Fish identification by genetic barcoding


 (c) Malte Damerau

New innovative approaches for the identification of fishes and fisheries products of diverse species and populations – a contribution to consumer safety and containment of illegal fisheries

Tracing the origin of fishes serves consumer safety and helps to contain illegal fishing. In this project East Atlantic fishes are characterized.

Background and Objective

The Central East Atlantic is a major source for fish imports to the European markets, including Germany. The relatively high species diversity and widespread lack of controls often leads to mislabeling of fisheries products. Such false declarations obscure illegal catches due to impossible traceability and may pose a risk for consumer safety. Especially processed fisheries products are often indistinguishable from each other by morphological characters. Hence, genetic methods for species determination gained increasing popularity. One important requirement for a successful genetic screening is the existence of validated standards. The aim of the project is to characterize all commercially important fish species from the East Atlantic genetically from voucher specimens by means of four genes. All data will be publicly available in a database.

Tracing the origin of migrating species is especially difficult. Exemplified for the heavily exploited yellow fin tuna (Thunnus albacares) the project is additionally intended to identify genetic markers that characterize manageable stocks by whole genome sequencing.

"Fische am genetischen Barcode erkennen" ist ein Teilprojekt von AutoMAt, dem Verbundprojekt "Anpassung und Weiterentwicklung von innovativen, nicht-invasiven Monitoringsystemen und Auswerteverfahren für die Fischereiforschung".


The Thünen Institute of Fisheries Ecology has a large collection of fishes from the East Atlantic. The DNA of these samples is isolated in the laboratory. Subsequently, specific fragments of mitochondrial and nuclear genes are amplified. These amplifications are finally sequenced and prepared for publication in our developed database.

The genome of the yellow fin tuna is sequenced by the whole-genome low-coverage method. First, total genomic dna is sheared into short fragments and subsequently amplified, read and combined to long dna sequences. Individual tags allow the simultaneous dna sequencing for multiple individuals, allowing the identification of markers, which characterize stocks.

Data and Methods

PCR based amplification of specific mitochondrial and nuclear gene fragments; Sanger sequencing of PCR products; whole-genome low-coverage sequencing (Illumina platform)


The genetic barcodes of 488 species and 882 individual samples have been characterized within the project. All data is publicly available in the curated data base For each sample additional data (e.g. sampling location and date, photographs) are provided for further reference. Especially control agencies and scientists have the possibility to upload their own DNA sequences for identification purposes. The data base continues to be updated and expanded.

The genomic analyses of the population structure of the yellowfin tuna has shown that atlantic and indo-pacific individuals belong to distinct populations with limited connectivity. The geographic origin of these fishes can be determined with only a few of the newly identified genetic markers, which has practical application for consumer safety and species conservation efforts. The project has proven that population structures can be detected by genomic comparisons for species which are characterized by relatively large population sizes and high mobility.

Links and Downloads


Involved Thünen-Partners

Involved external Thünen-Partners

Funding Body

  • Federal Office for Agriculture and Food (BLE)
    (national, öffentlich)


7.2013 - 12.2015

More Information

Projekt type:
Project status: finished


hits: 3

  1. Lopes EP, Monteiro V, Martins A, Coelho R, Freitas R, Blancke T, Hanel R (2021) Confirmed record of the roughear scad Decapterus tabl in the Cabo Verde Archipelago based on morphological and genetic data. Zoologia Caboverdiana 9(1):3-13
  2. Barth JM, Damerau M, Matschiner M, Jentoft S, Hanel R (2017) Genomic differentiation and demographic histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) population. Genome Biol Evol 9(4):1084-1098, DOI:10.1093/gbe/evx067
    pdf document (limited accessibility) 849 kb
  3. Damerau M, Freese M, Hanel R (2017) Multi-gene phylogeny of jacks and pompanos (Caragidae), including placement of monotypic vadigo Campogramma glaycos. J Fish Biol 92(1):190-202, DOI:10.1111/jfb.13509