112 research outputs found
Reducing microbial and human contamination in DNA extractions from ancient bones and teeth
Although great progress has been made in improving methods for generating DNA sequences from ancient biological samples, many, if not most, samples are still not amenable for analyses due to overwhelming contamination with microbial or modern human DNA. Here we explore different DNA decontamination procedures for ancient bones and teeth for use prior to DNA library preparation and high-throughput sequencing. Two procedures showed promising results: (i) the release of surface-bound DNA by phosphate buffer and (ii) the removal of DNA contamination by sodium hypochlorite treatment. Exposure to phosphate removes on average 64% of the microbial DNA from bone powder but only 37% of the endogenous DNA (from the organism under study), increasing the percentage of informative sequences by a factor of two on average. An average 4.6-fold increase, in one case reaching 24-fold, is achieved by sodium hypochlorite treatment, albeit at the expense of destroying 63% of the endogenous DNA preserved in the bone. While both pretreatment methods described here greatly reduce the cost of genome sequencing from ancient material due to efficient depletion of microbial DNA, we find that the removal of human DNA contamination remains a challenging problem
Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe
Little is known about the population history of Neandertals over the hundreds of thousands of years of their existence. We retrieved nuclear genomic sequences from two Neandertals, one from Hohlenstein-Stadel Cave in Germany and the other from Scladina Cave in Belgium, who lived around 120,000 years ago. Despite the deeply divergent mitochondrial lineage present in the former individual, both Neandertals are genetically closer to later Neandertals from Europe than to a roughly contemporaneous individual from Siberia. That the Hohlenstein-Stadel and Scladina individuals lived around the time of their most recent common ancestor with later Neandertals suggests that all later Neandertals trace at least part of their ancestry back to these early European Neandertals
Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry
Modern humans appeared in Europe by at least 45,000 years ago1–5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania7 and Siberia8 who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common
Genetic insights into the social organization of Neanderthals
Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans1–8, but the social organization of Neanderthal communities remains poorly understood. Here we present genetic data for 13 Neanderthals from two Middle Palaeolithic sites in the Altai Mountains of southern Siberia: 11 from Chagyrskaya Cave9,10 and 2 from Okladnikov Cave11—making this one of the largest genetic studies of a Neanderthal population to date. We used hybridization capture to obtain genome-wide nuclear data, as well as mitochondrial and Y-chromosome sequences. Some Chagyrskaya individuals were closely related, including a father–daughter pair and a pair of second-degree relatives, indicating that at least some of the individuals lived at the same time. Up to one-third of these individuals’ genomes had long segments of homozygosity, suggesting that the Chagyrskaya Neanderthals were part of a small community. In addition, the Y-chromosome diversity is an order of magnitude lower than the mitochondrial diversity, a pattern that we found is best explained by female migration between communities. Thus, the genetic data presented here provide a detailed documentation of the social organization of an isolated Neanderthal community at the easternmost extent of their known range
Style, Function and Cultural Transmission
Recent evolutionary approaches to the understanding of lithic variability take us back to long-standing issues in lithic studies to do with the claimed contrast between style and function and the Binford-Bordes debate of the 1960s concerning the factors that affect inter-assemblage variation. In fact, the style and function contrast is an unhelpful one, not least when considering the question of convergence. Taking the definition of style as ‘a way of doing’, all functions are carried out in locally specific ways that have a transmission history, although the extent to which the history of the attributes relevant to the function have been subject to random drift and innovation patterns, as opposed to selection, will vary. Moreover, in a subtractive technology like lithics the extent to which a transmission signal will be visible in an attribute like the angle of a cutting edge is unclear. The contrasting view is that, in the case of lithics, functional requirements will always call into existence the technical innovations to satisfy them, which in any case are not that difficult to find. The paper addresses these and related issues with reference to previous work by Shennan and colleagues on the use of material culture to identify within and between group variation, the extent to which isolation-by-distance in space and time can account for the similarities and differences between assemblages, and the role of phylogenetic methods
The formation of human populations in South and Central Asia
By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization’s decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages
Novel associations of UDP-glucuronosyltransferase 2B gene variants with prostate cancer risk in a multiethnic study
The changing role of china in the global illegal cigarette trade
This study explores the history of the illegal production, distribution, and smuggling of cigarettes in mainland China. Data were obtained from a content analysis of 931 media reports retrieved from LexisNexis for the time period 1975 until 2010, and from other open sources. The illegal cigarette trade first emerged in the form of violations of state tobacco monopoly regulations. In the course of the restructuring of the legal tobacco sector, which occurred under external political pressure to open the Chinese market to foreign competition, an illegal cigarette industry emerged which at first primarily produced fake Chinese brand cigarettes for the domestic black market. At the same time, China became a destination country for smuggled genuine Western brand cigarettes. It was only after effective crackdowns against cigarette smuggling and domestic distribution channels in the late 1990s that the Chinese illegal cigarette industry shifted to exporting large numbers of counterfeit Western brand cigarettes to black markets abroad. China’s current role as a leading supplier of counterfeit cigarettes is a result of the contradictions of the economic reform process and of external licit and illicit forces that worked toward opening up the Chinese tobacco sector to the outside world
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