Ancient DNA provides new insights into the origin of the Chinese domestic horse

Domestic horses played a pivotal role in ancient China, but their exact origin remains controversial. To investigate the origin of Chinese domestic horses, we analyzed mitochondrial DNA (mtDNA) from 35 horse remains, aged between 4000 and 2000 years, excavated from nine archaeological sites in northern China. The Chinese ancient horses exhibited high matrilineal diversity, falling into all the seven haplogroups (A–G) observed in modern horses. These results suggest that several maternal lines were introduced into the gene pool of Chinese horses in the past. Haplogroups A and F were more prevalent in ancient horses than the other haplogroups. Interestingly, only haplogroups A and F were present in the samples older than 4000 years, while the more recent horses (between 2000 and 3000 years BP) fell into all seven haplogroups. Comparison with DNA data of present-day horses suggests that haplogroup F is like to be an ancient haplogroup of East Asian origin. These analyses also suggest that the origin of Chinese domestic horses is complex, and external mtDNA input occurred after initial domestication. Our results indicate that the Chinese ancient horses are more related to the modern Mongolian horses. Lastly, our results cannot support the previous hypothesis that early Chinese domestic horses were derived from the Przewalski horse.     

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.     

The Status Problem of Iberian Holocene Equids: New Data from Cueva de El Mirador (Sierra de Atapuerca,Spain)

Equid remains are scarce and very fragmented in Iberian Neolithic and Bronze Age sites. Evidence suggesting that horses were domesticated does exist, but it is often inconclusive, thus leaving the question unanswered. Today, DNA analyses have provided information about a, most likely Iberian, nucleus of horse domestication, making it crucially important to expand the database. The Holocene sequence (6^th and 3^rd millennium cal bc ) of the Cueva de El Mirador (Sierra de Atapuerca, Spain) has yielded 92 equid remains distributed in 12 Neolithic and Bronze Age levels. In this paper, we present the study of the equid remains from the Cueva de El Mirador from an archaeozoological perspective, giving indirect evidence of horse domestication. Our results vary widely and lead to open interpretations about horse domestication and how humans used these animals. This study of horse remains focuses on species identification and on determining how humans economically used these animals. Copyright © 2014 John Wiley & Sons, Ltd.     

Taphonomic analysis of leporid remains obtained from modern Iberian lynx (Lynx pardinus) scats

Distinguishing leporid bones accumulated by diurnal raptors, owls, mammals and humans is essential to understand not only past human subsistence activities but also past ecology. This is particularly relevant in Iberian Palaeolithic sites where leporid remains usually constitute the most abundant taxon. As far as terrestrial mammal carnivores are concerned, the Iberian lynx (Lynx pardinus) would be the main leporid predator in the Iberian Peninsula. Up until now its contribution as a rabbit bone accumulator in archaeological sites has never been properly assessed. In order to investigate the taphonomic signature of this predator the analysis of 33 samples of modern Iberian lynx scats was carried out. Results show that leporid remains consumed by this carnivore appear very fragmented and exhibit a strong degree of corrosion digestion. Cranial elements are most abundant followed by long bones. Whereas there seem to be clear differences in relation to breakage and digestion alteration caused by owls, some of the patterns obtained are closest to those established with diurnal raptors.     

Ancient DNA Analysis of Anatolian Goat Remains Excavated from a Urartian Castle in Eastern Turkey

In recent years, mitochondrial diversity of goats has been extensively studied, in order to shed light on domestication processes. There are limited studies on genetic diversity and demographic history of Anatolian goat breeds, and these studies have focused only on modern goats. Until today, no research has been conducted on DNA analysis of ancient Anatolian goats. In the present study, seven ancient DNA samples of goat remains from Van‐Yoncatepe archaeological site in Eastern Anatolia, Turkey, dating 1000 BC, were successfully extracted and amplified for the first time. A 230‐bp fragment of mitochondrial DNA Hypervariable Region 1 of the samples was analyzed. All of the ancient sequences belonged to haplogroup A, which is the most widely distributed and frequently encountered haplogroup in modern goats. The results also pointed out that Anatolian ancient goats might have contributed to the genetic structure of modern goats in the Near East, the Mediterranean Region and South‐Southeastern Asia. Copyright © 2014 John Wiley & Sons, Ltd.     

Methods for the Study of Ancient Hair: Radiocarbon Dates and Gene Sequences from Individual Hairs

Genetic data from archaeological specimens provides a potent new approach for addressing questions in prehistory. Hair from archaeological sites is an important but overlooked data source amenable to molecular analysis. To date DNA identification from hair is limited to modern samples. Our study is the first to report DNA recovery from a 9800-year-old specimen. We report methods used to extract mitochondrial DNA and obtain accelerator mass spectrometry radiocarbon dates (AMS-¹⁴C) from hairs plucked from a piece of ancient bighorn sheep (Ovis canadensis nelsoni) skin found at Smith Creek Cave, Nevada. The ability to obtain reliable radiocarbon dates and DNA sequences from single ancient hairs opens new possibilities for addressing biological questions in prehistory.     

DNA analysis in charred grains of naked wheat from several archaeological sites in Spain

In the present work we attempt to recover endogenous ancient DNA from cereal grains preserved under different conditions: charred, partially charred and waterlogged. A total of 126 grains from naked wheat and 18 from barley from different sites on the Eastern Iberian Peninsula ranging from the beginning of agriculture in the region to the turn of the Common Era, were studied. Two different extraction protocols were used, a standard phenol–chloroform method and a silica-based DNA extraction procedure implemented for artificially charred seeds. Amplifications were directed to three markers: the large subunit of ribulose 1,5 biphosphate carboxylase (rbcL) and the microsatellite WCT12 in the chloroplast genome and the x and y subunits of the high molecular weight glutenin gene (Glu-1) in the nucleus. The first two were used to assess the preservation status of the samples, while with the third we tried to identify the wheat grains at species level. It was possible to obtain eleven positive amplifications in 8 partially charred seeds but only two amplifications of the Glu-1 gene from a single sample of the Early Bronze age were genome-specific. Different contamination sources were identified and reported. Cloning and alignment of sequenced clones showed a correspondence of the amplified fragment to modern wheat D genome haplotypes. This result suggests that the sample corresponds to hexaploid wheat (Triticum aestivum L.), thus being the first ancient DNA evidence to date for the cultivation of hexaploid wheat in the prehistoric agriculture of the Iberian Peninsula. Moreover, obtained results highlight contamination problems associated to the study of ancient archaeobotanical charred seeds suggest that the combination of a silica-based extraction method together with the amplification of specific targets is a good strategy for recovering endogenous ancient DNA from this kind of material.     

Presence of the genus Cuon in upper Pleistocene and initial Holocene sites of the Iberian Peninsula: new remains identified in archaeological contexts of the Mediterranean region

The dhole (Cuon alpinus) has been documented on the Iberian Peninsula throughout the Middle and Upper Pleistocene in archaeological and palaeontological contexts. However, this is an uncommon species among the Iberian quaternary faunae as a whole. This paper focuses on the remains of the genus Cuon recovered in three different sites of the Iberian Mediterranean region and their morphological and osteometrical study. By comparing these with fourteen complete skeletons of Canis lupus, as well as with other remains of C. alpinus, we intend to highlight some anatomical and metrical differences between Cuon and Canis that, added to those already published, could be a functional base-line for the identification of this genus. The identification of this species is complex, especially in archaeological contexts, and in some cases the dhole has been identified as Canis or Canidae. Furthermore, this paper explores the chronology of the presence of the dhole in the Iberian Peninsula and the different contexts where these animals have been recovered from.     

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.     

Examining histology to identify burned bone

Early research suggests that examination of the microscopic internal structure is a valid method for distinguishing burned from unburned bone in the archaeological record. This study compares burned and unburned modern bones with archaeological bones from Sibudu Cave (ca. 60,000 years ago) and Cave of Hearths (over 200,000 years ago) to more fully describe the heat-induced histological changes to bone. We also explore the effects of diagenesis on those changes to determine if histological evidence of burning preserves through fossilisation and diagenetic processes and can be successfully used to identify ancient burning. Application of this technique can help in addressing various issues, including the origins of controlled use of fire and understanding animal butchery and disposal.     

Evolving ecosystems: ecological data from an Iron Age small mammal accumulation at Alorda Park (Catalonia,Spain)

Small mammals are considered to be good indicators of ancient environments. One particular layer in a fortification tower of a Mediterranean Iberian village, Alorda Park (4th century BC), provided a large amount of well-preserved small mammal bones (about 19,200 remains) probably accumulated by barn owls (Tyto alba). Such an accumulation is rarely available from the Iron Age. It provides not only palaeoenvironmental data, but also further information about other studies such as morphometrics, ancient DNA and zoogeography. This article focuses on the ecological data, and attempts to develop an accurate taphonomic study to assess the reliability and statistical significance of this archaeological sample.     

The Quaternary fossil record of the genus Testudo in the Iberian Peninsula. Archaeological implications and diachronic distribution in the western Mediterranean

This paper explores the presence of tortoise remains and its meaning in Palaeolithic archaeological contexts. We focus on two topics: (1) the presence or absence of the genus Testudo from the Early Pleistocene to the Holocene in SW Europe; and (2) the relationship between Testudo and the palaeoclimatic and palaeoenvironmental conditions diachronically. In order to address this objective, we collected published and unpublished data from different sites on the eastern Iberian Peninsula. The results obtained by this study demonstrate that Testudo hermanni was the only tortoise present in this area until recent times and its presence in archaeological sites is almost always related to anthropic activities. Finally, the disappearance of Testudo from archaeological sites in some areas is related to climatic changes and events that occurred during the last stages of the Pleistocene.     

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.     

Who brought in the rabbits? Taphonomical analysis of Mousterian and Solutrean leporid accumulations from Gruta do Caldeirão (Tomar,Portugal)

In the Iberian Peninsula, leporids, and specifically rabbits, play a key role in the understanding of hunter-gatherer economies. They appear to have been especially important in the Tardiglacial, when large numbers of small prey animals and of the European rabbit (Oryctolagus cuniculus) in particular, are a ubiquitous feature of faunal assemblages from archaeological sites. Since a large number of non-human predators can also contribute to the formation of such assemblages, the ability to discriminate between bones accumulated by humans and by other kinds of predators is a key prerequisite to their interpretation. On the basis of systematic actualistic studies carried out on modern leporid remains produced by mammalian terrestrial carnivores, nocturnal and diurnal raptors, and humans, we identified diagnostic taphonomic indicators of the different predators. In this paper, the patterns observed on the modern material are applied to the taphonomical analysis of two archaeological samples of rabbit and hare remains from Mousterian and Solutrean layers of Gruta do Caldeirão, a cave site located in Central Portugal. Our results suggest that Eagle Owl (Bubo bubo) were mainly responsible for the Mousterian accumulations, whilst the Solutrean ones were most likely the result of human activity. These data support the notion that, in Iberia, significant reliance on rabbits does not become a feature of subsistence strategies until later Upper Palaeolithic times.     

Wild or domesticated? An ancient DNA approach to canid species identification in South Africa's Western Cape Province

The fragmentary remains typical of archaeological fauna can prove impossible to identify when confronted with closely related sympatric species. In southern Africa domesticated dogs (Canis familiaris) and black-backed jackals (Canis mesomelas) pose just such a problem, rendering difficult an accurate assessment of the timing of arrival of domesticated dogs in the region. Contextual evidence has suggested that canid remains from four Later Stone Age archaeological sites were likely to be domesticated dogs rather than jackals, and were subjected to ancient DNA analyses to determine species. Every tested specimen proved to derive from black-backed jackals. These data provide not only an unexpected window on southern African prehistory, but also highlight the value in applying ancient DNA techniques to archaeological species identification.     

Characterization of a current coprogenic sample originated by Canis lupus as a tool for identifying a taphonomic agent

We study a skeletal sample digested by Iberian wolf (Canis lupus signatus) in order to finding diagnostic features of digestion caused by this agent. The remains were taken from scats collected in different natural areas in the northwestern Iberian Peninsula. We tested different methods to recover the remains with the goal of not produce biases, and we evaluated the most appropriate methods. The results were compared with those reported by other authors who have also worked with samples digested by wolves. Bias during the procurement of the skeletal assemblages seems to be a significant cause of the differences observed between the samples. We found that it was necessary to fully recover all remains and individually analyze all modifications, even in small-sized remains. Taphonomic characterization was performed by analyzing physical and biochemical modifications. We believe that these results may be useful in the study of archaeological and paleontological assemblages.     

Feeding behaviour and taphonomic characterization of non-ingested rabbit remains produced by the Iberian lynx (Lynx pardinus)

The rabbit (Oryctolagus cuniculus) is usually the most abundant taxon found in the Palaeolithic and Epipalaeolithic archaeological sites of southern Europe and the Mediterranean Basin. These accumulations may be the result of different abiotic factors, biotic agents and/or the interaction of both. For these reasons, over the last decades actualistic research has been conducted on different predators of rabbits. Among them, the Iberian lynx (Lynx pardinus) is an excellent candidate for study because: 1) its diet is based almost exclusively on this leporids and 2) its historical distribution overlaps with one of the most interesting areas for small game research, the Iberian Peninsula and southern France. Here we present the taphonomical analysis of non-ingested rabbit remains collected from two Iberian lynx captive breeding centers located in southern Spain. Our results show: i) predominance of the distal segment of the appendicular skeleton; ii) variable breakage patterns, with a high proportion of whole bones of the autopodium and heavy breakage of the zeugopodium and stylopodium; iii) rare bone surface modifications. Comparison of these results with those obtained for other terrestrial carnivores, such as the fox, reveals great similarities, the only difference being the more abundant tooth marks present on fox non-ingested rabbit assemblages.     

Archaeogenetic study of prehistoric rice remains from Thailand and India: evidence of early <Emphasis Type="Italic">japonica</Emphasis> in South and Southeast Asia

We report a successful extraction and sequencing of ancient DNA from carbonized rice grains (Oryza sativa) from six archaeological sites, including two from India and four from Thailand, ranging in age from ca. 2500 to 1500 BP. In total, 221 archaeological grains were processed by PCR amplification and primary-targeted fragments were sequenced for comparison with modern sequences generated from 112 modern rice populations, including crop and wild varieties. Our results include the genetic sequences from both the chloroplast and the nuclear genomes, based on four markers from the chloroplast and six from the nuclear genome. These markers allow differentiation of indica rice from japonica rice, the two major subspecies of Asian rice (O. sativa) considered to have separate geographical origins. One nuclear marker differentiates tropical and temperate forms of subspecies japonica. Other markers relate to phenotypic variation selected for under domestication, such as non-shattering, grain stickiness (waxy starch) and pericarp colour. Recovery and identification of sequences from nuclear markers was generally poor, whereas recovery of chloroplast sequences was successful, with at least one of four markers recovered in 61 % of archaeological grains. This allowed for successful differentiation of indica or japonica subspecies variety, with japonica identified in all the Thai material and a mixture of indica and japonica chloroplasts in the two Indian assemblages. Rice subspecies was also assessed through conventional archaeobotanical methods relying on grain metrics, based on measurements from 13 modern populations and 499 archaeological grains. Grain metrics also suggest a predominance of japonica-type grains in the Southeast Asian sites and a mixture of japonica and indica in the Indian sites with indica in the minority. The similar results of grain metrics and ancient DNA (aDNA) affirm that grain measurements have some degree of reliability in rice subspecies identification. The study also highlights the great potential of ancient DNA recovery from archaeological rice. The data generated in the present study adds support to the model of rice evolution that includes hybridization between japonica and proto-indica.     

From Pre‐Roman Bailo To Roman Baelo: Long‐Term Landscape Dynamics In The Straits Of Gibraltar

The Straits of Gibraltar have been historically an important maritime axis of connection between the Mediterranean and Atlantic areas of the Iberian Peninsula. For this reason, most of the archaeological research has focused on the coastal settlements, but its broader archaeological landscape remains mostly unknown. In this paper, we present recent intensive surveys in which a wide range of sites was detected, dating from the eighth century BC to the fourteenth AD. The ancient landscape is thus reconstructed over a long‐term perspective. Prior to the Roman expansion, the earlier Bailo‐La Silla del Papa was an urban central place that supported a dense network of subordinate settlements. Later on, the central settlement was transported from inland to the coastal town of Baelo Claudia, but the territorial structure remained based on a similar pattern.     

Ancient DNA confirms a local origin of domesticated chenopod in eastern North America

Domesticated chenopod was an important starchy seed crop in eastern North America before the rise of maize agriculture. Domesticated chenopod first appeared in North America during the fourth millennium B.P., however its wild progenitor and site of domestication remain unresolved. Archaeological evidence suggests a local domestication in the Eastern Woodlands, while morphological similarities with modern Mexican cultivars indicate a possible introduction from Mesoamerica. To distinguish between these two scenarios, we isolate chloroplast DNA (cpDNA) from modern and archaeological North American chenopods sampled from across their geographic range. Our results demonstrate that the chenopod grown in the Eastern Woodlands was locally-derived, indicating that independent domestication events gave rise to the ancient eastern North American and modern Mexican cultivars. These results strengthen the argument for an entirely native pre-maize crop complex with chenopod as a major component.