圣水牛的家养/野生属性初步研究

水牛是现在中国南方稻作区的重要家畜之一。从更新世时期到全新世时期,中国南、北地区的考古遗址皆有水牛遗骸出土。本文从这些出土的水牛遗骸入手,综合其他学者的意见,对广泛出土于全新世时期遗址的圣水牛的家养/野生属性进行探讨,并提出了自己的观点。     

The evolution of rice: molecular vignettes on its origins and spread

The domesticated species Oryza sativa or Asian rice evolved starting approximately 9,000 years ago and from its centers of origin in China and India has subsequently spread throughout the Old World (and in historical times in the New World as well). This species is one of the key domesticated crop plants in the world and has emerged as a model for studying the origins and spread of domesticated taxa as well as in investigating the genetic basis for plant variation under domestication. Archaeological data has been critical in dissecting the origins and spread of rice throughout Asia, but molecular information has also provided a complementary approach to examining the evolutionary dynamics of this species. The evolutionary history of a species can leave its footprints within its genome. Moreover, genetic studies allow us to study the history of traits that do not leave an archaeological record—for example, grain stickiness or flowering time—which can provide insights into how crop species are adopted by different cultures. In this review, several molecular studies into the origin and spread of Asian rice are discussed and we explore the advances these genetic studies offer in our understanding of the evolution of domesticated species. We also explore how archaeological data can provide critical insights that can help refine genetic models of the origin and spread of domesticated species.     

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.     

Ancient molecules and human prehistory

Abstract

DNA and other molecules found in ancient remains are yielding new information about the origins, spread, interaction, and culture of early humans. Molecules of animal fats preserved in archaeological pottery have shown that in medieval societies people ate non-ruminant animals, such as pigs, but burned tallow from ruminants, such as sheep and cattle. Geochemical analysis of bitumen in the Middle East has documented ancient trade routes. Studies of molecular genetic diversity have shed light on when and how cattle were domesticated. Analysis of human hair from remains up to 5200 years old has revealed the diets of those ancient people. DNA recovered from other remains has also provided evidence for theories about the origins and spread of agriculture, and human migration into the Pacific.     

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.     

COMPLEX RELATIONSHIPS BETWEEN MITOCHONDRIAL AND NUCLEAR DNA PRESERVATION IN HISTORICAL DNA EXTRACTS*

‘Historical’ DNA obtained from specimens preserved in natural history collections has proven useful for addressing a wide variety of questions, such as the spread of domesticated species or changes in genetic diversity. With the development of high‐throughput sequencing techniques, there is an increasing focus on acquiring genetic information encoded by single‐copy nuclear DNA from historical DNA extracts. The development of efficient techniques to determine the level of nuclear DNA preservation in candidate specimens is necessary to maximize the data obtained from these analyses. Although current evidence suggests that a sample's mitochondrial DNA preservation predicts its nuclear DNA preservation, we show that the relationships between mitochondrial and nuclear DNA preservation are complex.     

An exploratory osteological study of the muscovy duck (Cairina moschata) (Aves: Anatidae) with implications for neotropical archaeology

The muscovy duck (Cairina moschata) (Aves: Anatidae) is the most enigmatic of the native New World animal domesticates. Although large and conspicuous, this duck is nonetheless rarely recovered in archaeological context. When identified, its domesticated status remains uncertain for lack of distinguishing criteria used to separate male from female and domestic from wild specimens. This study offers provisional criteria for osteological discrimination based upon an analysis of 34 museum skeletons. It applies these data to archaeological specimens recovered from the western lowlands of Ecuador, where muscovy duck, along with other domesticated animals may appear in contexts associated with prehispanic trade.     

Archaeological and Historical Materials as a Means to Explore Finnish Crop History

ABSTRACT

In Northern Europe, barley (Hordeum vulgare L.) has been cultivated for almost 6000 years. Thus far, 150-year-old grains from historical collections have been used to investigate the distribution of barley diversity and how the species has spread across the region. Genetic studies of archaeobotanical material from agrarian sites could potentially clarify earlier migration patterns and cast further light on the origin of barley landraces. In this study, we aimed to evaluate different archaeological and historical materials with respect to DNA content, and to explore connections between Late Iron Age and medieval barley populations and historical samples of barley landraces in north-west Europe. The material analysed consisted of archaeological samples of charred barley grains from four sites in southern Finland, and historical material, with 33 samples obtained from two herbaria and the seed collections of the Swedish museum of cultural history.

The DNA concentrations obtained from charred archaeological barley remains were too low for successful KASP genotyping confirming previously reported difficulties in obtaining aDNA from charred remains. Historical samples from herbaria and seed collection confirmed previously shown strong genetic differentiation between two-row and six-row barley. Six-row barley accessions from northern and southern Finland tended to cluster apart, while no geographical structuring was observed among two-row barley. Genotyping of functional markers revealed that the majority of barley cultivated in Finland in the late nineteenth and early twentieth century was late-flowering under increasing day-length, supporting previous findings from northern European barley.     

Domestic Pigs in Africa

The history of African pig breeds is still controversial due to the relative scarcity of archaeological and genetic data clarifying their origins. While these breeds might descend from Near Eastern pigs entering the continent via Egypt during the Neolithic, Africa may be a primary domestication locus for pigs, as indicated for other species such as cattle and donkeys. In this regard, characterisation of the mitochondrial gene pool of African pig breeds has revealed a very low frequency of Near Eastern alleles, suggesting that, if Fertile Crescent pigs played a part in the foundation of African breeds, their genetic signature has been substantially erased. Interestingly, genetic analysis of western and eastern African pig breeds has revealed a strong phylogeographic pattern, with the latter harbouring Far Eastern alleles at high frequencies. This finding is consistent with data obtained for chickens and confirms that livestock was transported in ancient times, from the Far East to Africa as a consequence of the Indian Ocean trade. European colonisation of Africa also involved the introduction of exotic swine breeds such as Iberian pigs. The confluence of the highly divergent European and Far Eastern Sus scrofa gene pools contributed to significantly enrich the genetic reservoir of African swine breeds, favouring their adaptation to environmental conditions that are often harsh. Conservation of this genetic legacy will be of utmost importance to ensure the prosperity of current resource-based subsistence farming systems in Africa.     

Ancient DNA supports lineage replacement in European dog gene pool: insight into Neolithic southeast France

We report palaeogenetic analysis of domesticated dog (Canis familiaris) remains excavated from three archaeological sites from southeast France and dating from Middle Neolithic. Ancient DNA analysis was attempted on teeth and bone samples taken from 11 dogs. Three 266-base-pair fragments of the mitochondrial genome Hypervariable Region I (HVR-I) could be retrieved and revealed two haplotypes belonging to HVR-I lineage C. These three sequences were compared to the sequences of Swedish and Italian Neolithic dogs and permitted to confirm that clade C was largely represented all over Western Europe during this period. One haplotype defined in Neolithic French dog was observed for the first time in Canis mtDNA, underlining the loss of mitochondrial diversity in Europe since the Neolithic. Finally, these results point out mitochondrial lineage replacement in Europe, since lineage C represents only 5% of extant European dogs. Altogether, these results support the proposition that palaeogenetic studies are essential for the reconstruction of the past demographic history and the domestication process of dogs.     

Incremental banding in dental cementum: Methods of preparation for teeth from archaeological sites and for modern comparative specimens

Analysis of incremental banding in dental cementum is a well-established means of determining the age and season of death of wild mammals. The dental cementum of domesticated mammals likewise can indicate age and season of death. Methods of preparation applicable to archaeological teeth differ from those used for modern specimens, however, and this paper describes two methods that have given excellent imaging on teeth of Bos taurus; one for modern teeth and the other for teeth from archaeological sites.     

It’s Getting Better All the Time: Comparative Perspectives from Oceania and West Africa on Genetic Analysis and Archaeology

Technological advances are making genetic data collection and analysis feasible on a scale unimaginable only a few years ago. Early genetic research using mitochondrial DNA and the Y chromosome provided important insights for macroscale modeling of regional and continent-wide population movements, but the capacity to study the entire genome now opens an era of finer-grained, mesoscale studies of regional and local population histories that are more compatible with the scale of archaeological analysis. The utility of integrating both types of data is illustrated by a case study from Oceania, where genetic studies were used to evaluate two models for the geographic origins of the populations that colonized Polynesia beginning ca. 3000 bp, bringing with them the distinctive Lapita cultural assemblage. A second case study considers the application of genetic studies to an understanding of Fulbe history, especially that of the pastoral Fulbe. Both archaeological and genetic data are underdeveloped for the key Fulbe homeland regions of Mauritania and Senegal, but recent research in the Middle Senegal Valley permits some conjectures on the history of Fulbe nomadic pastoralism. The article concludes with suggestions for a multidisciplinary research agenda to expand and upgrade the quality of relevant archaeological data, incorporate biodistance studies of human skeletal material, and improve and expand genetic sampling using more historically sensitive collection protocols.     

THE POTENTIAL MISUSE OF GENETIC ANALYSES AND THE SOCIAL CONSTRUCTION OF 'RACE'AND 'ETHNICITY'

The analysis of genetic material (such as DNA) has been attracting considerable attention for at least a decade. Recent years have seen the first application of genetic analysis to archaeological problems. In some circles DNA seems to be seen as a panacea for all ills. There is, however, little consideration of the methodological problems inherent in extrapolating from genetic information to ancient populations. In particular the assumption that genetic differences equal ethnic differences is challenged. The ethical implications for such research do not seem to have been addressed within the archaeological community.     

The role of canids in ritual and domestic contexts: new ancient DNA insights from complex hunter–gatherer sites in prehistoric Central California

This study explores the interrelationship between the genus Canis and hunter–gatherers through a case study of prehistoric Native Americans in the San Francisco Bay-Sacramento Delta area. A distinctive aspect of the region's prehistoric record is the interment of canids, variously classified as coyotes, dogs, and wolves. Since these species are difficult to distinguish based solely on morphology, ancient DNA analysis was employed to distinguish species. The DNA study results, the first on canids from archaeological sites in California, are entirely represented by domesticated dogs (including both interments and disarticulated samples from midden deposits). These results, buttressed by stable isotope analyses, provide new insight into the complex interrelationship between humans and canids in both ritual and prosaic contexts, and reveal a more prominent role for dogs than previously envisioned.     

Donkey Domestication

Donkeys are one of the least studied large domestic animals, even though they are economically important in many regions of the world. They are predominantly used as transport animals. Consequently, they are not kept in large numbers and this limits the number of archaeological specimens available for study. The donkey’s closest relative is the African wild ass, and genetic studies and zooarchaeological analyses of early donkeys indicate domestication of two genetically separate groups of wild asses in Africa. Maternal relationships revealed by mitochondrial DNA show that one group of donkeys was derived from the Nubian wild ass and that one was derived from an unknown ancestor distinct from the Somali wild ass.     

A Regional Approach to Ancient Urban Studies in Greece Through Multi-Settlement Geophysical Survey

The systematic exploration of large archaeological sites in the Mediterranean has evolved considerably since the “big dig” excavations. Pedestrian field surveying and remote sensing applications, including satellite and airborne image analysis, are now practical and relatively cost-efficient methods of characterizing large and diachronically diverse landscapes on regional scales. However, the use of geophysical techniques as a means for exploring manifold archaeological contexts is still in its infancy. In this paper, we highlight the advantages of archaeological geophysics to conduct regional surveys in the Mediterranean. Through a multi-site geophysical fieldwork campaign to investigate the patterns and dynamics of ancient cities in Greece, we show how geophysics offer new opportunities for characterizing the spatial attributes and regional dynamics of urban landscapes, and, in doing so, we make an argument for its wider adoption on regional survey projects.     

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.     

New data and new issues for the study of origin of rice agriculture in China

China was one of the major centers for the origin of agriculture in the world. The origins of agriculture in China, especially the origin of rice agriculture, made a significant contribution not only to the occurrence of Chinese civilization but also to the development of world history. Recently, the study on the origin of rice agriculture has attracted the attention of the academic community due to the dramatic development of archaeobotanical research in China. In recent years, the flotation technique has widely implemented in archaeological excavations in China. As the result, a tremendous amount of plant remains have been recovered from archaeological sites, including those much related to the study of early rice agriculture. The new data provide direct archaeological evidence for, and raise some new issues about, the origin of rice agriculture in China. For example, the rice remains from the Shangshan site, dated to ca. 10,000 cal. B.P., suggest the beginning of rice cultivation regardless of whether that rice was domesticated or not. The quantitative analysis of plant remains recovered by floatation from the Jiahu site, dated to ca. 8,000 cal. B.P., revealed that the subsistence of the Jiahu people mainly relied on fishing/hunting/gathering, while the products of rice cultivation and animal husbandry were only a supplement to their diet. The ongoing excavation, with floatation and water-sieving, at the Tianluoshan site, dated to 6,000 to 7,000 cal. B.P., suggests that rice farming, though important, was only part of a broader subsistence pattern of the Hemudu Culture, and rice domestication culminated after 6,500 B.P and the beginning of rice domestication remain unclear.     

Ancient olive DNA in pits: preservation,amplification and sequence analysis

The olive tree (Olea europaea) was domesticated by vegetative propagation of selected wild individuals with superior fruit. Later, new cultivars were established repeatedly from feral trees or from crosses between wild, feral, and domesticated trees. Thus the genetic background of many contemporary domesticated lines is a mixture of ancient cultivars and local wild trees. Ancient DNA may illuminate the complicated process of olive domestication because such DNA sequences provide data about ancient genomes that existed closer to the domestication events. Well preserved DNA must be available for such studies, even though in the Mediterranean region, where olive cultivation took place, the climatic conditions are not favorable for DNA preservation. To select for well preserved pits we measured their proportions of lignin by IR spectroscopy, and correlated this with parameters of DNA quality such as template length in an olive-specific repeat array, and template quantity as determined by real-time PCR amplification. Archaeological pits that passed these tests did contain high quality ancient DNA. We present the first ancient olive DNA sequences and compare them to modern wild, feral and domesticated lines.