Feather barbs as a good source of mtDNA for bird species identification in forensic wildlife investigations

Background: The ability to accurately identify bird species is crucial for wildlife law enforcement and bird-strikeinvestigations. However, such identifications may be challenging when only partial or damaged feathers areavailable for analysis.Results: By applying vigorous contamination controls and sensitive PCR amplification protocols, we found that itwas feasible to obtain accurate mitochondrial (mt)DNA-based species identification with as few as two featherbarbs. This minimally destructive DNA approach was successfully used and tested on a variety of bird species,including North American wild turkey (Meleagris gallopavo), Canada goose (Branta canadensis), blue heron (Ardeaherodias) and pygmy owl (Glaucidium californicum). The mtDNA was successfully obtained from ‘fresh’ feathers,historic museum specimens and archaeological samples, demonstrating the sensitivity and versatility of thistechnique.Conclusions: By applying appropriate contamination controls, sufficient quantities of mtDNA can be reliablyrecovered and analyzed from feather barbs. This previously overlooked substrate provides new opportunities foraccurate DNA species identification when minimal feather samples are available for forensic analysis

Active Whaling, Opportunistic Scavenging or Long-Distance Trading:Zooarchaeological, Palaeoproteomic, and Historical Analyses on Whale Exploitation and Bone Working in Anglo-Saxon Hamwic

THE ANGLO-SAXON SITE OF HAMWIC (modern Southampton, Hampshire, UK) has been identified as a major bone-working centre. Besides antler and terrestrial mammal bone, cetacean bone has been recovered in high quantities. These specimens primarily represent working waste. Using peptide mass fingerprinting of bone collagen (ZooMS), it was determined that the majority of these specimens derive from the currently highly endangered population of North Atlantic right whale (Eubalaena glacialis). Limited historical sources appear to suggest that whaling was undertaken by the Anglo-Saxons, or by the Normans on the other side of the English Channel prior to the eleventh century ad. Nevertheless, the primary method of acquisition for whale bone was through opportunistic scavenging and trading.</p

Medieval Whalers in the Netherlands and Flanders:Zooarchaeological Analysis of Medieval Cetacean Remains

Medieval historical sources suggest that cetacean exploitation was, for large parts of Europe, restricted to the social elite. This appears to have also been the case for the Netherlands and Flanders. It remains unclear, however, how frequently active hunting was undertaken, and which species were targeted. Zooarchaeological cetacean remains are often recovered from Medieval (AD 400-1600) sites in the Netherlands and Flanders, however the majority of these specimens have not been identified to the species level, leaving a substantial gap in our knowledge of past cetacean exploitation. By applying ZooMS, as well as morphological and osteometric analyses, these zooarchaeological specimens were identified to the species level. This analysis revealed that the North Atlantic right whale (Eubalaena glacialis), sperm whale (Physeter macrocephalus), and grey whale (Eschrichtius robustus) were frequently exploited. Active whaling appears to have been undertaken as well, especially in Flanders and in Frisia (the northern part of the Netherlands). Zooarchaeological cetacean remains appear to be present with relative frequency at high-status sites such as castles, as well as ecclesiastical sites, confirming the historical evidence that the social elite indeed did have a taste for cetacean meat. However, cetacean products were also available outside of elite and ecclesiastical contexts

Diet and Health in Middle Bronze Age Italy : a metaproteomic analysis of human dental calculus in two case-studies

Shotgun metaproteomics applied to dental calculus is a tool that is providing unprecedented insights in ancient diet and health reconstruction [1][2]. We apply a proteomic analysis of dental calculus deposits from individuals of two contemporaneous populations, Bovolone (Verona) and Sant’Abbondio (Pompeii), in order to provide more insight into the diet and health of individuals in middle Bronze Age Italy. Here we find that differences in protein preservation among individuals make comparing the two populations challenging. Nevertheless, we detect a number of dietary proteins, including wheats and eggs, which gains insight into food consumption practices during this period of social and economic change

Ancient mtDNA Analysis of Early 16th Century Caribbean Cattle Provides Insight into Founding Populations of New World Creole Cattle Breeds

The Columbian Exchange resulted in a widespread movement of humans, plants and animals between the Old and New Worlds. The late 15th to early 16th century transfer of cattle from the Iberian Peninsula and Canary Islands to the Caribbean laid the foundation for the development of American creole cattle (Bos taurus) breeds. Genetic analyses of modern cattle from the Americas reveal a mixed ancestry of European, African and Indian origins. Recent debate in the genetic literature centers on the ‘African’ haplogroup T1 and its subhaplogroups, alternatively tying their origins to the initial Spanish herds, and/or from subsequent movements of taurine cattle through the African slave trade. We examine this problem through ancient DNA analysis of early 16th century cattle bone from Sevilla la Nueva, the first Spanish colony in Jamaica. In spite of poor DNA preservation, both T3 and T1 haplogroups were identified in the cattle remains, confirming the presence of T1 in the earliest Spanish herds. The absence, however, of “African-derived American” haplotypes (AA/T1c1a1) in the Sevilla la Nueva sample, leaves open the origins of this sub-haplogroup in contemporary Caribbean cattle

Earliest Mexican Turkeys (Meleagris gallopavo) in the Maya Region: Implications for Pre-Hispanic Animal Trade and the Timing of Turkey Domestication

Late Preclassic (300 BC–AD 100) turkey remains identified at the archaeological site of El Mirador (Petén, Guatemala) represent the earliest evidence of the Mexican turkey (Meleagris gallopavo) in the ancient Maya world. Archaeological, zooarchaeological, and ancient DNA evidence combine to confirm the identification and context. The natural pre-Hispanic range of the Mexican turkey does not extend south of central Mexico, making the species non-local to the Maya area where another species, the ocellated turkey (Meleagris ocellata), is indigenous. Prior to this discovery, the earliest evidence of M. gallopavo in the Maya area dated to approximately one thousand years later. The El Mirador specimens therefore represent previously unrecorded Preclassic exchange of animals from northern Mesoamerica to the Maya cultural region. As the earliest evidence of M. gallopavo found outside its natural geographic range, the El Mirador turkeys also represent the earliest indirect evidence for Mesoamerican turkey rearing or domestication. The presence of male, female and sub-adult turkeys, and reduced flight morphology further suggests that the El Mirador turkeys were raised in captivity. This supports an argument for the origins of turkey husbandry or at least captive rearing in the Preclassic

A unified protocol for simultaneous extraction of DNA and proteins from archaeological dental calculus

Archaeological materials are a finite resource, and efforts should be made to minimize destructive analyses. This can be achieved by using protocols combining extraction of several types of biomolecules or microparticles, which decreases the material needed for analyses while maximizing the information yield. Archaeological dental calculus is a source of several different types of biomolecules, as well as microfossils, and can tell us about the human host, microbiome, diet, and even occupational activities. Here, we present a unified protocol allowing for simultaneous extraction of DNA and proteins from a single sample of archaeological dental calculus. We evaluate the protocol on dental calculus from six individuals from a range of time periods and estimated preservation states, and compare it against previously published DNA-only and protein-only protocols. We find that most aspects of downstream analyses are unaltered by the unified protocol, although minor shifts in the recovered proteome can be detected, such as a slight loss of hydrophilic proteins. Total protein recovery depends on both the amount of starting material and choice of extraction protocol, whereas total DNA recovery is significantly reduced using the unified protocol (mean 43%). Nevertheless, total DNA recovery from dental calculus is generally very high, and we found no differences in DNA fragment characteristics or taxonomic profile between the protocols. In conclusion, the unified protocol allows for simultaneous extraction of two complementary lines of biomolecular evidence from archaeological dental calculus without compromising downstream results, thereby minimizing the need for destructive analysis of this finite resource

Preservation of the metaproteome: variability of protein preservation in ancient dental calculus.

Proteomic analysis of dental calculus is emerging as a powerful tool for disease and dietary characterisation of archaeological populations. To better understand the variability in protein results from dental calculus, we analysed 21 samples from three Roman-period populations to compare: 1) the quantity of extracted protein; 2) the number of mass spectral queries; and 3) the number of peptide spectral matches and protein identifications. We found little correlation between the quantity of calculus analysed and total protein identifications, as well as no systematic trends between site location and protein preservation. We identified a wide range of individual variability, which may be associated with the mechanisms of calculus formation and/or post-depositional contamination, in addition to taphonomic factors. Our results suggest dental calculus is indeed a stable, long-term reservoir of proteins as previously reported, but further systematic studies are needed to identify mechanisms associated with protein entrapment and survival in dental calculus