This proposal has broader impacts in paleontological inquiry. This is Because the key to success in this line of inquiry often lies in the ability to identify samples with optimal preservation. An underlying pitfall is that we are far from understanding factors that limit the survival of ancient biomolecules. This has led to the sacrifice of numerous fossils for destructive analysis. An ultimate goal of our systematic study of bone diagenesis to redefine the way skeletal remains are selected for any variety of on going biomolecular studies. Several letters of support indicate the need for this data in developing their understanding of the paleoecological or characteristics of fossils at a particular site. The project also parallels work currently being conducted on collagen by MJC and other DNA research by AC. Each of the PI's teach various related courses and will host undergraduates, graduates and post-doctoral fellows in their laboratories. This proposal focuses on four related objectives. The first objective is to determine the limit of survival of DNA and OC from a set of samples stratified by time and depositional environment. Data emphasizing the enhanced stability of OC (Collins et al., 2000; McNulty et al., in press) suggest that it is likely to survive longer than DNA and may offer a genetic window into deep time. The second objective is to relate mineral characteristics (e.g. porosity) to the diagenetic state of protein and DNA (e.g. OC and collagen concentrations, abundance and types of OC-derived peptides, and copy number and amplifiable fragment size for DNA). Because preliminary data suggest predictive relationships between mineral characteristics and biomolecular survival, the third objective is to establish a reliable screening tool that identifies samples containing well-preserved biomolecules, based on mineralogical characteristics. Data on OC, DNA and collagen derive from our second objective. Our analyses typically take 20-500 mg of clean bone and, thus, result in little destruction. The fourth objective is to apply DNA sequencing (D-loop of the mitochondrial genome) and protein sequencing to elucidate the phylogeny of ancient muskox (Euceratherium, Praeovibos, Soergelia, Bootherium and Ovibos). Although this objective is not a primary focus of this grant, it reflects an intelligent strategy because these fossils will also be used for diagenetic studies. In addition to fulfilling these objectives, the intellectual merit of this proposal in part stems from using emerging technology (e.g. MALDI-MS, SAXS) to long-standing issues. The Ancient Biomolecules Center (AC) remains on the forefront of new applications of ancient DNA sequencing. The application of mass spectrometric techniques to ancient protein sequencing has provided the first complete protein sequences for >53,000 yr BP bones. We have shown definitively that protein and DNA sequences can derive from the same fossils. The broad public interest in this work was demonstrated by an enormous press response to our recent paper (Nielsen-Marsh et al., 2002): e,g, the BBC, Washington Post, Discovery Channel, Globe and Mail, The Telegraph, New Scientist and Naturwissenschaften. Building on our understanding of bone diagenesis toward the development of a screening tool is fundamental to the success of numerous lines of paleoecological research and will be imperative for protecting an irreplaceable component of the Earth's natural history.
