ArticlePublisher preview available

Age estimates for hominin fossils and the onset of the Upper Palaeolithic at Denisova Cave

To read the full-text of this research, you can request a copy directly from the authors.

Abstract and Figures

Bayesian modelling of chronometric, stratigraphic and genetic data from Denisova Cave provides a chronological framework for understanding Neanderthal and Denisovan presence at the site, as well as interactions between these groups.
This content is subject to copyright. Terms and conditions apply.
Age estimates for hominin fossils and the onset of
the Upper Palaeolithic at Denisova Cave
Katerina Douka1,2*, Viviane Slon3, Zenobia Jacobs4,5, Christopher Bronk Ramsey2, Michael V. Shunkov6,7,
Anatoly P. Derevianko6,8, Fabrizio Mafessoni3, Maxim B. Kozlikin6, Bo Li4,5, Rainer Grün9, Daniel Comeskey2, Thibaut Devièse2,
Samantha Brown1, Bence Viola10, Leslie Kinsley11, Michael Buckley12, Matthias Meyer3, Richard G. Roberts4,5, Svante Pääbo3,
Janet Kelso3 & Tom Higham2*
Denisova Cave in the Siberian Altai (Russia) is a key site for
understanding the complex relationships between hominin
groups that inhabited Eurasia in the Middle and Late Pleistocene
epoch. DNA sequenced from human remains found at this
site has revealed the presence of a hitherto unknown hominin
group, the Denisovans1,2, and high-coverage genomes from
both Neanderthal and Denisovan fossils provide evidence for
admixture between these two populations
. Determining the age
of these fossils is important if we are to understand the nature of
hominin interaction, and aspects of their cultural and subsistence
adaptations. Here we present 50 radiocarbon determinations
from the late Middle and Upper Palaeolithic layers of the site.
We also report three direct dates for hominin fragments and
obtain a mitochondrial DNA sequence for one of them. We apply
a Bayesian age modelling approach that combines chronometric
(radiocarbon, uranium series and optical ages), stratigraphic and
genetic data to calculate probabilistically the age of the human
fossils at the site. Our modelled estimate for the age of theoldest
Denisovan fossil suggests that this group was present at the site as
early as 195,000years ago (at 95.4% probability). All Neanderthal
fossils—as well as Denisova11, the daughter of a Neanderthal
and a Denisovan4—date to between 80,000 and 140,000years ago.
The youngest Denisovan dates to 52,000–76,000years ago. Direct
radiocarbon dating of Upper Palaeolithic tooth pendants and bone
points yielded the earliest evidence for the production of these
artefacts in northern Eurasia, between43,000and49,000calibrated
years before present (taken as 1950). On the basis of current
archaeological evidence, it may be assumed that these artefacts
are associated with the Denisovan population. It is not currently
possible to determine whether anatomically modern humans
were involved in their production, as modern-human fossil and
genetic evidence of such antiquity has not yet been identified in
the Altai region.
Denisova Cave preserves the longest and most notable Palaeolithic
sequence in northern Asia. It consists of three chambers: Main
Chamber, East Chamber and South Chamber (Supplementary
Information, section1). Excavations at the site have so far yielded the
remains of 12 hominins (Extended Data Fig.1 and Supplementary
Information, section3); most of these remains are small and highly
fragmentary. Despite this, the preservation of DNA in some of these
remains is very good and has enabled genome-wide data to be obtained
from both Neanderthal and Denisovan human remains, as well as from
cave sediments, enabling comparisons to be madebetween the two
The chronology of the site and the age of the recovered human
remains are key unresolved issues. Previous attempts at building a
chronology at Denisova Cave have used radiocarbon dating in the
uppermost sections, and thermoluminescence dating in the older
layers9. More recently, radiocarbon dating from the uppermost
Pleistocene layers in East Chamber revealed some age variations, which
were ascribed to taphonomic mixing and carnivore bioturbation2.
A set of optical ages
has been obtained from Pleistocene sedimentary
layers in all three chambers.
Here we report 50 radiocarbon determinations from 40 samples,
collected from the upper parts of the Pleistocene sequence (layers
9–12) in Main Chamber and East Chamber (Fig.1 and Extended Data
Table1). A further 23 samples were processed but did not yield suffi-
cient carbon for dating (Supplementary Information, section2). We
selected samples of charcoal, and humanly modified bone and arte-
facts (Extended Data Fig.2 and Supplementary Information, section2)
from locations that were deemed during excavation to be undisturbed.
Where possible, the samples were prepared using robust decontamina-
tion protocols, including collagen ultrafiltration and single amino acid
extraction of hydroxyproline from bones and teeth, and acid-base-wet
oxidation stepped-combustion (ABOx-SC) or acid-wet oxidation
stepped-combustion (AOx-SC) for charcoal (Supplementary
Information, section2).
All samples from layers 11.3, 11.4 and 12 in East Chamber, as well
as the directly dated Denisova11 bone11, pre-date the radiocarbon
age limit. In layer 11.2, we found two age clusters: three samples
have infinite ages, and three samples have finite calibrated ages
(Extended Data Table1). A horse tooth from layer 9.2 gave a result of
45,720–50,000calibrated years before present (cal. years ) (Oxford
radiocarbon laboratory code OxA-29859). This date is statistically
indistinguishable from the group of finite dates (treated with ultrafil-
tration and ABOx) from layer 11.2.
In Main Chamber, our radiocarbon ages reveal a depositional hiatus
between layers 12 and 11.4. Samples from layer 12 (at the end of the
Middle Palaeolithic) all gave infinite radiocarbon ages compared to
samples from layer 11.4, which date to between approximately 35,000
and 40,000cal. years  (Fig.1).
Four pendants made from red deer (Cervus elaphus) and elk (Alces
alces) teeth—which are often associated with Upper Palaeolithic
technocomplexes—provided results of ~32,000, ~40,000 and ~45,000cal.
years  (Fig.1 and Extended Data Fig.2). The oldest of these dates
(OxA-30963) is corroborated by a charcoal date (OxA-31506)
from the same stratigraphic location and year of excavation, and is
the earliest direct date for an artefact of this type in northern Eurasia.
1Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany. 2Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History
of Art, University of Oxford, Oxford, UK. 3Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. 4Centre for Archaeological Science, School
of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia. 5Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity
and Heritage, University of Wollongong, Wollongong, New South Wales, Australia. 6Institute of Archaeology and Ethnography, Russian Academy of Sciences Siberian Branch, Novosibirsk, Russia.
7Novosibirsk State University, Novosibirsk, Russia. 8Altai State University, Barnaul, Russia. 9Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland, Australia.
10Department of Anthropology, University of Toronto, Toronto, Ontario, Canada. 11Research School of Earth Sciences, The Australian National University, Canberra, Australian Capital Territory,
Australia. 12Manchester Institute of Biotechnology, University of Manchester, Manchester, UK. *e-mail:;
640 | NATURE | VOL 565 | 31 JANUARY 2019
© 2019 Springer Nature Limited. All rights reserved.
... -Denisova 15 is a bone splinter identified as Neanderthal by collagen peptide mass fingerprinting (Douka et al., 2019). ...
... More recently, a radiocarbon dating campaign of Denisova has yielded three dates for the Central chamber: one for layer 11.1, at 37.5 ± 1 ka BP (OxA-29861) and two for layer 11.4, 42.9 ± 2 ka BP (OxA-29872) and 41.2 ± 1.4 ka BP (OxA-30271; manufactured bone point) (Douka et al., 2015). This dating campaign was completed in 2016 and 2017 with the addition of 63 dating samples in both the Central chamber and the Eastern gallery (Douka et al., 2019). ...
... Layer 9, which material is clearly Upper Palaeolithic, yielded a surprisingly old date at 43-47 ka BP or 45-49 ka cal BP (Douka et al., 2015). This date has been recently confirmed by the radiocarbon dating of a second bone 5 at 46,300 ± 2,600 BP (OxA-36011; Douka et al., 2019). ...
Full-text available
The Altai range, in southern Russia, has yielded an important series of prehistoric assemblages in various contexts (caves, shelters and open-air sites). Recent anthropological and archaeological studies have established the significance of this area, with complex peopling events involving at least three different human species, Neanderthals, Modern Humans and Denisovans, the latter being exclusively associated with Altai assemblages. The cultural background of these hominins’ occupation is already well defined for the beginning of the Upper Palaeolithic. This study aims to better characterize the previous period’s productions, through one of its important cultural features, the Levallois technology.To address this issue, we have undertaken a review of material coming from the some of the key Altai sequences, while trying to reconstruct the different chaînes opératoires implemented for the production of the desired products that had been previously recognized as Levallois. The analysed artefacts cover a large time span, from Early Middle Palaeolithic (Denisova, stratum 22 of the Central Chamber, RTL dated to 220-280 ky) to layers associated with Upper Palaeolithic (Ust’-Kanskaya, strata 3 to 1), and come from both caves and open-air sites. This allowed us to establish a chronological comparison, as well as regional. Results have shown that the Levallois assemblages of the region are quite homogenous; also, that Levallois technology may not have been present in Altai as early as it has been previously claimed, with a difference of ~100.000 years; and finally, that it is mostly analogous to what we can find in neighbouring regions. These extra-regional common features probably express contacts and exchanges to and from the Altai region.
... Recent finds from Arabia also point to an association of the MP with anatomically modern humans during MIS 5 (Armitage et al., 2011;Groucutt et al., 2018). Hominin fossil, sediment DNA, and artefact evidence from the Altai Mountains (MIS 5-3) describe interactions and interstratification among Denisovans, Neanderthals, and H. sapiens, often with unclear technological associations (Derevianko, 2010;Douka et al., 2019;Rybin and Khatsenovich, 2020;Slavinsky et al., 2016;Slon et al., 2017). It appears that as the intensity of research increases in all of these regions, so does the complexity of evidence for Late Pleistocene hominin dispersals and authorship of artefact industries. ...
The Armenian Highlands and Caucasus comprise a pivotal region within the known Neanderthal biogeographic range. This topographically and eco-geologically diverse area is very rich in Middle Palaeolithic (MP) archaeology; however, it is still understudied. This chapter summarises results of recent fieldwork and current data on patterns and variability in MP site contexts, chronology, stone tool manufacture, technological organisation, land use, subsistence practices, and potential symbolic behaviour. MP hunter–gatherers were well adapted to Late Pleistocene mosaic landscapes and environmental-elevation gradients in the area. The spatial and temporal dynamics of the regional Middle to Upper Palaeolithic (UP) ‘transition’ are not fully resolved. Further research is likely to reveal complexity in the timing and nature of the disappearance of the MP and appearance of the UP, with implications for the replacement of Neanderthals by Homo sapiens in the region.
... Besides microbial degradation, the protein concentrations decrease with weathering and fossilization (Rapp Py-Daniel 2014). Therefore, the oldest bones suitable for stable isotope ratios of collagen are often found in cool environments where there was a relatively rapid burial, such as in the Denisova Cave in the Siberian Altai, where the oldest hominin collagen containing bone has been estimated to date to 195,000 years ago (Douka et al. 2019). For bones, collagen yields (more than 1%) and quality indices such as atomic carbon to nitrogen ratios (2.9-3.5) and percentage nitrogen content (more than 0.5%) are the most important preservation criteria (Ambrose 1990, Brock et al. 2012). ...
Full-text available
Stable isotope analysis of teeth and bones is regularly applied by archeologists and paleoanthropologists seeking to reconstruct diets, ecologies, and environments of past hominin populations. Moving beyond the now prevalent study of stable isotope ratios from bulk materials, researchers are increasingly turning to stable isotope ratios of individual amino acids to obtain more detailed and robust insights into trophic level and resource use. In the present article, we provide a guide on how to best use amino acid stable isotope ratios to determine hominin dietary behaviors and ecologies, past and present. We highlight existing uncertainties of interpretation and the methodological developments required to ensure good practice. In doing so, we hope to make this promising approach more broadly accessible to researchers at a variety of career stages and from a variety of methodological and academic backgrounds who seek to delve into new depths in the study of dietary composition.
... Denisovans are a group of archaic Homo, most closely related to Neanderthals but known only from a few scattered fossils and a range of genetic data collected from the fossils, cave sediments and modern day human populations (Reich et al., 2010(Reich et al., , 2011Slon et al., 2017aSlon et al., ,b, 2018Douka et al., 2019). Denisovans may have been widespread across Asia, potentially forming distinct populations with little inter-group contact (Pääbo, 2014(Pääbo, , 2015Kuhlwilm et al., 2016). ...
Full-text available
The Pleistocene archaeological record of mainland Southeast Asia (MSEA) is difficult to interpret, due to a sparsity of dated sites and a lithic record that is ill-suited to typological analysis. These challenges are compounded by the poorly constrained effects of tropical environments upon the deposition, preservation and degradation of archaeological cave sediments. These uncertainties restrict the interpretative potential of archaeological investigations, but the development of a rigorous, geoarchaeological framework of interpretation that is tailored to tropical cave sites offers an opportunity to improve research outcomes in MSEA and in tropical zones worldwide. Con Moong Cave (henceforth CMC), a Pleistocene archaeological site in North Vietnam, provided a small-scale example with which to explore the effects of tropical conditions upon archaeological site formation processes, and the potential of micro-geoarchaeological methods to overcome the difficulties of site interpretation in tropical zones. Research at CMC produced a depositional history for the site that revealed a correlation between sedimentation, the intensity of human occupation and changes in regional precipitation, as recognised in speleothem records in the published literature. Mineral suites from CMC’s guano deposits did not conform to established models of guano-driven diagenetic change and suggested that fluctuating hydrological conditions had led to diachronous episodes of mineral authigenesis. A shortage of reference data relevant to these processes meant it was not possible to conclusively relate these results to sedimentary palaeoenvironments or to understand their effects on assemblage taphonomy. Geo-ethnoarchaeological experiments were conducted to generate such a dataset, to enable hypothesis testing of the models of environmental changes at CMC and provide an assessment of the effects of tropical climates on sediment diagenesis.
... Свидетельства наличия усложненного метательного оружия, связанного с распространением современного человека в северной Евразии, поступают из Леванта и южной Европы (например, Shea, Sisk 2010;Sano et al. 2019;Yaroshevich, Kaufman, Marks 2021), и включают диагностические следы метательного излома пера, морфометрические признаки наконечников и особенности, связанные с насадом их на древки. Самое раннее указание на утепленную одежду (иглы с ушками) сейчас связано с появлением современного человека в Алтайском регионе на юге Сибири (Деревянко, Шуньков, Маркин 2014; Douka et al. 2019). Об использовании силков или ловушек можно судить по скоплениям заячьих останков древнее 40 тыс. ...
Full-text available
The East European Plain (EEP), which is the dominant landform on the continent of Europe, exhibits many parallels to the High Plains of North America with respect to landscape and biota. These parallels are reflected in the early prehistoric archaeological record of both regions and a “North American Plains (NAP) perspective” is applied here to the early Upper Paleolithic (EUP) between ~45 000 and ~30 000 cal BP of the EEP. As among First Peoples on the NAP, EUP groups on the EEP used the distribution of springs and the topography of an arid, open landscape to hunt large mammals individually and in small herds (especially horse and reindeer). Many sites contain features (e. g., carcass processing areas) analogous to those in archaeological sites on the NAP. EUP culture-stratigraphy for the EEP is reinterpreted from a “NAP perspective.”
... Sequencing results for such fossils allow us to analyze them at the genome level. The Neandertals were recognized as a distinct group of hominids with numerous fossils as well as stone tool assemblages (Krings et al., 1997;Heyes et al., 2016;Douka et al., 2019). Nevertheless, few fossils of the Denisovans, another distinct member of the Homo genus, have been found. ...
Full-text available
A comprehensive description of human genomes is essential for understanding human evolution and relationships between modern populations. However, most published literature focuses on local alignment comparison of several genes rather than the complete evolutionary record of individual genomes. Combining with data from the 1,000 Genomes Project, we successfully reconstructed 2,504 individual genomes and propose Divided Natural Vector method to analyze the distribution of nucleotides in the genomes. Comparisons based on autosomes, sex chromosomes and mitochondrial genomes reveal the genetic relationships between populations, and different inheritance pattern leads to different phylogenetic results. Results based on mitochondrial genomes confirm the "out-of-Africa" hypothesis and assert that humans, at least females, most likely originated in eastern Africa. The reconstructed genomes are stored on our server and can be further used for any genome-scale analysis of humans ( This project provides the complete genomes of thousands of individuals and lays the groundwork for genome-level analyses of the genetic relationships between populations and the origin of humans.
Résumé La concentration de sites aurignaciens dans la chaine montagneuse du Zagros (Iran, Iraq) implique deux conséquences importantes dans l’histoire ancienne du continent eurasiatique. D’une part, ce noyau central va diffuser (vers le Proche-Orient, l’Anatolie, le Caucase et la Crimée) les nouveaux modes de vie et la population moderne. D’autre part, cette situation géographique correspond à l’aire méridionale de la grande plaine asiatique, étendue depuis les Monts Altaï et centrée sur la Bactriane. Dans cette aire immense et giboyeuse, de perpétuelles innovations apparaissent tant dans les domaines comportementaux qu’anatomiques. Le Zagros est ainsi à la fois la frontière et le réservoir de l’humanité moderne, issue des expériences asiatiques centrales, celles qui vont se diffuser largement et finiront par se substituer au Paléolithique moyen européen.
Full-text available
An innovative protocol for the consolidation of ancient bone remains based on the use of nanometric HydroxyAPatite (HAP) was set up and tested through a multidisciplinary approach. A new protocol for the synthesis of HAP nanoparticles was developed, and the composition of the obtained nanomaterial was investigated through Fourier Transform Infrared Spectroscopy (FTIR) and X-Ray Diffraction (XRD); sizes, shape and morphology of the synthesized particles were studied by Scanning Electron Microscopy (SEM). The consolidation performance was evaluated by testing the new nanomaterial on degraded ancient bone findings. An increase of the mineral density and of the micro-hardness of the bone were observed. The new consolidation method was also tested to assess possible effects on the palaeogenetic analysis and radiocarbon dating on the treated bones. The consolidation treatment does not introduce any contaminations that could affect radiocarbon dating and has no general detrimental impact on the genetic characterization of the skeletal remains. This consolidation procedure represents a more compatible conservation tool with respect to traditional procedures: it has been shown that the treatment is effective, easily-applicable and compatible with post-consolidation analysis.
Purpose. Needle cases belong to “passive” bone tools, which store thin bone tools such as eyed needles or awls. Being an essential element of the technology of sewing complex clothing, needle cases and needles act as a marker of technological innovations, the spread of which in the Upper Palaeolithic contributed to the active population of the territory of Northern Eurasia. This study's objectives were to analyse and systematise published and archived data on the Upper Palaeolithic needle cases of Siberia and generalise the available information on the problems of interpreting the considered category of sewing kits, their archaeological, technological, cultural and chronological contexts. Results. The study results clearly show that the finds of bone needle cases have been identified and analysed in the materials of a minimal number of archaeological sites with different chronologies and associated with several cultural generations of the Upper Palaeolithic. Bone needle cases of Siberian sites, separated by hundreds and thousands of kilometres, show noticeable similarities in size, morphology, production technology, and ornamentation methods. Conclusion. Appearing for the first time in the Early Upper Palaeolithic, they are rare in Siberian sites and do not always accompany even mass finds of needles.
The sequencing of modern and ancient genomes from around the world has revolutionized our understanding of human history and evolution. However, the problem of how best to characterize ancestral relationships from the totality of human genomic variation remains unsolved. Here, we address this challenge with nonparametric methods that enable us to infer a unified genealogy of modern and ancient humans. This compact representation of multiple datasets explores the challenges of missing and erroneous data and uses ancient samples to constrain and date relationships. We demonstrate the power of the method to recover relationships between individuals and populations as well as to identify descendants of ancient samples. Finally, we introduce a simple nonparametric estimator of the geographical location of ancestors that recapitulates key events in human history.
Full-text available
The Altai region of Siberia was inhabited for parts of the Pleistocene by at least two groups of archaic hominins—Denisovans and Neanderthals. Denisova Cave, uniquely, contains stratified deposits that preserve skeletal and genetic evidence of both hominins, artefacts made from stone and other materials, and a range of animal and plant remains. The previous site chronology is based largely on radiocarbon ages for fragments of bone and charcoal that are up to 50,000 years old; older ages of equivocal reliability have been estimated from thermoluminescence and palaeomagnetic analyses of sediments, and genetic analyses of hominin DNA. Here we describe the stratigraphic sequences in Denisova Cave, establish a chronology for the Pleistocene deposits and associated remains from optical dating of the cave sediments, and reconstruct the environmental context of hominin occupation of the site from around 300,000 to 20,000 years ago.
Full-text available
Neanderthals and Denisovans are extinct groups of hominins that separated from each other more than 390,000 years ago1,2. Here we present the genome of 'Denisova 11', a bone fragment from Denisova Cave (Russia)3 and show that it comes from an individual who had a Neanderthal mother and a Denisovan father. The father, whose genome bears traces of Neanderthal ancestry, came from a population related to a later Denisovan found in the cave4-6. The mother came from a population more closely related to Neanderthals who lived later in Europe2,7 than to an earlier Neanderthal found in Denisova Cave8, suggesting that migrations of Neanderthals between eastern and western Eurasia occurred sometime after 120,000 years ago. The finding of a first-generation Neanderthal-Denisovan offspring among the small number of archaic specimens sequenced to date suggests that mixing between Late Pleistocene hominin groups was common when they met.
Full-text available
The presence of Neandertals in Europe and Western Eurasia before the arrival of anatomically modern humans is well supported by archaeological and paleontological data. In contrast, fossil evidence for Denisovans, a sister group of Neandertals recently identified on the basis of DNA sequences, is limited to three specimens, all of which originate from Denisova Cave in the Altai Mountains (Siberia, Russia). We report the retrieval of DNA from a deciduous lower second molar (Denisova 2), discovered in a deep stratigraphic layer in Denisova Cave, and show that this tooth comes from a female Denisovan individual. On the basis of the number of “missing substitutions” in the mitochondrial DNA determined from the specimen, we find that Denisova 2 is substantially older than two of the other Denisovans, reinforcing the view that Denisovans were likely to have been present in the vicinity of Denisova Cave over an extended time period. We show that the level of nuclear DNA sequence diversity found among Denisovans is within the lower range of that of present-day human populations.
Full-text available
DNA library preparation for high-throughput sequencing of genomic DNA usually involves ligation of adapters to double-stranded DNA fragments. However, for highly degraded DNA, especially ancient DNA, library preparation has been found to be more efficient if each of the two DNA strands are converted into library molecules separately. We present a new method for single-stranded library preparation, ssDNA2.0, which is based on single-stranded DNA ligation with T4 DNA ligase utilizing a splinter oligonucleotide with a stretch of random bases hybridized to a 3' biotinylated donor oligonucleotide. A thorough evaluation of this ligation scheme shows that single-stranded DNA can be ligated to adapter oligonucleotides in higher concentration than with CircLigase (an RNA ligase that was previously chosen for end-to-end ligation in single-stranded library preparation) and that biases in ligation can be minimized when choosing splinters with 7 or 8 random nucleotides. We show that ssDNA2.0 tolerates higher quantities of input DNA than CircLigase-based library preparation, is less costly and better compatible with automation. We also provide an in-depth comparison of library preparation methods on degraded DNA from various sources. Most strikingly, we find that single-stranded library preparation increases library yields from tissues stored in formalin for many years by several orders of magnitude.
Full-text available
RNA editing is a widespread post-transcriptional mechanism that can make a single base change on specific nucleotide sequence in an RNA transcript. RNA editing events can result in missense codon changes and modulation of alternative splicing in mRNA, and modification of regulatory RNAs and their binding sites in noncoding RNAs. Recent computational studies accurately detected more than 2 million A-to-I RNA editing sites from next-generation sequencing (NGS). However, the vast majority of these RNA editing sites have unknown functions and are in noncoding regions of the genome. To provide a useful resource for the functional effects of RNA editing in long noncoding RNAs (lncRNAs), we systematically analyzed the A-to-I editing sites in lncRNAs across human, rhesus, mouse, and fly, and observed an appreciable number of RNA editing sites which can significantly impact the secondary structures of lncRNAs and lncRNA-miRNA interactions. All the data were compiled into LNCediting, a user-friendly database ( LNCediting provides customized tools to predict functional effects of novel editing sites in lncRNAs. We hope that it will become an important resource for exploring functions of RNA editing sites in lncRNAs.
Rationale: For radiocarbon results to be accurate, samples must be free of contaminating carbon. Sample pre-treatment using an HPLC approach has been developed at the Oxford Radiocarbon Accelerator Unit (ORAU) as an alternative to conventional methods for dating heavily contaminated bones. This approach isolates hydroxyproline from bone collagen, enabling a purified bone-specific fraction to then be radiocarbon dated by accelerator mass spectrometry (AMS). Methods: Using semi-preparative chromatography and non-carbon based eluents, this technique enables the separation of underivatised amino acids liberated by hydrolysis of extracted bone collagen. A particular focus has been the isolation of hydroxyproline for single compound AMS dating since this amino acid is one of the main contributors to the total amount of carbon in mammalian collagen. Our previous approach, involving a carbon-free aqueous mobile phase, required a 2-step separation using two different chromatographic columns. Results: This paper reports significant improvements that have been recently made to the method to enable faster semi-preparative separation of hydroxyproline from bone collagen, making the method more suitable for routine radiocarbon dating of contaminated and/or poorly preserved bone samples by AMS. All steps of the procedure, from the collagen extraction to the correction of the AMS data, are described. Conclusions: The modifications to the hardware and to the method itself have reduced significantly the time required for the preparation of each sample. This makes it easier for other radiocarbon facilities to implement and use this approach as a routine method for preparing contaminated bone samples.
To date the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50 thousand years ago from Vindija Cave, Croatia to ~30-fold genomic coverage. She carried 1.6 differences per ten thousand base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10-20% more Neandertal DNA to be identified in present-day humans, including variants involved in LDL cholesterol levels, schizophrenia and other diseases.
Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples we detect Neandertal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy. Our work opens the possibility to detect the presence of hominin groups at sites and in areas where no skeletal remains are found.
The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ∼10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert. © 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved
If radiocarbon measurements are to be used at all for chronological purposes, we have to use statistical methods for calibration. The most widely used method of calibration can be seen as a simple application of Bayesian statistics, which uses both the information from the new measurement and information from the 14 C calibration curve. In most dating applications, however, we have larger numbers of 14 C measurements and we wish to relate those to events in the past. Bayesian statistics provides a coherent framework in which such analysis can be performed and is becoming a core element in many 14 C dating projects. This article gives an overview of the main model components used in chronological analysis, their mathematical formulation, and examples of how such analyses can be performed using the latest version of the OxCal software (v4). Many such models can be put together, in a modular fashion, from simple elements, with defined constraints and groupings. In other cases, the commonly used “uniform phase” models might not be appropriate, and ramped, exponential, or normal distributions of events might be more useful. When considering analyses of these kinds, it is useful to be able run simulations on synthetic data. Methods for performing such tests are discussed here along with other methods of diagnosing possible problems with statistical models of this kind.