Neanderthal Extinction Research Articles

Reconstructing Prehistoric Viral Genomes from Neanderthal Sequencing Data.

DNA viruses that produce persistent infections have been proposed as potential causes for the extinction of Neanderthals, and, therefore, the identification of viral genome remnants in Neanderthal sequence reads is an initial step to address this hypothesis. Here, as proof of concept, we searched for viral remnants in sequence reads of Neanderthal genome data by mapping to adenovirus, herpesvirus and papillomavirus, which are double-stranded DNA viruses that may establish lifelong latency and can produce persistent infections. The reconstructed ancient viral genomes of adenovirus, herpesvirus and papillomavirus revealed conserved segments, with nucleotide identity to extant viral genomes and variable regions in coding regions with substantial divergence to extant close relatives. Sequence reads mapped to extant viral genomes showed deamination patterns of ancient DNA, and these ancient viral genomes showed divergence consistent with the age of these samples (≈50,000 years) and viral evolutionary rates (10-5 to 10-8 substitutions/site/year). Analysis of random effects showed that the Neanderthal mapping to genomes of extant persistent viruses is above what is expected by random similarities of short reads. Also, negative control with a nonpersistent DNA virus does not yield statistically significant assemblies. This work demonstrates the feasibility of identifying viral genome remnants in archaeological samples with signal-to-noise assessment.

Homo sapiens reached the higher latitudes of Europe by 45,000 years ago

The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H. sapiens in eastern Europe1. Local hybridization between the two groups occurred2, but not on all occasions3. Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups4. One such technocomplex for which the makers are unknown is the Lincombian–Ranisian–Jerzmanowician (LRJ), which has been described in northwestern and central Europe5–8. Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H. sapiens remains in Eurasia. We show that early H. sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period.

Past human expansions shaped the spatial pattern of Neanderthal ancestry.

The worldwide expansion of modern humans (Homo sapiens) started before the extinction of Neanderthals (Homo neanderthalensis). Both species coexisted and interbred, leading to slightly higher introgression in East Asians than in Europeans. This distinct ancestry level has been argued to result from selection, but range expansions of modern humans could provide an alternative explanation. This hypothesis would lead to spatial introgression gradients, increasing with distance from the expansion source. We investigate the presence of Neanderthal introgression gradients after past human expansions by analyzing Eurasian paleogenomes. We show that the out-of-Africa expansion resulted in spatial gradients of Neanderthal ancestry that persisted through time. While keeping the same gradient orientation, the expansion of early Neolithic farmers contributed decisively to reducing the Neanderthal introgression in European populations compared to Asian populations. This is because Neolithic farmers carried less Neanderthal DNA than preceding Paleolithic hunter-gatherers. This study shows that inferences about past human population dynamics can be made from the spatiotemporal variation in archaic introgression.

Experience the precision of time: radiocarbon 3.0

Experience the precision of time: radiocarbon 3.0 RESOLUTION aims to achieve an accurate and highly resolved chronology back to 55 000 years BP (Before Present), using some new floating sections of fossil trees. In fact, with tree rings, the resolution will be an order of magnitude higher, and using the most recent advances in the AMS technique, we will obtain confidence intervals of only a few centuries in glacial times. In this way, we can establish in a precise way the timing of when Homo sapiens arrived in Europe, their interaction with Neanderthals and the final cause of the Neanderthal extinction. The project involves fieldwork in the Mediterranean and Southeast Europe to find more glacial trees, study the exist-ing collection of glacial conifers, exceptional 14C precision for 14C dates in the glacial, and the cutting-edge methodolo-gy linking floating tree-ring chronologies to 10Be on the ice core scale.

Demographic explanations of neanderthal extinction: a reply to Currie and Meneganzin

In a recent paper, Currie and Meneganzin (Biol Phil, 2022, 37, 50) critically engage with a recent demographic explanation of the demise of Neanderthals (Vaesen et al. 2019). Currie and Meneganzin suggest that, contrary to how it is (supposedly) presented, Vaesen et al.’s explanation is not (and in fact, could never be) ‘stand-alone’, i.e., competition and environmental factors always interfere with demographic ones. Here I argue that Currie and Meneganzin misconstrue what the study in question does and does not purport to show. I conclude that, in the relevant sense, the explanation Vaesen et al. provide is a standalone demographic one.

Natural selection and Neanderthal extinction in a Malthusian economy

Why are Homo sapiens the only human species living on this planet? Homo sapiens have lived on this planet for about 300,000 years. During most of their existence, early modern humans shared this planet with other archaic humans, such as Neanderthals and Denisovans. Why did the other archaic humans become extinct? To explore this question, this study develops a Malthusian model with natural selection of human species to explore how population dynamics of one group of humans may cause the extinction of another group. In my model, different groups of humans engage in hunting-gathering. The larger group of humans can occupy more land. Therefore, the expansion of one population causes the other population to shrink in a Malthusian economy. Which human population shrinks or even becomes extinct depends on structural parameters in the Malthusian model.

Did variants in inborn errors of immunity genes contribute to the extinction of Neanderthals?

Neanderthals were a species of archaic humans that became extinct around 40,000 years ago. Modern humans have inherited 1-6% of Neanderthal DNA as a result of interbreeding. These inherited Neanderthal genes have paradoxical influences, while some can provide protection to viral infections, some others are associated with autoimmune/auto-inflammatory diseases. We aim to investigate whether genetic variants with strong detrimental effects on the function of the immune system could have potentially contributed to the extinction of the Neanderthal population. We used the publically available genome information from an Altai Neanderthal and filtered for potentially damaging variants present in genes associated with inborn errors of immunity (IEI) and checked whether these variants were present in the genomes of the Denisovan, Vindija and Chagyrskaya Neanderthals. We identified 24 homozygous variants and 15 heterozygous variants in IEI-related genes in the Altai Neanderthal. Two homozygous variants in the UNC13D gene and one variant in the MOGS gene were present in all archaic genomes. Defects in the UNC13D gene are known to cause a severe and often fatal disease called hemophagocytic lymphohistiocystosis (HLH). One of these variants p.(N943S) has been reported in patients with HLH. Variants in MOGS are associated with glycosylation defects in the immune system affecting the susceptibility for infections. Although the exact functional impact of these three variants needs further elucidation, we speculate that they could have resulted in an increased susceptibility to severe diseases and may have contributed to the extinction of Neanderthals after exposure to specific infections.

Not by demography alone: Neanderthal extinction and null hypotheses in paleoanthropological explanation

Neanderthal extinction is a matter of intense debate. It has been suggested that demography (as opposed to environment or competition) could alone provide a sufficient explanation for the phenomenon. We argue that demography cannot be a ‘stand-alone’ or ‘alternative’ explanation of token extinctions as demographic features are entangled with competitive and environmental factors, and further because demography should not be conflated with neutrality.

An individual-based network model explains Neanderthal extinction through competitive exclusion

This paper presents an alternative social/economic explanation for the Neanderthals’ demise along similar lines with the competitive exclusion principle. We represent individuals as network nodes such that each link corresponds to an acquaintanceship between the respective nodes. We rely on the findings that Sapiens were more socially developed compared to Neanderthals. Running individual-based simulations under the assumption that Sapiens initially lived in larger and more connected groups, we illustrate how the two species’ social structures might have further evolved in opposite directions and how such an evolution might have favored Sapiens in their competition against Neanderthals.

Regional heterogeneity of environmental stressors for the Early, Middle and Late Palaeolithic European human populations related to the evolutionary lineage of Neanderthals

Pleistocene climatic fluctuations could play an important role in the development of the human phylogenetic line of Neanderthals. The aim of this study was to model how the climate-based physiological, cognitive, and vector-borne disease risk stressors for humans could vary in Europe by area and time from the Lower Palaeolithic era to the extinction of Neanderthals. For this purpose, the climatic requirements of the ancient humans were reconstructed based on the Early, Middle and Upper Palaeolithic occurrences of humans in Europe and its wider geographical environment for 8 Palaeolithic times and further six health and cold adaptation-related factors were also modelled. The adaptation of European human populations to the cool and volatile Pleistocene climate of Europe could gradually happen. While the Middle Palaeolithic humans in Europe lived in areas with long and medium-long vegetation periods and low or middle January mortality risk, in the late Palaeolithic the Neanderthal populations may have settled in areas with short ones. In January, these northern regions in the Late Palaeolithic era could be characterized by relatively high mortality risk. While the ancient humans of the Middle Palaeolithic era lived in such regions where the length of the thermal comfort season could be relatively long, the late Pleistocene humans of Europe occupied such regions where the thermal comfort season could be very short, and these humans should cover a large part of their body surface. However, the model results suggest that both humans of the Middle and Late Palaeolithic era should wear clothes in the coldest period of the winter in Europe. The Upper Palaeolithic populations could be less affected by such tick-borne diseases as Lyme borreliosis than the Early or the Middle Palaeolithic populations.

The upgrade in human evolution? It’s a matter of TIME!

The upgrade in human evolution? It’s a matter of TIME! RESOLUTION aims to achieve an accurate and highly resolved chronology back to 55,000 years BP (Before Present), to establish the timing of when Homo sapiens arrived in Europe, their interaction with Neanderthals and the final cause of Neanderthal extinction.

The discovery of an in situ Neanderthal remain in the Bawa Yawan Rockshelter, West-Central Zagros Mountains, Kermanshah.

Neanderthal extinction has been a matter of debate for many years. New discoveries, better chronologies and genomic evidence have done much to clarify some of the issues. This evidence suggests that Neanderthals became extinct around 40,000-37,000 years before present (BP), after a period of coexistence with Homo sapiens of several millennia, involving biological and cultural interactions between the two groups. However, the bulk of this evidence relates to Western Eurasia, and recent work in Central Asia and Siberia has shown that there is considerable local variation. Southwestern Asia, despite having a number of significant Neanderthal remains, has not played a major part in the debate over extinction. Here we report a Neanderthal deciduous canine from the site of Bawa Yawan in the West-Central Zagros Mountains of Iran. The tooth is associated with Zagros Mousterian lithics, and its context is preliminary dated to between ~43,600 and ~41,500 years ago.

Back to Uluzzo – archaeological, palaeoenvironmental and chronological context of the Mid–Upper Palaeolithic sequence at Uluzzo C Rock Shelter (Apulia, southern Italy)

ABSTRACTThe tempo and mode of Homo sapiens dispersal in Eurasia and the demise of Neanderthals has sparked debate about the dynamics of Neanderthal extinction and its relationship to the arrival of H. sapiens. In Italy, the so‐called ‘Transition’ from Neanderthals to H. sapiens is related to the Uluzzian technocomplex, i.e. the first archaeological evidence for modern human dispersal on the European continent. This paper illustrates the new chronology and stratigraphy of Uluzzo C, a rock shelter and Uluzzian key site located in the Uluzzo Bay in southern Italy, where excavations are ongoing, refining the cultural sequence known from previous excavations. Microstratigraphic investigation suggests that most of the deposit formed after dismantling of the vault of the rock shelter and due to wind input of loess deflated by the continental shelf. The occasional reactivation of the hydrology of the local karst system under more humid conditions further contributed to the formation of specific layers accumulating former Terra Rossa‐type soil fragments. Superposed on sedimentary processes, strong bioturbation and the mobilization and recrystallization of calcite have been detected. Optically stimulated luminescence (OSL) ages from Uluzzo C Rock Shelter are congruent with previously published radiocarbon ages obtained on shell beads and tephrachronology from adjacent sites preserving the Uluzzian technocomplex such as Grotta del Cavallo, confirming the onset for the Uluzzian in the area to ca. 39.2–42.0 ka. The OSL chronology from Uluzzo C also provides a terminus post quem for the end of the Mousterian in the region, constraining the disappearance of the Neanderthals in that part of Italy to ≥46 ± 4 ka.

Complexity in the Middle to Upper Paleolithic Transition in Peninsular Southern Europe and application of refugium concepts

AbstractDuring the Middle to Upper Paleolithic transition in the Balkan, Italian and Iberian peninsulas of southern Europe, late Neanderthal and early Anatomically Modern Human (AMH) populations may have overlapped in some capacity. Many of the hypotheses and models for the transition interval suggest that Neanderthal populations remained in, or migrated to, refugial zones while AMHs colonized areas not suitable for, or abandoned by, Neanderthals. However, many hypotheses and models have not been conclusively tested due to general issues impeding a clear understanding of the relevant archeological record and because of a lack of specificity in defining and applying the term ‘refugium’. This paper briefly summarizes what is known about the Middle to Upper Paleolithic transition in southern European Peninsulas and discusses some new directions in the use of refugium concepts in the study of Neanderthal extinction and AMH dispersal. We highlight the complexity of the archeological record in each region and in the studies of refugia more generally. Finally, we make an appeal for generating local, multi‐proxy paleoenvironmental and paleoclimatic records to address these complexities so that hypotheses and models integrating refugial concepts in explanations of the Middle to Upper Paleolithic transition can be properly formulated and tested.

Late Neanderthal subsistence strategies and cultural traditions in the northern Iberia Peninsula: Insights from Prado Vargas, Burgos, Spain

In order to better understand the causes and geographic patterns of Neanderthal demise it is necessary to broaden the focus of existing Neanderthal studies to include new sites from understudied regions, particularly those containing multi-level fossil and lithic records, and to improve regional-scale Neanderthal extinction frameworks using multiple dating techniques. To this end, we present an interdisciplinary study of the stratigraphy, chronology, pollen, fauna, lithic technology and human remains of the last Neanderthal level (Level N4) of Prado Vargas – a cave in northern Iberia, whose geographic location and chronology are ideal for investigating possible socio-economic and climatic influences on Neanderthal decline. Level N4 has yielded a rich Late Mousterian palimpsest indicative of repeated seasonal occupations, as well as a deciduous Neanderthal tooth, confirming the presence of children at the site. A wide range of human activities are detected in Level 4, with subsistence strategies demonstrating knowledgeable exploitation of the natural environs around the area. The site provides evidence for a distinctive recycling economy, including bone retouchers, recycling of cores, and intense (re)use of raw materials, which may reflect recurrent occupations or the particular cultural traditions of a regional group. Level N4 is dated to between 54.7 and 39.8 thousand years ago (ka) according to our new OSL and radiocarbon study. The late Neanderthal inhabitants of Prado Vargas were cold-adapted, and may have already been living in small, separate groups with marked territories and cultural traditions prior to the arrival of Homo sapiens in the Iberia Peninsula.

A Major Change in Rate of Climate Niche Envelope Evolution during Hominid History.

SummaryHomo sapiens is the only species alive able to take advantage of its cognitive abilities to inhabit almost all environments on Earth. Humans are able to culturally construct, rather than biologically inherit, their occupied climatic niche to a degree unparalleled within the animal kingdom. Precisely, when hominins acquired such an ability remains unknown, and scholars disagree on the extent to which our ancestors shared this same ability. Here, we settle this issue using fine-grained paleoclimatic data, extensive archaeological data, and phylogenetic comparative methods. Our results indicate that whereas early hominins were forced to live under physiologically suitable climatic conditions, with the emergence of H. heidelbergensis, the Homo climatic niche expanded beyond its natural limits, despite progressive harshening in global climates. This indicates that technological innovations providing effective exploitation of cold and seasonal habitats predated the emergence of Homo sapiens.

An Individual-based Network Model Explains Neanderthal Extinction through Competitive Exclusion

This paper presents a social/economic explanation for the Neanderthals' demise, along similar lines with the competitive exclusion theory, by considering the differences in both species' social structures and showing how those differences influenced the competition between them. Individuals are represented as the nodes of a network such that each link corresponds to an acquaintanceship between the respective nodes. We rely on the findings that Sapiens had superior social skills and social structure compared to Neanderthals; and running individual-based simulations, we illustrate how both species' social structures asymmetrically evolved and how such an evolution favored Sapiens in their competition against Neanderthals.

Speleothem record attests to stable environmental conditions during Neanderthal-modern human turnover in southern Italy.

The causes of Neanderthal-modern human (MH) turnover are ambiguous. While potential biocultural interactions between the two groups are still little known, it is clear that Neanderthals in southern Europe disappeared about 42 thousand years ago (ka) after cohabitation for ~3,000 years with MH. Among a plethora of hypotheses on Neanderthal extinction, rapid climate changes during the Middle to Upper Palaeolithic transition (MUPT) are regarded as a primary factor. Here we show evidence for stable climatic and environmental conditions during the MUPT in a region (Apulia) where Neanderthals and MH coexisted. We base our findings on a rare glacial stalagmite deposited between ~106 and ~27 ka, providing the first continuous western Mediterranean speleothem palaeoclimate archive for this period. The uninterrupted growth of the stalagmite attests to the constant availability of rainfall and vegetated soils, while its δ13C-δ18O palaeoclimate proxies demonstrate that Apulia was not affected by dramatic climate oscillations during the MUPT. Our results imply that, because climate did not play a key role in the disappearance of Neanderthals in this area, Neanderthal-MH turnover must be approached from a perspective that takes into account climatic and environmental conditions favourable for both species.

Timing of the Middle-to-Upper Palaeolithic transition in the Iberian inland (Cardina-Salto do Boi, Côa Valley, Portugal)

AbstractThe timing of the Neanderthal-associated Middle Palaeolithic demise and a possible overlap with anatomically modern humans (AMH) in some regions of Eurasia continues to be debated. The Iberian Peninsula is considered a possible refuge zone for the last Neanderthals, but the chronology of the later Middle Palaeolithic record has undergone revision and has increased the debate on the timing of Neanderthal extinction. Here we report on a study of the 5-m-thick archaeological stratigraphy of the Cardina-Salto do Boi, an open-air site located in inland Iberia, from which optically stimulated luminescence (OSL) ages were obtained for Middle and Upper Palaeolithic occupations preserved in overbank alluvial deposits. Geomorphology, archaeostratigraphy, stone-tool evolution, and OSL dating support the persistence of Neanderthals after 41 ka in central Iberia; the transition between the Middle Palaeolithic material culture and the AMH-associated Aurignacian blade and bladelet production is estimated to lie between 34.0 ± 2.0 ka and 38.4 ± 1.9 ka. Our results demonstrate that investigations focusing on different geomorphological situations are necessary to overcome the current limitations of the evidence and to establish more consistent models for Neanderthal disappearance and AMH expansion in the Iberian Peninsula.

Quantifying the potential causes of Neanderthal extinction: Abrupt climate change versus competition and interbreeding

Anatomically Modern Humans are the sole survivor of a group of hominins that inhabited our planet during the last ice age and that included, among others, Homo neanderthalensis, Homo denisova, and Homo erectus. Whether previous hominin extinctions were triggered by external factors, such as abrupt climate change, volcanic eruptions or whether competition and interbreeding played major roles in their demise still remains unresolved. Here I present a spatially resolved numerical hominin dispersal model (HDM) with empirically constrained key parameters that simulates the migration and interaction of Anatomically Modern Humans and Neanderthals in the rapidly varying climatic environment of the last ice age. The model simulations document that rapid temperature and vegetation changes associated with Dansgaard-Oeschger events were not major drivers of global Neanderthal extinction between 50 and 35 thousand years ago, but played important roles regionally, in particular over northern Europe. According to a series of parameter sensitivity experiments conducted with the HDM, a realistic extinction of the Neanderthal population can only be simulated when Homo sapiens is chosen to be considerably more effective in exploiting scarce glacial food resources as compared to Neanderthals.