Fig 1 - uploaded by Sally Wasef
Content may be subject to copyright.
Details of the locations and language groups of Aboriginal Australian samples. Light orange shading indicates the distribution and location of PamaNyungan language families. Orange shading indicates the distribution of non-Pama-Nyungan language families. Dashed lines show the approximate distribution of accepted major language subgroups as published in (20) with language names in italics. Red symbols indicate previously published mitochondrial or nuclear genomes; blue symbols indicate new unpublished data. Circles indicate contemporary Aboriginal Australian samples, and stars represent ancient individuals. Sample code abbreviations have been included in parentheses.
Source publication
After European colonization, the ancestral remains of Indigenous people were often collected for scientific research or display in museum collections. For many decades, Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return. However, many of these remains have no recorded provenance, making their repa...
Contexts in source publication
Context 1
... constructed comparative contemporary mitochondrial and nuclear DNA datasets based on self-reported language group affilia- tions (16,20), as well as geographic locations (Fig. 1). The contem- porary nuclear DNA dataset comprised 100 high-coverage nuclear genomes of Pama-Nyungan language-speaking Aboriginal Australians. A total of 112 mitogenomes showing Aboriginal Australian-specific mitochondrial haplogroups were included in the mitochondrial DNA analyses, including 17 previously published genomes (table S3) ...
Context 2
... Australian individuals (62.1%), the closest contempo- rary match was an individual from the same geographic region (within 235 km). Within this group, nine ancient individuals could be matched to a contemporary individual within 100 km, and six could be matched to individuals from the exact location from which the ancient remains originated (Fig. ...
Context 3
... finding and may potentially inform the time depth of these practices, it is less helpful for repatriation. In two instances (6.9%), the closest ancient mitochondrial matches were not from the same geo- graphic locations. In this case, the closest contemporary matches were individuals from opposite sides of Cape York Peninsula, some 635 km away ( Fig. 1). As the return to Place and Country of ancestral remains is of paramount importance to many Aboriginal Australian commu- nities, repatriation to an incorrect Country would be problematic. Therefore, the use of mitochondrial DNA alone is not recommended for repatriation. ...
Context 4
... constructed comparative contemporary mitochondrial and nuclear DNA datasets based on self-reported language group affilia- tions (16,20), as well as geographic locations (Fig. 1). The contem- porary nuclear DNA dataset comprised 100 high-coverage nuclear genomes of Pama-Nyungan language-speaking Aboriginal Australians. A total of 112 mitogenomes showing Aboriginal Australian-specific mitochondrial haplogroups were included in the mitochondrial DNA analyses, including 17 previously published genomes (table S3) ...
Context 5
... Australian individuals (62.1%), the closest contempo- rary match was an individual from the same geographic region (within 235 km). Within this group, nine ancient individuals could be matched to a contemporary individual within 100 km, and six could be matched to individuals from the exact location from which the ancient remains originated (Fig. ...
Context 6
... finding and may potentially inform the time depth of these practices, it is less helpful for repatriation. In two instances (6.9%), the closest ancient mitochondrial matches were not from the same geo- graphic locations. In this case, the closest contemporary matches were individuals from opposite sides of Cape York Peninsula, some 635 km away ( Fig. 1). As the return to Place and Country of ancestral remains is of paramount importance to many Aboriginal Australian commu- nities, repatriation to an incorrect Country would be problematic. Therefore, the use of mitochondrial DNA alone is not recommended for repatriation. ...
Similar publications
After European colonization, the ancestral remains of Indigenous people were often collected for scientific research or display in museum collections. For many decades, Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return. However, many of these remains have no recorded provenance, making their repa...
Citations
... DNA analysis is being proposed as a means of determining relationships between recently excavated ancestral remains and living populations (e.g. Wright et al. 2018), but as far as we are aware has yet to be used in relation to museum collections. Ancient DNA analyses have been successfully applied to determine Indigenous ancestry for excavated Indigenous Ancestral Remains in the USA and Canada, although in such cases, provenance is known so the issues are different. ...
... While thousands of paleogenomes have now been generated from remains found in temperate climates, paleogenomes from humid tropical regions remain rare due to the comparatively poor preservation of genetic material [47]. Nonetheless, the first paleogenomic studies of individuals from Mainland Southeast Asia (MSEA) [48], Oceania [49][50][51][52], and ISEA [53] have begun to emerge in the past five years, including the first paleogenomes from Wallacea. ...
Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic diversity. However, a comprehensive understanding of these fundamental questions has been impeded by the lack of inclusion of many Indigenous populations in genomic surveys, including those from the Wallacean archipelago (which comprises islands of present-day Indonesia located east and west of Wallace’s and Lydekker’s Lines, respectively) and the former continent of Sahul (which once combined New Guinea and Australia during lower sea levels in the Pleistocene). Notably, these regions have been important areas of human evolution throughout the Late Pleistocene, as documented by diverse fossil and archaeological records which attest to the regional presence of multiple hominin species prior to the arrival of anatomically modern human (AMH) migrants. In this review, we collate and discuss key findings from the past decade of population genetic and phylogeographic literature focussed on the hominin history in Wallacea and Sahul. Specifically, we examine the evidence for the timing and direction of the ancient AMH migratory movements and subsequent hominin mixing events, emphasising several novel but consistent results that have important implications for addressing these questions. Finally, we suggest potentially lucrative directions for future genetic research in this key region of human evolution.
... There has been advocacy for an African American Graves Protection and Repatriation Act modeled on the existing NAGPRA (Dunnavant et al., 2021). A recent study suggests that it may be possible in the future to use genomic methods to identify the source of remains for which provenance is unknown (Wright et al., 2018). ...
As organizations that facilitate collaboration and communication, scientific societies have an opportunity, and a responsibility, to drive inclusion, diversity, equity, and accessibility in science in academia. The American Association for Anatomy (AAA), with its expressed and practiced culture of engagement, can serve as a model of best practice for other professional associations working to become more inclusive of individuals from historically underrepresented groups. In this publication, we acknowledge anatomy's exclusionary past, describe the present face of science in academia, and provide recommendations for societies, including the AAA, to accelerate change in academia. We are advocating for scientific societies to investigate inequities and revise practices for inclusivity; develop and empower underrepresented minority leadership; and commit resources in a sustained manner as an investment in underrepresented scientists who bring diverse perspectives and lived experiences to science in academia.
... Unfortunately, similar quality genomic datasets for contemporary Indigenous Australians do not currently exist. From a genomics perspective, Australia remains relatively understudied and for some locations the available evidence is restricted to mitochondrial data only (van Holst Pellekaan, 2013;Malaspinas et al., 2016;Bergström et al., 2016;Nagle et al., 2017;Tobler et al., 2017;Wright et al., 2018;Wasef et al., 2020). ...
... A serious limitation on research moving forward is the issue of who can access and use these data. As an example, the whole modern genomic dataset for Indigenous Australians, which is one of the largest, is currently not publicly shared (Malaspinas et al., 2016;Wright et al., 2018). These restrictions are a point of considerable concern for Indigenous communities and many researchers (Kowal et al., 2017;Wasef et al., 2020) and greatly limit opportunities for engagement with Aboriginal partners. ...
... Together we showed that the complexities of human social life (such as inter-tribal marriage) and the impacts of colonisation on Indigenous Australians meant that even full genome comparisons may not correctly identify an individual's tribal affiliation . In addition to new findings the research also illustrated how future research relating to the biology of Indigenous Australians could be undertaken (Wright et al., 2018;Collard et al., 2019;Wasef et al., 2020;Adams et al., 2020). ...
It has long been accepted that the Indigenous groups of Australia's Cape York Peninsula have numerous cultural traits that were adopted from people in New Guinea and/or the Torres Strait Islands after the formation of the Torres Strait around 8000 years ago. However, opinions differ on whether the movement of the traits in question was accompanied by gene flow events. Some argue for a significant amount of gene flow resulting from voyages from New Guinea and the Torres Strait Islands down the east coast of Cape York. Others contend that there was only contact at the northern end of the Cape and that the cultural traits spread through down-the-line transmission. In recent years partnerships between Australian institutions and Indigenous communities in Cape York have led to new genetic research that provides benefits to both parties. We review the currently available genetic data that have the potential to shed light on this issue, concluding that the data are inconsistent with significant gene flow between Indigenous Australians and Papuan people between 8000 years ago and the colonial period. There are indications of gene flow, but it most likely occurred in the Pleistocene rather than the Holocene. As such, the currently available genomic data do not support the hypothesis that the diffusion of cultural traits from New Guinea and/or the Torres Strait Islands into Cape York was accompanied by gene flow. The data suggest instead that the cultural traits most probably spread via down-the-line trade, exchange, and imitation. Our review highlights the gaps in the available genomic information from contemporary and ancestral descendants of Australia's first settlers, and we suggest that researchers adopt a more collaborative approach, involving Indigenous communities and their knowledge in project design, data collection, and dissemination, in future genomic studies in Australia.
... Where appropriate, permission was also obtained from the Queensland Parks and Wildlife Service. Samples from living people were obtained under a permit issued by the Griffith University Human Research Ethics Committee (see Malaspinas et al. [2016] and Wright et al. [2018b] for details). ...
... A second study to which the project contributed focused on the possibility of using genomic data as a basis for repatriating unprovenanced Aboriginal remains (J.L. Wright et al. 2018b). In this study, ten nDNA and 27 mtDNA genomes from pre-European (up to 1540 BP) individuals of known provenance were sequenced and compared to 100 modern Aboriginal genomes. ...
... They were able to further elucidate the nature of these interactions by showing that the spread of genes was unidirectional, from New Guinea to Australia. In line with these findings, Wright et al. (2018b) estimated that their skeletal samples from Cairns and the Flinders Island Group had ca. 13% Papuan-related ancestry. ...
In this paper we outline a worked example of the combined use of genetic data and archaeological evidence. The project focuses on Queensland’s Cape York Peninsula and has two goals. One is to shed new light on the population history of the region. The other is to develop a methodology to facilitate repatriation of the remains of Aboriginal Australians. After providing some background to the project and outlining its main activities, we summarize our key findings to date. Subsequently, we discuss what the project has taught us about the prehistory of Cape York, the potential for DNA research and isotope chemistry to assist research institutions and Aboriginal communities with the repatriation of unaffiliated remains, and the process of conducting combined genetic and archaeological research.
Aboriginal manufacture and use of pottery was unknown in Australia prior to European settlement, despite well-known ceramic-making traditions in southern Papua New Guinea, eastern Indonesia, and the western Pacific. The absence of ancient pottery manufacture in mainland Australia has long puzzled researchers given other documented deep time Aboriginal exchange networks across the continent and the close proximity of pottery-bearing Lapita and post-Lapita maritime communities in the western Pacific with ocean-going watercraft and sophisticated navigation abilities. We report the oldest securely dated ceramics found in Australia from archaeological excavations on Jiigurru (Lizard Island Group) on the Great Barrier Reef, northeast Australia. Comprehensive radiocarbon dating and Bayesian modelling constrains ceramic deposition to between 2950–2545 cal BP and 1970–1815 cal BP. This timing overlaps with late Lapita and post-Lapita ceramic traditions of southern Papua New Guinea. Geological characterisation of the sherds strongly suggests local manufacture as the vessels belong to three temper and clay groups locally sourced to northeast Australia, and most likely to Jiigurru. The oldest occupation layers date to 6510–5790 cal BP, making Jiigurru the earliest offshore island occupied on the northern Great Barrier Reef. The results demonstrate that northeast Australian First Nations communities had sophisticated canoe voyaging technology and open-sea navigational skills and were intimately engaged in ancient maritime networks, connecting them with peoples, knowledges, and technologies across the Coral Sea region.
Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference datasets1–3. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here we apply population-scale whole-genome long-read sequencing⁴ to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large insertion–deletion variants (20–49 bp; n = 136,797), structural variants (50 b–50 kb; n = 159,912) and regions of variable copy number (>50 kb; n = 156). The majority of variants are composed of tandem repeat or interspersed mobile element sequences (up to 90%) and have not been previously annotated (up to 62%). A large fraction of structural variants appear to be exclusive to Indigenous Australians (12% lower-bound estimate) and most of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short tandem repeats throughout the genome to characterize allelic diversity at 50 known disease loci⁵, uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among short tandem repeat sequences. Our study sheds new light on the dimensions and dynamics of genomic structural variation within and beyond Australia.
Ancient DNA (aDNA) has added a wealth of information about our species’ history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples.
Since the arrest of the Golden State Killer in the US in April 2018, forensic geneticists have been increasingly interested in the investigative genetic genealogy (IGG) method. While this method has already been in practical use as a powerful tool for criminal investigation, we have yet to know well the limitations and potential risks. In this current study, we performed an evaluation study focusing on degraded DNA using the Affymetrix Genome-Wide Human SNP Array 6.0 platform (Thermo Fisher Scientific). We revealed one of the potential problems that occur during SNP genotype determination using a microarray-based platform. Our analysis results indicated that the SNP profiles derived from degraded DNA contained many false heterozygous SNPs. In addition, it was confirmed that the total amount of probe signal intensity on microarray chips derived from degraded DNA decreased significantly. Because the conventional analysis algorithm performs normalization during genotype determination, we concluded that noise signals could be genotype-called. To address this issue, we proposed a novel microarray data analysis method without normalization (nMAP). Although the nMAP algorithm resulted in a low call rate, it substantially improved genotyping accuracy. Finally, we confirmed the usefulness of the nMAP algorithm for kinship inferences. These findings and the nMAP algorithm will make a contribution to the advance of the IGG method.
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.
