Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

Effects of marine biofertilisation on Celtic bean carbon, nitrogen and sulphur isotopes: Implications for reconstructing past diet and farming practices.

RATIONALE: The application of fertilisers to crops can be monitored and assessed using stable isotope ratios. However, the application of marine biofertilisers (e.g., fish, macroalgae/seaweed) on crop stable isotope ratios has been rarely studied, despite widespread archaeological and historical evidence for the use of marine resources as a soil amendment. METHODS: A heritage variety of Celtic bean, similar in size and shape to archaeobotanical macrofossils of Vicia faba L., was grown in three 1 × 0.5 m outdoor plots under three soil conditions: natural soil (control); natural soil mixed with macroalgae (seaweed); and 15 cm of natural soil placed on a layer of fish carcasses (Atlantic cod). These experiments were performed over two growing seasons in the same plots. At the end of each growing season, the plants were sampled, measured and analysed for carbon, nitrogen and sulphur stable isotope ratios (δ13 C, δ15 N, δ34 S). RESULTS: The bean plants freely uptake the newly bioavailable nutrients (nitrogen and sulphur) and incorporate a marine isotopic ratio into all tissues. The bean δ15 N values ranged between 0.8‰ and 1.0‰ in the control experiment compared with 2‰ to 3‰ in the macroalgae crop and 8‰ to 17‰ in the cod fish experiment. Their δ34 S values ranged between 5‰ and 7‰ in the control compared with 15‰ to 16‰ in the macroalgae crop and 9‰ to 12‰ in the cod fish crop. The beans became more 13 C-depleted (δ13 C values: 1-1.5‰ lower) due to crop management practices. CONCLUSIONS: Humans and animals consuming plants grown with marine biofertilisers will incorporate a marine signature. Isotopic enrichment in nitrogen and sulphur using marine resources has significant implications when reconstructing diets and farming practices in archaeological populations.

Sex estimation of teeth at different developmental stages using dimorphic enamel peptide analysis.

OBJECTIVES: This study tests, for the first time, the applicability of a new method of sex estimation utilizing enamel peptides on a sample of deciduous and permanent teeth at different stages of mineralization, from nonadults of unknown sex, including perinates. MATERIALS AND METHODS: A total of 43 teeth from 29 nonadult individuals aged from 40 gestational weeks to 19 years old were analyzed. The sample included pairs of fully mineralized and just developing teeth from the same individual. The individuals were from four archaeological sites in England: Piddington (1st-2nd centuries AD), Coach Lane, Victoria Gate, and Fewston (all 18th-19th centuries). A method that identifies sex chromosome-linked isoforms of the peptide amelogenin from human tooth enamel was applied. The method utilizes a minimally destructive acid etching procedure and subsequent nano liquid chromatography tandem mass spectrometry. RESULTS: It was possible to determine the sex of 28 of the nonadult individuals sampled (males = 20, females = 8, undetermined = 1). Only one sample failed (CL9), due to insufficient mineralization of the sampled tooth enamel. Data are available via ProteomeXchange with identifier PXD021683. DISCUSSION: Sufficient peptide material to determine sex can be recovered even from the crowns of developing perinatal teeth that are not fully mineralized. The minimally destructive and inexpensive (compared to ancient DNA) nature of this procedure has significant implications for bioarchaeological studies of infancy and childhood.

Sex determination of human remains from peptides in tooth enamel.

The assignment of biological sex to archaeological human skeletons is a fundamental requirement for the reconstruction of the human past. It is conventionally and routinely performed on adults using metric analysis and morphological traits arising from postpubertal sexual dimorphism. A maximum accuracy of ∼95% is possible if both the cranium and os coxae are present and intact, but this is seldom achievable for all skeletons. Furthermore, for infants and juveniles, there are no reliable morphological methods for sex determination without resorting to DNA analysis, which requires good DNA survival and is time-consuming. Consequently, sex determination of juvenile remains is rarely undertaken, and a dependable and expedient method that can correctly assign biological sex to human remains of any age is highly desirable. Here we present a method for sex determination of human remains by means of a minimally destructive surface acid etching of tooth enamel and subsequent identification of sex chromosome-linked isoforms of amelogenin, an enamel-forming protein, by nanoflow liquid chromatography mass spectrometry. Tooth enamel is the hardest tissue in the human body and survives burial exceptionally well, even when the rest of the skeleton or DNA in the organic fraction has decayed. Our method can reliably determine the biological sex of humans of any age using a body tissue that is difficult to cross-contaminate and is most likely to survive. The application of this method will make sex determination of adults and, for the first time, juveniles a reliable and routine activity in future bioarcheological and medico-legal science contexts.

Carbon, nitrogen and sulphur isotope data of archaeological fish and mammal bone collagen from Lithuania.

Until relatively recently, stable sulphur isotope analysis of bone collagen was seldom undertaken in bioarchaeological research. With increasing frequency, its application has proven useful in reconstructing palaeodiets and palaeoecologies, as well as identifying potential migration and mobility patterns. Here, sulphur (δ34S) isotope analysis, together with carbon (δ13C) and nitrogen (δ15N), was performed on six fish and 34 mammal bone collagen samples from 14 prehistoric sites in Lithuania dating from the Late Mesolithic (ca. 7000-5000 cal BC) to the Late Bronze Age (ca. 1100-500 cal BC). We present the first δ34S data from Lithuania, including coupled δ13C and δ15N data, offering a crucial dataset for future research to explore spatial and temporal variability in the region and beyond.

Cattle Management for Dairying in Scandinavia's Earliest Neolithic.

New evidence for cattle husbandry practices during the earliest period of the southern Scandinavian Neolithic indicates multiple birth seasons and dairying from its start. Sequential sampling of tooth enamel carbonate carbon and oxygen isotope ratio analyses and strontium isotopic provenancing indicate more than one season of birth in locally reared cattle at the earliest Neolithic Funnel Beaker (EN I TRB, 3950-3500 cal. B.C.) site of Almhov in Scania, Sweden. The main purpose for which cattle are manipulated to give birth in more than one season is to prolong lactation for the production of milk and dairy-based products. As this is a difficult, intensive, and time-consuming strategy, these data demonstrate complex farming practices by early Neolithic farmers. This result offers strong support for immigration-based explanations of agricultural origins in southern Scandinavia on the grounds that such a specialised skill set cannot represent the piecemeal incorporation of agricultural techniques into an existing hunter-gatherer-fisher economy.