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\begin{document}

\title{More than dirt: sedimentary ancient DNA and Indigenous Australia}



\author[1]{Dawn Lewis}%
\author[2]{Rebecca Simpson}%
\author[3]{Azure Hermes}%
\author[2]{Alex Brown}%
\author[1]{Bastien Llamas}%
\affil[1]{The University of Adelaide}%
\affil[2]{Telethon Kids Institute}%
\affil[3]{Australian National University National Centre for Indigenous Genomics}%


\vspace{-1em}



  
  \date{May 24, 2024}


\begingroup
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\selectlanguage{english}
\begin{abstract}
The rise of sedimentary ancient DNA (sedaDNA) studies has opened up new
possibilities for studying pre-historic ecology. The use of sediments to
identify organisms even where macroscopic remains are limited or no
longer exist is an exciting and potentially ground-breaking area of
genomics. There are special considerations however when managing this
substrate in Indigenous Australian contexts. Sediments and soils are
often considered as waste by-products during archaeological and
paleontological excavations, and as such are not typically considered of
high value in ethical considerations in traditional western research.
Nevertheless, the product of sedaDNA work -- genetic information from
past fauna, flora, microbial communities, and human ancestors -- is
likely to be of cultural value for Indigenous peoples. We argue that the
integration of Traditional Knowledges into sedaDNA research would a)
allow identification of sensitive, secret, or sacred genomic data, and
b) improve research outcomes by providing ecological context for species
through multi-millennia oral histories.%
\end{abstract}%



\sloppy


More than dirt: sedimentary ancient DNA and Indigenous Australia

\emph{Authors}

Ms Dawn Alison Lewis

Ms Rebecca Simpson

Mrs Azure Hermes

Professor Alex Brown

Associate Professor Bastien Llamas

Dawn A Lewis\textsuperscript{1,2,\#}, Rebecca
Simpson\textsuperscript{3,4}, Azure Hermes\textsuperscript{3}, Alex
Brown\textsuperscript{3,4}, Bastien Llamas\textsuperscript{1,2,3,4}

\textsuperscript{1} Australian Centre for Ancient DNA, School of
Biological Sciences and Environment Institute, University of Adelaide,
SA 5005, Australia

\textsuperscript{2} ARC Centre of Excellence for Australian Biodiversity
and Heritage, University of Adelaide, Adelaide, SA 5005, Australia

\textsuperscript{3} National Centre for Indigenous Genomics, Australian
National University, Canberra, ACT 2601, Australia

\textsuperscript{4} Black Ochre Data Labs, Telethon Kids Institute,
Adelaide, SA 5000, Australia

\textsuperscript{\#} Corresponding author: dawn.lewis@adelaide.edu.au

\emph{Acknowledgements:}

This work is supported by funding from an NHMRC Synergy Grant
(ID:2011277). DL is~supported~by~The University of Adelaide Research
Scholarship (Indigenous) Research Training Program Scholarship
(Indigenous) and~The Julia Konig Bequest Award - For Indigenous
Students.~RS is supported by The Australian National University
Indigenous Postgraduate Research Fellowship. AB is supported by an NHMRC
Senior Researcher Fellowship (\#1137563).\emph{}

\emph{Abstract}

The rise of sedimentary ancient DNA (sedaDNA) studies has opened up new
possibilities for studying pre-historic ecology. The use of sediments to
identify organisms even where macroscopic remains are limited or no
longer exist is an exciting and potentially ground-breaking area of
genomics. There are special considerations however when managing this
substrate in Indigenous Australian contexts. Sediments and soils are
often considered as waste by-products during archaeological and
paleontological excavations, and as such are not typically considered of
high value in ethical considerations in traditional western research.
Nevertheless, the product of sedaDNA work -- genetic information from
past fauna, flora, microbial communities, and human ancestors -- is
likely to be of cultural value for Indigenous peoples. We argue that the
integration of Traditional Knowledges into sedaDNA research would a)
allow identification of sensitive, secret, or sacred genomic data, and
b) improve research outcomes by providing ecological context for species
through multi-millennia oral histories.

\emph{Keywords}

TEK; ancient DNA; Indigenous; Aboriginal;

\emph{Benefit sharing / positionality statement}

This article is an opinion piece designed to communicate the
responsibilities of ecological researchers in Australia as that research
pertains to the emerging field of sedimentary ancient DNA and Indigenous
communities. As such, there is no new data to provide or site. The
authors identify in the following ways. DL is a Woolwonga woman, AB is a
Wadi Wadi and Yuin Nation man, and BL is a non-Indigenous man, and they
are visitors to the Kaurna Land on which they live and work; RS is a
Kaurna/Narungga woman from South Australia and Indigenous Fijian from
SavuSavu, Fiji Islands, currently living and working on her Kaurna
homelands; AH is a Walubara Yidinji woman, from Cairns, Far North
Queensland who is a visitor to the Ngunnawal Land on which she lives and
works. All authors endeavour to walk on these respective Country with
care. This work aims to highlight the importance of researcher
collaboration with the diverse Indigenous identities in modern day
Australia. The authors hold no authority to represent all Indigenous
peoples across Australia and thank those who entrust their knowledge to
their care.

\emph{Introduction}

Modern day Indigenous Australia is comprised of two distinct cultures:
Aboriginal and Torres Strait Islander. Each culture is comprised of
hundreds of distinct Nations or Tribes that in practice should be
considered as discrete entities with their own laws, lore and
relationships with non-Indigenous Australia. Aboriginal and Torres
Strait Islander peoples (hereafter respectfully referred to as
Indigenous peoples) have been connected with ancestral lands, seas and
waterways since time immemorial according to oral traditions, to the
point where the term ``Country'' defines the place, the biota and
microbiota, as well as peoples' culture, language, spirituality,
identity, familial and social bonds, and stories. As a western echo to
Traditional Knowledge, archaeological evidence suggests Australia has
been occupied by humans for at least fifty millennia (Clarkson et al.,
2017; Dortch \& Malaspinas, 2017; O'Connor, Louys, Kealy, \& Samper
Carro, 2017). The continuing transgenerational and strong cultural
relationship with Country links the ecological health of the Australian
landscape with human occupation from at least midway through the late
Pleistocene, and continues to evolve with the introduction of non-native
biota (Fletcher, Hall, \& Alexandra, 2021; Trauernicht, Murphy,
Tangalin, \& Bowman, 2013; Turner \& McDonald, 2010, pp. 117, 176-188).
Ancient DNA studies reach into these time periods and can be used to
enlighten local and regional ecological history (Alter, Newsome, \&
Palumbi, 2012; Hofman, Rick, Fleischer, \& Maldonado, 2015).

\emph{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,
Lorenz, \& Wackernagel, 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 PCR, or polymerase chain reaction (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 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).

\emph{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, traditional sub-fossil
taxonomic identification (Pansu et al., 2015; P\selectlanguage{ngerman}érez, Liu, Hengst, \&
Weyrich, 2022; Slon et al., 2017; Thomas et al., 2022). Recovered
sedaDNA has come 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). Natural variation in geology and biotic factors
will mean the severity of stratum translocation will likely vary within
and between sites. To address this, Massilani et al. (2022) assert that
their technique of impregnating sediment samples with resin not only
reduces post-sampling translocation but also allows for clearer
assessment of post-depositional movement.

Viable sedaDNA was initially recovered in areas of permafrost when
researchers at the University of Copenhagen successfully extracted DNA
from sedimentary (dry silty) cores in 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 mtDNA between
\textasciitilde{}100ka to \textasciitilde{}200ka (Slon et al., 2017;
Vernot et al., 2021). More recently, shotgun sequencing of 25ka-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).

\emph{Using sedaDNA to assess the impact of cultural ecological
management}

Anthropogenic transformation can lead to significant changes to a
landscape (Garcés-Pastor et al., 2021), and sedaDNA may assist in
assessing these effects through time to inform contemporary ecological
management plans. Environmental conditions and drivers can be revealed
through microbial (Pérez et al., 2022), fungal (Talas, Stivrins, Veski,
Tedersoo, \& Kisand, 2021) and plant (Edwards et al., 2021; Hudson et
al., 2022) 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
around the world, including Aboriginal Australians (Coughland \& Petty,
2012). Also referred to as cultural burning, the fire-based ecological
practices of Aboriginal peoples go as far back as the early Holocene
(Matthew A Adeleye, Haberle, Connor, Stevenson, \& Bowman, 2021) and
have had clear ecological impacts on animal and plant populations
(Matthew Adesanya Adeleye, Haberle, Ondei, \& Bowman, 2022; Bowman,
1998). Associating ecological communities identified by sedaDNA in
stratigraphic horizons with the concentration of charcoal in the
sediment can elucidate the effects of fire on the local environment.

Landscapes subject to cultural burnings have greater habitat diversity
than comparable regions (Bliege Bird, Bird, Codding, Parker, \& Jones,
2008), and 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 by
cultural burning vary by social and geographic necessity (Gott, 2005;
Hill, Griggs, \& Bamanga Bubu Ngadimunku, 2000; Yibarbuk et al., 2001).
The cultural entwining of fire practices cannot be disentangled from
socio-cultural 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
\emph{mitika}(\emph{Bettongia leseur} or rat-kangaroo) with a cessation
in cultural burning (Burrows \& Christensen, 1990). In south east
Australia, annual burnings kept scrublands open for seed germination and
movement across Country and in the north maintained diversity of food
sources from both plants and animals on Yolngu Country (Gott, 2005;
Yibarbuk et al., 2001). The Kuku-Yulanji people of Tropical North East
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 of vegetative
diversity is beneficial to humans and other animals (Bell, Plummer, \&
Taylor, 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. Further,
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
(Matthew Adesanya 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
clearly important in understanding Australian ecology now and in the
past and connecting Traditional Knowledges with sedaDNA has the
potential to inform ecological management practices.

\emph{Traditional Knowledges as sources of information}

Researchers have benefited greatly from bridging Traditional Knowledges
and the predominant Western systems of knowledge keeping. For example,
Noongar (western Australia), Wiradjuri (eastern Australia), Yolngu
(northern Australia) Warlpiri (central Australia) and many more Nations,
have been specifically acknowledged by modern astrophysicists as keepers
of navigational and calendar systems, as well as notable 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).

Through the demonstrated anthropocentric Knowledge and given the close
relationship of Indigenous peoples in Australia to Country, it is
understood that Traditional Knowledges carry in-depth scientific
understanding for the complexity of the environment. In cases where the
oral history of an area can be shared, Traditional Knowledges can
accurately indicate changes in weather or resources use, or add to our
understanding of inter-species interactions, particularly for species
that are poorly studied. In the context of determining the drivers
and/or impact of ecological change, there is no doubt that sedaDNA
studies would benefit from the inter-connectedness with millennia of
oral history and Traditional Knowledges.

\emph{Receiving Traditional Knowledges is a gift, not a right}

It is important for researchers to manage their expectations regarding
receiving Traditional Knowledges as Indigenous peoples in Australia
continue to recover from intergenerational traumas stemming from
historic, and often continuing, colonial practices. Academic Australia
has a largely British, or otherwise Euro-centric, history that includes
the reverence of humans above all else. Although Indigenous Australians
greatly revere the remains of Old People (ancestors), Indigenous
genomics in Australia encompasses the entirety of Aboriginal and Torres
Strait Islander connectedness to land, flora, and fauna. Akarre Elder
Margaret \emph{Kemarre} Turner (Order of the Medal of Australia)
demonstrates this as ``The Land \emph{is} us, and we are the Land.''
(Turner \& McDonald, 2010, p. 15). The relationships between Land and
Indigenous peoples are not abstract, they are 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, Robinson, \& Hunter, 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
\emph{Kemmare}teaches that Aboriginal lore requires plants 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 could be utilised by Indigenous peoples to connect
oral histories with modern science. Much Traditional Knowledge however,
has been repressed and consequently, the continued research on
Indigenous peoples, plants and animals is likely to perpetuate harmful
colonial narratives, regardless of researchers' intent (Z. Roberts,
2022). Balancing the potential for sedaDNA research with the risk to
harm Indigenous peoples can only be done with direct input and control
from Traditional Owners.

Considering the responsibilities of Indigenous peoples in caring for
Country is important for researchers that undertake genomic analyses in
Australia, where they reasonably 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'' (P. 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 have responsibility 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, Herczog, Hudson, Russell, \&
Stall, 2021) when disseminating sedaDNA data.

In such an area, where efforts are made to understand Traditional
Knowledges, non-Indigenous researchers may become frustrated at the
hesitancy of Indigenous peoples to share their stories, particularly as
they relate to ecological, or otherwise non-human entities. But
remembering that sediments should be treated with full recognition of
their Indigeneity, respecting the sovereignty of Traditional Owners in
decision making means they have the right to retain or otherwise mediate
the dispersal of that Knowledge (potentially applying Bio-Cultural and
Traditional Knowledge label systems (Mc Cartney et al., 2022). Research
that engages with, but does not dominate or claim ownership of,
Traditional Knowledges will not only improve the ethical standing of the
researcher but improve research outcomes through a more holistic
understanding of species history.

\emph{Conclusion}

Indigenous genomics, in particular the study of sedaDNA, is a powerful
tool that has the potential to provide Indigenous Nations of Australia
with links to their kin and improve ecological research. Respectfully
improving the relationship of academic institutions and researchers with
Indigenous peoples will be difficult, however, as the historic forced
suppression of Traditional Knowledges and Traditional Knowledge systems,
in conjunction with the abduction and embezzlement of Indigenous
artefacts (including kin/totem flora and fauna), has created
intergenerational mistrust of academic activities. The result is a
current gap of Indigenous inclusion in rapidly developing areas of
genomic science such as sedaDNA. Given the breadth of genomic
information from Country available through sedaDNA analysis, engaging
Indigenous peoples is key to ensure each Nation is in control of their
own narrative.

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\emph{Author contributions}

DL conceptualised and wrote the initial paper; BL, AB, AH and RS
contributed to the writing of the paper.

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