Fishing for DNA (without bycatch)

Thijs is not the only one visiting the KU Leuven in Belgium this spring (March-May 2019). While he is out in the field fishing for sticklebacks, I am fishing for DNA in the lab with my Belgian colleague Els De Keyzer and Congolese visiting scientist Fidel Muterezi Bukinga.

Our work focuses on the Lake Tanganyika sardine (Limnothrissa miodon) and sprat (Stolothrissa tanganicae), which are the centre of my project “Population genomics and phylogeography of freshwater sardines of Central Africa”. These two species have a similar lifestyle to their marine counterparts (like herring, sardine, anchovy, …), and are comparably important to the fisheries of Lake Tanganyika. Over half of the lake’s catch is made up of these small fishes, making them an indispensable food source for the inhabitants of the surrounding countries.

The Tanganyika sprat, fresh from Lake Tanganyika (photo credit: Charlotte Huyghe).

Els has been working on the fisheries of Lake Tanganyika for over 2 years now, and has recently published a study showing the lack of population structure in the Tanganyika sprat, highlighting the need for integrated management across country borders (read more here). Now we are asking ourselves if the same is true for the Tanganyika sardine, and if the observed patterns are stable over time. To find out, we are extending Els' study to the Tanganyika sardine, and to different seasons and years.

At the moment, we are preparing our fish for RAD-tag sequencing, a widely used reduced representation DNA sequencing technique based on known cut sites of restriction enzymes.

First step of getting DNA: dissections.

To get from fish to RAD-tag sequences, we first need to dissect our fish and extract pure DNA from the samples. This DNA is then subjected to a restriction enzyme digestion, barcoding and amplification, so we end up with a high amount of digested DNA fragments to sequence.

We plan to use the generated genomic data to delineate the population structure of our species and monitor it over time. This work is important to inform fisheries management and ensure the continued productivity of the Lake Tanganyika fishery. If you'd like to know more about the project, click here.

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