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Identifying invasive alien species using DNA

Being tasked with the monitoring of invasive alien species (IAS) occurring in Flanders, the Agency for Nature and Forests of the Flemish Government needs to be able to accurately identify the species involved and to distinguish them from their related species. Within this framework, the Agency contacted the Barcoding Facility for Organisms and Tissues of Policy Concern (BopCo) to help determine if faecal droppings found in a nature reserve near Antwerp belonged to native deer or to the invasive Reeves’ muntjac (Muntiacus reevesi).

Keywords: invasive alien species (IAS), EU Regulation, online DNA sequence data, DNA barcoding, BopCo, Muntiacus reevesi

"Genetic barcoding of these muntjac droppings proved to be rapid, cheap, and very informative. It is clear that this method holds great power to support us in the further management of invasive species."

Bram D'hondt, Agency for Nature and Forests of the Flemish Government

The Agency for Nature and Forests manages more than 37,000 hectares of parks, forests and nature areas in Flanders. It is the competent authority in Flanders for the implementation of the EU Regulation on invasive alien species (1143/2014). The Regulation requires authorities to take action on pathways of unintentional introduction, to take measures for the early detection and rapid eradication of these species, and to manage species that are already widely spread in their territory.


Non-native species introduced into Europe can be of policy concern since some of them may reproduce and disperse rapidly in a new territory, establish viable populations and finally negatively impact native species. Hence non-native species may disrupt ecosystems, affect crops and livestock, and introduce vector-borne diseases or parasites, thus impacting human health and socio-economic activities. Non-native species causing such adverse effects are called Invasive Alien Species (IAS). In order to protect native biodiversity and ecosystems, and to mitigate the potential impact on human health and socio-economic activities, the problem of IAS is tackled in Europe by EU Regulation 1143/2014 on measures to be implemented across all EU member states. These measures require accurate methods for the identification of IAS when suspicious biological material is encountered.

Reeves’ muntjac, Muntiacus reevesi, is a small deer native to southeast China and Taiwan that is included in the list of IAS of EU concern. Its presence in Flanders is monitored and managed by the Agency for Nature and Forests. In order to do so, the Agency needs to be able to identify it correctly and distinguish it from the native deer species. In this context, the Agency sent two suspect faecal samples to BopCo for identification.



Since morphology-based species identifications are not always possible (e.g. cryptic species, trace material, early life-stages), BopCo uses a DNA barcoding approach. This is a species identification method that uses DNA sequence data (“DNA barcodes”) to compare an unknown sample to a database of reference sequences of well-identified species. The rationale is that the divergence of nucleotide sequences among different species is larger than the nucleotide divergence among conspecific sequences. DNA sequence data can thus facilitate the identification of IAS samples, especially when morphological characteristics are absent or uninformative.

Against this background, BopCo evaluates the usefulness of publicly available reference DNA sequence data to reliably identify the IAS of EU concern. The results of these evaluations are presented as factsheets (one per IAS) that can be consulted by anyone interested in this topic. Each factsheet consists of (i) a short introduction to the specific IAS, compiling information on its classification, as well as its native and invasive distribution, and (ii) a critical evaluation of the current usefulness of publicly available reference DNA sequences to identify a given IAS.

To assure correct species identifications, the online libraries of reference DNA sequences need to include a large number of sequences of (i) the IAS under investigation from different geographic areas (native and introduced) to assess the intraspecific sequence divergence, and (ii) closely related species, in order to evaluate the interspecific sequence divergence.

In the case of the faecal samples, the information compiled in the factsheet for the Reeves’ muntjac allowed for a quick selection of the most informative DNA markers.

Used components of the LifeWatch Infrastructure

Barcoding Facility for Organisms and Tissues of Policy Concern (BopCo)

BopCo acts as a focal point for identifying biological materials upon request, by providing access to the expertise and infrastructure necessary to identify organisms of policy concern and their derived products. Identifications can rely on traditional morphology-based approaches employing the taxonomic expertise and specimen collections at the Royal Belgian Institute of Natural Sciences (RBINS) and the Royal Museum for Central Africa (RMCA). However, when morphological identifications are not possible (e.g. early life stages, cryptic species, processed food items), DNA sequence data (or other DNA based methods) are used for species identifications. In order to do so, BopCo has access to fully equipped DNA laboratories at both RBINS and RMCA.




Meganck, K., Smitz, N., Gombeer, S., Van Bourgonie, YR., Backeljau, T. & De Meyer, M. 'DNA barcoding to identify invasive alien species targeted by EU policies'. 8th International Barcode of Life Conference, 17–20 June 2019. Trondheim, Norway.

Meganck, K., Smitz, N., Gombeer, S., Van Bourgonie, Y.R., Backeljau, T. & De Meyer, M. ‘Identifying Invasive Alien Species by DNA-barcoding: possibilities, gaps and pitfalls‘. 25th Congress of Zoology, 14-15 December 2018, Antwerp, Belgium.

Smitz, N., Meganck, K., Gombeer, S., Van Bourgonie, Y.R., De Meyer, M. & Backeljau, T. 'Invasive Alien Species in Belgium (IAS): examining the utility of GenBank and BOLD for species identifications'. 24th Congress of Zoology, 23-24 November 2017, Wageningen, The Netherlands.

Gombeer, S., Meganck, K., Van Bourgonie, Y.R., Smitz, N., De Meyer, M. & Backeljau, T. ‘Aliens in Europe’. 7th International Barcode Of Life Conference, 20-24 November 2017, Kruger National Park, South Africa.




Useful links

Image credits

  • Muntiacus reevesi By gailhampshire [CC BY 2.0]
  • Molecular laboratory By BopCo
  • Muntiacus reevesi By David Bygott [CC BY-NC-SA 2.0]