1.1 Sedimentary ancient DNA

Sedimentary ancient DNA (sedaDNA) can be found both intracellularly in small pieces of tissue, and extracellularly, particularly adsorbed with negatively charged minerals and biomolecules (Massilani et al., 2022; Pedersen et al., 2015; Pedreira-Segade et al., 2018; Wnuk et al., 2020). Allophane from volcanic soils and montmorillonite clay mineral have a high affinity to nucleic acids (Huang et al., 2014) and while these molecular interactions can protect the DNA molecules over time (Blum et al., 1997), they may also impede the DNA extraction and in vitro amplification processes (Pedersen et al., 2015; Wnuk et al., 2020). For example, humic acids are known inhibitors of enzymes used to amplify DNA in vitro—using a standard molecular biology method called polymerase chain reaction (PCR; Simmons & Cross, 2013, p. 276). The humic acids and metal ions commonly found in soils and sands have similar characteristics to DNA molecules and as such bind nucleotides and inhibit DNA isolation (Pedersen et al., 2015; Wnuk et al., 2020). Horizon-stabilising techniques have indicated that targeting organic inclusions in sediment samples impregnated with resin can yield high DNA content and limit these inhibiting factors, resulting in better DNA sequencing library preparation efficiency than when analysing loose sediments (Massilani et al., 2022).

1.2 Non-ecological applications of sedaDNA

This article focusses on the ecological potential of sedaDNA, but there are potential impacts in other academic and social contexts. It is important to note the interdisciplinary potential of sedaDNA research in fields such as archaeology, zoology, medicine, evolutionary biology and related disciplines. For example, sedaDNA has been used to identify anatomically modern humans and hominins (Gelabert et al., 2021; Slon et al., 2017; Vernot et al., 2021; Zavala et al., 2021), providing new lines of evidence that complement traditional archaeological science. The identification of ancient humans and hominins through sedaDNA analysis can have significant social and cultural implications, particularly for Indigenous communities by providing a new dimension to life history studies of Indigenous ancestors. Furthermore, sedaDNA research can have significant implications for the study of evolutionary biology and the origins of species. By analysing sedaDNA from a range of sedimentary contexts, researchers can gain insights into the evolutionary history of various organisms, including those that are difficult to study through traditional methods. This information can have practical applications, such as in the conservation of endangered species or the management of invasive species.

1.3 Using sedaDNA in ecological studies

The use of sedaDNA in ecological studies is currently limited, but it is emerging as a powerful methodological framework as specialised statistical analyses are being developed (Chen & Ficetola, 2020). Techniques for the extraction, isolation and downstream analysis of ancient DNA are now so advanced that ancient sediments can be used as a genetic substrate to complement, or replace entirely, traditional subfossil taxonomic identification (Pansu et al., 2015; Pérez et al., 2022; Slon et al., 2017; Thomas et al., 2022). Recovered sedaDNA comes from across the tree of life, including microbes, plants and animals (Chen & Ficetola, 2020; Pansu et al., 2015; Pérez et al., 2022; Slon et al., 2017; Thomas et al., 2022; Willerslev et al., 2003).

The prospect of extracting genetic material from sediments with stable strata would allow a high-resolution temporal view of the landscape and offer new insights into ecological variation. Recent evidence from Denisova cave suggests that millimetre-scale sediment horizons can be locally stabilised over time (Massilani et al., 2022). The translocation of sedimentary strata, however, whether by climatic or biotic forces, will likely remain the primary confounding factor in sedaDNA studies (Pedersen et al., 2015). Work by Haile et al. (2007) in Aotearoa New Zealand found both moa and sheep DNA together despite never cohabiting in the region. It is expected that natural variation in geology and biotic factors will mean the severity of stratum translocation varies within and between sites and therefore caution should be taken to assess the whole context for potential translocation of genetic material (Arnold et al., 2010; Haile et al., 2007). Furthermore, Haile et al.'s work did find that wind did not contaminate sedaDNA. Recently, Massilani et al. (2022) assert that their technique of impregnating sediment samples with resin not only reduces postsampling translocation but also allows for clearer assessment of postdepositional reworking.

Viable sedaDNA was initially recovered in areas of permafrost when researchers at the University of Copenhagen successfully extracted DNA from sediments in Siberia and Aotearoa New Zealand (Willerslev et al., 2003). They also extracted extinct moa DNA from the sand in direct contact with a moa bone. Mitochondrial DNA has been successfully recovered from a variety of species across the mid to late Pleistocene (Slon et al., 2017). Denisova cave has yielded hominin DNA spanning the last ~100,000 years of the Pleistocene (Slon et al., 2017; Vernot et al., 2021; Zavala et al., 2021). More recently, shotgun sequencing of 25,000-year-old European sediments allowed the retrieval of genome-wide sequences from humans, wolves and bison, offering insights into the recent evolution of all three species (Gelabert et al., 2021).

1.4 Traditional Knowledges as sources of information

Researchers have benefited greatly from bridging Traditional Knowledges and the predominant academic systems of knowledge keeping. This is evidenced by the specific acknowledgments made by modern astrophysicists to Indigenous Nations such as the Noongar (Western Australia), Wiradjuri (Eastern Australia), Yolngu (Northern Australia), Warlpiri (Central Australia) and many more. These Indigenous communities have long been recognised as keepers of navigational and calendar systems, as well as having knowledge of astrophysical phenomena of cyclical and individual incidence (Forster, 2021; Norris, 2016).

Indigenous genetic knowledge has been demonstrated in Indigenous marriage systems. Briefly, traditional marriage is often determined by the moiety to which a person belongs (Turner & McDonald, 2010, p. 23). These moieties have their own names in their Nation's language, but may be referred to in English as ‘skin groups’ in some regions; these moieties have strong connectedness with Country for which members of that group are responsible (Turner & McDonald, 2010, pp. 25, 28, 30). Gamilaraay academic Dr. Jarrod Field demonstrated mathematically the genetic benefits of the Gamilaraay traditional marriage system (Field, 2021). Such systems, which differ between Aboriginal Nations, prevent ‘wrong-way’ marriages (Turner & McDonald, 2010, pp. 25, 29), resulting in lower-than-expected relatedness in contemporary populations of such small size that Western tradition would assume the opposite (McWhirter et al., 2014).

Given the close relationship of Indigenous peoples in Australia to Country and the demonstrated anthropocentric knowledge, it is widely understood that Traditional Knowledges contain in-depth scientific understanding of the complex symbiosis and natural cycles of the environment. Traditional Knowledge can provide valuable insights into the ecological changes that have occurred in a particular area over time. This knowledge can accurately indicate changes in weather patterns or resource use and can also contribute to our understanding of interspecies interactions, particularly for species that have been poorly studied.

In the context of determining the drivers and impacts of ecological change, there is no doubt that sedaDNA studies would benefit from the insights gained from Traditional Knowledges. Millennia of oral history and Traditional Knowledges are interconnected with the natural environment, which can provide valuable context and additional data to support the findings of sedaDNA studies. By incorporating Traditional Knowledge into research on environmental change, we can gain a more comprehensive understanding of how ecosystems have been impacted and how they may continue to change in the future.

The incorporation of Traditional Knowledges into academic research has the potential to enrich scientific understanding and provide unique insights that are not available through traditional academic systems alone. By working in collaboration with Indigenous communities and acknowledging their knowledge and expertise, researchers can develop more comprehensive and culturally sensitive approaches to research.

1.5 Meaningful engagement of Indigenous peoples when utilising sedaDNA

Indigenous Australian peoples have been disposed and displaced since the declaration of terra nullius and accompanying British invasion in the late 18th century (Huebner et al., 2020). Internationally, the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity (2011; Nagoya Protocol) aims to promote ‘fair and equitable’ benefit sharing. There is explicit inclusion of Traditional Knowledges used for genetic research within the Nagoya Protocol (Articles 3, 5, 7, 10–13, 16, 18, 21, 22). Although Australia is a party to the Convention, it has yet to ratify the Protocol itself. The Australian Government states that ‘existing domestic measures are consistent with the Protocol’ Department of Climate Change Energy and Water (2021). The Australian Institute for Aboriginal and Torres Strait Islander Studies (AIATSIS) produced a Code of Ethics for Aboriginal and Torres Strait Islander Research in 2020 (AIATSIS, 2020), which can be broadly applied to both research and other work that may impact Indigenous peoples in Australia. Therefore, work with sedaDNA easily falls under the purview of this code in both nonhuman and human genomic research applied to sediment, despite being a nascent field. It is noted that AIATSIS is not a governing body of Indigenous Australians, and therefore, individual nation, clan or tribal sovereignty should be the priority when engaging with Traditional Owners. This may include actively seeking out local language (particularly where English is a second, third or fourth language for a group) and ensuring that researchers understand the wording and concept reflected in Indigenous languages, rather than simply requiring Indigenous peoples to understand the often-technical language of the researchers. SedaDNA researchers in Australia should treat the AIATSIS Code of Ethics as a starting point or minimum standard from which to further develop an appropriate framework for the Indigenous Nation or Nations with whom they work. International researchers may also find the Code useful in non-Australian contexts, though care should be taken to treat Global Indigenous Nations as individual and sovereign entities.

Recent efforts have highlighted the responsibility of researchers in their handling of human and nonhuman remains. In Aotearoa New Zealand, guidelines have been established for genomic research involving Taonga species and Māori people (Hudson et al., 2016, 2021). Additionally, Alpaslan-Roodenberg et al. (2021) have outlined five general guidelines for using human remains in research, which include adhering to legal regulations, creating a study plan, minimising damage, engaging with stakeholders and adherence to open data principles. This paper has since been criticised with respect to the disregarding of Indigenous data sovereignty principles and the relevance of broad stakeholder engagement, which Alpaslan-Roodenberg et al. couple with the assertion that stakeholder approval prior to publication may jeopardise the scientific process (Kowal et al., 2023). Kowal et al. (2023) stress that Alpaslan-Roodenberg et al. (2021) disregard Indigenous data sovereignty principles and the importance of Indigenous community engagement. They contend that community engagement is not only ethical but also necessary for understanding the perspectives of stakeholders and ensuring that research is conducted in a culturally appropriate manner. The authors highlight examples of successful community partnerships in ancient DNA research, emphasising that such partnerships should be built on trust, transparency and equitable power-sharing. They conclude that community partnerships should be a fundamental aspect of ethical ancient DNA research and call for a rethinking of the current approach to research on Indigenous remains and cultural heritage.

As researchers, it is crucial that we remain mindful of the multiple stakeholders involved in ancient DNA research, including those with academic or commercial interests. We must ensure that Indigenous stakeholder sensibilities are not subverted or sidelined and that Indigenous voices are not overwhelmed by the perspectives of other stakeholders. This can be achieved through meaningful engagement with Traditional Owners and other Indigenous stakeholders and by empowering them to maintain control over research on their people and Country. While international guidelines and principles can serve as useful starting points for Australian researchers, it is important to recognise that they may not fully represent the unique perspectives and needs of Indigenous Australians. To ensure appropriate engagement with Indigenous peoples, researchers should look to the United Nations Declaration on the Rights of Indigenous Peoples (2007) for guidance. The Declaration emphasises the importance of free, prior, and informed consent and the right of Indigenous peoples to control research on their traditional knowledge and cultural heritage. To meet these standards, Traditional Owners should be given direct input into research design and decision-making, including the power to offer permission or rejection of any proposed research. Researchers should also strive to engage with Indigenous stakeholders in a culturally appropriate and respectful manner, taking care to prioritise local language and knowledge systems. Ultimately, building strong and equitable partnerships with Indigenous communities is crucial for ethical ancient DNA (including sedaDNA) research that is both scientifically rigorous and culturally sensitive.

There are currently no nondestructive tests to ascertain the quantity of ancient DNA within a sample either biological or sedimentary. As such, sampling relies on the experience of laboratory technicians to target the most probable source of DNA. This can mean making a decision about which skeletal element should be used in ancient DNA analysis or the quantity of sample needed to increase the likelihood of a result. In sediments, we do not have to contend with the appropriateness of sampling a femur as opposed to a skull, we do however need to clarify the expectations of sample size, storage and repatriation and protocols to guide this work aligned with community interests and cultural obligations.

The scientific collection of biological materials from Indigenous Australians has historically been done in nonconsensual ways (Huebner et al., 2020). In many cases, samples have been collected without the knowledge or consent of the individuals or communities from which they were taken. University and hospital sample storage facilities are notorious for containing decades-old materials long since forgotten by a researcher who has moved elsewhere or retired. The discovery of such a collection of Aboriginal and Torres Strait Islander biological samples is how the National Centre for Indigenous Genomics came to be formed at the Australian National University (Easteal et al., 2020; Hermes et al., 2021). The centre was established with the aim of addressing the ethical, legal and social implications of genetic research on Indigenous peoples.

In the case of contemporary sample collection, it is crucial to engage with Traditional Owners early in the research process to establish how long the original samples may be kept before being returned to the community, if known. It is also essential to consider the secondary biological products produced during the DNA extraction process, such as a pellet of bone precipitate or ‘leftover’ stock samples that were not used for extraction.

For waste products that do not pose a risk to people or the environment, researchers should provide the option to return them to Country in a way that aligns with the community's governance systems and cultural practices. For example, a smoking ceremony may be conducted to allow the sample by-product to be passed through cleansing smoke and returned to the earth or a fire. By returning extraction by-products to the community, Traditional Owners can make decisions about their land and maintain control over their cultural heritage. Further forms of researcher engagement are suggested in Table 1.

1.6 Using sedaDNA to assess the impact of cultural ecological management

Anthropogenic transformation can lead to significant changes in the landscape over time (Garcés-Pastor et al., 2021). SedaDNA can assist in assessing these changes and inform contemporary ecological management plans. Environmental conditions and drivers can be revealed through microbial (Pérez et al., 2022), fungal (Talas et al., 2021) and plant (Edwards et al., 2021; Hudson et al., 2022; Parducci et al., 2017) sedaDNA. This would be of great benefit in areas where Traditional Knowledges are drawing the attention of non-Indigenous stakeholders, such as the fire-based ecology in Australia. Ecological management practices that utilise fire are integrated in many cultures worldwide, including Aboriginal Australians (Coughlan & Petty, 2012). Also referred to as cultural burning, the fire-based ecological practices of Indigenous peoples date back to the early Holocene (Adeleye, Haberle, Connor, Stevenson, & Bowman, 2021) and have had clear ecological impacts on animal and plant populations (Adeleye et al., 2022; Bowman, 1998). By associating ecological communities identified by sedaDNA in stratigraphic horizons with the concentration of charcoal in the sediment, we can elucidate the effects of fire on the local environment.

Landscapes that undergo cultural burnings have greater habitat diversity than comparable regions (Bliege Bird et al., 2008). The cumulative effects of fire practice over generations lead to the maintenance of high biodiversity (Bliege Bird et al., 2008). The anthropological justifications for this ecological manipulation through cultural burning vary by social and geographic necessity (Gott, 2005; Hill et al., 2000; Yibarbuk et al., 2001). It is not possible to separate the cultural entwining of fire practices from sociocultural practices (Yibarbuk et al., 2001). The following represent examples of diversity in the practical applications of cultural burnings and are not an exhaustive or exclusive list for the different Indigenous peoples mentioned. Peoples of the Ngaanyatjarra language group in the Western Desert of Australia have associated a decline in desert mammals, specifically the mitika (Bettongia lesueur or rat-kangaroo) with a cessation in cultural burning (Burrows & Christensen, 1990). In southeast Australia, annual burnings kept scrublands open for seed germination and movement across Country, while in the north, they maintained diversity of food sources from both plants and animals on Yolngu Country (Gott, 2005; Yibarbuk et al., 2001). The Kuku-Yalanji people of tropical northeast Australia manage the interface of tropical rainforest and open grass-and-bush lands and each environment's unique resources, through cultural burning (Hill et al., 2000). Some Australian seeds have an obligate fire response to germinate, and the increase in vegetative diversity is beneficial to humans and other animals (Bell et al., 1993; Gott, 2005). Identifying changes in sedaDNA communities associated with changes in charcoal concentration would allow identification of wildfires both natural and anthropogenic, where a plateau in species diversity associated with higher charcoal concentration could indicate the presence of cultural burnings. Furthermore, and with relevance to contemporary ecology, cultural burning can control wildfire spread (Coughlan & Petty, 2012; Mariani et al., 2022). It is reported that Traditional Knowledges of fire practices have adapted in many cases to manage the landscape formed by European colonisation (Adeleye, Connor, Haberle, Herbert, & Brown, 2021; Coughlan & Petty, 2012; Hill et al., 2000; Yibarbuk et al., 2001). Collectively, Traditional Knowledges that mediate cultural burning are crucial in understanding Australian ecology in the past and present. Connecting Traditional Knowledges with sedaDNA has the potential to inform ecological management practices.

1.7 Receiving Traditional Knowledges is a gift, not a right

It is important for researchers to manage their expectations when seeking to receive Traditional Knowledges from Indigenous peoples in Australia, who are still recovering from intergenerational traumas caused by historic and ongoing colonial practices. Academic Australia has a predominantly British or Euro-centric history that prioritises humans above all else. However, Indigenous genomics in Australia encompasses Aboriginal and Torres Strait Islander connectedness to land, flora and fauna. Akarre Elder Margaret Kemarre Turner (Order of the Medal of Australia) aptly summarises this by stating, ‘The Land is us, and we are the Land.’ (Turner & McDonald, 2010, p. 15). The relationship between Indigenous peoples and the Land is not abstract but tangible and meaningful.

Indigenous Australians have rules surrounding their Country's biota, dictated through lore and stories, which often relate to the breeding and hunting seasons as well as other aspects of care for totem animals (Raven et al., 2021; Robinson & Raven, 2020; Steffensen, 2020, p. 95). Indeed, an emu is as much an ancestor as Old People are, though the strength of this connectedness may depend on an individual's familial lines (Raven et al., 2021). Aunty Margaret Kemmare teaches that Aboriginal lore requires plants to be respected for stories, food and medicine and that some trees are considered to have become human (Turner & McDonald, 2010, pp. 156–161). These kinship ties integrate obligations to care for Country in perpetuity, in the past, present and future, and the meaning of which varies with each Nation as they do with the landscape (Raven et al., 2021; Robinson & Raven, 2020). SedaDNA can connect oral histories with modern science; however, Traditional Knowledges have been supressed during colonial occupation. As a result, the continued research on Indigenous peoples, plants and animals is likely to perpetuate harmful colonial narratives, regardless of researchers' intentions (Roberts, 2022). Balancing the potential for sedaDNA research with the risk of harming Indigenous peoples can only be achieved with direct input from Traditional Owners.

Considering the responsibilities of Indigenous peoples in caring for Country is important for researchers who undertake genomic analyses in Australia, where they inevitably encounter all aspects of Indigenous genomics. Like the people who inhabit the continent, the Australian landscape is diverse, from red desert to snowy mountains and even the ‘oldest surviving rainforest in the world’ (Roberts et al., 2021). Consequently, land management by Indigenous peoples differs between Nations along with specialised ways of knowing, learning and being (Raven et al., 2021). The interconnectedness of Indigenous peoples and the land they are responsible for has developed over thousands of generations, and the health of the land is so entwined with the health of the people that one cannot be separated from the other (Raven et al., 2021; Robinson & Raven, 2020; Turner & McDonald, 2010, pp. 114, 115). Therefore, when considering Indigenous sedaDNA work, due respect is owed to the biota from across the tree of life that leave their DNA traces in the sediment. As a direct practical consequence, it is paramount to balance CARE and FAIR principles (Carroll et al., 2021) when disseminating sedaDNA data.

In this area, where efforts are made to understand Traditional Knowledges, non-Indigenous researchers may feel frustrated at the hesitancy of Indigenous peoples to share their stories, particularly as they relate to ecological, or otherwise nonhuman entities. However, it is important to recognise that sediments should be treated with full recognition of their Indigeneity and respecting the sovereignty of Traditional Owners in decision-making. They have the right to retain or otherwise mediate the dispersal of that Knowledge. Research that engages with Traditional Knowledges without dominating or claiming ownership will not only improve the ethical standing of the researcher but also lead to more holistic understanding of species history and the creation of equitable partnerships between communities, Elders and researchers.