DNA analysis of archaeological sheep remains from China

Recent research has thrown considerable light on the history of the domestic sheep, but has not extended to ancient sheep specimens. In the present study, ancient DNA analysis was carried out on eight archaeological sheep remains recovered from Erlitou archaeological site in Henan Province (ca. 2100–1800 B.C.) to explore the genetic structure of ancient sheep and the phylogenetic relationship between ancient and modern sheep. We analyzed the control region sequences and coding regions of mitochondrial DNA from the remains by direct sequencing and restriction fragment length polymorphism analysis, respectively. Our results reveal that all ancient sheep belong to lineage A defined by modern sheep sequences. Phylogenetic analysis shows that neither argali (Ovis ammon) nor urial (Ovis vignei) mtDNA is closely related to Erlitou ancient sheep. In addition, our results suggest that ancient DNA analysis can serve as a powerful tool in tracing prehistoric population movement.     

Fuel, Fire and Heat: an experimental approach to highlight the potential of studying ash and char remains from archaeological contexts

As in traditional societies today ancient societies probably selected different fuels to meet specific heat requirements. Char and ash, the end products of fire, are often found in abundance in archaeological contexts. These end products can provide information regarding (i) the original fuel resource and type, (ii) the characteristics of the fire and (iii) combined with other archaeological evidence shed further light on possible socio-economic activity(-ies) associated with that fire. The three main fuel resources would have been (i) modern vegetation, (ii) fossil fuel and (iii) animal by-products. Local availability and abundance would have influenced the choice made.In this study an experimental approach was adopted to try and distinguish between the three different fuel resources that are known to have been used by ancient societies (and continue to be used by traditional societies today) from their char and ash remains to help determine original fuel-type and understand the relative heating properties. For this end one fuel-type from each fuel resource listed above, namely wood, peat and cow dung, was chosen.     

Recovery of DNA from archaeological insect remains: first results,problems and potential

We report the recovery of short fragments of PCR amplifiable ancient DNA from exoskeletal fragments of the grain weevil Sitophilus granarius (L.) extracted from Roman and medieval deposits in Northern England. If DNA preservation in archaeological insect remains is widespread then many applications in the spheres of evolutionary studies and archaeology can be conceived, some of which are outlined.     

Ancient DNA typing of archaeological pig remains corroborates historical records

The recent increase in both the abundance and taxonomic range of DNA sequence data in public repositories makes it possible to determine the maternal origin of lineages of faunal archaeological material by characterizing its mitochondrial DNA. Among the most commonly represented taxa are domesticated animals, for which extensive genetic characterization has revealed high levels of genetic diversity and (in at least some cases) strong phylogeographic clustering. Such information has significant implications not only for characterizing important aspects of the occupation history of archaeological sites, but also in providing novel insights into colonisation history and the scale and scope of trade and exchange networks. This can be done through studying the origins and dispersal of proxy organisms such as commensal and domesticated animals, as well as economically important wild fauna. To illustrate this approach, we compare historical records of maritime movement of people and pigs from two sites on Lord Howe Island, Australia, to phylogeographic results of DNA extracted from pig bones.     

Genetic analysis of archaeological wood remains: first results and prospects

A total of 51 ancient oak wood samples originating from various European archaeological sites, dating from the Neolithic period to the 18th century, were assayed for the presence of reproducible chloroplast (cp) DNA sequences. Five polymorphic chloroplast fragments were targeted. Only five of the samples could be fully genetically characterised, revealing four different oak cpDNA haplotypes. In all cases, the haplotypes detected on ancient woods and the haplotypes characterised from fresh samples from the same localities matched. Overall, this congruence is consistent with a genetic continuity between ancient and modern European oaks, confirming the hypothesis that the mapped genetic patterns largely reflect the original structure that established during the post-glacial. This stability of the genetic structure implies that, in the future, the technique could be used to infer or confirm the transport of wood by man, providing interesting perspectives for the genetic analysis of ancient woods.     

The molecular palaeoecology of geese: identification of archaeological goose remains using ancient DNA analysis

The remains of six species of geese are commonly recovered from archaeological sites in Britain dating from the Saxon and later periods. However, identification of this material to species level is hampered by a lack of morphological variation and a large overlap in size. To address this issue we obtained DNA sequence data for a section of the mitochondrial cytochrome b gene from modern samples of each species, and successfully identified several DNA markers for Branta species. No markers were found within the cytochrome b gene for the genus Anser. Ancient DNA techniques were then used to recover DNA from goose bones excavated from two archaeological sites. The DNA sequences enabled identification of Barnacle goose (Branta leucopsis) from one site and confirmed the presence of Anser species at another. © 1998 John Wiley & Sons, Ltd.     

Accurate sex identification of ancient human remains using DNA shotgun sequencing

Accurate identification of the biological sex of ancient remains is vital for critically testing hypotheses about social structure in prehistoric societies. However, morphological methods are imprecise for juvenile individuals and fragmentary remains, and molecular methods that rely on particular sex-specific marker loci such as the amelogenin gene suffer from allelic dropout and sensitivity to modern contamination. Analyzing shotgun sequencing data from 14 present-day humans of known biological sex and 16 ancient individuals from a time span of 100 to ∼70,000 years ago, we show that even relatively sparse shotgun sequencing (about 100,000 human sequences) can be used to reliably identify chromosomal sex simply by considering the ratio of sequences aligning to the X and Y chromosomes, and highlight two examples where the genetic assignments indicate morphological misassignment. Furthermore, we show that accurate sex identification of highly degraded remains can be performed in the presence of substantial amounts of present-day contamination by utilizing the signature of cytosine deamination, a characteristic feature of ancient DNA.     

Identification of pastoral sites using stable nitrogen and carbon isotopes from bulk sediment samples: a case study in modern and archaeological pastoral settlements in Kenya

The identification of pastoral sites in the East African archaeological record is problematic. Recently, a method for the identification of degraded livestock enclosure sediments had been developed that takes into account the geoarchaeological indicators of micromorphology, phytolith concentrations and the mineral assemblages. This suite of indicators may not always be present in degraded livestock enclosure sediments. This study presents an additional indicator by which degraded livestock enclosure sediments may be identified, namely the isotopic composition of organic nitrogen measured on bulk sediment samples. We studied a highly controlled ethnoarchaeological sequence of abandoned Maasai livestock enclosure sediments sampled in Rombo area, southern Kenya. The results were compared to archaeological sediments from the Elmenteitan Pastoral Neolithic site of Sugenya, southwestern Kenya, radiocarbon dated to ca. 2000 BP (uncalibrated). The sediments from both sites were studied using all four types of analyses, i.e., micromorphology, mineralogy, phytolith concentrations, and stable carbon and nitrogen isotopic compositions on bulk sediment samples. The results show that in abandoned livestock enclosure sediments of known ages a significant enrichment in the heavy nitrogen isotope (¹⁵N) occurs, and that carbon isotopic compositions may be useful for differentiating cattle from caprine enclosures following their dietary preferences (i.e., grazers vs. browsers). A similar pattern of ¹⁵N enrichment is observed in sediments sampled within the site of Sugenya while sediments sampled outside the site's perimeter are generally depleted in ¹⁵N. The micromorphological, mineralogical and phytolith analyses support the conclusion that the sediments from within the site of Sugenya represent degraded livestock enclosure sediments. The carbon isotopic composition from the degraded dung deposits strongly suggests that livestock kept at Sugenya were cattle. Overall, this study presents new empirical data that can be used for the identification of livestock enclosures, and shows that the isotopic signatures and geoarchaeological indicators can preserve for at least two millennia.     

The identification of archaeological dung deposits on the basis of remains of predatory mites (Acari; Gamasida)

The results of a study of recent predatory mite faunas, characteristic of the dung of different domestic animal species, forms the basis of a two-step identification method for archaeological dung deposits. The method is illustrated by a study of the remains of the predatory mites found in 12 mediaeval dung samples from the north of The Netherlands.     

Fossil dogs and wolves from Palaeolithic sites in Belgium,the Ukraine and Russia: osteometry,ancient DNA and stable isotopes

Using multivariate techniques, several skulls of fossil large canids from sites in Belgium, Ukraine and Russia were examined to look for possible evidence of the presence of Palaeolithic dogs. Reference groups constituted of prehistoric dogs, and recent wolves and dogs. The fossil large canid from Goyet (Belgium), dated at c. 31,700 BP is clearly different from the recent wolves, resembling most closely the prehistoric dogs. Thus it is identified as a Palaeolithic dog, suggesting that dog domestication had already started during the Aurignacian. The Epigravettian Mezin 5490 (Ukraine) and Mezhirich (Ukraine) skulls are also identified as being Palaeolithic dogs. Selected Belgian specimens were analyzed for mtDNA and stable isotopes. All fossil samples yielded unique DNA sequences, indicating that the ancient Belgian large canids carried a substantial amount of genetic diversity. Furthermore, there is little evidence for phylogeographic structure in the Pleistocene large canids, as they do not form a homogenous genetic group. Although considerable variation occurs in the fossil canid isotope signatures between sites, the Belgian fossil large canids preyed in general on horse and large bovids.     

New methods for the identification of evidence for bitting on horse remains from archaeological sites

This article describes alterations to equid lower second premolars and diastemata from a series of known life history equids and a number of archaeological horse specimens from the British Iron Age. Two new methods for recording bit wear are proposed involving the analysis of the extent and morphology of enamel/dentine exposure on the anterior edge of LP2s and analysis of the extent of new bone formation and bone loss to the diastema of the mandible. It is suggested that when a bit is used on a horse it acts more frequently on the anterior margin of the LP2 than has previously been thought and that repeated contact between the bit and the LP2s and diastemata results in recognisable damage to these areas of the mouth.     

The distinction between freshwater- and terrestrial-based diets: methodological concerns and archaeological applications of sulphur stable isotope analysis

Sulphur isotopes in archaeological bone collagen are not routinely analysed in palaeodietary studies. Here we investigate the potential contribution that sulphur isotope analysis can provide toward the study of ancient human diet and economy, with particular emphasis on the distinction between freshwater and terrestrial consumers. For material from the Late Bronze Age site of Chicha in the south-western Eurasian forest-steppe, sulphur isotopes effectively separate freshwater and terrestrial animal food resources. The sulphur isotope data coupled with nitrogen isotope values from Chicha reflect a dietary reliance upon freshwater animal protein (fish) for the Late Bronze Age inhabitants. In contrast, sulphur isotope values for freshwater and terrestrial potential food species from the Eneolithic site of Bil'shivtsi in western Ukraine were indistinguishable, demonstrating that δ³⁴S values cannot always be relied upon to identify freshwater and terrestrial consumers. The data from this study support the adoption of δ³⁴S analysis as a standard component of palaeodietary studies; apart from its potential to distinguish freshwater from terrestrial consumers, it can provide supplementary dietary information not evident from the carbon and nitrogen isotope data. In addition, certain indices are considered that may be used to assess the validity of sulphur isotope data, as currently exist for carbon and nitrogen. According to the analysis of modern collagen samples, N:S appears to be a broad indicator of collagen sulphur isotope quality. However, more work needs to be done to establish an effective means by which highly-altered sulphur isotope values can be identified and thereby removed from consideration.     

Preservation potential of charcoal in alkaline environments: an experimental approach and implications for the archaeological record

Charcoalified plant material (usually wood) has been described as being inert with a high preservation potential. Although usually black on both the outside and inside, the physical and chemical properties differ as a function of temperature and time of exposure to a heat source. Post-depositional processes however may exert additional affects on charcoalified material and introduce bias into the archaeological record. This work explores the influence of alkaline conditions, often encountered in the soil environment, on the preservation potential of charcoalified material. Charcoal, experimentally produced at different temperatures, was exposed to a number of solutions of potassium hydroxide and calcium hydroxide with different pHs, to simulate exposure to alkaline soil conditions. Under these conditions chemically mediated physical interactions occur resulting in fragmentation of the charcoal samples into (very) small pieces the size of which depends upon the initial temperature of charcoalification. Moreover further interactions result in a decrease in reflectance relative to samples not exposed to alkaline conditions. Although experimentally driven the potential for physical loss of charcoal from a particular site coupled with the reduction in (expected) reflectance of any resident material, has important implications for any conclusions drawn regarding the archaeological record.     

Biosocial archaeology of the Early Neolithic: Synthetic analyses of a human skeletal population from the LBK cemetery of Vedrovice,Czech Republic

Bioarchaeology is a powerful tool in the examination of prehistoric collections of human skeletal remains. Application of a few bioarchaeological techniques (ancient DNA, carbon and nitrogen stable isotopes, and dental micro-wear) to the human osteological remains from the Early Neolithic LBK settlement of Vedrovice (Moravia), has allowed us to reconstruct not only broad cultural patterns but also the life histories of the individuals with insights into diet, migrations, ancestry, personal identity, social position and life experience. Vedrovice acted as a gateway settlement for a farming community with close ties to western Hungary and northeast Bohemia. The individuals showed clear differences in status and migration histories, giving glimpses of more complex social practices and patterns than could have been determined through the traditional culture-historical studies.     

Biomolecular archaeology of ancient tuberculosis: response to “Deficiencies and challenges in the study of ancient tuberculosis DNA” by Wilbur et al. (2009)

It is sixteen years since the first detection of Mycobacterium tuberculosis DNA in archaeological specimens, yet the validity of findings continues to be questioned. Rigorous scientific scrutiny and debate is valuable and has led to a coalescence of procedures and precautions amongst those actively engaged in this work. It is disappointing that these good practices are not recognised by certain scientists whose primary expertise is in the related fields of archaeology, palaeopathology, and eukaryote ancient DNA. There is a danger that by constant repetition, disputable and inadequately justified concerns will assume the status of self-perpetuating myths and misunderstandings. We discuss these issues with reference to a recent article in this journal, in which clear peer-reviewed scientific data were specifically targeted as part of a general critique of the field of the palaeomicrobiology of tuberculosis. We believe we have given sufficient evidence and cogent argument to persuade the unbiased reader that the views in the critique by Wilbur et al. are unjustified.     

A bioarchaeological study of a Western Basin tradition cemetery on the Detroit River

Archaeological monitoring of construction in a Windsor city park on the Detroit River led to the discovery of an isolated cemetery containing the remains of eight individuals assigned to the Late Woodland Western Basin Tradition. At the request and consent of the contemporary First Nation community, tissue samples from five individuals were subjected to radiocarbon dating, mtDNA, and stable isotope analysis to confirm cultural affiliation and further understand the subsistence practices of these people. Radiocarbon dating placed the cemetery at the transition from the Younge phase (AD 900–1200) to the Springwells phase (AD 1200–1400). The stable carbon and nitrogen isotope results provide an unexpected but fuller understanding of Late Woodland Western Basin Tradition subsistence. All individuals were as enriched in carbon as those found on Iroquoian horticulturalist sites to the east, suggesting a very high reliance on maize. Nitrogen isotope values indicate that the protein component of the diet was comprised largely of high trophic level food sources, likely fish. An in situ osteological analysis identified a high number of carious lesions in the visible teeth, also suggesting a diet high in carbohydrates. The mtDNA findings support the antiquity of the Western Basin presence in Northeast North America through genetic links with the Hind Site, an Archaic site in southern Ontario. These results underscore the importance of such studies for providing novel insight into the archaeological histories and lifeways of this distinct Late Woodland tradition. This study also emphazises the need to work with descendant communities to provide them with information on the past that reflects their distinct heritage in the lower Great Lakes region.     

Aspartic acid racemization variability in ancient human remains: implications in the prediction of ancient DNA recovery

The extent of racemization of aspartic acid (Asp) – expressed as d/l ratio – has been used as a marker of biomolecular degradation in ancient remains. However, Asp racemization rate is highly variable, and depends on biochemical and geochemical factors. In this paper we aim to determine to which extent the fraction analyzed and the kind of sample used may influence the d/l Asp ratios. Other factors, such as burial site and sample preservation conditions, are also considered.     

Using ancient DNA identification and osteometric measures of archaeological Pacific salmon vertebrae for reconstructing salmon fisheries and site seasonality at Dionisio Point,British Columbia

Determining the diversity of salmon species represented in archaeological contexts is critical to understanding patterns of salmon harvesting and consumption, storage practices and seasonal patterns of resource exploitation by precontact peoples of the Northwest Coast. We present species determinations generated for salmon vertebrae from the Dionisio Point site (DgRv-003) in coastal southwestern British Columbia, a well-preserved village site that dates to between 1500 and 1300 cal BP. Molecular species identification was possible for 70 Pacific salmonid vertebral elements recovered from one excavated plankhouse at the site. Coupled with osteometric measures, we determine that residents of the plankhouse fished primarily for chum, sockeye and pink salmon, with a lesser emphasis on chinook, coho and steelhead. These results indicate a diverse fishery that likely occurred between July and December, suggesting a mid summer through winter season of occupation for the village.     

A new miniSTR heptaplex system for genetic fingerprinting of ancient DNA from archaeological human bone

The analysis of short tandem repeats (STRs) is a useful tool in various contexts of ancient DNA research. Main applications are the reconstruction of kinship, identification, and authentication. Here we describe a short amplicon autosomal short tandem repeat (miniSTR) heptaplex system for the amplification of D13S317, D21S11, D18S51, TH01, D5S818, FGA and Amelogenin from highly degraded DNA as an inexpensive alternative to commercially available kits. All primers were newly designed and the amplicon length of all systems is less than 200 bp, with the exception of some rare alleles in the FGA and D21S11 systems. To validate the suitability of this system for typing STRs from human specimens with low DNA preservation we systematically tested it on 20 skeletal samples from four archaeological sites representing different burial environments and time spans since death. Finally, to test the sensitivity of the heptaplex system, we analyzed serial dilutions of control DNA and ancient DNA extracts. Using the system we were able to reproducibly obtain full STR profiles, down to a concentration of 0.06 ng DNA. Even with 0.004 ng DNA partial profiles could be amplified. The accumulated power of discrimination for the six selected STR loci is 0.99999984, plus the option of genetic sex determination through Amelogenin. The tests conducted prove that the system presented is efficient and especially suited for cases where STRs have to be typed and sex has to be assessed from human specimens with highly degraded DNA.     

Crops and weeds: the role of weed functional ecology in the identification of crop husbandry methods

This paper brings together the results of five present-day studies of arable weed ecology, and applies these to the identification of past crop husbandry regimes on the basis of archaeobotanical weed assemblages. The contrasting husbandry regimes covered by the present-day studies include irrigation and dry farming, fallowing and rotation, intensive and extensive cultivation, and autumn and spring sowing. The weed floras associated with these regimes were analysed in terms of the functional ecology of the species represented. These same functional attributes, that distinguished contrasting regimes, were then measured for the weed species found accompanying crop seeds in two archaeobotanical studies, of the Islamic site of Khirbet Faris, S. Jordan and Neolithic sites in central Europe. Analyses using these functional measurements resulted in the identification of irrigation at the former and in the identification of sowing time and intensive cultivation at the latter.