Before and after farming: The genetic structure of South China and Southeast Asia.

In this issue of Cell, Wang et al. harness ancient DNA methods to produce and analyze new genomic data from 31 individuals from South China, dated between 500 and 10,000-12,000 years ago. The study reveals a complex interplay between groups of three different genetic ancestries and provides a new perspective on interactions and agricultural dispersals in South China and Southeast Asia.

Ancient human DNA recovered from a Palaeolithic pendant.

Artefacts made from stones, bones and teeth are fundamental to our understanding of human subsistence strategies, behaviour and culture in the Pleistocene. Although these resources are plentiful, it is impossible to associate artefacts to specific human individuals1 who can be morphologically or genetically characterized, unless they are found within burials, which are rare in this time period. Thus, our ability to discern the societal roles of Pleistocene individuals based on their biological sex or genetic ancestry is limited2-5. Here we report the development of a non-destructive method for the gradual release of DNA trapped in ancient bone and tooth artefacts. Application of the method to an Upper Palaeolithic deer tooth pendant from Denisova Cave, Russia, resulted in the recovery of ancient human and deer mitochondrial genomes, which allowed us to estimate the age of the pendant at approximately 19,000-25,000 years. Nuclear DNA analysis identifies the presumed maker or wearer of the pendant as a female individual with strong genetic affinities to a group of Ancient North Eurasian individuals who lived around the same time but were previously found only further east in Siberia. Our work redefines how cultural and genetic records can be linked in prehistoric archaeology.

Innovative ochre processing and tool use in China 40,000 years ago.

Homo sapiens was present in northern Asia by around 40,000 years ago, having replaced archaic populations across Eurasia after episodes of earlier population expansions and interbreeding1-4. Cultural adaptations of the last Neanderthals, the Denisovans and the incoming populations of H. sapiens into Asia remain unknown1,5-7. Here we describe Xiamabei, a well-preserved, approximately 40,000-year-old archaeological site in northern China, which includes the earliest known ochre-processing feature in east Asia, a distinctive miniaturized lithic assemblage with bladelet-like tools bearing traces of hafting, and a bone tool. The cultural assembly of traits at Xiamabei is unique for Eastern Asia and does not correspond with those found at other archaeological site assemblages inhabited by archaic populations or those generally associated with the expansion of H. sapiens, such as the Initial Upper Palaeolithic8-10. The record of northern Asia supports a process of technological innovations and cultural diversification emerging in a period of hominin hybridization and admixture2,3,6,11.

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.

Earliest known human burial in Africa.

The origin and evolution of hominin mortuary practices are topics of intense interest and debate1-3. Human burials dated to the Middle Stone Age (MSA) are exceedingly rare in Africa and unknown in East Africa1-6. Here we describe the partial skeleton of a roughly 2.5- to 3.0-year-old child dating to 78.3 ± 4.1 thousand years ago, which was recovered in the MSA layers of Panga ya Saidi (PYS), a cave site in the tropical upland coast of Kenya7,8. Recent excavations have revealed a pit feature containing a child in a flexed position. Geochemical, granulometric and micromorphological analyses of the burial pit content and encasing archaeological layers indicate that the pit was deliberately excavated. Taphonomical evidence, such as the strict articulation or good anatomical association of the skeletal elements and histological evidence of putrefaction, support the in-place decomposition of the fresh body. The presence of little or no displacement of the unstable joints during decomposition points to an interment in a filled space (grave earth), making the PYS finding the oldest known human burial in Africa. The morphological assessment of the partial skeleton is consistent with its assignment to Homo sapiens, although the preservation of some primitive features in the dentition supports increasing evidence for non-gradual assembly of modern traits during the emergence of our species. The PYS burial sheds light on how MSA populations interacted with the dead.

SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS.

MOTIVATION: Zooarchaeology by Mass Spectrometry (ZooMS) is a palaeoproteomics method for the taxonomic determination of collagen, which traditionally involves challenging manual spectra analysis with limitations in quantitative results. As the ZooMS reference database expands, a faster and reproducible identification tool is necessary. Here we present SpecieScan, an open-access algorithm for automating taxa identification from raw MALDI-ToF mass spectrometry (MS) data. RESULTS: SpecieScan was developed using R (pre-processing) and Python (automation). The algorithm's output includes identified peptide markers, closest matching taxonomic group (taxon, family, order), correlation scores with the reference databases, and contaminant peaks present in the spectra. Testing on original MS data from bones discovered at Palaeothic archaeological sites, including Denisova Cave in Russia, as well as using publicly-available, externally produced data, we achieved >90% accuracy at the genus-level and ∼92% accuracy at the family-level for mammalian bone collagen previously analysed manually. AVAILABILITY AND IMPLEMENTATION: The SpecieScan algorithm, along with the raw data used in testing, results, reference database, and common contaminants lists are freely available on Github (https://github.com/mesve/SpecieScan).

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

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 populations3. 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 AD 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.

The genome of the offspring of a Neanderthal mother and a Denisovan father.

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.

Large-scale application of palaeoproteomics (Zooarchaeology by Mass Spectrometry; ZooMS) in two Palaeolithic faunal assemblages from China.

The application of Zooarchaeology by Mass Spectrometry (ZooMS) on Pleistocene sites in Europe and northern Asia has resulted in the discovery of important new hominin fossils and has expanded the range of identified fauna. However, no systematic, large-scale application of ZooMS on Palaeolithic sites in East Asia has been attempted thus far. Here, we analyse 866 morphologically non-diagnostic bones from Jinsitai Cave in northeast China and Yumidong Cave in South China, from archaeological horizons dating to 150-10 ka BP. Bones from both sites revealed a high degree of collagen preservation and potentially time-related deamidation patterns, despite being located in very distinct environmental settings. At Jinsitai, we identified 31 camel bones, five of which were radiocarbon dated to 37-20 ka BP. All dated specimens correspond to colder periods of Marine Isotope Stages 3 and 2. We regard the presence of camels at Jinsitai as evidence of wild camels being a megafauna taxon targeted, most likely by early modern humans, during their expansion across northeast Asia. This large-scale application of ZooMS in China highlights the potential of the method for furthering our knowledge of the palaeoanthropological and zooarchaeological records of East Asia.

Cytoplasmic long noncoding RNAs are differentially regulated and translated during human neuronal differentiation.

The expression of long noncoding RNAs is highly enriched in the human nervous system. However, the function of neuronal lncRNAs in the cytoplasm and their potential translation remains poorly understood. Here we performed Poly-Ribo-Seq to understand the interaction of lncRNAs with the translation machinery and the functional consequences during neuronal differentiation of human SH-SY5Y cells. We discovered 237 cytoplasmic lncRNAs up-regulated during early neuronal differentiation, 58%-70% of which are associated with polysome translation complexes. Among these polysome-associated lncRNAs, we find 45 small ORFs to be actively translated, 17 specifically upon differentiation. Fifteen of 45 of the translated lncRNA-smORFs exhibit sequence conservation within Hominidea, suggesting they are under strong selective constraint in this clade. The profiling of publicly available data sets revealed that 8/45 of the translated lncRNAs are dynamically expressed during human brain development, and 22/45 are associated with cancers of the central nervous system. One translated lncRNA we discovered is LINC01116, which is induced upon differentiation and contains an 87 codon smORF exhibiting increased ribosome profiling signal upon differentiation. The resulting LINC01116 peptide localizes to neurites. Knockdown of LINC01116 results in a significant reduction of neurite length in differentiated cells, indicating it contributes to neuronal differentiation. Our findings indicate cytoplasmic lncRNAs interact with translation complexes, are a noncanonical source of novel peptides, and contribute to neuronal function and disease. Specifically, we demonstrate a novel functional role for LINC01116 during human neuronal differentiation.

The Initial Upper Paleolithic of the Altai: New radiocarbon determinations for the Kara-Bom site.

The Initial Upper Paleolithic (IUP) is one of the most important phases in the recent period of the evolution of humans. During a narrow period in the first half of Marine Isotope Stage 3 laminar industries, accompanied by developed symbolism and specific blade technology, emerged over a vast area, replacing different variants of the Middle Paleolithic. In western Eurasia, the earliest appearance of IUP technology is seen at the Boker Tachtit site, dated ca. 50 ka cal BP. The earliest evidence of IUP industries in the Balkans and Central Europe, linked to the spread of Homo sapiens, has been dated to around 48 ka cal BP. A key area of IUP dispersals are the mountains and piedmont of southern Siberia and eastern Central Asia. One of the reference assemblages here is Kara-Bom, an open-air site in the Siberian Altai. Three major settlement phases are distinguished in the sediment sequence. In this paper, we present the results of new radiocarbon determinations and Bayesian models. We find that the latest phase of the IUP, Upper Paleolithic 1 ('UP1') is bracketed between 43 and 35 ka cal BP (at 95.4% probability). The earliest IUP phase, 'UP2', begins to accumulate from ca. 49 ka cal BP and ends by ca. 45 ka cal BP. The Middle Paleolithic 'MP2' assemblages all fall prior to 50 ka cal BP. We can detect a spatial distribution of dates from the geographic core of the IUP beyond the Altai where it appears around 47-45 ka cal BP. The current distribution of dates suggests a west-east dispersal of the IUP technocomplex along the mountain belts of Central Asia and South Siberia.

A refined chronology for the Middle and early Upper Paleolithic sequence of Riparo Mochi (Liguria, Italy).

The Riparo Mochi rock shelter, located on the Ligurian coast of Italy, is one of the most important early Upper Paleolithic sites on the Mediterranean rim. Its ∼10-m-deep stratigraphy comprises a Mousterian sequence, followed by various development stages of the Upper Paleolithic. A series of radiometric dates on marine shells bearing traces of human modification has provided a chronological framework for the final Mousterian and the Proto-Aurignacian of the site. Based on modeling results, the end of the Mousterian was dated between 44.0 and 41.8 ka cal BP (68% probability) and the beginning of the Proto-Aurignacian between 42.7 and 41.6 ka cal BP (68% probability). However, these estimates were based on a limited number of radiocarbon ages in the Mousterian levels. Here, we report new dating of the Mochi sequence using luminescence techniques, along with new radiocarbon measurements. The combination of these results using a Bayesian modeling approach allows for the first time the establishment of a more precise timing for the Mousterian occupation at the site. We show that Mousterian groups were already present at Riparo Mochi by at least 65 ka and continued to occupy the site for another 20 ka. The transition to the earliest Upper Paleolithic at the site is centered around 44.3-41.1 ka (95.4% probability), providing our best age estimate for the beginning of the Early Upper Paleolithic and the establishment of modern human groups in the Balzi Rossi. The sequence continues upward with a more evolved Aurignacian phase and a Gravettian phase starting at ∼26 ka or earlier.

Long non-coding RNAs in development and disease: conservation to mechanisms.

Our genomes contain the blueprint of what makes us human and many indications as to why we develop disease. Until the last 10 years, most studies had focussed on protein-coding genes, more specifically DNA sequences coding for proteins. However, this represents less than 5% of our genomes. The other 95% is referred to as the 'dark matter' of our genomes, our understanding of which is extremely limited. Part of this 'dark matter' includes regions that give rise to RNAs that do not code for proteins. A subset of these non-coding RNAs are long non-coding RNAs (lncRNAs), which in particular are beginning to be dissected and their importance to human health revealed. To improve our understanding and treatment of disease it is vital that we understand the molecular and cellular function of lncRNAs, and how their misregulation can contribute to disease. It is not yet clear what proportion of lncRNAs is actually functional; conservation during evolution is being used to understand the biological importance of lncRNA. Here, we present key themes within the field of lncRNAs, emphasising the importance of their roles in both the nucleus and the cytoplasm of cells, as well as patterns in their modes of action. We discuss their potential functions in development and disease using examples where we have the greatest understanding. Finally, we emphasise why lncRNAs can serve as biomarkers and discuss their emerging potential for therapy. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

A refined chronology for the Gravettian sequence of Abri Pataud.

Abri Pataud (France) is the type site in studies focusing on the appearance of modern humans and the development of classic Upper Paleolithic technocomplexes in Europe. It contains important evidence of successful adaptation strategies of modern humans to new territories and in response to sharply changing climatic conditions that characterized Marine Isotope Stages 3 and 2. Despite being for decades one of the best excavated and most studied Paleolithic sites, the chronology of Abri Pataud has lacked precision and revealed large discrepancies. The chronology of the lowermost part of the sequence (Levels 14-5) was refined in 2011 with the publication of 32 new radiocarbon determinations, mainly from the Aurignacian levels. In contrast, the Gravettian levels (Levels 5-2) remained poorly dated until now. Here, we present 18 new radiocarbon dates on cut-marked animal bones from the Gravettian part of the site, which complete the dating of this important sequence. The determinations are analyzed using Bayesian statistical modeling, and the results allow us to place the start of the Gravettian at the site between ∼33,000 and 32,000 cal BP (∼29,000-28,000 BP). We discuss the succession of the Gravettian facies across the sequence (Bayacian, Noaillian, Rayssian), as well as the likely duration of each archaeological level. With a total of more than 50 radiocarbon determinations, Abri Pataud offers secure information for the appearance and development of the technocomplexes linked with early modern humans and their establishment in western Europe. Based on published genetic data, it appears that it is the Gravettian hunter-gatherers and subsequent human groups, rather than the earlier Aurignacian and pre-Aurignacian groups, that contributed to the genetic signature of later and living Europeans. Hence, elucidating the precise timing of the Gravettian appearance has broad implications in our understanding of late human evolution across Europe.

Genome sequence of a 45,000-year-old modern human from western Siberia.

We present the high-quality genome sequence of a ∼45,000-year-old modern human male from Siberia. This individual derives from a population that lived before-or simultaneously with-the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000-13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10(-9) to 0.6 × 10(-9) per site per year, a Y chromosomal mutation rate of 0.7 × 10(-9) to 0.9 × 10(-9) per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10(-8) to 3.2 × 10(-8) per site per year based on the age of the bone.

The timing and spatiotemporal patterning of Neanderthal disappearance.

The timing of Neanderthal disappearance and the extent to which they overlapped with the earliest incoming anatomically modern humans (AMHs) in Eurasia are key questions in palaeoanthropology. Determining the spatiotemporal relationship between the two populations is crucial if we are to understand the processes, timing and reasons leading to the disappearance of Neanderthals and the likelihood of cultural and genetic exchange. Serious technical challenges, however, have hindered reliable dating of the period, as the radiocarbon method reaches its limit at ∼50,000 years ago. Here we apply improved accelerator mass spectrometry (14)C techniques to construct robust chronologies from 40 key Mousterian and Neanderthal archaeological sites, ranging from Russia to Spain. Bayesian age modelling was used to generate probability distribution functions to determine the latest appearance date. We show that the Mousterian ended by 41,030-39,260 calibrated years bp (at 95.4% probability) across Europe. We also demonstrate that succeeding 'transitional' archaeological industries, one of which has been linked with Neanderthals (Châtelperronian), end at a similar time. Our data indicate that the disappearance of Neanderthals occurred at different times in different regions. Comparing the data with results obtained from the earliest dated AMH sites in Europe, associated with the Uluzzian technocomplex, allows us to quantify the temporal overlap between the two human groups. The results reveal a significant overlap of 2,600-5,400 years (at 95.4% probability). This has important implications for models seeking to explain the cultural, technological and biological elements involved in the replacement of Neanderthals by AMHs. A mosaic of populations in Europe during the Middle to Upper Palaeolithic transition suggests that there was ample time for the transmission of cultural and symbolic behaviours, as well as possible genetic exchanges, between the two groups.

Ancient crops provide first archaeological signature of the westward Austronesian expansion.

The Austronesian settlement of the remote island of Madagascar remains one of the great puzzles of Indo-Pacific prehistory. Although linguistic, ethnographic, and genetic evidence points clearly to a colonization of Madagascar by Austronesian language-speaking people from Island Southeast Asia, decades of archaeological research have failed to locate evidence for a Southeast Asian signature in the island's early material record. Here, we present new archaeobotanical data that show that Southeast Asian settlers brought Asian crops with them when they settled in Africa. These crops provide the first, to our knowledge, reliable archaeological window into the Southeast Asian colonization of Madagascar. They additionally suggest that initial Southeast Asian settlement in Africa was not limited to Madagascar, but also extended to the Comoros. Archaeobotanical data may support a model of indirect Austronesian colonization of Madagascar from the Comoros and/or elsewhere in eastern Africa.

Direct radiocarbon dating and DNA analysis of the Darra-i-Kur (Afghanistan) human temporal bone.

The temporal bone discovered in the 1960s from the Darra-i-Kur cave in Afghanistan is often cited as one of the very few Pleistocene human fossils from Central Asia. Here we report the first direct radiocarbon date for the specimen and the genetic analyses of DNA extracted and sequenced from two areas of the bone. The new radiocarbon determination places the find to ∼4500 cal BP (∼2500 BCE) contradicting an assumed Palaeolithic age of ∼30,000 years, as originally suggested. The DNA retrieved from the specimen originates from a male individual who carried mitochondrial DNA of the modern human type. The petrous part yielded more endogenous ancient DNA molecules than the squamous part of the same bone. Molecular dating of the Darra-i-Kur mitochondrial DNA sequence corroborates the radiocarbon date and suggests that the specimen is younger than previously thought. Taken together, the results consolidate the fact that the human bone is not associated with the Pleistocene-age deposits of Darra-i-Kur; instead it is intrusive, possibly re-deposited from upper levels dating to much later periods (Neolithic). Despite its Holocene age, the Darra-i-Kur specimen is, so far, the first and only ancient human from Afghanistan whose DNA has been sequenced.

Chronometric investigations of the Middle to Upper Paleolithic transition in the Zagros Mountains using AMS radiocarbon dating and Bayesian age modelling.

The Middle to Upper Paleolithic transition is often linked with a bio-cultural shift involving the dispersal of modern humans outside of Africa, the concomitant replacement of Neanderthals across Eurasia, and the emergence of new technological traditions. The Zagros Mountains region assumes importance in discussions concerning this period as its geographic location is central to all pertinent hominin migration areas, pointing to both east and west. As such, establishing a reliable chronology in the Zagros Mountains is crucial to our understanding of these biological and cultural developments. Political circumstance, coupled with the poor preservation of organic material, has meant that a clear chronological definition of the Middle to Upper Paleolithic transition for the Zagros Mountains region has not yet been achieved. To improve this situation, we have obtained new archaeological samples for AMS radiocarbon dating from three sites: Kobeh Cave, Kaldar Cave, and Ghar-e Boof (Iran). In addition, we have statistically modelled previously published radiocarbon determinations for Yafteh Cave (Iran) and Shanidar Cave (Iraqi Kurdistan), to improve their chronological resolution and enable us to compare the results with the new dataset. Bayesian modelling results suggest that the onset of the Upper Paleolithic in the Zagros Mountains dates to 45,000-40,250 cal BP (68.2% probability). Further chronometric data are required to improve the precision of this age range.

Early dispersal of modern humans in Europe and implications for Neanderthal behaviour.

The appearance of anatomically modern humans in Europe and the nature of the transition from the Middle to Upper Palaeolithic are matters of intense debate. Most researchers accept that before the arrival of anatomically modern humans, Neanderthals had adopted several 'transitional' technocomplexes. Two of these, the Uluzzian of southern Europe and the Châtelperronian of western Europe, are key to current interpretations regarding the timing of arrival of anatomically modern humans in the region and their potential interaction with Neanderthal populations. They are also central to current debates regarding the cognitive abilities of Neanderthals and the reasons behind their extinction. However, the actual fossil evidence associated with these assemblages is scant and fragmentary, and recent work has questioned the attribution of the Châtelperronian to Neanderthals on the basis of taphonomic mixing and lithic analysis. Here we reanalyse the deciduous molars from the Grotta del Cavallo (southern Italy), associated with the Uluzzian and originally classified as Neanderthal. Using two independent morphometric methods based on microtomographic data, we show that the Cavallo specimens can be attributed to anatomically modern humans. The secure context of the teeth provides crucial evidence that the makers of the Uluzzian technocomplex were therefore not Neanderthals. In addition, new chronometric data for the Uluzzian layers of Grotta del Cavallo obtained from associated shell beads and included within a Bayesian age model show that the teeth must date to ~45,000-43,000 calendar years before present. The Cavallo human remains are therefore the oldest known European anatomically modern humans, confirming a rapid dispersal of modern humans across the continent before the Aurignacian and the disappearance of Neanderthals.