Catching the Past: Discovering the legacy of historic Atlantic cod exploitation using ancient DNA

¬Humans have used the natural resources of the oceans for thousands of years. For communities around the North Atlantic Ocean, Atlantic cod (Gadus morhua) in particular is of great economic and cultural value. In the last century, the industrial exploitation of cod has been associated with population collapse and phenotypic changes that lead to economic loss, i.e. fish mature at an earlier age and remain smaller. Nevertheless, it is unclear if such periods of intense fishing have had lasting genomic impacts, making it difficult to quantify the full extent of human impact. The main aim of this project is to investigate if the intensive exploitation of cod over thousands of years has affected their population demography or has led to evolutionary change. By extracting DNA from ancient fish remains (up to 9000 years old) we compare the genetic profiles of these fish to those from modern reference databases. The age of the ancient fish remains allows us to investigate patterns of cod diversity from those periods that predate extensive human influence. We also develop novel genetic approaches to trace the extend of historical trade of throughout northern Europe. So far, our temporal analyses show no substantial loss of genetic diversity with high effective population sizes and an absence of major evolutionary change. We have further improved our ability to trace source populations of Atlantic cod from archaeological sites improving our understanding of a temporally and spatially expanding fishing trade.

We processed over 500 historic and ancient Atlantic cod samples from Norway, the Netherlands, Germany, Denmark, Sweden and the United Kingdom. As subset of these has been sequenced to medium/higher coverage (~5 to 10X) for detailed evolutionary inference. These data have been used to address a range of evolutionary questions (see publications). During this work we were challenged by unexpectedly poor DNA preservation of many specimens. We addressed this challenge by developing a novel program to deal with specimens with such poor DNA preservation. This new program (BAMscorer) allows us to obtain useful data from the far majority of ancient specimens that we have processed.

Humans have exploited the naturally abundant resources of marine ecosystems since prehistoric times. One of these resources, Atlantic cod (Gadus morhua), is of profound economic and cultural value for communities around the North Atlantic Ocean. The history of exploitation for this species dates back millennia, which makes it difficult to quantify the extent of human impact. While contemporary influence of industrial fishing is associated with population collapse and phenotypic changes that lead to economic loss, it is unclear if past episodes of intensive fishing have wrought analogous demographic and evolutionary changes. Therefore, the true anthropogenic impacts on the ecology of exploited fish populations remain unclear. Given the projected increase in anthropogenic pressure on marine resources, a better understanding of such effects is urgently needed. Here, we obtain genome-wide data from archaeological bones up to 9000 years old and ask if an intensive exploitation history covering millennia has inflicted demographic and selective changes on Atlantic cod. We reconstruct long-term patterns of cod diversity from those periods predating extensive human influence and simultaneously identify the source populations of Viking Age and medieval fish trade. Our unprecedented spatiotemporal approach allows us to assess associations between expanding fisheries, population decline and anthropogenic selection, as well as answer specific archaeological questions. Overall, the combination of the latest genomic tools and material of distinctive importance will yield unparalleled insights in the natural and cultural history of a major marine resource.