The identification of poultry processing in archaeological ceramic vessels using in-situ isotope references for organic residue analysis.

Poultry products are rarely considered when reconstructing pottery use through organic residue analysis, impinging upon our understanding of the changing role of these animals in the past. Here we evaluate an isotopic approach for distinguishing chicken fats from other animal products. We compare the carbon isotopes of fatty acids extracted from modern tissues and archaeological bones and demonstrate that archaeological bones from contexts associated with pottery provide suitable reference ranges for distinguishing omnivorous animal products (e.g. pigs vs. chickens) in pots. When applied to pottery from the Anglo-Saxon site of Flixborough, England, we succeeded in identifying residues derived from chicken fats that otherwise could not be distinguished from other monogastric and ruminant animals using modern reference values only. This provides the first direct evidence for the processing of poultry or their products in pottery. The results highlight the utility of ‘in-situ’ archaeological bone lipids to identify omnivorous animal-derived lipids in archaeological ceramic vessels

A new strategy for enhancing imputation quality of rare variants from next-generation sequencing data via combining SNP and exome chip data

Background: Rare variants have gathered increasing attention as a possible alternative source of missing heritability. Since next generation sequencing technology is not yet cost-effective for large-scale genomic studies, a widely used alternative approach is imputation. However, the imputation approach may be limited by the low accuracy of the imputed rare variants. To improve imputation accuracy of rare variants, various approaches have been suggested, including increasing the sample size of the reference panel, using sequencing data from study-specific samples (i.e., specific populations), and using local reference panels by genotyping or sequencing a subset of study samples. While these approaches mainly utilize reference panels, imputation accuracy of rare variants can also be increased by using exome chips containing rare variants. The exome chip contains 250 K rare variants selected from the discovered variants of about 12,000 sequenced samples. If exome chip data are available for previously genotyped samples, the combined approach using a genotype panel of merged data, including exome chips and SNP chips, should increase the imputation accuracy of rare variants. Results: In this study, we describe a combined imputation which uses both exome chip and SNP chip data simultaneously as a genotype panel. The effectiveness and performance of the combined approach was demonstrated using a reference panel of 848 samples constructed using exome sequencing data from the T2D-GENES consortium and 5,349 sample genotype panels consisting of an exome chip and SNP chip. As a result, the combined approach increased imputation quality up to 11 %, and genomic coverage for rare variants up to 117.7 % (MAF < 1 %), compared to imputation using the SNP chip alone. Also, we investigated the systematic effect of reference panels on imputation quality using five reference panels and three genotype panels. The best performing approach was the combination of the study specific reference panel and the genotype panel of combined data. Conclusions: Our study demonstrates that combined datasets, including SNP chips and exome chips, enhances both the imputation quality and genomic coverage of rare variants

Aquatic Resources in Foodcrusts: Identification and Implication

NoFoodcrusts, the charred surface deposits on pottery vessel surfaces, provide a rich source of data regarding container function. This article reviews recent applications focusing on the detection of aquatic resources (marine and freshwater) in pottery vessels using a range of analytical approaches including bulk isotope measurements of carbon and nitrogen, lipid biomarker analysis, and compound-specific carbon isotope determinations. Such data can help to evaluate the presence of reservoir effects when undertaking radiocarbon dating of foodcrust samples. In particular, molecular and isotopic analysis can aid in the selection of suitable candidates for C-14 where it can be demonstrated that aquatic resources are unlikely to contribute to the residue. Prospects for compound-specific C-14 analysis of lipids in foodcrusts and ceramic-absorbed residues are also discussed

Aquatic Resources in Foodcrusts: Identification and Implication

NoFoodcrusts, the charred surface deposits on pottery vessel surfaces, provide a rich source of data regarding container function. This article reviews recent applications focusing on the detection of aquatic resources (marine and freshwater) in pottery vessels using a range of analytical approaches including bulk isotope measurements of carbon and nitrogen, lipid biomarker analysis, and compound-specific carbon isotope determinations. Such data can help to evaluate the presence of reservoir effects when undertaking radiocarbon dating of foodcrust samples. In particular, molecular and isotopic analysis can aid in the selection of suitable candidates for C-14 where it can be demonstrated that aquatic resources are unlikely to contribute to the residue. Prospects for compound-specific C-14 analysis of lipids in foodcrusts and ceramic-absorbed residues are also discussed

The White Stuff: Milking in the Outer Scottish Isles

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Did the first farmers of central and eastern Europe produce dairy foods?

Although the origins of domestic animals have been well-documented, it is unclear when livestock were first exploited for secondary products, such as milk. The analysis of remnant fats preserved in ceramic vessels from two agricultural sites in central and eastern Europe dating to the Early Neolithic (5900-5500 cal BC) are best explained by the presence of milk residues. On this basis, the authors suggest that dairying featured in early European farming economies. The evidence is evaluated in the light of analysis of faunal remains from this region to determine the scale of dairying. It is suggested that dairying — perhaps of sheep or goats — was initially practised on a small scale and was part of a broad mixed economy

Comparison of three DNA extraction methods on bone and blood stains up to 43 years old and amplification of three different gene sequences

Extraction of amplifiable DNA-from degraded human material in the forensic context remains a problem, and maximization of yield and elimination of inhibitors of the Polymerase Chain Reaction (PCR) are important issues which rarely feature in comparative studies. The present work used PCR amplification of three DNA sequences (HLA DPB1, amelogenin and mitochondrial) to assess the efficiency of three methods for extracting DNA (sodium acetate, magnetic beads and glass-milk) from 32 skeletal samples and 25 blood stains up to 43 years old. The results, analyzed using multivariate statistics, confirmed that the extraction method was crucial to the subsequent detection of amplification products; the glass-milk protocol performed better than sodium acetate, which was better than magnetic beads. Successful amplification also depended on gene sequence, multiple copy mitochondrial sequences performing best; however, with the singly copy sequences, the longer HLA DPB1 (327 bp) being detected just as often as the shorter amelogenin (106/112 bp). Amplification products were obtained more frequently from blood stains than bone, perhaps reflecting differences inherent in the material, and from younger compared with older specimens, though plateauing seemed to occur after 10 years. PCR inhibitors were more frequent in sodium acetate extracts

Sulphur isotope variation in archaeological marine fauna from northern Europe

We undertook combined stable carbon, nitrogen and sulphur isotope analysis of marine and terrestrial faunal remains from two prehistoric coastal shell middens in Denmark. The aim of the investigation was to establish whether sulphur isotopes were useful in discriminating terrestrial and marine consumers in this region. We found that sulphur isotopes do separate marine and terrestrial fauna but, contrary to our expectations, we observed a negative correlation between δ34S and δ13C values for marine fauna. We conclude that similar studies over a broader geographical range are needed before sulphur isotopes can be reliably used to study coastal resource exploitation