Received: 6 June 2022
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Revised: 1 September 2022
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Accepted: 5 September 2022
DOI: 10.1002/edn3.363
C O M M E N TA R Y
Environmental DNA surveys of African biodiversity: State of
knowledge, challenges, and opportunities
Sophie von der Heyden
Evolutionary Genomics Group, University
of Stellenbosch, Matieland, South Africa
Correspondence
Sophie von der Heyden, Evolutionary
Genomics Group, University of
Stellenbosch, Private Bag X1, Matieland,
7602, South Africa.
Email: svdh@sun.ac.za
Abstract
Environmental DNA surveys have become a well-­established tool for detecting natural communities, showing excellent promise for supporting biodiversity monitoring,
conservation, and management efforts. Africa is a continent of exceptional biodiversity, threatened not only by anthropogenic pressures but also by a general lack of
research capacity and infrastructure, limiting evaluation and monitoring of ecosystems. This commentary explores the use of environmental DNA in surveying natural
diversity, a rapidly moving field, within the context of capturing Africa's natural capital. Through an extensive literature search and filtering, 65 papers from 22 countries
were identified, with research from Madagascar and Africa forming the bulk of the
literature (~38%), with many countries only represented by one to three papers. There
was a diverse range of studies, with more than half reporting on communities or diet
analyses; freshwater and marine research are underrepresented, accounting for ~5%
of studies. There were some papers on disease monitoring, particularly in freshwater.
Disturbingly, representation of authors was highly skewed and highlights the ongoing
inequality of scientific publishing and the extent of parachute science; one-­third of
papers (n = 21) reported no African representation, in contrast with the 18 papers that
had either first or senior authors affiliated with an institution in Africa. The remainder
of the papers (n = 27) had at least one author affiliated with an African institution. In
addition, less than half of papers reported appropriate sampling permits. Importantly
and with a concerted global effort, building long-­term capacity, through meaningful
and equitable relationships will help increase self-­sustaining science around technologies based on eDNA, thus ensuring not only biodiversity but also humanitarian benefits across Africa.
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I NTRO D U C TI O N
much of which supports crucial ecosystem services and ~16% of
the global population. From the Cape Floristic region at the tip of
The African continent and associated islands, both in the Indian and
the continent to the desert and mountainous regions of northern
Atlantic oceans, is without a doubt one of the biodiversity jewels
Africa, the African continent harbors eight of the world's biodiver-
of the world. Its uniqueness of natural biodiversity is unparalleled,
sity hotspots (Myers et al., 2000), ranging from temperate to tropical
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium,
provided the original work is properly cited.
© 2022 The Author. Environmental DNA published by John Wiley & Sons Ltd.
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Environmental DNA. 2023;5:12–17.
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and high to low rainfall areas and diverse ecosystems such as rain-
authorship contributions and also touches on permitting. As such
forests to deserts with some of the lowest rainfall globally. As else-
this work provides insights into the future of eDNA surveys in Africa,
where, urbanization (Güneralp et al., 2017), agricultural expansion
whilst highlighting the necessity for equitable access to ensure that
and land cover changes (Brink & Eva, 2009; Marchant et al., 2018),
not only African biodiversity is documented and accounted for, but
alien and invasive species (Linders et al., 2021), overexploitation
that the continent can thrive through capacity building, equal ac-
(Riggio et al., 2018) and the effects of climate change (Dejene, 2018;
cess, and applied solutions to safeguarding biodiversity through the
Pecl et al., 2017) all threaten Africa's unique biodiversity and the
exciting technologies that eDNA offers.
ecosystem services they provide (Archer et al., 2021).
Although patterns of biodiversity in Africa are broadly understood, there remain ongoing challenges for monitoring species and
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M E TH O D S
communities. This is especially problematic in the context of climate
change, where species are known to shift their ranges in response to
A Web of Science search was carried out in February 2022 with
environmental variation (Brodie et al., 2021; Carvalho et al., 2021;
the following search terms (“Country” AND eDNA) OR (“Country”
Dejene et al., 2021; Pecl et al., 2017) and it is likely that for the vast
AND “environmental DNA”) OR (metabarcoding AND “Country”) OR
majority of African biodiversity, contemporary distribution patterns
(“Country” and “eDNA metabarcoding”) where “country” was sub-
or even broad habitat requirements, which would allow for pre-
stituted for each of the 58 countries in Africa. In addition, a search
dictive modeling of future ranges, are undocumented. This lack of
for “Country” AND “environmental DNA” AND “biomonitoring” was
biodiversity knowledge limits opportunities for maximizing conser-
carried out to ensure that the first round of searches did not exclude
vation and management opportunities that can benefit biodiversity
papers with a biomonitoring focus. Following Antich et al. (2021),
and people and strengthen their resilience under climatic change
the term “environmental DNA” was used to generally include “any
(Dejene, 2018; Kapuka & Hlásny, 2021).
DNA extracted from an environmental sample.” All papers were ex-
Given the numerous logistical and financial challenges associated
ported into an Excel database for further assessment. Papers with
with monitoring biodiversity, particularly in remote or deep aquatic
the sole focus on microbial diversity were not included for analyses
ecosystems, environmental DNA surveys have become a well-­
and only papers with multicellular eukaryotes retained (with the ex-
established as a tool for detecting natural communities from water,
ception of two studies that focused on the gut microbiota of host
sediment, and even air (Deiner et al., 2017; Gaither et al., 2022;
animals); methods papers were also excluded. In addition, one paper
Ruppert et al., 2019; Thomsen & Willerslev, 2015). Environmental
from Mozambique was excluded as the work was not conducted in
DNA approaches have been used to detect rare, endangered, or in-
the country but rather in the Mozambique Channel; relevant papers
vasive species (Franklin et al., 2019; Wilcox et al., 2013) and even
from La Reunion and Mayotte (n = 7) were also not included in the
contributed toward our understanding of population genetic struc-
final list given their designations as overseas departments of France,
turing in natural populations (Adams et al., 2019). Species monitoring
rather than independent African states.
based on eDNA surveys has been shown to be comprehensive and
Post filtering and retention, papers were scanned and broadly
likely have broad applicability in conservation and management (Bani
divided into the following categories: (1) Marine, terrestrial, or
et al., 2020; Barnes & Turner, 2016; Beng & Corlett, 2020). However,
freshwater; (2) community or diet study or gut microbiome or par-
despite the numerous benefits of carrying out biodiversity surveys
asite or species detection (but excluding parasites such as free-­
using eDNA and the general ease with which to collect samples,
living parasites such as schistosomiasis, which were included in
generating data is complex, requiring specialized DNA extraction
“parasites”). To identify the spread of eDNA studies across Africa
venues, as well as access to advanced sequencing platforms (e.g.,
the country where each study took place was noted, as well as
Illumina MiSeq or HiSeq). Such challenges have likely led to uneven
the composition of the authors on the paper; specifically, (1) the
applications of eDNA surveys globally, with tropical regions, South
number of papers with first or senior authors affiliated with an
America, and Africa reporting significantly fewer eDNA studies than
institution in Africa, (2) the number of papers with an author af-
the Northern Hemisphere (for example in freshwater surveys Belle
filiated with an African institution elsewhere on the author line (ex-
et al., 2019) and there have been calls to ensure more equal access
cluding first/senior authors) and (3) the number of papers without
to data generated from eDNA biodiversity surveys to ensure better
any African representation. The latter was carried out to identify
uptake and application (Berry et al., 2021). Paradoxically, Africa's im-
African participation in developing environmental DNA barcoding
portance to global biodiversity and associated ecosystem services
and to gauge the extent of “parachute science,” that is instances
will be severely undermined without equitable access to eDNA tech-
where researchers from one country (primarily the global North)
nologies and all the benefits this offers for biodiversity monitoring.
conduct studies in another (mostly the global South), without
This commentary explores environmental DNA surveys from a wide
including or engaging with people from that nation, effectively
range of environmental samples in order to provide a state of knowl-
sidelining researchers or other stakeholders from a scientific inves-
edge of the field in Africa. In addition to investigating the applicabil-
tigation (Asase et al., 2020; de Vos & Schwartz, 2022; Stefanoudis
ity of eDNA for biodiversity surveys, this commentary also explores
et al., 2021). Finally, for each paper, it was noted whether a collec-
the “academic” origin of eDNA research through investigating
tion or research permit was provided.
26374943, 2023, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/edn3.363 by Namibia Hinari NPL, Wiley Online Library on [01/12/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
von der
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R E S U LT S A N D D I S CU S S I O N
3.1 | Environmental DNA surveys have diverse
applications in Africa
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3.2 | Unequal representation of host nations on
eDNA-­based research and a lack of research permits
Representation of authors was surprisingly skewed and highlights the
ongoing inequality of scientific publishing and in particular parachute
The WoS search returned 103 papers, with 65 retained after assess-
science. Only ~28% of papers had first or senior authors affiliated with
ment (excluded papers were either not focused on eDNA or reported
African institutions in “host nations” (i.e., where the research was car-
on free-­living microbial communities; available in Table S1). The ma-
ried out; Figure 1), which is fewer than the 32% of papers that had no
jority of studies were carried out on terrestrial ecosystems (n = 51),
African institution affiliated authors listed on the author line, although
with only nine and five focusing on marine or freshwater systems, re-
some of these papers list African participants in acknowledgments for
spectively. There was a wide geographic spread in the 22 countries
enabling research through fieldwork and support. The remainder of
in which eDNA surveys were carried out, but for many of these only
publications had some African representation as middle authors. Most
between one and five studies were recorded (Figure 1). Research from
of the latter category only had one or two African authors and only
only two countries, Madagascar (n = 10) and South Africa (n = 15)
one country, South Africa, had papers where all authors were associ-
made up ~38% of all eDNA studies. There was a wide array of study
ated with African institutions. These findings show a deep disconnect
systems, but community and diet studies made up the bulk of the re-
of African researchers from what is happening elsewhere globally,
search (~70%; Figure 1), with ~23% of papers having a focus on either
which is highly problematic given the accelerating developments in
free-­living or internal parasites, the latter particularly mammals. Gut
the field. This is further underscored by how many papers listed per-
microbiome and species detections studies made up less than 2% of
missions for accessing environmental samples, with less than half of
all studies (Figure 1). There was a diverse range of focal taxa, from
the papers providing details on permits or similar. Permits were most
fungal communities associated with root systems of trees, to large
likely to be reported when working in Madagascar, South Africa, or
charismatic mammal species such as cheetahs, rhinos, and elephants.
those studies focusing on large mammals. It was surprising that pa-
Studies carried out in freshwater systems, targeted either invasive
pers without explicit permit statements were published, given that the
species (such as Silver carp) or parasite detection. Several papers fo-
majority of established publishers require collection and permission
cused on agricultural aspects, including detection and dynamics of
information, highlighting that publishers need to do better on report-
pest species and their management, as well as the detection of human
ing requirements. Finally, although not explicitly analyzed, the vast
diseases, not only in freshwater systems but also mammalian hosts.
majority of funding stemmed from outside of Africa (with only South
F I G U R E 1 Map of Africa providing an overview of the number of papers on environmental DNA surveys retrieved for each country
(central panel), as well as a subset of taxonomic diversity targeted in studies (green panel). The top graph shows the different categories of
eDNA research (note that “species detection” excludes parasites), whereas the bottom graph notes authorship of studies. The size of the
circles on the main map indicates the number of studies.
26374943, 2023, 1, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/edn3.363 by Namibia Hinari NPL, Wiley Online Library on [01/12/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
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research field but extends to other biological areas such as human
BOX 1
health, genomics, and biodiversity monitoring (Chu et al., 2014;
Stephenson & Ruiz de Pas, 2022; Svardal et al., 2020). For example,
There are many exciting opportunities for expanding eDNA
Svardal et al. (2020) highlight numerous barriers when carrying out
workflows and studies in Africa. Although several global
genomic research in Africa, with a lack of access to resources and
initiatives such as the Ocean Best Practices (OBIS) and
finances probably the largest inhibitors to growing genomic capac-
UNESCO have environmental DNA working groups, these
ity in Africa. Parachute science is another significant challenge
by themselves are not sufficient to address the inequality
identified in this commentary, as it has been elsewhere (Asase
of research. As such, the recommendations below echo
et al., 2020; de Vos & Schwartz, 2022; Stefanoudis et al., 2021).
those made elsewhere (see for example Chu et al., 2014;
Unlike working directly with plants or animals, environmental DNA
O'Connell et al., 2017; Schmeller et al., 2017; Stephenson
samples from water and sediment are particularly easy to collect,
& Ruiz de Pas, 2022; Svardal et al., 2020):
transport and process, making them more susceptible to collection
1. Meaningful collaborations that include African re-
and transport without permits. This makes it difficult to enforce
searchers and allow for capacity building for long-­term
eDNA work, particularly if there is a lack of oversight from funding
self-­sufficiency, thereby minimizing dependence on ex-
bodies and publishers. This challenge has to be addressed outside
ternal researchers. This includes the identification of
of Africa and lies predominantly with researchers themselves, who
research problems and co-­creation of projects, includ-
have ethical obligations toward the biodiversity capital of other
ing access to funding. Although some efforts are made
nations. Further, the importance of the identification of research
around citizen science and citizen involvement is laud-
and knowledge gaps and the co-­creation of projects by African and
able and important, alone it is not substitutes for knowl-
other partners, to fill those gaps is not only crucial for bridging
edge sharing and meaningful collaborations at a higher
the science-­p olicy interface but has the potential to revolution-
level.
ize how science can be applied to solve real-­world challenges. For
2. Ensuring and enabling access to eDNA biodiversity data
example, in this review, one paper dealt specifically with human
through standardizing repositories and eDNA reporting,
health and monitoring disease vectors but did not include African
which includes not only data but also methods (Berry
collaborators for whom such data is relevant for managing disease
et al., 2021), in order to facilitate researchers unable to
or provide any insights as to how the data might be used to bet-
fund international travel access to the latest in eDNA
ter manage vector-­b orne disease. This shows a vast disconnect
developments.
between research through parachute science, which can only
3. Publishers and funders must ensure that appropriate
limit the development of science and its application. Overall, for
and valid permits/permissions for sample collection are
African biodiversity research to fully benefit from the exciting op-
obtained and reported.
portunities that environmental DNA surveys have to offer, deep,
4. Continued building of DNA barcode databases to allow
for more accurate linking of specimens from eDNA data,
long-­term, and equitable working relationships are foundational to
achieving fully integrated and self-­sustaining eDNA research.
thus supporting conservation, management, and spatial
planning (Bani et al., 2020; Cristescu, 2014).
AC K N OW L E D G M E N T
I sincerely thank Courtney Gardiner for help with the creative artwork and Wiley Publishers for granting a waiver that supported the
OA fees for this paper.
Africa providing significant financial support to environmental DNA
research). As such funding bodies, including those supported through
C O N FL I C T O F I N T E R E S T
the EU and NSF need to do more to provide oversight and to positively
The author declares no conflict of interest.
influence their grantholders not only regarding appropriate permitting
but also to ensure meaningful participation of researchers and other
DATA AVA I L A B I L I T Y S TAT E M E N T
stakeholders for capacity development, especially for countries out-
No new data was generated for this article.
side their immediate jurisdiction.
ORCID
3.3 | A way forward for eDNA biomonitoring
in Africa
Although the diverse range of eDNA-­
based research in Africa
is encouraging, numerous challenges remain (see Box 1), but a
global approach will find solutions. This is not unique to the eDNA
Sophie von der Heyden
https://orcid.org/0000-0001-9166-976X
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S U P P O R T I N G I N FO R M AT I O N
Additional supporting information can be found online in the
Supporting Information section at the end of this article.
How to cite this article: von der Heyden, S. (2023).
Environmental DNA surveys of African biodiversity: State of
knowledge, challenges, and opportunities. Environmental
DNA, 5, 12–17. https://doi.org/10.1002/edn3.363
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