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.     

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.     

DNA analysis of archaeological rabbit remains from the American Southwest

Ancient DNA analysis was carried out on 20 archaeological rabbit remains from an early Pueblo II period site in Colorado (circa 1000 A.D.) to explore the possibility of obtaining accurate rabbit genus and species identifications. The presence of abundant rabbit remains at archaeological sites in the American Southwest indicates the importance of rabbit species in the subsistence economy and ritual activities of early aboriginal populations. The study of these remains is hindered by the difficulty of accurate identification due to the fragmentary nature of the bones and the lack of genus- and species-specific morphological features.A short cytochrome b gene fragment was amplified and sequenced to produce a genetic profile for each bone sample. At the genus level, the DNA identifications were consistent with those based on the analysis of mandible morphology for the majority of specimens. When compared to species-specific reference DNA sequences, Lepus americanus and Lepus californicus samples were easily identified. Identification of an unexpected L. americanus (snowshoe hare) from the remains provided new information concerning hunting ranges or exchange between groups in the region. Sylvilagus nuttallii and Sylvilagus audubonii, however, could not be confidently differentiated at this point due to the difficulty in obtaining accurate species-specific reference sequences.The inability to obtain such reference sequences can be a serious problem for DNA species identification of non-domestic animals that lack population-level genetic data and have few sequences available in GenBank. The lack of the DNA data increases the possibility that inappropriate reference sequences could be applied, resulting in false species identification even when authentic DNA is retrieved and amplified from ancient remains.     

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.     

Wild or domesticated: DNA analysis of ancient water buffalo remains from north China

Recent zooarchaeological studies on water buffalo (Bubalus sp.) remains from China and south Asia question the traditional view that water buffalo were first domesticated in Neolithic China over 7000 years ago. The results from several recent population genetic studies of modern domesticated buffalo (Bubalus bubalis) are not consistent with each other, placing the original center of buffalo's domestication in south Asia, southeast Asia, or China. This paper reports a study using an ancient DNA approach to analyze water buffalo remains from Neolithic sites in north China to investigate their affinities with modern domesticated water buffalo, and to shed light on the origin of modern domesticated water buffalo in China.A 169 bp fragment of D-loop mitochondrial DNA was successfully amplified and verified for 13 of 24 bone samples obtained from seven archaeological sites along the Wei River valley in Shaanxi Province, China. The bone samples which yielded positive DNA can be dated to 8000–3600 cal. BP. The phylogenetic analysis of the obtained DNA sequences along with modern water buffalo sequences indicated that the ancient water buffalos were not the direct ancestor of modern domesticated water buffalo. However, the phylogenetic analysis, along with BLAST searches of these ancient DNA sequences, did demonstrate their relatedness to water buffalo more so than to any other bovid species, confirming the existence of indigenous wild (but now extinct) water buffalo species (B. mephistopheles) in ancient China.The DNA analysis of these ancient remains failed to establish direct links between modern domesticated water buffalo (B. bubalis) and indigenous water buffalo (B. mephistopheles) from ancient China. If further DNA studies of more ancient remains from other regions of China confirm the observation of solely indigenous water buffalo species in ancient China, it would suggest modern water buffalo might not have been first domesticated in China.     

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.     

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.     

Ancient bacterial DNA (aDNA) in dental calculus from archaeological human remains

The purpose of this study was to identify reactive bacterial aDNA in archaeological human dental calculus. Dental calculus was collected from a middle/late Neolithic human skull from Hulbjerg passage grave, Langeland, Denmark and prepared for transmission electron microscopy (TEM) or gold-labeled antibody TEM. TEM showed calcified, as well as non-calcified bacteria. Immunogold labeling occurred over the cytoplasmic portions of the sectioned bacteria. The result demonstrated that it is possible to identify aDNA sequences from bacteria in archaeological material of considerable age by this technique.     

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.     

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.     

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.     

Amplification and sequencing of Trichuris trichiura ancient DNA extracted from archaeological sediments

Despite high prevalence of Trichuris trichiura infection, PCR-based analysis on T. trichiura from archaeological samples has not been established so far. In the present study, we sought to perform PCR-based amplification of T. trichiura aDNA using the sediments from medieval tomb of Korea. The presence of Trichuris eggs were first detected by microscopic observation; then confirmed by PCR-based aDNA analysis. Obtained sequence showed 100% homology to that of the small subunit ribosomal RNA (SSUrRNA) gene of T. trichiura but distinct from that of other Trichuris species. PCR-based aDNA analysis in this study can serve as effective method to confirm the presence of T. trichiura eggs in the soils or coprolites collected from archaeological sites.     

考古发掘现场出土脆弱遗迹提取方法研究述评

考古发掘现场脆弱遗迹提取关系到遗迹长期保存及后续保护修复,因此要求提取方法科学、严谨,所用材料安全、有效。本文以考古发掘现场文物保护与修复工作实际出发,总结了提取材料的要求与原则,回顾了考古发掘现场出土脆弱遗迹所用的石膏提取、聚氨酯泡沫提取、环十二烷提取以及薄荷醇提取等几种方法的使用情况,评述了其提取工艺及性能,并对考古发掘现场出土脆弱遗迹提取方法未来研究方向进行了展望。     

Assessing the reliability of pRIA for identifying ancient proteins from archaeological contexts

The use of immunological techniques for identifying the origin of proteins and inferring foodstuffs exploited by prehistoric occupations has been conducted for several decades. Cases of experimental laboratory and archaeological studies have shown the potential of these techniques for reliable results. However, very few of these case studies employ archaeological sites that have excellent preservation and high-resolution spatial contexts between identifiable faunal remains, features, and stone tools. We present an assessment of the identification reliability of one immunological technique, protein radioimmunoassay (pRIA), using faunal remains and stone tools from two sites from arctic and subarctic contexts. The results of this research indicate that, even in contexts with excellent preservation, the identifications produced by the pRIA technique are subject to misidentification and cross-reactions due to diagenetic alteration of proteins. We propose a higher minimum reaction value (percent binding of labeled antibody) that mitigates these effects, and renders the pRIA results more reliable for ancient, poorly preserved organic remains.     

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.     

Rice archaeological remains and the possibility of DNA archaeology: examples from Yayoi and Heian periods of Northern Japan

Japanese rice cultivation in paddy fields has 2,400∼3,000 years of history. Most of modern Japanese rice varieties are classified as Temperate-japonica (Tm-J). Few landraces are recognized as Tropical-japonica (Tr-J) only in southwestern Japan. However, ancient DNA studies and phytolith analysis suggest that Tr-J strains were more popular in the past than now. Maekawa is a complex archaeological site composed of paddies dated from the Yayoi (2,100 years BP) to the Heian (1,100 years BP) periods. Phytolith analysis indicates that intensive rice cultivation was practiced in both periods, but there was no cultivation in the intervening period. Morphological features of bulliform phytoliths suggest that Tr-J was cultivated during both periods. Locally, rice cultivation during the Heian period was brought to a close by a flood event, in which immature rice plants were pulled down and buried in silt to be preserved in a quasi-carbonized/ waterlogged state. Ancient DNA (aDNA) analysis of the carbonized plant culm from Heian Maekawa recovered chloroplast DNA sequences of the 6C7A plastid subtype, which is common to both Tr-J and Tm-J, whereas two plastid subtypes, such as 6C7A and also 7C6A, were found in aDNA of carbonized grains from the Tareyanagi site of the Yayoi period. The latter plastid subtype was specific only to Tr-J. In order to better characterize the past rice populations, modern landraces collected in the local area were classified with morphophysiological traits. Some of the landraces were found to carry several traits of Tr-J, including bulliform phytolith types, but mixed with Tm-J traits. Based on the discontinuous distribution of rice phytoliths between the Yayoi and the Heian period, the early introduction of rice cultivation may have been discontinuous and locally reintroduced after a ∼1,000-year hiatus, but with a genetically different rice population. Such populations were composed from Tr-J like strains as shown by landraces but with reduced diversity in plastid types. Through such changes, since the Yayoi era, Tr-J was largely replaced by Tm-J, although ancient Tr-J continued to participate in the genetic makeup of later rice populations and may have aided the local adaptation of introduced Tm-J.     

The origin of the Juch'uypampa Cave mummies: strontium isotope analysis of archaeological human remains from Bolivia

Previous analyses of strontium isotopes from human bone and teeth have identified diverse patterns of residential mobility in the South Central Andes during the Middle Horizon (AD 500–1100). During this time, the large polity of Tiwanaku exerted great influence over what are now southern Peru, northern Chile, northwestern Argentina and Bolivia. Recently, five naturally-mummified individuals were discovered in the cave of Juch'uypampa in the Pulacayo region of southern Bolivia. Although these individuals were buried with a number of fine Tiwanaku-style grave goods as well as non-Tiwanaku items, the burial site is isolated and does not conform to the pattern of large Tiwanaku-affiliated cemeteries and residential sites outside of the Lake Titicaca Basin. Strontium isotope analysis was performed on enamel from two adult men and bone from a third adult male in order to test the hypotheses that one or more of the males was from either the Tiwanaku heartland in the Lake Titicaca Basin, the Chilean oasis of San Pedro de Atacama, which contains a series of cemeteries with Tiwanaku-style grave goods, or the local area in which they were buried. Results show that two individuals likely spent their childhood in the local area where they were interred, while the third man probably spent at least the last twenty years of his life in that region before being buried there. This raises interesting questions regarding the nature of Tiwanaku influence in southern Bolivia and the relationship between the Juch'uypampa mummies and the Tiwanaku polity.     

A new calibration of the XRD technique for the study of archaeological burned human remains

A new calibration of human bones as a function of programmed temperature (200–1000 °C) and time (0, 18 and 60 min) is presented and discussed in order to investigate the issues related to the study of cremated bone remains by using the powder X-ray diffraction approach. The experimental results confirm the growth of hydroxylapatite crystallites as a function of the applied temperature, with a sigmoid behaviour that has been parameterized to the experimental data points. Particularly, it was observed that the thermal treatments for 60 min anticipate of about 100 °C the effects that are otherwise observed after the treatments for 0 min. The developed procedure was subsequently applied to cremated remains of various archaeological sites of Spain and supplied precise information not only about the temperature reached during the funerary rites, but also on the presumed duration for the cremation.     

Genetic sexing to determine the optimal discriminant functions for the analysis of archaeological remains from El Hierro (Canary Islands)

A correct sex assignment of a given bone or bone fragment is of paramount importance for the archaeologist, anthropologist and in forensic medicine. Discriminant functions, combining several anthropometric measurements obtained from individuals with known sex are useful tools for this purpose, but it is essential to know exactly the sex from which the measures are obtained. This is an easy task in modern populations, but it is problematic in ancient ones, since even when the entire skeleton is available, diagnosis of sex is not 100% accurate. Sexing by genetic methods by amplifying the first intron of the amelogenin gene constitutes a much more accurate method for sexing bones and may be the gold standard for further elaboration of discriminant functions which may serve for sexing new bones dug up in future excavations. With this aim we have genetically sexed 52 (out of 59) tibiae belonging to the prehispanic population of El Hierro, in the Canary Islands, identifying 18 women and 34 men, and then, performed discriminant functions combining several anthropometric variables. These functions show a high accuracy in sex diagnosis (94.2%; area under ROC curve = 0.954 with the best of the functions), so that they allow correct sexing of tibiae or tibiae fragments (only proximal third, distal third or midshaft). Thus, genetic sexing obviates the problem of finding an accurate gold standard for the elaboration of discriminant functions for ancient bones. This method could be applied to other populations of different antiquity and different ethnicity.