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Archaeology meets Environmental Genomics: implementing sedaDNA in the study of the human past

Authors:

Abstract

Sedimentary ancient DNA (sedaDNA) has become one of the standard applications in the field of paleogenomics in recent years. It has been used for paleoenvironmental reconstructions, detecting the presence of prehistoric species in the absence of macro remains and even investigating the evolutionary history of a few species. However, its application in archaeology has been limited and primarily focused on humans. This article argues that sedaDNA holds a significant potential in addressing key archaeological questions concerning the origins, lifestyles and environments of past human populations. Our aim is to facilitate the integration of sedaDNA into the standard workflows in archaeology as a transformative tool and thereby unleashing its full potential for studying the human past. Ultimately, we not only underscore the challenges inherent in the sedaDNA field but also provide a research agenda for essential enhancements needed for implementing sedaDNA into the standard workflows of archaeologists.
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Archaeology meets Environmental Genomics:
implementing sedaDNA in the study of the human
past
Kadir Toykan Özdoğan ( k.t.ozdogan@uu.nl )
Utrecht University
Pere Gelabert
University of Vienna
Neeke Hammers
ADC ArcheoProjecten
N. Ezgi Altınışık
Hacettepe University
Arjen Groot
Wageningen Environmental Research
Gertjan Plets
Utrecht University
Research Article
Keywords: sedaDNA, ancient DNA, archaeogenemics, ancient metagenomics, bioarchaeology,
environmental archaeology
Posted Date: November 8th, 2023
DOI: https://doi.org/10.21203/rs.3.rs-3568244/v1
License: This work is licensed under a Creative Commons Attribution 4.0 International License. 
Read Full License
Additional Declarations: No competing interests reported.
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Abstract
Sedimentary ancient DNA (sedaDNA) has become one of the standard applications in the eld of
paleogenomics in recent years. It has been used for paleoenvironmental reconstructions, detecting the
presence of prehistoric species in the absence of macro remains and even investigating the evolutionary
history of a few species. However, its application in archaeology has been limited and primarily focused
on humans. This article argues that sedaDNA holds a signicant potential in addressing key
archaeological questions concerning the origins, lifestyles and environments of past human populations.
Our aim is to facilitate the integration of sedaDNA into the standard workows in archaeology as a
transformative tool and thereby unleashing its full potential for studying the human past. Ultimately, we
not only underscore the challenges inherent in the sedaDNA eld but also provide a research agenda for
essential enhancements needed for implementing sedaDNA into the standard workows of
archaeologists.
1. Introduction
Ancient DNA or shortly
aDNA
refers to all DNA fragments of once lived organisms. Most ancient DNA
studies that address archeological questions focus on the use of human remains to study past human
ancestry, mostly testing the effect of migration in historical events. Yet, the studies that also explore the
evolutionary and population history of other taxa are becoming more abundant (Kistler et al., 2020;
MacHugh et al., 2017).
Despite most paleogenomic studies using macroscopic organic remains, an increasing number of studies
look for ancient DNA in environmental samples. Modern environmental DNA (eDNA) might be preserved
in water (Thomsen et al., 2012), soil (Taberlet et al., 2012) or air (de Groot et al., 2021). However, eDNA in
archaeological context is typically recovered from sediments (either from terrestrial or aquatic sites), in
which case it is referred to as sedimentary ancient DNA or
sedaDNA
. SedaDNA samples hold genetic
information of all living organisms that have interacted with a given layer or context. In
paleoenvironmental research, sedaDNA has been embraced as the main methods for reconstructing past
environments.
Studies using permafrost, cave, and lake sediments have helped answer questions about extinct
hominins and large mammal species in prehistory (Gelabert et al., 2021; Parducci et al., 2017; Vernot et
al., 2021; Wang et al., 2021). Yet, these studies have so far mostly studied a few distinct species, thus not
making use of the full potential that sedaDNA has to offer, e.g. the recovery of a broad biodiversity.
Furthermore, archaeological sedaDNA studies to date focused mainly on prehistoric periods, leaving
biodiversity assessments from historical periods largely untouched.
However, before sedaDNA becomes a standard method in archaeology, concerted action is required. The
sedaDNA eld is in continuous development; new lab methods are being developed, along with tailor-
made bioinformatic approaches to process the big amount of genomic data. Both developments require
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highly specialized skills and as a result, debates on advantages and disadvantages of sedaDNA
applications are highly technical, which makes the eld dicult to explore for archaeologists, perhaps
even more so than any new method in archaeology. Moreover, it is highly tempting to become enchanted
with the technique and have too much trust in it. If we want to avoid the boom-and-bust cycle typical for
many methods (Jones & Bösl, 2021; Lebrasseur et al., 2018) we need to collectively develop a research
agenda. To make sedaDNA a cornerstone in archaeology, we need to bridge the gap between on the one
side archaeology and on the other side (ancient) environmental metagenomics.
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Table 1
Common terms used in sedaDNA studies.
Term Meaning
Ancient DNA (aDNA) DNA fragments obtained from fossils and ancient sediments
Environmental DNA DNA fragments obtained from environmental sources
Ancient
environmental DNA
(aeDNA)
Ancient DNA obtained from ancient environmental sources
Sedimentary ancient
DNA (sedaDNA) Ancient DNA obtained from ancient sediment samples
Paleogenomics The scientic eld of reconstructing and analyzing ancient genomic material
Metagenomics The study of genetic material recovered from samples contains multiple
organisms.
Ancient
metagenomics Metagenomics of ancient DNA samples
Permafrost Surface materials (e.g. soil, subsoil) that remain consistently frozen
regardless of seasonal variations.
Pathogen A general term for microorganisms that cause diseases
Mitochondrial DNA
(mtDNA) Maternally inherited DNA that is present in a separate organelle, i.e
mitochondria, rather than nucleus of the cell
Phylogenetic tree A tree-shaped graph that shows evolutionary relationship between
organisms
Polymerase chain
reaction (PCR) A commonly method used for enzymatic amplication of DNA out of cell
Shotgun sequencing A method for sequencing random fragments from a DNA library
Target enrichment /
target capture A laboratory method for selecting DNA fragments belonging chosen taxa in a
DNA library
Contamination Undesired DNA fragments from outside the sample, mostly modern DNA
Authentication Determining whether the recovered DNA is ancient or not
Damage pattern Specic chemical alterations occurred in DNA molecules in the post-mortem
period that are used for authenticating ancient DNA
Cross-contamination Contamination occurred between samples
Based on a structured literature review, the authors of this paper will outline the fundamental principles of
sedaDNA and their successful applications. We will, then, identify on which fronts it can contribute to
archaeology and on which not. Subsequently, we will offer a research agenda highlighting the needed
developments and approaches for eciently implementing sedaDNA into archaeological research.
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2. Current approaches and applications of sedaDNA
2.1. Sources
The eld of paleogenomics reconstructs and analyzes genomic information from any sample type and
uses it for identifying taxa and acquiring deeper information about past organisms. However, ancient
DNA for most archaeogenomic research is extracted directly from larger preserved organic artifacts and
ecofacts such as human or animal bones, and macro-botanical remnants. In well-preserved contexts (e.g.
permafrost) soft tissues of organisms may be preserved that can be sampled directly (Maixner et al.,
2016).
Sedimentary ancient DNA, however, is most likely found in micro remains or coprolites (Massilani et al.,
2022) or bound to minerals in the soil (Kjær et al., 2022). Due to the natural decomposition of organic
materials, sedaDNA is damaged, degraded, fragmented, and intermixed (Orlando et al., 2021).
Furthermore, a single ancient sediment sample most likely contains ancient DNA from a broad range of
species, animal, vegetal, bacteria and fungi, as well as -in most cases- DNA of recent origin of a suite of
organisms from the same range of taxonomic groups. These characteristics heavily determine and
restrict the methodological workow for sedaDNA analysis.
2.2. Workow
Similar to aDNA studies for sedaDNA follow strict protocols and workow consisting of (1) sampling, (2)
laboratory-based data generation, and (3) bioinformatic processing (see Fig.1). Per step, multiple
protocols can be available and choices in this respect have direct implications for the types of questions
that can be tackled.
2.2.1
. Sampling
Although there are protocols throughout the whole workow to prevent, detect and lter out
contamination with DNA molecules from present-day sources, such contamination is to be avoided as
much as possible already in the rst steps of the workow to maximize the amount of useful information
gained per sample. Therefore, sedaDNA sampling requires sterile disposable materials, specialized
protective clothing and careful handling including multiple steps to clean materials and sediment
surfaces. To avoid not only the inuence of present-day DNA but also cross-contamination with actual
ancient DNA from other contexts or nearby soil layers, sedaDNA samples are to be taken either from the
inside of soil sampling cores (Murchie et al., 2021) or directly from archeological sections after removing
the air-exposed top layer (Wang et al., 2021). Since aDNA fragments are highly degraded and fragmented,
signals of DNA degradation and sequenced fragment lengths can be used to authenticate aDNA and to
detect contamination (Peyrégne & Prüfer, 2020).
2.2.2. Data generation: Laboratory process
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For the same reasons, the extraction of aDNA from sedimentary samples happens in an ultra-clean (i.e.,
contamination-free) aDNA lab (Fulton & Shapiro, 2019). Since ancient DNA is heavily fragmented,
extraction methods are designed to target only those small fragments of aDNA. Thus, most modern
contaminants are eliminated during the extraction (Dabney et al., 2013). Sediment samples are prone to
disruption of lab analysis mainly due to humic acids, heavy metals and complex proteins naturally
occurring in organically rich sediment which is called inhibition. A series of additional protocols have
been developed to minimize the impact of such inhibitors (Armbrecht et al., 2020; Murchie et al., 2021;
Rohland et al., 2018; Slon et al., 2017; Wang et al., 2021).
For the analysis of the DNA pool of a whole community of organisms, a specic workow is imperative,
that is capable of parallel identication of individual taxa. In principle, various approaches are available.
One of the approaches, DNA metabarcoding zooms in on one or a few regions of the genome which are
known to show variation among the taxa studied (Armbrecht et al., 2020). Available fragments of those
‘barcode regions’ are then multiplied via PCR amplication and the DNA code of all resulting copies is
translated into a letter code in a digital le (i.e., a ‘sequence read’). This translation is done in parallel for
all copies in a process called ‘high-throughput sequencing’ (Illumina Cooperation, 2023a). While DNA
metabarcoding secures data for informative parts of the genome (enhancing chances for species-level
identications) and downstream data analysis is relatively straightforward, a huge downside of this
method is the inability to screen the resulting dataset for any remaining modern contaminants. While
tools are available to assess that detected taxa is either modern or ancient (see below), such tools cannot
be applied on the products of the metabarcoding approach.
Another method, referred to as metagenomics, requires amplication of all DNA fragments in the original
DNA extract regardless of their position in the genome. This so-called ‘shotgun metagenomics’ approach
results in a much more complex dataset yet does allow an authenticity check for each single taxon.
DNA metabarcoding has been the method of choice in the majority of recent sedaDNA-based
palaeoenvironmental studies. Authenticity checks can be less crucial for the type of research questions
explored there, which are mainly general shifts in community composition across time and space. Yet,
applications of sedaDNA in an archeological setting are often driven by questions of the presence or
absence of particular taxa at certain locations of moments in time. In such cases, avoiding false-positive
detection of a taxon in a particular sample is crucial. For archeological applications, metagenomics is
therefore the method of choice. Hence, it becomes evident that informatic techniques centered on the
comparative analysis of multiple taxa, that integrate robust statistical discrimination methods, emerge as
the most dependable and effective means to assess the presence of taxa (Vogel et al., 2023).
The untargeted data collection via metagenomics may require a deeper sequencing (i.e., collection of
DNA codes for a larger subset of fragments from the DNA extract) to gather sucient data for parts of
the genome that a discriminatory among species or genetic variants within species. To reduce costs
and/or enhance data volume especially for more detailed studies at the level of e.g., populations, strains
or individuals, new approaches are developed to enrich the DNA pool for discriminatory fragments prior to
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sequencing. Such target enrichment works by capturing regions of interest by hybridization to tailor-made
probes attached to magnetic beads, which can then be isolated from the pool using magnetic pulldown
(Illumina Cooperation, 2023b).Hence, apart from tailoring the resolution to meet project-specic inquiries,
the method chosen is also contingent upon the budget.
Ultimately, the resolution of generated data is a vital element in sedaDNA studies and can be dened in
two layers: i) covering more diverse organisms in the sample or ii) gaining deeper knowledge on relevant
organisms. While the former corresponds to metagenomics or metabarcoding, the latter can be achieved
by using the targeted enrichment approach. The choice of the method depends on the archaeological
research question.
2.2.3. Data processing: Bioinformatics
Bioinformatics, which represents the analytical step of these kinds of studies, is a crucial step, especially
now that advanced sequencing and extraction techniques are yielding vast amounts of data.
Bioinformatic tools help researchers to (1) detect contamination, (2) perform the authentication, and (3)
taxonomic classication. An aspect of bioinformatics specic to metagenomic analysis as a tool for
biodiversity screening is the assignment of DNA sequences to specic taxa (species, or higher taxonomic
levels). This process requires matching each individual sequence read against databases containing
reference sequences of known taxa. Different bioinformatic tools have been published that automate this
process (Hübler et al., 2019; Pochon et al., 2023; Yates et al., 2021).
After determining which organisms are present in a sample and authenticating them, it is possible to do
further deeper analyses on the sequences of a selected taxon, depending on the quantity and quality of
the recovered data. For instance, the co-occurrence of certain organisms can be used as an indicator of
environmental dynamics (Wang et al., 2021), the co-occurrence of two closely related species in the same
sample might be disentangled (Pedersen et al., 2021) or the population history of a species from a
specic site (Vernot et al., 2021) may be determined.
When high-quality genomes are available for particular species, combined with the tools offered by
population genetics, it is possible to explore not only the presence/absence of species but also profound
changes in genome structure and function. This sheds light on the underlying evolutionary pressures.
2.3. Application of sedaDNA in paleoenvironmental studies
& archaeology
A key feature of environmental samples, in contrast to aDNA samples from macro remains, is that it
contains traces of DNA from multiple taxa preserved at the same time and space. Therefore, data yielded
from sedaDNA studies offers a groundbreaking advancement in the eld of evolutionary research, by
enriching our understanding not only in terms of spatial distribution but also by adding a crucial temporal
dimension.
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In the existing literature, researchers have employed various sources for isolating sedaDNA, as shown in
Table2. Source material varies considerably due to the diverse environmental conditions found on Earth's
surface, such as permafrost, aquatic and terrestrial sediments, among others. Whilst the choice of the
source material is based on the specic research objectives.
Table 2
Selected articles that used various types of sediments as aDNA source.
Sources of
sedaDNA Literature
Lake sediment Pedersen et al. 2016, Graham et al., 2016, Wang et al. 2017, Ahmed et al. 2018,
Parducci et al., 2019, Schulte et al., 2020, Moguel et al., 2021, Lammers et al.,
2021, Rijal et al., 2021, Wang et al. 2021, Hebda et al., 2022,
Marine sediment Smith et al., 2015, Gaffney et al., 2020, Armbrecht et al., 2020
Rock shelter
sediment Braadbaart et al., 2020
Midden sediment Seersholm et al., 2016, Moore et al., 2020, Borry et al., 2020
Cave sediment Slon et al., 2017, Ardelean et al., 2020, Zhang et al., 2020, Gelebert et al., 2021,
Zavala et al., 2021, Pedersen et al., 2021, Vernot et al., 2021
Swamp forest
sediment Dommain et al. 2020
Permafrost Liang et al. 2021, Wang et al. 2021, Murchie et al. 2021, Murchie et al., 2022
Latrine/pond/well
sediment Søe et al. 2018, Tams et al., 2018, Sabin et al., 2020,
Aquatic sediments have provided valuable information on past ecosystems through both
bioarcheological and genetic analyses (Parducci et al., 2019). By using lake sediments, researchers
recovered ancient DNA from organisms belonging to a variety of taxa (Capo et al., 2021), and marine
sediments have been used to analyze oral and faunal changes through time (Armbrecht et al., 2020;
Gaffney et al., 2020; Smith et al., 2015). Furthermore, several studies showed that it is possible to secure
and reconstruct chloroplast and mitochondrial genomes, eciently enough to perform population
genomic analyses by using aquatic sediments (Lammers et al., 2021; Wang et al., 2021).
Permafrost sediments have also been used for reconstructing quaternary environments mostly from high
latitudes of the northern hemisphere (Fernandez-Guerra et al., 2023; Kjær et al., 2022; Murchie et al., 2021,
2022; Wang et al., 2021). Recent studies showed that DNA could be preserved at least 2million years in
permafrost. This provides a unique opportunity to reconstruct ancient environments starting from the
Late Pliocene and to uncloak the alterations of climate, vegetation and other living communities in time
and space (Kjær et al., 2022). Thanks to its ability to reconstruct genomes, this type of data allows to
reveal evolutionary histories of species (Murchie et al., 2021, 2022; Wang et al., 2021).
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Meanwhile, sedaDNA has also been used for the recovery of ancient DNA, present in archaeological sites.
It allows us to determine the presence of human groups and study temporal changes such as the
extinction of Neanderthals. While it could be collected from alongside any retrieved bone (thus limiting
the need to damage the bone), human ancient DNA can in some cases also be retrieved from soil in the
absence of bones, potentially tremendously enlarging sample sizes and spatiotemporal coverage of
future population genetic studies (Gelabert et al., 2021; Pedersen et al., 2021; Slon et al., 2017; Zavala et
al., 2021). The same, in principle, applies to other faunal, as well as oral taxa.
We can name two main applications of this technique in the Paleolithic contexts: 1) First, the
determination of presence or absence of an specic taxon such as humans in a space and time and 2)
second, while more recent and/or well-preserved contexts sedaDNA has the potential to yield more detail
(higher taxonomic resolution), and may detect additional organisms that are usually not observed in
current methods due to bad preservation conditions. It can potentially enable us to gain access to more
sample locations for a given period, a development that we now see in the application of sedaDNA to
paleoenvironmental reconstructions.
SedaDNA holds promise in addressing recent historical questions. Faunal, oral or microbial
compositions of a given environment change with human activity in some historical cornerstones (i.e.
agricultural activities). Series of temporal sampling from the archaeological cores and investigation of
compositional alterations in these samples may allow, for example, the understanding of the history of
urbanization and its effects on the environment or temporal differences in vegetation due to various
effects.
3. Added Value of sedaDNA in Archaeology
Within the subelds of geoarchaeology, zooarchaeology, and archaeobotany, ecofacts are used to tackle
fundamental archaeological research questions. Most studies to date use macro- or microscopic visual
classication to identify past environments, species, and subsistence practices. Consequently, these
methods are time-consuming and costly. Furthermore, morphological data is sometimes inadequate to
distinguish closely related species. The principles of sedaDNA and the rst trials of the method on
archaeological contexts highlight metagenomic approaches that have the potential to transform those
subelds. Yet, like any method, sedaDNA has limitations and visual-based inspection of ecofacts may
yield more or better information in some cases. Therefore, the potential of sedaDNA in comparison to
other ancient DNA sources (i.e., macro remains) or conventional archaeological methods depends on the
type of question at hand and the type and resolution of data required to provide answers to that question.
This potential is summarized in Table3 and justied in more detail below.
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Table 3
Potential of sedaDNA for answering different types of archaeologically relevant research questions (* ‘-’:
limited, ‘+’: promising, ‘++’: signicant).
Main questions Specic topics Conventional methods Ancient DNA
Microscopic
inspection
(e.g.
palynology)
Macroscopic
inspection Macro
remains Sediments
What did they
eat? Diet composition
(plants and animals) ++ ++ ++ ++
Storage and
transportation of
food products
+ + + ++
Food preparation
procedures + ++ - -
How healthy
were they? Detection of illness
and disease - ++ - -
Presence of
pathogens and
parasites (including
zoonoses)
+ - ++ +
Hygiene and
healthcare indicators ++ ++ ++ ++
How did they
control their
environment?
Land management
and spatial planning ++ + ++ ++
Agricultural practices ++ + ++ ++
Usage of wild
animals (hunting
and gathering)
- ++ ++ ++
Domestication
practices - ++ ++ +
Effects on wild
populations and
natural ecosystems
+ + + ++
Movement of
domestic livestock
and plants during
migrations
++ ++ ++ ++
Interbreeding of
domestic varieties - - ++ +
What did the
environment
look like?
Ecosystem status
and complexity ++ - - ++
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Indicators of climatic
uctuations through
biodiversity
++ - - ++
Indicators of past
landforms ++ - - ++
Indicators of natural
disasters (e.g.
volcanic eruptions)
+ - - +
Who were they
and where did
they come from?
Mobility of people
during their lifetimes - - - -
Individual and
population level
migrations
- - ++ +
Diversity within the
population - - ++ +
Relatedness of given
individuals - - ++ -
3.1. What did they eat?
Organic remains are important indicators to reconstruct past subsistences, diets and cultural preferences.
Micro- and macroscopic methods based on morphological characteristics currently dene
archaeozoological and archaeobotanical research. Increasingly, isotope ratios are also used for
reconstructing diets (DeNiro, 1987; Hedges & Reynard, 2007; Katzenberg, 2008; Larsen et al., 2019;
Richards et al., 2001).
While off-site contexts such as ponds, and ditches can provide important insights into the fauna and ora
consumed during a period (Reitz & Shackley, 2012) especially latrines, occupation layers and trash
contexts as are often rich in organic remains and provide evidence about the consumption of plants and
animals. For the study of animal products, macrofaunal assemblages remain the main source of
information. Microscopic analyses of e.g. pollen, and phytoliths provide the most important line of
evidence for plants (Larsen et al., 2019; Santini et al., 2022; Warnock & Reinhard, 1992).
Ancient DNA analysis of micro and macro remains can increase the taxonomic resolution to which they
can be identied (Hagan et al., 2020; Kuch & Poinar, 2012; Maixner et al., 2021; Nodari et al., 2021; Oskam
et al., 2012). Also ancient DNA analysis of human remains can provide evidence for adaptations to
consumption changes. For example, the presence or diversity of genes coding for certain enzymes may
signal certain diets (Fan et al., 2016; Rees et al., 2020).
As ancient DNA theoretically can be recovered from almost any archaeological context containing
organic material, sedaDNA can be an ecient way in identifying key biomarkers. It may provide a faster
way to scan pollen deposits without rst extracting pollen. Furthermore, sedaDNA can provide a high level
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of taxonomic detail as DNA extracted from ecofacts. It may especially be valuable to allow the
identication of species of which micro- or macro-remains are notoriously absent from the archeological
records due to preservation conditions. Likewise, sedaDNA may help to identify unrecognizable
fragments and remains of food products in storage vessels (Drieu et al., 2020).
While sedaDNA holds potential for consumption practices, its potential to answer questions on food
preparation procedures is more limited. Here, biochemical techniques can make a difference (Hendy,
2021). Furthermore, DNA cannot differentiate between different parts of the same species. Likewise, it is
always likely a consumption plant is present in a context because its pollen was blown in from the
surroundings (de Groot et al., 2021).
Contexts such as latrines that are less inuenced by external factors and abundantly rich in organic
remains are especially suited for or sedaDNA research into consumption practices. Clearly, sedaDNA and
archaeozoological/botanical studies are not mutually exclusive, but complementary. Not only can such
methods provide nal proof for the presence of a taxon, visual inspection also provides more nal proof
of culinary processing (Martín et al., 2014; Medina et al., 2012; Yravedra et al., 2012).
3.2. How was their health?
Osteological approaches are essential in studying individual life histories. Macroscopic inspection of
human remains enables us to identify diseases (Ortner, 2011). Traumas and healing patterns give
insights into the daily life of individuals and the social and medical institutions around them (Altınışık et
al., 2022; Spikins et al., 2018). Dental inspection (development, caries, wear etc.) enables the
reconstruction of oral health and dietary habits (Larsen et al., 2019).
While human remains are an important source, they are not often available due to preservation conditions
and burial practices, hampering systematic analysis. Findings of ancient pathogens can provide
additional information and can be recovered from sediments rich in human feces. These contain
microfossil remains associated with bacteria and viruses such as fungi and parasites. (Sabin et al., 2020;
Warnock & Reinhard, 1992). Eggs of intestinal parasites (e.g. helminths) are generally well preserved in
latrines and coprolites and have been the focus of paleoparasitological research for decades (Reinhard et
al., 1986). While techniques for extraction and examination have been rened, overlap in morphological
characters often limits identication beyond genus level (Søe et al., 2018). The integration of techniques
from genetics into paleoparasitology has advanced abilities to identify eggs extracted from latrines or
coprolites to the species level (Loreille et al., 2001e et al., 2015).
Recent exploratory studies have shown that sedaDNA has the potential to be a versatile method for the
recovery of ancient parasite DNA from soil (Søe et al., 2018). Depending on DNA preservation, direct
extraction of sedaDNA could be a cost-effective alternative for sieving eggs from the sediment. Although
larger numbers of eggs can be inspected by sieving them from the sediment, metagenomic analysis of a
small sediment sample may already yield a large diversity of soil- and meat-borne parasites (Søe et al.,
2018).
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Over the past decade dental calculus, bone tissues, and dentine have been subject to aDNA analysis for
identifying ancient protists, and bacterial and viral pathogens (de-Dios et al., 2023; Enard & Petrov, 2018;
Greenbaum et al., 2019; Guzmán-Solís et al., 2021; Margaryan et al., 2018). However, ancient pathogen
DNA from environmental sources remains understudied but presents itself as an important domain for
future innovation (Malyarchuk et al., 2022).
3.3. How did they domesticate fauna and ora?
A central research question in archaeology remains the domestication of the fauna and ora.
Macrofaunal and archaeobotanical remains have been used to distinguish domestic species from their
wild counterparts and identify markers of domestication. Visual comparison has been central in
pinpointing the origin of domestication events of different species (Price & Hongo, 2020). Unfortunately,
for many species, it is not always possible to distinguish domestic and wild species since they are still
physically close to each other. In such cases, tracing domestication events by using ancient DNA from
organic remains becomes a more reliable alternative. There have been numerous genetic studies to detect
evolutionary splits of wild and domestic species, as well as hybridization events afterward (Bergström et
al., 2022). However, these ancient DNA studies still require well-preserved macroscopic organic remains.
Here, sedaDNA has the potential to ll in the gaps on the map between sites where such remains have
been found, and thereby help researchers gure out the geographical distribution of domesticated species
and, given sucient quantity and quality of data, even the origins of those species. Likewise, sedaDNA
may help to increase spatial coverage of historical distribution maps of wild species, as well as -on a
more local scale- assessment of their presence in the surroundings of humans. A drawback of using
sedaDNA for the detection of specic domesticated or wild variants of a taxon is that such variants may
be hard to distinguish in case of low DNA yields from a certain taxon, quality or availability of references,
postmortem damage (Atağ et al., 2022) and in some cases when samples have DNA from multiple
closely related taxa.
3.4. What was their environment?
Humans not only alter plants and animals, but human action is also prescribed by the environment. Biotic
and abiotic factors dene livelihood practices and are thus crucial for the interpretation of sites. A suite of
faunal and botanic processes enables us to directly reconstruct both the biodiversity around a site and
indirectly abiotic factors such as climate.
Certain archaeological contexts can also act as catchments where organic materials from the local or
regional environment slowly accumulate (e.g. wells, deep canals, peat bogs or lakes). Microbotanical
(pollen) and microfaunal (diatoms and insects) remain valuable sources for identifying key biomarkers
that yield important insights into past landscapes and climate (Chevalier et al., 2020; Reitz & Shackley,
2012).
Therefore, in many paleoenvironmental studies, sedaDNA has already been embraced as a fast, cost-
effective and detailed alternative to palynology (Armbrecht et al., 2020; Gaffney et al., 2020; Murchie et
Page 14/26
al., 2021, 2022; Smith et al., 2015; Wang et al., 2021). These studies mostly use samples from permafrost
or lake sediments. Archaeological contexts that are now used for environmental reconstruction through
traditional methods, thus, can easily be used with the same methods.
However, cautionary selection and interpretation of contexts are needed as sedaDNA does not
discriminate between material originating from wild populations and material originating from human
practices, unless a clear signal of domestication is found. Furthermore, with traditional methods pollen
can be quantied, providing insights into the dominance and divergence between species. Metagenomic
analysis of pollen may provide trustworthy relative abundances among the observed taxa but fails to
provide absolute densities, making it more dicult to make quantitative distribution assessments per
species.
3.5. Who were they and where did they come from?
Human mobility is proven to have been considerable throughout history (Lazaridis et al., 2014). While
moving, people spread ideas, norms, and livelihood strategies. In the past, material culture was a central
source for tracing human mobility. Important advances in the natural sciences have ensured that for the
last two decades, DNA and isotopic ratios collected from human remains have been the main information
sources for studying paleo-mobility (Bentley et al., 2003; Brettell et al., 2012; Duxeld et al., 2020;
Pospieszny et al., 2023; Shaw et al., 2016).
As contemporary human DNA also enables us to map migrations routes and the genetic proximity of
populations to each other (Gilbert et al., 2022), DNA from ancient individuals provides information about
when and how population movements occurred. Therewith, answering important archaeological
questions became possible, such as the distribution of certain languages or cultures (Fernandes et al.,
2020; Wang et al., 2021).
Ancient human DNA from sediments might be advantageous when there are no human remains available
because of several reasons, such as preventing destructive sampling, ethical concerns, the type of burial,
or the absence of human remains in a site due to preservation levels. Despite the lower quality of data,
studies have shown that it is possible to study the ancestry of individual genomes found from soil,
enabling the performance of population genetics analyses with the absence of bone material (Gelabert et
al., 2021; Pedersen et al., 2022). One of the limitations of this type of study, however, is that the recovered
mtDNA or genomic data might originate from multiple individuals. This adds a layer of complexity to the
population genetics analyses, which rely on the comparison of diverse genomic positions between
individuals. A composite sequence that originates from multiple biological sources will present more
variable positions than a real single genome, adding articial divergence to the recovered consensus
sequences (Gelabert et al., 2021).
3.6. Summary: potential and position of sedaDNA in future
archaeology
Page 15/26
SedaDNA has the capacity to recover genetic material from unidentied taxa, or from taxa with scarce
remains. Therefore, it presents itself as an essential method that can truly revolutionize our study of past
consumption practices. Also, for the reconstruction of past landscapes and mapping of environmental
change, it holds great potential. SedaDNA also has the potential to tackle other research questions,
especially when certain organic remains are unavailable, have not been preserved, or are too costly for the
excavators. However, sedaDNA is not the magic solution and single method that can solve all research
questions.
Despite such limitations, we contend that sedaDNA has the potential to contribute to archaeology on
three fronts:
1. Because of its versatility in cost-effectively identifying taxa from a given sample, it can add unseen
details to archaeobotany, archaeozoology and geoarchaeology, and identify taxa which are
impossible to classify due to taphonomy or lack of morphological distinctiveness.
2. Since it can map changes in consumption practices and the environment when zooming in on
specic biomarkers, it can make existing models more ne-grained and provide us with detailed
insights into changes over time.
3. It has the potential to straightforwardly map the absence or presence of key species, the technique
presents itself as an ideal scanning or preliminary evaluation tool to assess the potential of a context
or site for further analysis with traditional techniques.
4. Possibility to recover genomes of key species, including humans with absence of bones which
provides a broader temporal and spatial distribution patterns of those taxa.
Clearly, sedaDNA is not to replace existing methods. Rather it should become part of the toolkit of those
allied subelds studying organic remains. Perhaps its biggest potential lies in its role as a scanning
method preceding further analysis.
4. Towards a research agenda for sedaDNA in Archaeology
With the decreasing sequencing costs, and improving laboratory and computational methods, sedaDNA
is on track to become a standard method in archaeology. However, at this moment, sedaDNA remains an
innovative application that has only been tested on a limited range of archeological contexts and
research questions. We need to ensure that we do not end up in a “hype cycle” where everybody is blindly
enchanted by the potential of sedaDNA and the technique is widely applied without focus and criticism
(Jones & Bösl, 2021).
We argue that concerted collaborative research across international labs is needed to ensure sedaDNA
becomes a trustworthy cornerstone in the study of the human past. Thus, a shared research agenda is
imperative to focus methodological developments and thereby arrive at the right conditions so
fundamental research questions in archaeology can be addressed with sedaDNA. We argue that in order
to become adopted as a standard method by archaeologists, ve main topics require concerted attention.
Page 16/26
(1) Clean sampling strategies more easily integrated into the archaeological workow need to be
developed. The current workow requires trained DNA experts. However, archaeological (rescue)
excavations often are ad hoc, making it dicult to plan and consistently sample those context rich in
organics. Therefore, archaeologists would need to have the tools and knowledge at hand to sample those
high potential contexts. This requires a standardized protocol executable for archaeologists that is both
versatile and sterile enough for further extraction in the lab.
(2) Increasing the data resolution for specic archaeological research questions:The resolution layer and
correspondingly, data generation strategies in sedaDNA depends on the research question as mentioned
in the workow section (see 2.2.) above. A comprehensive research plan based on research questions
and budget should be made before data generation to increase the feasibility and eciency of the
method. To explore the full biodiversity of an environmental community, one should aim to encompass
the widest range of different organisms, typically achieved through metabarcoding or when
authentication is crucial, shotgun metagenomics. On the other hand, for a more in-depth exploration of a
specic organism, targeted enrichment is often the preferred method for a high-resolution analysis. The
eciency of targeted enrichment depends signicantly on prior knowledge of the genomic diversity of the
relevant organism. Well-studied species (e.g., humans and domesticates), generally possess relatively
high-quality reference genomes and diversity panels. However, for most, the scarcity of data results in
limited prior knowledge. In the latter case, capture probe design can be challenging and requires
competent know-how. This could potentially decrease the resolution of the data. The long-term solution is
accumulating data from a wide variety of organisms in time, while a more immediate approach lies in
openly releasing designed probes along with publications.
(3) More comprehensive reference databases to increase the quality of taxonomic and evolutionary
estimations. Since the taxonomic classications heavily depend on the reference genomes available, the
lack thereof creates false positives and negatives during the analysis. To tackle it, more reference
genomes from different taxa are needed. Existing initiatives beyond archaeology show that sequencing
genomes of relevant species can increase the quality of bioinformatic species determination.
(4) Fostering an open science perspective where raw data and methodological protocols are shared:Such
an approach helps other scientists use the similar methods for their own studies or help them avoid
double work for certain aspects of their studies. Next to those, when the shared data is raw and
unprocessed sequencing data, it allows other scientists to re-use it for comparison or certain types of
analyses that were not done during the actual study, due to different focus or a limited time. Once the raw
data is shared it becomes a good resource for other scientists and contributes to the growth of the
scientic eld.
(5) Multi-proxy comparisons between sedaDNA and other archaeological methods: The comparison of
results of sedaDNA with e.g., pollen analysis enables us to explore the limits and blind spots of sedaDNA.
This information will help us in positioning sedaDNA in the archaeological workow and thus solve the
Page 17/26
important question: at which stage can sedaDNA bring added value and be eciently integrated into the
current workow.
5. Conclusion
SedaDNA has become an essential tool in the eld of paleogenomics while its applications for
archaeology remain limited. This article highlighted the vast potential of sedaDNA to address pressing
archaeological questions. Especially, the research questions related to diets, origins, and environments of
ancient human populations are yet to unleash this potential. However, it is evident that future studies
need to overcome several key challenges. These are mainly about its applicability in archaeological
workows, data resolution and quality and comprehensive reference databases. Our primary goal is to
facilitate a broader use and to unlock the full potential of sedaDNA in archaeological research. The
optimization of sedaDNA’s use in archaeological research will provide newly found perspectives in the
pursuit of a deeper understanding of the human past. Therefore, a concerted collaboration between
sedaDNA labs is needed if it would become a cornerstone of the archaeological practice.
Declarations
Acknowledgements
This paper derives from the project ‘Constructing the
Limes
: Employing citizen science to understand
borders and border systems from the Roman period until today’ (C-Limes), funded by the Dutch Research
Council (NWO) as part of the Dutch Research Agenda. (2021–2026, Project number: NWA.1292.19.364).
Pere Gelabert was funded by FWF under project P–36433: “Social genomics in Late Antique and Early-
Medieval Societies”’. Ezgi Altınışık was funded by TÜBİTAK Project No: 121Z485. Lastly, we would like to
extend our appreciation to Irene Mena for creating the illustration on sedaDNA workow (see Fig.1).
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Figures
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Figure 1
An illustration of basic sedaDNA workow for archaeologists’ toolkit.
... SedaDNA can thus go beyond standard archaeogenetic research rooted in fossils, which is necessarily a death assemblage. It may instead present a life assemblage (13), reflecting on aspects of human site use, population dynamics, and structuring of domestic spaces (14). But to transcend the question of "who was here," we need to develop and employ analytical approaches that acknowledge and take advantage of the highly variable sedimentary record. ...
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Haplotype-based analyses have recently been leveraged to interrogate the fine-scale structure in specific geographic regions, notably in Europe, although an equivalent haplotype-based understanding across the whole of Europe with these tools is lacking. Furthermore, study of identity-by-descent (IBD) sharing in a large sample of haplotypes across Europe would allow a direct comparison between different demographic histories of different regions. The UK Biobank (UKBB) is a population-scale dataset of genotype and phenotype data collected from the United Kingdom, with established sampling of worldwide ancestries. The exact content of these non-UK ancestries is largely uncharacterized, where study could highlight valuable intracontinental ancestry references with deep phenotyping within the UKBB. In this context, we sought to investigate the sample of European ancestry captured in the UKBB. We studied the haplotypes of 5,500 UKBB individuals with a European birthplace; investigated the population structure and demographic history in Europe, showing in parallel the variety of footprints of demographic history in different genetic regions around Europe; and expand knowledge of the genetic landscape of the east and southeast of Europe. Providing an updated map of European genetics, we leverage IBD-segment sharing to explore the extent of population isolation and size across the continent. In addition to building and expanding upon previous knowledge in Europe, our results show the UKBB as a source of diverse ancestries beyond Britain. These worldwide ancestries sampled in the UKBB may complement and inform researchers interested in specific communities or regions not limited to Britain.
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Ancient environmental DNA (aeDNA) is a crucial source of information for past environmental reconstruction. However, the computational analysis of aeDNA involves the inherited challenges of ancient DNA (aDNA) and the typical difficulties of eDNA samples, such as taxonomic identification and abundance estimation of identified taxonomic groups. Current methods for aeDNA fall into those that only perform mapping followed by taxonomic identification and those that purport to do abundance estimation. The former leaves abundance estimates to users, while methods for the latter are not designed for large metagenomic datasets and are often imprecise and challenging to use. Here, we introduce euka , a tool designed for rapid and accurate characterisation of aeDNA samples. We use a taxonomy‐based pangenome graph of reference genomes for robustly assigning DNA sequences and use a maximum‐likelihood framework for abundance estimation. At the present time, our database is restricted to mitochondrial genomes of tetrapods and arthropods but can be expanded in future versions. We find euka to outperform current taxonomic profiling tools and their abundance estimates. Crucially, we show that regardless of the filtering threshold set by existing methods, euka demonstrates higher accuracy. Furthermore, our approach is robust to sparse data, which is idiosyncratic of aeDNA, detecting a taxon with an average of 50 reads aligning. We also show that euka is consistent with competing tools on empirical samples. euka 's features are fine‐tuned to deal with the challenges of aeDNA, making it a simple‐to‐use, all‐in‐one tool. It is available on GitHub: https://github.com/grenaud/vgan . euka enables researchers to quickly assess and characterise their sample, thus allowing it to be used as a routine screening tool for aeDNA.
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This article presents the first direct archaeological evidence of nixtamalization, a chemical process that improves the nutritional value of maize, among the ancient Maya people of Guatemala. Analysis of microbotanical remains recovered from two chultunes, pits cut into bedrock, in a Late and Terminal Classic period residential group at the site of San Bartolo, Petén, Guatemala, provides the first archaeological recovery of maize starch spherulites, a unique byproduct of nixtamalization, and thus the earliest direct evidence of nixtamalization in the archaeological record. The presence of helminth eggs within the same contexts indicates that, at some point in their use life, the pits were used as latrines and as middens for the disposal of domestic refuse, likely including nejayote, wastewater from nixtamalization. These findings shed light on the daily lives of ancient Maya commoners and inform discussions of subsistence and waste management in Maya cities.