Final Report Summary - ORCA (Optimizing Research tools for Cetaceans in Archaeology)
Whale hunting has been practiced by a variety of cultures worldwide for thousands of years, and played a key economic and sociological role especially in pre-contact North-America. Today, whales belong to one of the most threatened groups of mammals, almost exclusively due to the industrial hunting practices of the last few centuries. Archaeological investigations into the history of whaling are vital for understanding the long-term exploitation of these important marine mammals, and also because they can provide essential ecological baseline data on whale populations prior to industrial overhunting. Previous investigations both into the pre-history of whaling and contemporary impacts of whale hunting have been hampered by difficulties in the accurate identification of fragmentary archaeological cetacean remains. Innovative new biomolecular approaches, however, can provide accurate information on the distribution, diversity and population sizes of whale populations through time. My project, “ORCA: Optimizing Research tools for Cetaceans in Archaeology”, developed new biomolecular approaches for the taxonomic identification of archaeological whale remains. Both species identification and genetic data were then applied to archaeological whale remains on three continents to explore the long-term exploitation and historical ecology of cetacean populations, with a key focus on the historical demography of gray whales.
Through ORCA, I addressed the pressing need for rapid, inexpensive biomolecular approaches for accurate whale species identification. First, I tested a new identification protocol that compares collagen peptide fingerprints with the fingerprints from known samples using mass spectrometry (ZooMS - Zooarchaeology Mass Spectrometry). Following training in MALDI-TOF and MS/MS, I refined the ZooMS for cetacean remains through the rapid screening and direct sequencing of archaeological and museum collagen from known species. These data were combined with recently published species diagnostic peptide masses to create a cetacean collagen database, which was then tested using archaeological whale remains to assess its reliability, accuracy and precision in terms of taxonomic identifications. Comparisons with DNA based identification methods demonstrated that ZooMS consistently produced accurate taxonomic identifications to the genus or family level, although it lacked the discriminatory power of DNA based methods when analysing closely related cetacean species. The power of ZooMS lay in its ability to identify bone fragments from non-cetacean species (e.g. human, pinniped, ruminant) that had been morphologically misidentified as whales, as well as with whale bones samples that had failed DNA analysis due to the presence of inhibitory substances.
In further refining biomolecular identification approaches, I tested micro-sampling approaches using both ZooMS and DNA based techniques. While the micro-sampling approach for ZooMS failed to consistently yield adequate quantities of collagen for an unambiguous taxonomic identification, the micro-sampling technique for DNA-based identification could produce accurate and consistent species identifications using as little as 3 mg of archaeological bone powder. These micro-sampling techniques are imperative for dealing with precious museum samples, or worked whale bones artifacts. Once optimized, this microsampling technique was applied to a 1000-year-old carved whale bone artifact from the East Coast of the United States demonstrating the utility and practicality of micro-sampling for museums and other biological archives.
Following technical optimization, through ORCA, I explored how accurate species based identifications affected current hypotheses on the prehistory of whale hunting and exploitation in the South Atlantic and Mediterranean. In both regions, biomolecular methods revealed cetacean taxa that had not been identifiable morphologically, and in some cases, significantly revised the data concerning species distributions, human preferences and cetacean exploitation strategies. Finally, through the analysis of over 60 ancient remains from the northeast Pacific and North Atlantic, I attempted to document the distinct demographic histories of Atlantic and Pacific gray whale (Eschrichtius robustus). Following training in bait-capture enrichment, next-generation sequencing, and bioinformatics, I tested whether a hybridization approach to ‘capture’ mitochondrial DNA from paleontological samples over 40,000 years old would yield sufficient genome coverage for demographic modelling. These analyses indicated extensive variability in the quantity of endogenous DNA that could be retrieved from ancient (often water-logged) samples, and the need for further optimization of hybridization capture approaches.
Through ORCA, I was able to bring the concept of DNA and protein-based identification methods to the wider public, through public outreach activities and lectures. Additionally, the project has developed new links with researchers in North and South America and Europe, including the University of Georgia, University of Manitoba, Simon Fraser University, ICSE-Universidad Nacional de Tierra del Fuego, the Archéologie des Sociétés Méditerranéennes, University of Montpellier, Cardiff Osteoarchaeology Research Group, Zoological Society of London, and Natuurhistorisch museum, Rotterdam. These new collaborations have opened up novel research directions in cetacean exploitation, with ramifications not only for the understanding of the past, but for future whale conservation.
Through ORCA, I addressed the pressing need for rapid, inexpensive biomolecular approaches for accurate whale species identification. First, I tested a new identification protocol that compares collagen peptide fingerprints with the fingerprints from known samples using mass spectrometry (ZooMS - Zooarchaeology Mass Spectrometry). Following training in MALDI-TOF and MS/MS, I refined the ZooMS for cetacean remains through the rapid screening and direct sequencing of archaeological and museum collagen from known species. These data were combined with recently published species diagnostic peptide masses to create a cetacean collagen database, which was then tested using archaeological whale remains to assess its reliability, accuracy and precision in terms of taxonomic identifications. Comparisons with DNA based identification methods demonstrated that ZooMS consistently produced accurate taxonomic identifications to the genus or family level, although it lacked the discriminatory power of DNA based methods when analysing closely related cetacean species. The power of ZooMS lay in its ability to identify bone fragments from non-cetacean species (e.g. human, pinniped, ruminant) that had been morphologically misidentified as whales, as well as with whale bones samples that had failed DNA analysis due to the presence of inhibitory substances.
In further refining biomolecular identification approaches, I tested micro-sampling approaches using both ZooMS and DNA based techniques. While the micro-sampling approach for ZooMS failed to consistently yield adequate quantities of collagen for an unambiguous taxonomic identification, the micro-sampling technique for DNA-based identification could produce accurate and consistent species identifications using as little as 3 mg of archaeological bone powder. These micro-sampling techniques are imperative for dealing with precious museum samples, or worked whale bones artifacts. Once optimized, this microsampling technique was applied to a 1000-year-old carved whale bone artifact from the East Coast of the United States demonstrating the utility and practicality of micro-sampling for museums and other biological archives.
Following technical optimization, through ORCA, I explored how accurate species based identifications affected current hypotheses on the prehistory of whale hunting and exploitation in the South Atlantic and Mediterranean. In both regions, biomolecular methods revealed cetacean taxa that had not been identifiable morphologically, and in some cases, significantly revised the data concerning species distributions, human preferences and cetacean exploitation strategies. Finally, through the analysis of over 60 ancient remains from the northeast Pacific and North Atlantic, I attempted to document the distinct demographic histories of Atlantic and Pacific gray whale (Eschrichtius robustus). Following training in bait-capture enrichment, next-generation sequencing, and bioinformatics, I tested whether a hybridization approach to ‘capture’ mitochondrial DNA from paleontological samples over 40,000 years old would yield sufficient genome coverage for demographic modelling. These analyses indicated extensive variability in the quantity of endogenous DNA that could be retrieved from ancient (often water-logged) samples, and the need for further optimization of hybridization capture approaches.
Through ORCA, I was able to bring the concept of DNA and protein-based identification methods to the wider public, through public outreach activities and lectures. Additionally, the project has developed new links with researchers in North and South America and Europe, including the University of Georgia, University of Manitoba, Simon Fraser University, ICSE-Universidad Nacional de Tierra del Fuego, the Archéologie des Sociétés Méditerranéennes, University of Montpellier, Cardiff Osteoarchaeology Research Group, Zoological Society of London, and Natuurhistorisch museum, Rotterdam. These new collaborations have opened up novel research directions in cetacean exploitation, with ramifications not only for the understanding of the past, but for future whale conservation.