Periodic Reporting for period 1 - MAFRI (Molecular Ancient Fish Remains Identification)
Período documentado: 2016-06-09 hasta 2018-06-08
Anthropogenic effects on oceans including pollution, climate change, habitat destruction, and overfishing are threatening the viability of fish stocks and the health of the ocean. In 2010, the FAO reported 30% of fish stocks were overexploited, depleted, or recovering from depletion, but it is likely much higher. Creating evidence-based fisheries management policies, critical to long-term ocean health, requires data on the natural variation and responses to environmental and anthropogenic pressures in healthy fish populations. However, as most, if not all, of the living fish populations, are unhealthy this is difficult. Archaeology offers an alternative line of evidence to help overcome this issue by providing detailed, long-range histories of local inshore fisheries and their exploitation by humans. The sheer diversity of species (~30,000) means that conventional zooarchaeological approaches combined with limited reference collections struggle to identify the vast majority of remains below family level with zooachaeologists estimating that only 4-10% of fish bones are identified to species. Such low-resolution information prevents archaeology from usefully contributing to studies of past fishing, let alone contributing to current management issues. MAFRI explored the possibilities of employing of ZooMS, recently described as a ‘Game Changing Technique’ using archaeological material to directly address ecological questions. The hope is that ZooMS can greatly improve this resolution and help identify diversity within the earliest fish populations exploited by humans and thus how much this has been impacted by fishing pressures. This can include tracking invasive species in the past, such as carp and exploring past population distributions to predict how fish populations might be affected by warmer waters caused by climate change.
MAFRI began to explore the question of the Medieval fish trade. Working with archaeoichthyologists she compared the archaeozoological identifications with those from the ZooMS analysis. Typically when the bones could be identified morphologically there was agreement, ZooMS proving its value when there was an insufficient detail to identify the origin. Following a successful presentation at the ICAZ Fish Remains Working Group MAFRI was invited to participate in a number of other projects in collaboration with archaeoichthyologists. These projects included (i) expanding the freshwater fish identifications to include several species from the Perch family in order to identify very small fish bones from archaeological sites in Eastern Europe (ii) identifying North Atlantic salmon and trout species in order to better understand the fishing behavior of the hunters in Neolithic Scotland and (iii) identifying Atlantic tuna, freshwater eels in Japan, and several species of marine sharks in New Zealand and South Africa..
Undoubtedly the most significant finding was the fact that it was possible to successfully use ZooMS to identify fish remains even between members of the same genus. It was gratifying that so many different researchers from around the world became aware of the potential of the method to aid their diagnosis. The ongoing interest and collaborations that have resulted from the project are extensive. Consequently, although there has yet to be a stand-out moment for the research, MAFRI has laid the groundwork for a number of ongoing projects. Kristine’s appointment to the MPI Jena, mean that this work will continue making the methods and databases developed during the project accessible to a wider group of researchers.
One key element of the MAFRI project was to communicate the research to as wide an audience as possible. Kristine led other Marie Curie postdoctoral fellows, Horizon 2020 PhD students, and Chef Presenter, Phil Leverington to produce a yearly event through the award Winning York Festival of Ideas which introduced members of the general public to the concept of fishing in the archaeological record and the importance of healthy aquatic ecosystems today over the course of two days. The event educated several hundred people each year with activities for adults and children and was featured in an article by the British Academy. In addition, Kristine participated in outreach events with Cawood Historical Society for school age students and adults, Science Trails at the University of York for school-age students, and several archaeological groups for lectures for adults. Kristine also participated in online outreach as a guest host for a week on the twitter pages @biotweeps and @iamscicomm and was featured as a Human of York, though the University of York. This outreach work continues through the online platforms www.fish-n-ships.palaeome.org and on Twitter at @FishNShipsUK
Undoubtedly the most significant finding was the fact that it was possible to successfully use ZooMS to identify fish remains even between members of the same genus. It was gratifying that so many different researchers from around the world became aware of the potential of the method to aid their diagnosis. The ongoing interest and collaborations that have resulted from the project are extensive. Consequently, although there has yet to be a stand-out moment for the research, MAFRI has laid the groundwork for a number of ongoing projects. Kristine’s appointment to the MPI Jena, mean that this work will continue making the methods and databases developed during the project accessible to a wider group of researchers.
One key element of the MAFRI project was to communicate the research to as wide an audience as possible. Kristine led other Marie Curie postdoctoral fellows, Horizon 2020 PhD students, and Chef Presenter, Phil Leverington to produce a yearly event through the award Winning York Festival of Ideas which introduced members of the general public to the concept of fishing in the archaeological record and the importance of healthy aquatic ecosystems today over the course of two days. The event educated several hundred people each year with activities for adults and children and was featured in an article by the British Academy. In addition, Kristine participated in outreach events with Cawood Historical Society for school age students and adults, Science Trails at the University of York for school-age students, and several archaeological groups for lectures for adults. Kristine also participated in online outreach as a guest host for a week on the twitter pages @biotweeps and @iamscicomm and was featured as a Human of York, though the University of York. This outreach work continues through the online platforms www.fish-n-ships.palaeome.org and on Twitter at @FishNShipsUK
The ZooMS method relies upon collagen preserved in fish bone fragments, and it can be applied anywhere where collagen is preserved. Let us imagine collagen as three chains of beads, each more than 1000 beads long. The twenty different beads have different sizes and shapes. Comparing these chains between species, at first glance the chains look identical. On closer inspection, here and there one or more beads are different. This difference may amount to only one bead change in a chain of more than 1000 beads. As these chains are very long they are very difficult to analyse, so we rely on the use of another protein, an enzyme called trypsin, that will cleave the sequence at specific points (it will only cut at two particular types of ‘bead’, the amino acids Arginine and Lysine). These fragments (peptides) of varying length and sequence create what is known as a peptide mass fingerprint. Modern mass spectrometers can rapidly measure the mass of (a subset of) these fragments. If one or more of the fragments has a different mass, this can be rapidly detected, and therefore the sequence difference and thus the species identified and the animal of origin of the parchment established. Within MAFRI the major advances were to improve the prediction of peptide mass fingerprint patterns for fish using genomic data. A particular delight of the project was the willingness of researchers to share their early data from sequencing projects so that Kristine was able to literally ‘fish’ out the collagen genes required for the analysis. This work highlights a real challenge with furthering this work, the sheer diversity of fish collagen sequences is daunting, although it does (as in the case of the salmonids) enable the resolution to species which is not the case in mammals, where resolution is more typically limited to species.
One interesting example of the nature of interdisciplinary collaboration that has resulted from MAFRI is a conversation during an outreach event between Kristine an expert in European Medieval History who works on Medieval maps. Kristine was talking about the average size of fish has decreased greatly through time and then pointed out that some of the illustrations of sea monster fish on the Medieval maps were species that although now are considered fairly small, in the past would have grown to over two meters long. The historian did not realize that the species of fish on the maps would have ever been large enough to pose an actual threat to fishing boats during the Medieval period and thus although still fanciful were not as fanciful as she once thought.
One interesting example of the nature of interdisciplinary collaboration that has resulted from MAFRI is a conversation during an outreach event between Kristine an expert in European Medieval History who works on Medieval maps. Kristine was talking about the average size of fish has decreased greatly through time and then pointed out that some of the illustrations of sea monster fish on the Medieval maps were species that although now are considered fairly small, in the past would have grown to over two meters long. The historian did not realize that the species of fish on the maps would have ever been large enough to pose an actual threat to fishing boats during the Medieval period and thus although still fanciful were not as fanciful as she once thought.