Recent dating of extinct Atlantic gray whale fossils, (Eschrichtius robustus), Georgia Bight and Florida, western Atlantic Ocean

Paleoproteomics

Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.

New Holocene grey whale (Eschrichtius robustus) material from North Carolina: the most complete North Atlantic grey whale skeleton to date

Skeletal remains and historical accounts indicate that grey whales (Eschrichtius robustus) existed in the North Atlantic Ocean from the Pleistocene into the seventeenth century. Fossil and sub-fossil occurrences in this basin are rare, distributed from the east coast of the United States to Iceland and Europe. Here, we report an incomplete skeleton of a Holocene grey whale from Pender County, North Carolina, USA. This specimen represents a physically immature individual and is the most complete North Atlantic grey whale specimen reported to date. It comprises 42 cranial and postcranial elements, including the cranium, parts of the rostrum, both mandibles, both scapulae, humeri, radii and ulnae, most of the vertebral column anterior to the lumbar region and numerous ribs. Its provenance near the inlet of a large estuary is consistent with previous findings from the southeastern USA and parallels the species' habitat use in Baja California breeding and calving grounds in the North Pacific Ocean. Radiocarbon dating indicates an age of 827 ± 172 years before present. Cut marks on multiple skeletal elements indicate that the animal was butchered, suggesting some level of human exploitation of the species in the southeastern USA in the twelfth century, approximately 500 years prior to its extirpation in the North Atlantic.

Leveraging palaeoproteomics to address conservation and restoration agendas

Archaeological and paleontological records offer tremendous yet often untapped potential for examining long-term biodiversity trends and the impact of climate change and human activity on ecosystems. Yet, zooarchaeological and fossil remains suffer various limitations, including that they are often highly fragmented and morphologically unidentifiable, preventing them from being optimally leveraged for addressing fundamental research questions in archaeology, paleontology, and conservation paleobiology. Here, we explore the potential of palaeoproteomics—the study of ancient proteins—to serve as a critical tool for creating richer, more informative datasets about biodiversity change that can be leveraged to generate more realistic, constructive, and effective conservation and restoration strategies into the future.

Species identification of Australian marsupials using collagen fingerprinting

The study of faunal remains from archaeological sites is often complicated by the presence of large numbers of highly fragmented, morphologically unidentifiable bones. In Australia, this is the combined result of harsh preservation conditions and frequent scavenging by marsupial carnivores. The collagen fingerprinting method known as zooarchaeology by mass spectrometry (ZooMS) offers a means to address these challenges and improve identification rates of fragmented bones. Here, we present novel ZooMS peptide markers for 24 extant marsupial and monotreme species that allow for genus-level distinctions between these species. We demonstrate the utility of these new peptide markers by using them to taxonomically identify bone fragments from a nineteenth-century colonial-era pearlshell fishery at Bandicoot Bay, Barrow Island. The suite of peptide biomarkers presented in this study, which focus on a range of ecologically and culturally important species, have the potential to significantly amplify the zooarchaeological and paleontological record of Australia.

Natal origin of Namibian grey whale implies new distance record for in-water migration

We use genomics to identify the natal origin of a grey whale found in the South Atlantic, at least 20 000 km from the species core range (halfway around the world). The data indicate an origin in the North Pacific, possibly from the endangered western North Pacific population, thought to include only approximately 200 individuals. This contributes to our understanding of Atlantic sightings of this species known primarily from the North Pacific, and could have conservation implications if grey whales have the potential for essentially global dispersion. More broadly, documenting and understanding rare extreme migration events have potential implications for the understanding of how a species may be able to respond to global change.