAus, CCT CONICET-CENPAT), Puerto Madryn, Chubut, Argentina
| | - Rubén Ricardo Romero Saihueque
- Dirección de Asuntos Indígenas, Subsecretaría de Derechos Humanos, Ministerio de Gobierno y Justicia del Chubut, Rawson, Chubut, Argentina
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de Mexico (UNAM), Santiago de Querétaro, Mexico
| | - María Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus, CCT CONICET-CENPAT), Puerto Madryn, Chubut, Argentina
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Cortez AD, Lippert D, Davis JL, Nicholas G, Malhi RS, Weyrich LS, Claw KG, Bader AC, Colwell C. Extracting the practices of paleogenomics: A study of ancient DNA labs and research in relation to Native Americans and Indigenous peoples. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023. [PMID: 36799477 DOI: 10.1002/ajpa.24714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/18/2023]
Abstract
OBJECTIVES The field of paleogenomics has rapidly grown, influencing a range of scientific fields and drawing notice from the public. In the United States, this work is especially salient for Native Americans, who are frequently the subject of ancient DNA analyses, but are less frequently included as researchers, collaborators, or advisors. This article seeks to deepen our understanding of the current state of paleogenomics so that the field can center Indigenous peoples and their experiences, knowledges, and stakes in the research process. MATERIALS AND METHODS We conducted 31 semi-structured interviews with researchers from three paleogenomics labs located in North America and Europe. We used a responsive interviewing technique where the interview resembled a conversation around a set of questions that could change depending upon the interviewee's answers and experiences. We then employed a theme-based analysis of the interviews. RESULTS Through this analysis, we are able to identify practices in the field related to training, the structuring of labs and projects, consent, data control, Ancestor care, and funding that influence various forms of engagement with Indigenous peoples, and which foster or delimit ethical commitments to descendant communities. DISCUSSION This research not only elucidates contemporary practices in paleogenomics labs but also identifies specific areas of potential intervention to help researchers work toward ethical and collaborative paleogenomic research with Indigenous peoples. Using these results, researchers and community advocates can work toward reorienting the field of paleogenomics toward ethical research with Indigenous peoples.
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Affiliation(s)
| | - Dorothy Lippert
- Repatriation Office, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jenny L Davis
- American Indian Studies, Department of Anthropology, University of Illinois Urbana Champaign, Champaign, Illinois, USA
| | - George Nicholas
- Department of Archaeology, Simon Fraser University, Burnaby, Canada
| | - Ripan S Malhi
- Department of Anthropology, Carl R Woese Institute for Genomic Biology, University of Illinois Urbana Champaign, Champaign, Illinois, USA
| | - Laura S Weyrich
- Department of Anthropology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Katrina G Claw
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Alyssa C Bader
- Department of Anthropology, McGill University, Montreal, Canada
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9
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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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Cerdeña JP, Grubbs V, Non AL. Racialising genetic risk: assumptions, realities, and recommendations. Lancet 2022; 400:2147-2154. [PMID: 36502852 DOI: 10.1016/s0140-6736(22)02040-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 09/07/2022] [Accepted: 10/14/2022] [Indexed: 12/13/2022]
Affiliation(s)
- Jessica P Cerdeña
- Yale School of Medicine, Yale University, New Haven, CT, USA; Department of Anthropology, University of Connecticut, Storrs, CT, USA
| | - Vanessa Grubbs
- Department of Ambulatory and Preventive Medicine, Alameda Health System, Oakland, CA, USA
| | - Amy L Non
- Department of Anthropology, University of California, San Diego, CA, USA.
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