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INTRODUCTION
Trends in DNA barcoding and metabarcoding
Sarah J. Adamowicz, James S. Boatwright, Frédéric Chain, Brian L. Fisher, Ian D. Hogg,
Florian Leese, Darío A. Lijtmaer, Monica Mwale, Amanda M. Naaum, Xavier Pochon,
Dirk Steinke, John-James Wilson, Susanna Wood, Jianping Xu, Sen Xu, Xin Zhou,
and Michelle van der Bank
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This open-access special issue features 12 full articles international DNA barcoding research community. Sev-
representing emerging trends from the international DNA eral contributions focus upon the unique biota of Africa.
barcoding community. Several articles highlight how A number of African institutions, particularly in South
DNA-based techniques are elucidating the species diver- Africa but elsewhere as well, harbour rich research pro-
sity, biogeography, and conservation status of Africa’s grams in biodiversity, DNA barcoding, molecular phylo-
biodiversity. Another prominent theme is the movement
genetics, molecular wildlife forensics, and evolutionary
towards big biodiversity data using high-throughput,
community ecology (e.g., Adeoba et al. 2019; Yessoufou
individual-based DNA barcoding methods, which pre-
serve voucher specimens and abundance data, as well as et al. 2019). Moreover, the 7th International Barcode of
bulk sample-based metabarcoding. Methodological de- Life Conference was recently held at Kruger National
velopments are enhancing the detection of specific spe- Park, South Africa, from November 20–24, 2017, marking
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cies and whole communities using environmental DNA the first time this biennial conference series was hosted
(eDNA) barcoding and metabarcoding. Data are also ex- on the African continent (Adamowicz et al. 2017).
panding in terms of genetic coverage; in this issue, a new Key trends in contemporary DNA barcoding research
database is established for a secondary fungal DNA barcode include large-scale analyses of the biodiversity, evolution-
marker, and multi-kingdom, multi-marker biodiversity ary history, and conservation status of the biota of Africa;
surveys are gaining traction. DNA barcode sequence data, increasing use of DNA-based methods for wildlife forensics
often combined with complementary markers or tax- and for marketplace product authentication; cross-over of
onomic information, are increasingly contributing to
cutting-edge methods from genomics into biodiversity re-
large-scale phylogenetic projects, with implications
search; growing interest in the development and applica-
for understanding evolutionary history, community
tions of environmental DNA (eDNA) techniques; and the
structure, and conservation priorities.
integrative analysis of biomes and species interactions
Focus on African biodiversity (Adamowicz et al. 2017). A strong signature of interna-
This special issue of peer-reviewed papers focuses tional collaboration and authorship is also a consistent
upon research trends and biological findings from the pattern among researchers in the DNA barcoding com-
munity and reflects a global research network (Adamowicz While individual-based methods provide abundance
and Steinke 2015; Adamowicz et al. 2017; also see refer- data, substantial research attention is also being directed
ences herein). to exploring prospects for more efficient biodiversity
Here, our team of invited Guest and Regular Associate data collection. In this issue, Zizka et al. (2019) present a
Editors is pleased to introduce a special issue of 12 open- methodological study of biodiversity detection by eDNA
access articles that use or develop DNA barcoding and metabarcoding from the fixative used to store bulk mac-
related techniques to further the study of biodiversity, roinvertebrate samples. By constructing known mock
evolution, and conservation. This will be followed by the communities, they compare species recovery from the
publication of a larger virtual special issue, comprised of sample fixative against DNA barcoding of specimens as
an array of papers from the 7th Conference plus addi- well as bulk sample metabarcoding. Their results are
tional related contributions published across multiple encouraging, showing in general good species recovery,
issues of Genome. In addition to a geographic focus on the albeit with variable DNA sequence read counts. The
biota of Africa in multiple contributions, this special is- authors suggest that classical DNA barcoding or bulk
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sue showcases three main scientific trends. metabarcoding may be preferred when a more compre-
hensive biodiversity survey is needed, yet eDNA metabar-
Large-scale biodiversity analyses
A dominant trend in DNA barcoding research, exem- coding from preservative is a promising alternative for
plified in this special issue, is the development of new large-scale, efficient, and cost-effective biodiversity
approaches for acquiring big biodiversity data. For exam- studies.
ple, deWaard et al. (2019) present protocols for efficient, The challenges of detecting species in the wild using
high-throughput biodiversity surveys of arthropod sam- molecular approaches are also highlighted by Wood et al.
ples, using a workflow that combines Malaise trap sam- (2019), who compare surveys of marine environments con-
pling, specimen sorting, DNA barcoding via unidirectional ducted by SCUBA divers against results obtained using
sequencing, grouping specimens into species-like units quantitative PCR (qPCR) performed on eDNA and eRNA.
Their detection rates with qPCR are lower than for diver
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In addition to capturing more total biodiversity, multi- phological approaches to estimate fruit fly infestation
marker approaches can also increase confidence in iden- rates as well as the diversity and associations of parasi-
tifications within taxonomic groups. Meyer et al. (2019) toid wasps in both wild and cultivated olives in South
promote a multi-marker approach for fungal DNA bar- Africa. In their study, Powell and colleagues discovered
coding. They introduce a new database for the secondary concordance between the different lines of evidence and
DNA barcode marker, Translational Elongation Factor 1␣ a new understanding of the diversity and parasitism
(TEF1␣), for fungi. Complementing the ITS marker, which
rates in olives.
was established in 2012 as the standard for fungi (Schoch
Phylogenetic methods applied to DNA barcodes are
et al. 2012), TEF1␣ is proposed to increase resolution at
also being used to elucidate biogeographic history and
the species level. Confidence in identifications is espe-
evolutionary rates, particularly over recent geological
cially important in clinical settings when dealing with
pathogenic species. Formal establishment of multiple time periods, because commonly used DNA barcode
markers mirrors the multi-marker approach for plant markers yield a phylogenetic signal at low taxonomic
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DNA barcoding and opens new potential avenues for levels. Loeza-Quintana et al. (2019) generate phylogenetic
DNA barcoding applications as well as fundamental re- hypotheses for trans-Arctic marine invertebrates and
search in biodiversity patterns and systematics. compare phylogeographic patterns against the timeline
of the recurrent openings and closures of the Bering
Tree of life and phylogenetic diversity
Strait. By arranging the biogeographic and geological/
A third research trend involves working towards more
complete phylogenetic trees and using phylogenetic climatic evidence in a harmonized timeline, they pro-
hypotheses to study ecological and evolutionary mecha- pose a recalibrated molecular clock for northern marine
nisms. Methods for building phylogenetic trees vary, invertebrates. This research involving many allopatric
such as through de novo phylogenetic reconstruction sister pairs—and with molluscan fossil evidence used to
using multi-marker datasets or hybrid taxonomic and validate the biogeography-based calibrations—has re-
phylogenetic approaches. By participating in large-scale sulted in an upward revision of rates of molecular evolu-
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biodiversity surveys and DNA sequencing campaigns, tion in the mitochondrial cytochrome c oxidase subunit
the international DNA barcoding research community is I (COI) gene compared to commonly cited prior marine
establishing new ways to fill in leaves on the tree of life clock calibration studies. These findings are expected to
and is achieving more comprehensive phylogenetic cov- inform rates of diversification as well as the correlation
erage than was considered possible a decade ago. between evolutionary events and the geological and cli-
A notable example of this trend is this issue’s contri- matic history of marine regions.
bution by Adeoba et al. (2019), who combine taxonomic
There is also an increasing tendency in the DNA barcod-
and DNA barcode sequence data to create a new phylo-
ing community, particularly among botanical researchers,
genetic hypothesis for species belonging to the fish
to use DNA barcode loci to construct whole-community
family Cyprinidae in Africa. They conclude that there is
a significant phylogenetic signal in the distribution of phylogenies. For Robben Island, South Africa, Yessoufou
heightened extinction risk, meaning that more unique et al. (2019) generate a community-wide phylogenetic tree
evolutionary history would be lost than expected by and reveal an association between higher phylogenetic di-
chance alone should currently threatened species be per- versity within native communities and lower risk of local-
mitted to go extinct. This pattern could cause the loss of scale invasion by non-native species. They also pinpoint
unique ecosystem functions as well as inherently valu- differences in biological traits, such as flowering time,
able, unique life forms. Adeoba et al. (2019) also highlight pollination syndrome, and breeding mode, between non-
the identities and distributions of species of special rel- native and native species. Their work contributes to an
evance for conservation due to their global evolutionary understanding of factors governing invasion processes
uniqueness and threatened status. Their approach high- and the importance of preserving phylogenetically di-
lights the utility of building comprehensive phylogenetic verse native plant communities.
hypotheses at the species level yet also draws attention to
Moving into the aquatic environmental microbiome,
deficits in taxonomic, geographic, and genetic marker
Farrell et al. (2019) conduct bacterial metabarcoding and
coverage in public biological data bases. Increasing cov-
phylogenetic analysis using the 16S rRNA gene on uncul-
erage across these domains would open new research
tured water samples from watering holes in Kruger
avenues in conservation phylogenetics and DNA-based
biodiversity tracking, informing conservation prioritiza- National Park and found spatially and phylogenetically
tion efforts. structured communities. This environmental microbiome
Taxonomic and phylogenetic approaches are also approach could be paired in the future with multi-marker
being used to elucidate biodiversity and ecological metabarcoding, including the macrobiota, to examine bio-
interactions among species of socio-economic impor- logical associations between the prokaryotes and eu-
tance. Powell et al. (2019) combine molecular and mor- karyotes and to track spatial and temporal changes.
1. Cristescu Melania E., Donaldson Michael R.. 2019. Genome’s 60th anniversary. Genome 62:4, iii-iv. [Citation] [Full Text] [PDF]
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