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Molecular Ancient Fish Remains Identification

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Old bones point the way in fisheries management

How fish populations will respond to changes in fishing practices and the environment is one of the most important questions facing fisheries management. With fish stocks under pressure, accurate histories of man-made and environmental change are needed to create a tool for developing effective management policies.

Food and Natural Resources

Archaeology can provide detailed, long-range histories of local inshore fisheries and their exploitation by humans, but only if the techniques for identifying and analysing fishbones are improved. However, the identification of fish bones and scales to species is often difficult or impossible using current methods, meaning that fish are often not described at species level in archaeological reports and diversity is likely underrepresented in the archaeological literature. As part of the Marie Skłodowska-Curie Individual Fellowships grant scheme, the EU-funded Horizon 2020 MAFRI project addressed this challenge by developing the Zooarchaeology by Mass Spectrometry (ZooMS) fishbone identification system. The rapid and inexpensive system uses protein barcoding to identify proteins in the collagen associated with the bones. Cross discipline collaboration The ZooMS technique involves peptide fingerprinting of collagen to detect known peptide sequences and rapidly identify bones collected from archaeological digs and archives. Collagen is the main structural protein in bones and scales and this approach can be applied wherever collagen is preserved. Mass spectra reflect the differences in protein sequence and can therefore be reproducibly linked to a particular protein or fragment. “For mammals, sufficient sequence information is available, but, for freshwater fish, species are highly diverse, and few sequences are currently available,” says researcher Dr Kristine Korzow Richter, the Marie Skłodowska-Curie fellow. Researchers used ZooMS to build a framework for species-level identification, creating a database of fish collagen sequences and testing the method at several archaeological sites. This involved collaborating with modern and archaeological fish experts to acquire bone reference material and for mining genomic databases for genetic reference material. “It is now possible to successfully use ZooMS to identify ancient fish remains even between members of the same genus,” explains Dr Korzow Richter. Improved identification Working closely alongside archaeological experts, they compared the identified fish remains from archaeological sites with those from the ZooMS analysis. “Typically, when the bones could be identified morphologically there was agreement, ZooMS proving its value when (as is common in fish remains) there was insufficient detail to identify their origin,” claims Dr Korzow Richter. “The sheer diversity of species means that conventional zooarchaeological approaches combined with limited reference collections struggle to identify most remains below family level. Zooachaeologists estimate that only 4-10 % of fish bones are identified at the species level,” observes Dr Korzow Richter. Such low-resolution information can prevent archaeology from understanding the complete picture of past fishing activities and contributing to current management issues. ZooMS will help to improve this resolution and identify diversity within the fish populations exploited by humans. This may include tracking past invasive species, like carp and exploring past population distributions to predict how fish populations may be affected by warmer waters caused by climate change. “With this new technique archaeologists can provide more accurate histories of fisheries, leading to better fisheries management policies in the future,” concludes Dr Korzow Richter.

Keywords

MAFRI, fish, archaeological, ZooMS, protein, collagen, sequence, peptide

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