Authenticated DNA from ancient wood remains

BACKGROUND: The reconstruction of biological processes and human activities during the last glacial cycle relies mainly on data from biological remains. Highly abundant tissues, such as wood, are candidates for a genetic analysis of past populations. While well-authenticated DNA has now been recovered from various fossil remains, the final 'proof' is still missing for wood, despite some promising studies. SCOPE: The goal of this study was to determine if ancient wood can be analysed routinely in studies of archaeology and palaeogenetics. An experiment was designed which included blind testing, independent replicates, extensive contamination controls and rigorous statistical tests. Ten samples of ancient wood from major European forest tree genera were analysed with plastid DNA markers. CONCLUSIONS: Authentic DNA was retrieved from wood samples up to 1,000 years of age. A new tool for real-time vegetation history and archaeology is ready to use.     

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.     

Using ancient mtDNA to reconstruct the population history of northeastern North America

Mitochondrial DNA (mtDNA) was extracted and analyzed from the skeletal remains of 44 individuals, representing four prehistoric populations, and compared to that from two other prehistoric and several contemporary Native American populations to investigate biological relationships and demographic history in northeastern North America. The mtDNA haplogroup frequencies of ancient human remains from the Morse (Red Ocher tradition, 2,700 BP) and Orendorf (Mississippian tradition, 800 BP) sites from the Central Illinois River Valley, and the Great Western Park (Western Basin tradition, 800 BP) and Glacial Kame (2,900 BP) populations from southwestern Ontario, change over time while maintaining a regional continuity between localities. Haplotype patterns suggest that some ancestors of present day Native Americans in northeastern North America have been in that region for at least 3,000 years but have experienced extensive gene flow throughout time, resulting, at least in part, from a demic expansion of ancestors of modern Algonquian-speaking people. However, genetic drift has also been a significant force, and together with a major population crash after European contact, has altered haplogroup frequencies and caused the loss of many haplotypes.     

Analysis of the fuel wood used in Late Bronze Age and Early Iron Age copper mining sites of the Schwaz and Brixlegg area (Tyrol,Austria)

Charcoal analysis was carried out as part of an interdisciplinary project focusing on the copper mining history of the former mining area of Schwaz and Brixlegg, a region pivotal as a copper source in prehistoric Europe. The goal was to use remains of carbonised wood to investigate environmental implications of prehistoric mining, as well as to gain new insight about the ancient mining technique of fire-setting. Charcoal samples from seven copper mining sites (Late Bronze Age to Early Iron Age) were analysed. The results reveal a strong preference for coniferous wood as fuel in fire-setting, but not in ore smelting/roasting processes. Species composition at the ore-processing sites indicates moderate forest degradation processes caused by human intervention.     

Trees Underground: New Insights into Trees and Woodmanship in South-east England c. AD 800–1300

Summary

Study of wood recovered from waterlogged archaeological sites in London reveals much about the trees that grew in the city's hinterland between about AD 800 and 1300. Tentative reconstructions of some specific types of trees and ‘treeland’ have been made by combining three-dimensional recording of the timbers and roundwood with examination of how the wood was used, tree-ring analysis, species identification and experimental work in ancient woodland. It has also been possible to gain some appreciation of general trends during the mediaeval period such as the intensification of woodland management and the disappearance of wildwood conditions.     

河南灵井许昌人遗址鬣狗粪化石的初步研究

河南灵井许昌人遗址是我国近年来发掘的最为重要的古人类遗址之一。该遗址中出土了大量的石器、骨器、动物化石、粪便化石等遗存以及人类头盖骨化石等。我们对该遗址出土的鬣狗粪化石进行了类型学及其包含的微体化石等方面研究,从分析统计结果来看,鬣狗粪化石中包含了丰富的古信息,如古寄生虫卵、动物毛发、孢粉、植硅体、真菌等。本文主要针对鬣狗粪化石中古寄生虫卵及动物毛发进行分析,探讨了作为寄主鬣狗罹患的寄生虫病,以及鬣狗的食物来源等情况,为深入理解更新世晚期人类适应环境与气候提供新的证据。     

A methodological approach to the study of archaeological cereal meals: a case study at Çatalhöyük East (Turkey)

This paper presents an integrated methodology for the analysis of archaeological remains of cereal meals, based on scanning electronic microscopic analyses of microstructures of charred food fragments from Neolithic Çatalhöyük (Turkey). The remains of cereal foods as ‘bread-like’ or ‘porridge-like’ small charred lumps of various amalgamated plant materials are frequently recovered from Neolithic and later archaeological sites in southwest Asia and Europe. Cereal food remains have recently attracted interest because the identification of their plant contents, the forms of food that they represent and the methods used in their creation can provide unique information about ancient culinary traditions and routine food processing, preparation and cooking techniques. Here, we focus on three methodological aspects: (1) the analysis of their composition; (2) the analysis of their microstructure to determine preparation and cooking processes; (3) the comparison with experimental reference materials. Preliminary results are presented on the botanical composition and cooking processes represented by the charred cereal preparations found at Neolithic Çatalhöyük (Turkey), for example cereals processed into bread, dough and/or porridge.     

Holocene changes in the ecology of northern fur seals: insights from stable isotopes and archaeofauna

The remains of northern fur seals (Callorhinus ursinus) are among the most abundant of pinniped elements recovered from mainland coastal archaeological sites in both California and Oregon. This is surprising as all contemporary northern fur seals breed exclusively on offshore islands, primarily at high latitudes, and the species is otherwise pelagic. The vulnerability of these animals to human predation suggests that either humans were foraging much further offshore than has been presumed or alternatively that the ecology of these animals has shifted during the late Holocene. We used isotopic and archaeofaunal analysis of the remains of pinnipeds from the middle to late Holocene of central and northern California to clarify the breeding and foraging behavior, and migration patterns of these ancient animals. The carbon and nitrogen isotope compositions of ancient northern fur seals reveal that these animals fed as far offshore as they do today, and that they remained at middle latitudes throughout the year. From an archaeological site at Moss Landing, California, we identified 16 skeletal elements from at least 12 very small northern fur seal pups. From another site near Mendocino, California, we identified the remains of at least 6 pups. We estimate the size and age of 5 of the young animals using sex-specific regressions of body length on the short dentary length derived from measurements of modern specimens. Our estimates indicate these ancient pups were substantially smaller, and therefore younger, than modern 3-month-old northern fur seal pups from similar latitudes and their nitrogen isotope compositions suggest they had not been weaned. As present-day northern fur seals do not leave their rookeries until they are at least 4 months old, we consider it highly unlikely that these ancient pups swam to these mainland locations from some distant island rookery. While there are numerous nearshore rocky outcrops along the Mendocino Coast, which may have supported small breeding colonies, the Moss Landing site is centered on a 40-km-long sandy beach, and is more than 120 km from what at the time were the nearest offshore islands. We conclude that northern fur seal adult females, subadults, and pups whose remains were recovered at the Moss Landing archaeological site must have been taken at a mainland rookery. Evidence that northern fur seals once bred on the mainland at this central California location suggests that the abundant remains of these animals at numerous other archaeological sites along the California coast also reflect the presence of nearby mainland rookeries. Based on the relative abundance of their remains in ancient human occupation sites and the widespread distribution of sites where their remains have been found, it appears that northern fur seals were once the predominant pinniped throughout a region where they now only rarely occur. Furthermore, their presence along the central and northern California coasts appears to have once severely limited the distribution of other pinnipeds, which are now common to the region.     

Developing Markets for Certified Wood Products: Greening the Supply Chain for Construction Materials

A growing worldwide movement is seeking to promote the greening of the construction sector. At the design level, proponents of frameworks such as LEED (Leadership in Energy and Environmental Design) seek to motivate designers and building owners to employ environmentally desirable materials. A prominent component of this approach is boosting availability of “green” building materials through programs that will certify to buyers that materials meet environmental standards. For wood products, this has resulted in several forms of “green certification” for forest management. Increasingly large areas of forest are now being certified worldwide. Yet it remains difficult for designers of green buildings, or consumers seeking green furniture, to obtain certified wood products. Many, if not most, of the logs now being harvested on green certified forest land worldwide are not reaching the store shelf with a certified label. Marketing certified wood all the way to the retail shelf has proved to be much harder than initially thought by proponents of certified products. This article explains the sources of these difficulties and outlines an approach to identifying products with high potential for marketing as certified products. Because of complex, multilevel supply chains for many wood products, support is required at all processing and distribution levels for a product to reach the retail customer with its green label. Market participants' purchase size and frequency, basis for product selection, buying influences, and price sensitivity are evaluated to identify product and market approaches likely to increase success rates for certified wood products. The article concludes with recommendations for expanding markets for green building materials.     

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.     

Mitochondrial DNA sequences from a 7000-year old brain.

Pieces of mitochondrial DNA from a 7000-year-old human brain were amplified by the polymerase chain reaction and sequenced. Albumin and high concentrations of polymerase were required to overcome a factor in the brain extract that inhibits amplification. For this and other sources of ancient DNA, we find an extreme inverse dependence of the amplification efficiency on the length of the sequence to be amplified. This property of ancient DNA distinguishes it from modern DNA and thus provides a new criterion of authenticity for use in research on ancient DNA. The brain is from an individual recently excavated from Little Salt Spring in southwestern Florida and the anthropologically informative sequences it yielded are the first obtained from archaeologically retrieved remains. The sequences show that this ancient individual belonged to a mitochondrial lineage that is rare in the Old World and not previously known to exist among Native Americans. Our finding brings to three the number of maternal lineages known to have been involved in the prehistoric colonization of the New World.     

A 400,000-year-old Acheulean assemblage associated with the Aroeira-3 human cranium (Gruta da Aroeira,Almonda karst system,Portugal)

Bifaces dominate the Acheulean stone tools recovered during the archaeological excavation of layer X of Gruta da Aroeira, dated to 389–436 ka. Faunal remains and a human cranium were found in association with this lithic assemblage. The raw materials used are mostly quartz and quartzite cobbles available in the vicinity of the site. Technological and systematic analysis shows that there are no Levallois elements and suggests that on-site knapping consisted of the reduction of centripetal cores. Flake cleavers are absent. Use-wear analysis indicates the processing of hard materials, mainly wood. Gruta da Aroeira represents one of the few Middle Pleistocene sites that provide securely dated diagnostic human remains and associated Acheulean lithics, thus representing a major step forward in our understanding of the variability of westernmost Europe's Acheulean and of the human populations that made it.     

Trifolieae and related seeds from archaeological contexts: problems in identification

Small legume seeds are commonly recovered from Epipalaeolithic and Early Neolithic sites in north Africa and south-west Asia, often as a high proportion of the total plant remains. Their role is uncertain, but it is thought that small-seeded legumes may once have been a human food resource. They are difficult to identify. The gross morphology and testa surface micromorphology have been investigated in fresh seeds of members of the tribe Trifolieae and some related tribes in the same subfamily Faboideae. The separation of the four genera Medicago, Melilotus, Trifolium, and Trigonella has been attempted by multivariate analysis of seed characters that can be seen in experimentally charred seed specimens. The characters used have also been observed in well-preserved ancient charred small legume seeds, and so can be readily used for the purpose of identification. Although identification to the level of species is rarely possible, identification to generic level could provide information useful for the interpretation of this category of ancient plant remains.     

Plant Remains from an Archaeological Site as Indicators of Vegetation and Agricultural Practice Between (3320±400) and (2080±80) yr BP in Gangetic West Bengal, India

Diverse plant remains recovered from an archaeological site of Chalcolithic-Early Historic age in the Bhairabdanga area of Pakhanna (latitude 23°25′N, longitude 87°23′E), situated on the west bank of the Damodar river, Bankura district, West Bengal, India, include food grains, wood charcoals, and palynomorphs. Radiocarbon dating of the recovered biological remains reveal the age of the site as (3320±400) to (2080±80) yr BP. The food grains were identified as Oryza sativa L. and Vigna mungo L, and seeds of Brassica cf.campestris L. were also found; these indicate the agricultural practice and food habits of the ancient people living at Pakhanna from the Chalcolithic to the Early Historic period. Sediments including plant remains have been broadly divided into two zones, considering archaeological findings and radiocarbon dating. Analysis of the plant remains (i.e. wood charcoals and palynomorphs) in addition to cultivated food grains has revealed that a rich vegetation cover existed in this area, with a prevailing tropical and humid climate,comprising the timber-yielding plants Shorea sp., Terminalia sp., and Tamarindus sp., with undergrowths of diverse shrubs and herbs during the Chalcolithic period (zone Ⅰ) dated (3320±400) yr BP. Comparatively poorer representation and frequency of plant remains indicate a drier climate during the Early Historic period (zone Ⅱ) dated as (2110±340) to (2080±80) yr BP. Comparisons of the archaeobotanical data recovered from the Chalcolithic and Early Historic period and also a principle components analysis indicate a change in the climate of the area from tropical and humid at (3 320 ± 400) yr BP to tropical and drier conditions at (2110±340) to (2080±80) yr BP. The present-day tropical, dry deciduous vegetation of the area suggests that climate change has occurred in the area since the contemporaneous past. The plant remains database has been utilized to reconstruct the settlement pattern of the community living in the site between (3320±400) and (2080±80) yr BP. The community settled near the riverbank, practicing cultivation.     

DNA content and distribution in ancient feathers and potential to reconstruct the plumage of extinct avian taxa

Feathers are known to contain amplifiable DNA at their base (calamus) and have provided an important genetic source from museum specimens. However, feathers in subfossil deposits generally only preserve the upper shaft and feather ‘vane’ which are thought to be unsuitable for DNA analysis. We analyse subfossil moa feathers from Holocene New Zealand rockshelter sites and demonstrate that both ancient DNA and plumage information can be recovered from their upper portion, allowing species identification and a means to reconstruct the appearance of extinct taxa. These ancient DNA sequences indicate that the distal portions of feathers are an untapped resource for studies of museum, palaeontological and modern specimens. We investigate the potential to reconstruct the plumage of pre-historically extinct avian taxa using subfossil remains, rather than assuming morphological uniformity with closely related extant taxa. To test the notion of colour persistence in subfossil feathers, we perform digital comparisons of feathers of the red-crowned parakeet (Cyanoramphus novaezelandiae novaezelandiae) excavated from the same horizons as the moa feathers, with modern samples. The results suggest that the coloration of the moa feathers is authentic, and computer software is used to perform plumage reconstructions of moa based on subfossil remains.     

Charred olive stones: experimental and archaeological evidence for recognizing olive processing residues used as fuel

After extracting oil from olives a residue is left usually referred to as the olive oil processing residue (OPR). This study explores the way in which ancient societies may have used OPR as fuel for fires to generate heat and the various issues that are related to the residues of this fuel. After drying, the high heating value and structure of OPR makes it an excellent and efficient fuel. Upgrading OPR further, through thermal conversion or charring, provides an even more efficient fuel (COPR), with a hotter and smoke free flame, a higher heating value and which is lighter in mass and thus easier to transport. After a fire is extinguished two types of remains of the fuel are left i.e. char and ash. Analyses on both remains, recovered from archaeological deposits, could be used as a source of information on fuel utilization. Laboratory experiments on charred modern OPR and stones show that by measuring their reflectance and analyzing their structure under reflected light microscopy, OPR and COPR can be distinguished in the charred material recovered from three archaeological sites in Greece and Syria. Based on these investigations it is suggested that on the three sites COPR was used as fuel. Ash, sampled together with the char, provides the possibility of investigating if other types of fuel were used, apart from OPR or COPR. On the investigated sites no ash was collected, but the analysis of the modern OPR showed that the properties of its ash could be used to distinguish it from other types of fuel. Ash from modern OPR and olive stones showed the presence of phytoliths. The often discussed issue related to the sharpness and smoothness of the edges of charred fragmented olive stones was investigated. The results showed that this is not a reliable criterion for recognizing olive oil production. It is recommended that in addition to the identification of the botanical material more properties of the remains of fuels should be analysed. To prevent destroying and losing char and ash as a result of excavation activities such as flotation and sieving, special measures have to be taken. The results show that analysing char and ash may provide valuable information on the (pyro)technology practised in ancient societies.     

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 .     

Spatiotemporal fluctuations of population structure in the Americas revealed by a meta-analysis of the first decade of archaeogenomes

Objectives

Since 2010, genome-wide data from hundreds of ancient Native Americans have contributed to the understanding of Americas' prehistory. However, these samples have never been studied as a single dataset, and distinct relationships among themselves and with present-day populations may have never come to light. Here, we reassess genomic diversity and population structure of 223 ancient Native Americans published between 2010 and 2019.

Materials and Methods

The genomic data from ancient Americas was merged with a worldwide reference panel of 278 present-day genomes from the Simons Genome Diversity Project and then analyzed through ADMIXTURE, D-statistics, PCA, t-SNE, and UMAP.

Results

We find largely similar population structures in ancient and present-day Americas. However, the population structure of contemporary Native Americans, traced here to at least 10,000 years before present, is noticeably less diverse than their ancient counterparts, a possible outcome of the European contact. Additionally, in the past there were greater levels of population structure in North than in South America, except for ancient Brazil, which harbors comparatively high degrees of structure. Moreover, we find a component of genetic ancestry in the ancient dataset that is closely related to that of present-day Oceanic populations but does not correspond to the previously reported Australasian signal. Lastly, we report an expansion of the Ancient Beringian ancestry, previously reported for only one sample.

Discussion

Overall, our findings support a complex scenario for the settlement of the Americas, accommodating the occurrence of founder effects and the emergence of ancestral mixing events at the regional level.