No evidence of Neandertal admixture in the mitochondrial genomes of early European modern humans and contemporary Europeans

Neandertals, the archaic human form documented in Eurasia until 29,000 years ago, share no mitochondrial haplotype with modern Europeans. Whether this means that the two groups were reproductively isolated is controversial, and indeed nuclear data have been interpreted as suggesting that they admixed. We explored the range of demographic parameters that may have generated the observed mitochondrial diversity, simulating 3.0 million genealogies under six models differing as for the relationships among contemporary Europeans, Neandertals, and Upper Palaeolithic European early modern humans (EEMH), who coexisted with Neandertals for millennia. We compared by Approximate Bayesian Computations the simulation results with mitochondrial diversity in 7 Neandertals, 3 EEMH, and 150 opportunely chosen modern Europeans. A model of genealogical continuity between EEMH and contemporary Europeans, with no Neandertal contribution, received overwhelming support from the analyses. The maximum degree of Neandertal admixture, under the model of gene flow supported by nuclear data, was estimated at 1.5%, but this model proved 20-32 times less likely than a model without any gene flow. Nuclear and mitochondrial evidence might be reconciled if smaller population sizes led to faster lineage sorting for mitochondrial DNA, and Neandertals shared a longer period of common ancestry with the non-African's than with the African's ancestors.     

A 28,000 years old Cro-Magnon mtDNA sequence differs from all potentially contaminating modern sequences

Background

DNA sequences from ancient speciments may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal) and early modern (Cro-Magnoid) Europeans.

Methodology/Principal Findings

We typed the mitochondrial DNA (mtDNA) hypervariable region I in a 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23) and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences.

Conclusions/Significance:

The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans.     

Complex History of Admixture between Modern Humans and Neandertals

Recent analyses have found that a substantial amount of the Neandertal genome persists in the genomes of contemporary non-African individuals. East Asians have, on average, higher levels of Neandertal ancestry than do Europeans, which might be due to differences in the efficiency of purifying selection, an additional pulse of introgression into East Asians, or other unexplored scenarios. To better define the scope of plausible models of archaic admixture between Neandertals and anatomically modern humans, we analyzed patterns of introgressed sequence in whole-genome data of 379 Europeans and 286 East Asians. We found that inferences of demographic history restricted to neutrally evolving genomic regions allowed a simple one-pulse model to be robustly rejected, suggesting that differences in selection cannot explain the differences in Neandertal ancestry. We show that two additional demographic models, involving either a second pulse of Neandertal gene flow into the ancestors of East Asians or a dilution of Neandertal lineages in Europeans by admixture with an unknown ancestral population, are consistent with the data. Thus, the history of admixture between modern humans and Neandertals is most likely more complex than previously thought.     

Late archaic and modern Homo sapiens from Europe, Africa, and Southwest Asia: Craniometric comparisons and phylogenetic implications

The craniometric affinities among Neandertals. Upper Palcolithic Europeans, early anatomically modern Southwest Asians, and archaic and modern Africans are investigated using univariate and multivariate methods. For the first time, it is possible to analyse the North African finds Dar-es-Soltane 5, Nazlet Khater, and Wadi Kubbaniya. It was not possible to include the Neandertals from Central Europe due to their poor state of preservation. The results point to, first, a basic distinction between Neandertals on the one hand and modern humans from all geographic regions on the other, and, secondly, to great similarities between modern African and European populations. Late archaic sapiens specimens from Africa were more similar to Upper Paleolithic Europeans than were the Neandertals. The results do not support the hypothesis that a regional evolution giving rise to modern humans took place in Europe. The results are, however, consistent with the hypothesis that modern populations originated in Africa and spread to Europe from there.     

The Date of Interbreeding between Neandertals and Modern Humans

Comparisons of DNA sequences between Neandertals and present-day humans have shown that Neandertals share more genetic variants with non-Africans than with Africans. This could be due to interbreeding between Neandertals and modern humans when the two groups met subsequent to the emergence of modern humans outside Africa. However, it could also be due to population structure that antedates the origin of Neandertal ancestors in Africa. We measure the extent of linkage disequilibrium (LD) in the genomes of present-day Europeans and find that the last gene flow from Neandertals (or their relatives) into Europeans likely occurred 37,000–86,000 years before the present (BP), and most likely 47,000–65,000 years ago. This supports the recent interbreeding hypothesis and suggests that interbreeding may have occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa.     

Is human longevity a consequence of cultural change or modern biology?

Increased longevity, expressed as the number of individuals surviving to older adulthood, represents a key way that Upper Paleolithic Europeans differ from earlier European (Neandertal) populations. Here, we address whether longevity increased as a result of cultural/adaptive change in Upper Paleolithic Europe, or whether it was introduced to Europe as a part of modern human biology. We compare the ratio of older to younger adults (OY ratio) in an early modern human sample associated with the Middle Paleolithic from Western Asia with OY ratios of European Upper Paleolithic moderns and penecontemporary Neandertals from the same region. We also compare these Neandertals to European Neandertals. The difference between the OY ratios of modern humans of the Middle and Upper Paleolithic is large and significant, but there is no significant difference between the Neandertals and early modern humans of Western Asia. Longevity for the West Asian Neandertals is significantly more common than for the European Neandertals. We conclude that the increase in adult survivorship associated with the Upper Paleolithic is not a biological attribute of modern humans, but reflects important cultural adaptations promoting the demographic and material representations of modernity.     

Diagnostic differences in mandibular P4 shape between Neandertals and anatomically modern humans

This study uses elliptical Fourier analysis to quantify shape differences observed in the P(4) crown of Neandertals and anatomically modern humans. Previously, P(4) shape was assessed qualitatively, and results suggested marked differences between Neandertals and anatomically modern humans (Bailey [2002] New Anat. 269:148-156). The goal of this study was to investigate the P(4) shape in more detail, quantifying it in order to determine its utility for taxonomic classification and phylogenetic analysis. A comparison of mean shapes confirms that the mesiolingual portion of the P(4) is truncated in Neandertals, and that this produces a distinctively asymmetrical P(4). A randomization test confirms that the shape difference between Neandertals and anatomically modern humans is significant. Principal component and discriminant function analyses indicate that the relative size of the lingual portion of the tooth also affects tooth shape, with the lingual portion of the Neandertal P(4) being narrower than that of anatomically modern humans. Classification of P(4) crown shapes using discriminant functions analysis is far from perfect. While 86.4% of the teeth were correctly classified, classification was much better for anatomically modern humans (98.1%) than it was for Neandertals (65%). Fortunately, crown shape is but one of several diagnostic characters of the P(4) crown. P(4) crown asymmetry can be added to the growing list of dental morphological characters distinguishing Neandertals from anatomically modern humans. Moreover, based on a comparison of mean tooth shapes in fossil and recent humans, symmetry, rather than asymmetry, appears to be the primitive state, and the high frequency of P(4) asymmetry is likely derived in Neandertals.     

A morphometric analysis of maxillary molar crowns of Middle-Late Pleistocene hominins

This study explores the significance of shape differences in the maxillary first molar crowns of Neandertals and anatomically modern humans. It uses morphometric analysis to quantify these differences and to investigate how the orientation of major cusps, relative cusp base areas and occlusal polygon area influence crown shape. The aims of this study were to 1) quantify these data to test whether the tooth shapes of Neandertals and anatomically modern humans differ significantly and 2) to explore if either of the shapes is derived relative to earlier fossil hominins. Data were collected from digital occlusal photographs using image-processing software. Cusp angles, relative cusp base areas and occlusal polygon areas were measured on Neandertals (n=15), contemporary modern humans (n=62), Upper Paleolithic humans (n=6), early anatomically modern humans (n=3) and Homo erectus (n=3). Univariate and multivariate statistical tests were used to evaluate the differences between contemporary modern humans and Neandertals, while the much sparser data sets from the other fossil samples were included primarily for comparison. Statistically significant differences reflecting overall crown shape and internal placement of the crown apices were found. Neandertals are distinguished from contemporary humans by possessing maxillary first molars that 1) are markedly skewed; 2) possess a narrower distal segment of the occlusal polygon compared to the mesial segment; 3) possess a significantly smaller metacone and a significantly larger hypocone; and 4) possess a significantly smaller relative occlusal polygon area reflecting internally placed cusps. Differences in relative cusp base areas of the hypocone and metacone may contribute to the shape differences observed in Neandertals. However, early anatomically modern humans possessing a pattern of relative cusp base areas similar to Neandertals lack their unusual shape. That the morphology observed in non-Neandertal fossil hominins is more anatomically modern human-like than Neandertal-like, suggests that this distinctive morphology may be derived in Neandertals.     

Post-glacial partitioning of mitochondrial genetic variation in the field vole

Genetic markers are often used to examine population history. There is considerable debate about the behaviour of molecular clock rates around the population-species transition. Nevertheless, appropriate calibration is critical to any inference regarding the absolute timing and scale of demographic changes. Here, we use a mitochondrial cytochrome b gene genealogy, based entirely on modern sequences and calibrated from recent geophysical events, to date the post-glacial expansion of the Eurasian field vole (Microtus agrestis), a widespread temperate mammal species. The phylogeographic structure reflects the subsequent expansion of populations that went through bottlenecks at the time of the Younger Dryas (ca 12,000 years BP) rather than the Last Glacial Maximum (LGM, ca 24,000 years BP), which is usually seen as the time when present-day patterns were determined. The nucleotide substitution rate that was estimated here, ca 4 × 10(-7) substitutions/site/year, remains extremely high throughout the relevant time frame. Calibration with similarly high population-based substitution rates, rather than long-term rates derived from species divergence times, will show that post-LGM climatic events generated current phylogeographic structure in many other organisms from temperate latitudes.     

Who made the Aurignacian and other early Upper Paleolithic industries?

The Aurignacian is typically taken as a marker of the spread of anatomically modern humans into Europe. However, human remains associated with this industry are frustratingly sparse and often limited to teeth. Some have suggested that Neandertals may, in fact, be responsible for the Aurignacian and the earliest Upper Paleolithic industries. Although dental remains are frequently considered to be taxonomically undiagnostic in this context, recent research shows that Neandertals possess a distinct dental pattern relative to anatomically modern humans. Even so, it is rare to find mandibles or maxillae that preserve all or most of their teeth; and, the probability of correctly identifying individuals represented by only a few teeth or a single tooth is unknown. We present a Bayesian statistical approach to classifying individuals represented exclusively by teeth into two possible groups. The classification is based on dental trait frequencies and sample sizes for ‘known’ samples of 95 Neandertals and 63 Upper Paleolithic modern humans. In a cross validation test of the known samples, 89% of the Neandertals and 89% of the Upper Paleolithic modern humans were classified correctly. We then classified an ‘unknown’ sample of 52 individuals: 34 associated with Aurignacian or other (non-Châtelperronian) early Upper Paleolithic industries, 15 associated with the Châtelperronian, and three unassociated. Of the 34 early Upper Paleolithic-associated individuals, 29 were assigned to modern humans, which is well within the range expected (95% of the time 26-33) with an 11% misclassification rate for an entirely modern human sample. These results provide some of the strongest evidence that anatomically modern humans made the Aurignacian and other (non-Châtelperronian) early Upper Paleolithic industries.     

Early Upper Paleolithic Man and Late Middle Paleolithic Tools

The appearance of anatomically modern Homo sapiens in Europe, the Near East, and Africa must represent either an in situ evolution of Neandertals or a migration. Those who suggest the latter claim a sudden replacement of Neandertals by anatomically modern Homo sapiens. However, the "evidence" actually cited claims only the sudden replacement of Middle by Upper Paleolithic industries. We criticize the migration explanation on two grounds. (1) There is no "sudden replacement" of Middle Paleolithic by Upper Paleolithic industries, but rather a gradual change in the frequencies of already present tools. Numerous sites in these areas exhibit transitional industries. (2) Concomitantly, there is no morphological evidence indicating a "sudden replacement" of hominids. There is no absolute association between anatomically modern Homo sapiens and Upper Paleolithic industries. Instead, the evidence clearly shows that early anatomically modern Homo sapiens is a late Middle Paleolithic local phenomenon .     

No evidence of Neandertal mtDNA contribution to early modern humans

The retrieval of mitochondrial DNA (mtDNA) sequences from four Neandertal fossils from Germany, Russia, and Croatia has demonstrated that these individuals carried closely related mtDNAs that are not found among current humans. However, these results do not definitively resolve the question of a possible Neandertal contribution to the gene pool of modern humans since such a contribution might have been erased by genetic drift or by the continuous influx of modern human DNA into the Neandertal gene pool. A further concern is that if some Neandertals carried mtDNA sequences similar to contemporaneous humans, such sequences may be erroneously regarded as modern contaminations when retrieved from fossils. Here we address these issues by the analysis of 24 Neandertal and 40 early modern human remains. The biomolecular preservation of four Neandertals and of five early modern humans was good enough to suggest the preservation of DNA. All four Neandertals yielded mtDNA sequences similar to those previously determined from Neandertal individuals, whereas none of the five early modern humans contained such mtDNA sequences. In combination with current mtDNA data, this excludes any large genetic contribution by Neandertals to early modern humans, but does not rule out the possibility of a smaller contribution.     

Ancient DNA: would the real Neandertal please stand up?

Mitochondrial DNA sequences recovered from eight Neandertal specimens cannot be detected in either early fossil Europeans or in modern populations. This indicates that, if Neandertals made any genetic contribution at all to modern humans, it must have been limited, though the extent of the contribution cannot be resolved at present.     

Paleoclimate during Neandertal and anatomically modern human occupation at Amud and Qafzeh, Israel: the stable isotope data

The δ¹³C(en) and δ¹⁸O(en) values of goat and gazelle enamel carbonate indicate that Neandertals at Amud Cave, Israel (53-70 ka) lived under different ecological conditions than did anatomically modern humans at Qafzeh Cave, Israel (approximately 92 ka). During the Last Glacial Period, Neandertals at Amud Cave lived under wetter conditions than those in the region today. Neither faunal species ate arid-adapted C₄ plants or drought-stressed C₃ plants. The variation in gazelle δ¹⁸O(en) values suggests multiple birth seasons, which today occur under wetter than normal conditions. The magnitude and pattern of intra-tooth variation in goat δ¹⁸O(en) values indicate that rain fell throughout the year unlike today.Anatomically modern humans encountered a Qafzeh Cave region that was more open and arid than Glacial Period Amud Cave, and more open than today's Upper Galilee region. Goat δ¹³C(en) values indicate feeding on varying amounts of C₄ plants throughout the year. The climate apparently ameliorated higher in the sequence; but habitats remained more open than at Amud Cave. Both gazelles and goats fed on C₃ plants in brushy habitats without any inclusion of C₄ plants. The magnitude of intra-tooth variation in goat δ¹⁸O(en) values, however, suggest that some rain fell throughout the year, and the relative representation of woodland dwelling species indicates the occurrence of woodlands in the region.Climate differences affecting the distribution of plants and animals appear to be the significant factor contributing to behavioral differences previously documented between Neandertals and anatomically modern humans in the region. Climate forcing probably affected the early appearances of anatomically modern humans, although not the disappearance of Neandertals from the Levant.     

Do modern humans and Neandertals have different patterns of cranial integration?

Studies of cranial differences between modern humans and Neandertals have identified several characteristics for which the two groups differ in their mean values, the proportional relationships with other traits, or both. However, the limited number of fairly complete Neandertals has hindered investigations into patterns of integration – covariance and correlation among traits – in this fossil group. Here, we use multiple approaches specifically designed to deal with fragmentary fossils to test if metric cranial traits in Neandertals fit modern human patterns of integration. Based on 37 traits collected from a sample of 2524 modern humans from Howells’ data set and 20 Neandertals, we show that overall patterns of cranial integration are significantly different between Neandertals and modern humans. However, at the same time, Neandertals are consistent with a modern human pattern of integration for more than three-quarters of the traits. Additionally, the differences between the predicted and actual values for the deviating traits are rather small, indicating that the differences in integration are subtle. Traits for which Neandertals deviate from modern human integration patterns tend to be found in regions where Neandertals and modern humans are known to also differ in their mean values. We conclude that the evolution of patterns of cranial integration is a cause for caution but also presents an opportunity for understanding cranial differences between modern humans and Neandertals.     

Revisiting dental fluctuating asymmetry in neandertals and modern humans

Previous studies have suggested that Neandertals experienced greater physiological stress and/or were less capable of mitigating stress than most prehistoric modern human populations. The current study compares estimates of dental fluctuating asymmetry (DFA) for prehistoric Inupiat from Point Hope Alaska, the Late Archaic, and Protohistoric periods from Ohio and West Virginia, and a modern sample from Ohio to Neandertals from Europe and Southwest Asia. DFA results from developmental perturbation during crown formation and is thus an indicator of developmental stress, which previous studies have found to be higher in Neandertals than in several modern human populations. Here, we use recent methodological improvements in the analysis of fluctuating asymmetry suggested by Palmer and Strobeck (Annu Rev Ecol Syst 17 ( 1986 ) 391–421, Developmental instability: causes and consequences ( 2003a ) v.1–v.36, Developmental instability: causes and consequences ( 2003b ) 279–319) and compare the fit of Neandertal DFA Index values with those of modern humans. DFA estimates for each of the modern population samples exceeded measurement error, with the Inupiat exhibiting the highest levels of DFA for most tooth positions. All significant Neandertal z‐scores were positive, exceeding the estimates for each of the modern prehistoric groups. Neandertals exhibited the fewest significant differences from the Inupiat (9.2% of values are significant at P < 0.05), while for the other modern prehistoric groups more than 10% of the Neandertal z‐scores are significant at P < 0.05, more than 90% of these significant scores at P < 0.01. These results suggest that the Inupiat experienced greater developmental stress than the other prehistoric population samples, and that Neandertals were under greater developmental stress than all other prehistoric modern human samples. Am J Phys Anthropol 149:193–204, 2012. © 2012 Wiley Periodicals, Inc.     

New data on the late Neandertals: Direct dating of the Belgian Spy fossils

In Eurasia, the period between 40,000 and 30,000 BP saw the replacement of Neandertals by anatomically modern humans (AMH) during and after the Middle to Upper Paleolithic transition. The human fossil record for this period is very poorly defined with no overlap between Neandertals and AMH on the basis of direct dates. Four new ¹⁴C dates were obtained on the two adult Neandertals from Spy (Belgium). The results show that Neandertals survived to at least ≈36,000 BP in Belgium and that the Spy fossils may be associated to the Lincombian–Ranisian–Jerzmanowician, a transitional techno‐complex defined in northwest Europe and recognized in the Spy collections. The new data suggest that hypotheses other than Neandertal acculturation by AMH may be considered in this part of Europe. Am J Phys Anthropol, 2009. © 2008 Wiley‐Liss, Inc.     

尼安德特人基因组学研究进展

尼安德特人是现代人最近的旁支,也是化石资料最丰富的古人类。在现代人起源问题的争论中,尼安德特人对现代人是否有遗传贡献是一个焦点问题。文章综述了近年来关于尼安德特人线粒体基因组和核基因组的研究进展,初步研究表明尼安德特人可能对现代人有遗传贡献,这引发了人们对现代人起源问题的重新思考。藉尼人基因组研究经验进行的古人类基因组学研究将有望揭开现代人起源的谜团,并丰富进化生物学相关领域的理论体系。     

Brief communication: The distribution of perikymata on Qafzeh anterior teeth

Recent studies have suggested that Neandertals and modern humans differ in the distribution of perikymata (enamel growth increments) over their permanent anterior tooth crowns. In modern humans, perikymata become increasingly more compact toward the cervix than they do in Neandertals. Previous studies have suggested that a more homogeneous distribution of perikymata, like that of Neandertals, characterizes the anterior teeth of Homo heidelbergensis and Homo erectus as well. Here, we investigated whether Qafzeh anterior teeth (N = 14) differ from those of modern southern Africans, northern Europeans, and Alaskans (N = 47–74 depending on tooth type) in the percentage of perikymata present in their cervical halves. Using the normally distributed modern human values for each tooth type, we calculated Z‐scores for the 14 Qafzeh teeth. All but two of the 14 Qafzeh teeth had negative Z‐scores, meaning that values equal to these would be found in the bottom 50% of the modern human samples. Seven of the 14 would be found in the lowest 5% of the modern human distribution. Qafzeh teeth therefore appear to differ from those of modern humans in the same direction that Neandertals do: with generally lower percentages of perikymata in their cervical regions. The similarity between them appears to represent the retention of a perikymata distribution pattern present in earlier members of the genus Homo, but not generally characteristic of modern humans from diverse regions of the world. Am J Phys Anthropol 2010. © 2009 Wiley‐Liss, Inc.