[MARMAM] new publication on marine mammal eDNA surveys

Elena Agnese Valsecchi elena.valsecchi at unimib.it
Thu Feb 6 09:42:17 PST 2020

Dear MARMAM readers,
My co-authors and I are pleased to announce the publication of our new article
in Environmental DNA:

Novel universal primers for metabarcoding environmental DNA surveys of
marine mammals and other marine vertebrates

Elena Valsecchi, Jonas Bylemans, Simon J. Goodman, Roberto Lombardi, Ian
Carr, Laura Castellano, Andrea Galimberti, Paolo Galli (2020)


Link to open access https://onlinelibrary.wiley.com/doi/full/10.1002/edn3.72

Metabarcoding studies using environmental DNA (eDNA) and high throughput
sequencing (HTS) are rapidly becoming an important tool for assessing and
monitoring marine biodiversity, detecting invasive species, and supporting
basic ecological research. Several barcode loci targeting teleost fish and
elasmobranchs have previously been developed, but to date primer sets
focusing on other marine megafauna, such as marine mammals have received
less attention. Similarly, there have been few attempts to identify
potentially ‘universal’ barcode loci which may be informative across
multiple marine vertebrate Orders. Here we describe the design and
validation of two new sets of primers targeting hypervariable regions of
the vertebrate mitochondrial 12S and 16S rRNA genes, which have conserved
priming sites across virtually all cetaceans, pinnipeds, elasmobranchs,
boney fish, sea turtles and birds, and amplify fragments with consistently
high levels of taxonomically diagnostic sequence variation. ‘*In silico*’
validation using the OBITOOLS software showed our new barcode loci
outperformed most existing vertebrate barcode loci for taxon detection and
resolution. We also evaluated sequence diversity and taxonomic resolution
of the new barcode loci in 680 complete marine mammal mitochondrial genomes
demonstrating that they are effective at resolving amplicons for most taxa
to the species level. Finally, we evaluated the performance of the primer
sets with eDNA samples from aquarium communities with known species
composition. These new primers will potentially allow surveys of complete
marine vertebrate communities in single HTS metabarcoding assessments,
simplifying workflows, reducing costs, and increasing accessibility to a
wider range of investigators.


Elena Valsecchi, PhD

*Marine eDNA Group, MaRHE Center (**http://www.marhe.unimib.it/

*Adjunct Professor of Marine Vertebrate Zoology *

*Department of Environmental and Earth Sciences
(**https://www.disat.unimib.it/en <https://www.disat.unimib.it/en>**),

*University of Milano-Bicocca. Piazza della Scienza 1, 20126 Milan, Italy*
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