Ancient DNA: Using molecular biology to explore the past

Ancient DNA has been discovered in many types of preserved biological material, including bones, mummies, museum skins, insects in amber and plant fossils, and has become an important research tool in disciplines as diverse as archaeology, conservation biology and forensic science. In archaeology, ancient DNA can contribute both to the interpretation of individual sites and to the development of hypotheses about past populations. Site interpretation is aided by DNA-based sex typing of fragmentary human bones, and by the use of genetic techniques to assess the degree of kinship between the remains of different individuals. On a broader scale, population migrations can be traced by studying genetic markers in ancient DNA, as in recent studies of the colonisation of the Pacific islands, while ancient DNA in preserved plant remains can provide information on the development of agriculture.     

Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops

Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of origin. Using archaeogenomics and computational models, we can observe genome evolution directly and understand how plants adapted to the human environment and the regional conditions to which agriculture expanded. We have applied various archaeogenomics approaches as exemplars to study local adaptation of barley to drought resistance at Qasr Ibrim, Egypt. We show the utility of DNA capture, ancient RNA, methylation patterns and DNA from charred remains of archaeobotanical samples from low latitudes where preservation conditions restrict ancient DNA research to within a Holocene timescale. The genomic level of analyses that is now possible, and the complexity of the evolutionary process of local adaptation means that plant studies are set to move to the genome level, and account for the interaction of genes under selection in systems-level approaches. This way we can understand how plants adapted during the expansion of agriculture across many latitudes with rapidity.     

Phytoliths Analysis for the Discrimination of Foxtail Millet (Setaria italica) and Common Millet (Panicum miliaceum)

Foxtail millet (Setaria italica) and Common millet (Panicum miliaceum) are the oldest domesticated dry farming crops in Eurasia. Identifying these two millets in the archaeobotanical remains are still problematic, especially because the millet grains preserve only when charred. Phytoliths analysis provides a viable method for identifying this important crop. However, to date, the identification of millet phytoliths has been questionable, because very little study has been done on their morphometry and taxonomy. Particularly, no clear diagnostic feature has been used to distinguish between Foxtail millet and Common millet. Here we examined the anatomy and silicon structure patterns in the glumes, lemmas, and paleas from the inflorescence bracts in 27 modern plants of Foxtail millet, Common millet, and closely related grasses, using light microscopy with phase-contrast and microscopic interferometer. Our research shows that five key diagnostic characteristics in phytolith morphology can be used to distinguish Foxtail millet from Common millet based on the presence of cross-shaped type, regularly arranged papillae, Ω-undulated type, endings structures of epidermal long cell, and surface ridgy line sculpture in the former species. We have established identification criteria that, when used together, give the only reliable way of distinguishing between Foxtail millet and Common millet species based on their phytoliths characteristics, thus making a methodological contribution to phytolith research. Our findings also have important implications in the fields of plant taxonomy, agricultural archaeology, and the culture history of ancient civilizations.     

Ancient plant DNA in archaeobotany

Plant diaspores, tissues and wood are preserved in natural and anthropogenic sediments. Also, over the past centuries, plants have been collected in herbaria. These plant remains carry macroscopic and molecular information, making them a rich source for reconstructing past plant use, agriculture, diet or vegetation—they are thus proxies for past economies, ecology, migrations or trade. This article focuses on the application of ancient DNA analyses from plants excavated at Holocene archaeological sites. A short methodological section is added to illustrate possibilities and limitations of ancient DNA research in plants.     

The ethnolinguistic identity of the domesticators of Asian rice

Linguistic palaeontology permits the identification of two language families whose linguistic ancestors pose the likeliest candidates for the original domesticators of rice, viz. Hmong-Mien and Austroasiatic. In the 2009 model, the ancient Hmong-Mien was identified as the primary domesticators of Asian rice, and the ancient Austroasiatics as the secondary domesticators. Recent rice genetic research leads to the modification of this model for rice domestication, but falls short of identifying the original locus of rice domestication. At the same time, the precise whereabouts of the Austroasiatic homeland remains disputed. Linguistic evidence unrelated to rice agriculture has been adduced to support a southern homeland for Austroasiatic somewhere within the Bay of Bengal littoral. The implications of new rice genetic research are discussed, the linguistic palaeontological evidence is reassessed, and an enduring problem with the archaeology of rice agriculture is highlighted.     

方兴未艾的古代DNA的研究

保留在古代生物遗骸中的遗传物质DNA是一种重要的遗传资源。古代DNA的研究对于了解包括人类在内的各种生物的起源、进化和迁徙有重要意义。古代DNA的研究有其自身的特点,并且已经取得一系列重要成就。本文综述古代DNA研究的历史、方法和进展。 Abstract：DNA present in ancient samples can be recovered,amplified and analysed.It opens a new window for genetic analysis in many different disciplines,such as anthropology,archaeology,human population genetics,animal and plant evolutionary taxonomy and forensic science.In general,ancient DNA is rare in quantity,damaged in quality.To ensure the reproducibility and reliability of the results,great cares should be taken,such as various measurements against contamination and phylogenetic analysis of ancient DNA sequences.In this paper we review recovery,amplification and analysis of ancient DNA,also discuss the guidelines to ensure the authenticity of ancient DNA and the recent advances in ancient DNA study.     

How ancient DNA may help in understanding the origin and spread of agriculture

The origin and spread of agriculture have been central questions in archaeology for the last 75 years and are increasingly being addressed by a multidisciplinary approach involving biologists, ecologists, geographers and anthropologists as well as archaeologists. Molecular genetics has the potential to make an important contribution, especially by enabling the number of times that a crop or animal was domesticated to be determined. Molecular genetics can also assign approximate dates to domestication events, identify the wild progenitor of a domesticate, and provide new forms of evidence relevant to agricultural spread. With wheat, molecular genetical studies of modern plants have suggested that einkorn was domesticated just once but that emmer might have been domesticated more than once. Ancient DNA studies of animal remains have benefited from progress made with equivalent analyses of human bones, and with plant material there have been clear demonstrations of DNA preservation in desiccated seeds. Charred remains have also been shown to contain ancient DNA but this finding is unexpected in view of the high temperatures to which these seeds have supposedly been exposed. Ancient DNA studies of wheat remains have been used in taxonomic identification and in assessment of the possible bread-making quality of the wheat grown at an Early Bronze Age site in Greece.     

试论动物考古中的小哺乳动物研究

小哺乳动物种类及其数量,在哺乳动物中占据大多数。它们是自然界生态链中非常重要的、不可缺少的环节。它们体质进化较快,大部分种类居住区域选择性强,种群活动范围比较小。所以研究小哺乳动物种群面貌及其生态特征,可以帮助我们判断古遗址相对时代,解析历史时期的生态演变。小哺乳动物的生态指示性,能够帮助我们准确复原和研究古遗址环境背景。它们的分布状况及很多生态规律,在帮助我们研究古遗址环境卫生及古居民住房条件等方面有独特作用。小哺乳动物种群变化与人类经济生产的互动性,以及它们与人类的伴栖关系、人类对小哺乳动物资源的开发和利用等,均是动物考古工作中应该重视和积极开展研究的内容。开展小哺乳动物研究,需要必要的工作计划、专业技术和实验设备。我国旧石器时代的小哺乳动物考古已取得丰硕成果,新石器时代及其以后的小哺乳动物考古尚有待加强。小哺乳动物研究工作的拓展,将会有力促进动物考古学进展,促使动物考古在考古学实践中发挥出更大作用。     

Ancient plant DNA: review and prospects

Ancient DNA has received much attention since the mid-1980s, when the first sequence of an extinct animal species was recovered from a museum specimen. Since then, the majority of ancient DNA studies have focused predominantly on animal species, while studies in plant palaeogenetics have been rather limited, with the notable exception of cultivated species found in archaeological sites. Here, we outline the recent developments in the analysis of plant ancient DNA. We emphasize the trend from species identification to population-level investigation and highlight the potential and the difficulties in this field, related to DNA preservation and to risks of contamination. Further efforts towards the analysis of ancient DNA from the abundant store of fossil plant remains should provide new research opportunities in palaeoecology and phylogeography. In particular, intraspecific variation should be considered not only in cultivated plants but also in wild taxa if palaeogenetics is to become a fully emancipated field of plant research.     

Optimization of DNA Recovery and Amplification from Non-Carbonized Archaeobotanical Remains

Ancient DNA (aDNA) recovered from archaeobotanical remains can provide key insights into many prominent archaeological research questions, including processes of domestication, past subsistence strategies, and human interactions with the environment. However, it is often difficult to isolate aDNA from ancient plant materials, and furthermore, such DNA extracts frequently contain inhibitory substances that preclude successful PCR amplification. In the age of high-throughput sequencing, this problem is even more significant because each additional endogenous aDNA molecule improves analytical resolution. Therefore, in this paper, we compare a variety of DNA extraction techniques on primarily desiccated archaeobotanical remains and identify which method consistently yields the greatest amount of purified DNA. In addition, we test five DNA polymerases to determine how well they replicate DNA extracted from non-charred ancient plant remains. Based upon the criteria of resistance to enzymatic inhibition, behavior in quantitative real-time PCR, replication fidelity, and compatibility with aDNA damage, we conclude these polymerases have nuanced properties, requiring researchers to make educated decisions as to which one to use for a given task. The experimental findings should prove useful to the aDNA and archaeological communities by guiding future research methodologies and ensuring precious archaeobotanical remains are studied in optimal ways, and may thereby yield important new perspectives on the interactions between humans and past plant communities.     

Crop processing of <Emphasis Type="Italic">Olea europaea</Emphasis> L.: an experimental approach for the interpretation of archaeobotanical olive remains

Archaeobotanical research, ethnographic observations and laboratory experiments are put together to create model sequences of olive processing, which are developed, presented and explored as an aid for the interpretation of rich archaeobotanical assemblages of Olea. We conclude that the remains of different processing stages are reasonably distinctive in the archaeobotanical record and assist in the identification of different types of olive remains, such as fragmented olive stones, the inner kernels, and fruit flesh     

Ancient DNA studies

Now that the hype surrounding Jurassic Park has settled down and we have become relatively used to dramatic headlines announcing the recovery of DNA from exotic fossilized remains, scientists working on ancient DNA are beginning to reflect on the long-term prospects and implications of the subject.¹ The science of ancient DNA has grown exponentially since its birth only ten years ago, and despite serious technical difficulties, it promises to become a revolutionary research tool in anthropology and molecular evolution. The use of bone DNA typing in particular has already yielded useful insights into Polynesian prehistory as well as spectacular applications in the forensic identification of skeletal remains.     

Garden variety seeds? Botanical remains from the Petra Garden and Pool Complex

Archaeobotanical samples recovered during the 2004, 2005, 2009 and 2011 excavation seasons at the Petra Garden and Pool Complex (PGPC) in Jordan examined plants that were preserved during different phases of use of the site. The analysis of these remains attempts to determine what plants would have been grown in the garden in antiquity. Results indicated that the material recovered likely represented plants that had been preserved elsewhere in the area and then deposited in the garden to act as fertilizer. The remains were generally charred and were probably derived from fuel and/or waste deposits as it does not appear that the garden was catastrophically burned. Although it is difficult to ascertain garden variety plants under these preservation conditions, an analysis of the archaeobotanical data from the PGPC addresses the questions of what and how plants functioned in the local and regional economy, and how the role of the garden changed through time, in addition to providing insight into the general environmental or ecological conditions present in southern Jordan from the Late Hellenistic through Late Byzantine/Post-Classical periods. Although ornamental species represent a small fraction of materials collected, the presence of these taxa may indicate their occurrence in the garden. Even if garden plants are not readily identifiable, this study aids in addressing the larger issues of trade, economy and environment of this ancient city, as well as the feasibility of identifying garden plants in antiquity.     

Experimental approaches to understanding variation in grain size in Panicum miliaceum (broomcorn millet) and its relevance for interpreting archaeobotanical assemblages

The dimensions of archaeobotanical grains identified as Panicum miliaceum (broomcorn millet) vary greatly in size. This is illustrated by the remains from the archaeological site of Zanovskoe in eastern Ukraine (5th–1st centuries cal. b.c.). We carried out experimental work on broomcorn millet plants and grains, aiming at a comprehensive understanding of factors that may have contributed to variation in the grain size of broomcorn millet in archaeobotanical assemblages. We analyzed the dependence of grain size variation on selected environmental and taphonomic factors. Our results indicate that immaturity is more likely than environmental stress to account for small grain size in broomcorn millet plants. Depending on charring temperature and time, immature broomcorn millet grains can withstand charring and are potentially preserved in archaeological assemblages. Depending on maturity level, such grains vary in size and shape. These results are potentially important for accurate identification of archaeobotanical specimens.     

Ancient DNA as a multidisciplinary experience

Investigation into DNA from archeological remains offers an inestimable tool for unraveling the history of humankind. However, a series of basic and technical difficulties renders the analysis of ancient DNA (aDNA) molecules troublesome, depending either on their own peculiar characteristics or on the complexity of processes affecting the bone matrix over time, all compromising the preservation of ancient DNA. This review underlines the contribution of many different disciplines, in particular molecular biology and genetics, to overcome these obstacles. The role of each expertise is illustrated to appropriately address the questions arising in aDNA investigations.     

夏家店等古人骨DNA的提取、扩增及序列分析

古DNA从距今 2 0 0 0～ 50 0 0年的古代人骨 (编号为 :M89,ⅢM11,ⅢM12和AM4 )中提取出来 ,利用聚合酶链式反应分别对线粒体DNA中MTND4 基因中 112 10～ 11414(2 0 5bp)以及RegionV中 8196～ 83 16(12 1bP)进行了扩增 ,并被测序 .实验结果表明古代人骨中仍存在有大量的遗传信息 ,通过提取、扩增可以得到真实可靠的序列 .对序列进行比较发现 112 4 8,112 4 9,112 83及 112 93为易发生突变的位点 .结果经同源性分析后发现 ,ⅢM11和ⅢM12有很高同源性 ,而M89和AM4与ⅢM11和ⅢM12的同源性却比较低 .这对人类学、考古学及分子进化的研究有重要的辅助作用 .     

Paleobot.org: establishing open-access online reference collections for archaeobotanical research

Difficulty in accessing high quality reference materials has been a limiting factor in the advancement of archaeobotanical research. However, new developments in online open source content management technology and faster downloading capabilities make high quality and low cost dynamic online curation of archaeobotanical reference images increasingly feasible. We describe the establishment of Paleobot.org, an open access online reference collection database for macrobotanical, microbotanical and isotopic data to help standardize and improve the identification of archaeobotanical remains.     

Macro-Process of Past Plant Subsistence from the Upper Paleolithic to Middle Neolithic in China: A Quantitative Analysis of Multi-Archaeobotanical Data

Detailed studies of the long-term development of plant use strategies indicate that plant subsistence patterns have noticeably changed since the Upper Paleolithic, when humans underwent a transitional process from foraging to agriculture. This transition was best recorded in west Asia; however, information about how plant subsistence changed during this transition remains limited in China. This lack of information is mainly due to a limited availability of sufficiently large, quantified archaeobotanical datasets and a paucity of related synthetic analyses. Here, we present a compilation of extensive archaeobotanical data derived from interdisciplinary approaches, and use quantitative analysis methods to reconstruct past plant use from the Upper Paleolithic to Middle Neolithic in China. Our results show that intentional exploitation for certain targeted plants, particularly grass seeds, may be traced back to about 30,000 years ago during the Upper Paleolithic. Subsequently, the gathering of wild plants dominated the subsistence system; however, this practice gradually diminished in dominance until about 6~5 ka cal BP during the Middle Neolithic. At this point, farming based on the domestication of cereals became the major subsistence practice. Interestingly, differences in plant use strategies were detected between north and south China, with respect to (1) the proportion of certain plant taxa in assemblages, (2) the domestication rate of cereals, and (3) the type of plant subsistence practiced after the establishment of full farming. In conclusion, the transition from foraging to rice and millet agriculture in China was a slow and long-term process spanning 10s of 1000s of years, which may be analogous to the developmental paths of wheat and barley farming in west Asia.     

古人类骨中羟磷灰石的XRD和喇曼光谱分析

人骨残骸是生物考古的主要对象,而骨骼污染鉴别是样品选择的依据,也是生物考古的前提。利用X射线衍射（XRD）和喇曼光谱相结合的方法,通过对新疆克雅河圆沙古城遗传出土的人类骨骼中羟磷灰石的分析,来辨析骨骼污染程度。研究结果表明,两种方法的有机结合,准确反映了骨骼中羟磷石结晶度的变化,从而可简单、较为有效地鉴别古代人类骨骼样品的污染。     

Functional interpretation of archaeobotanical data: Making hay in the archaeological record

Hay malting and hay meadows have long been of fundamental ecological, economic and social importance in temperate Europe. A variety of archaeological sources suggests that hay making may date back to the Iron Age, but direct archaeobotanical evidence for this practice is problematic. Past grassland communities are imperfectly represented and preserved in archaeobotanical assemblages, and ancient meadow and pasture communities may not resemble present-day communities in terms of management practices or botanical composition. This paper explores the potential of FIBS (Functional Interpretation of Botanical Surveys) in the archaeobotanical investigation of ancient grassland management. The botanical composition of present-day grassland communities was analysed in terms of functional attributes (e.g. canopy height) relevant to cutting, grazing and habitat productivity. The utility of these attributes for distinguishing between present-day meadow, pasture and unmanaged grassland communities has been evaluated. Similar analyses were performed on archaeobotanical data from Neolithic to post-Medieval northwestern and central Europe. Functional shifts over time, interpreted in the light of the functional analysis of modern grassland, suggest that hay-making was well established by the Iron Age. Avenues are suggested for the refinement and further development of the FIBS methodology in the archaeobotanical investigation of grassland management.