Neanderthal and Denisova genetic affinities with contemporary humans: Introgression versus common ancestral polymorphisms

Analyses of the genetic relationships among modern humans, Neanderthals and Denisovans have suggested that 1–4% of the non-Sub-Saharan African gene pool may be Neanderthal derived, while 6–8% of the Melanesian gene pool may be the product of admixture between the Denisovans and the direct ancestors of Melanesians. In the present study, we analyzed single nucleotide polymorphism (SNP) diversity among a worldwide collection of contemporary human populations with respect to the genetic constitution of these two archaic hominins and Pan troglodytes (chimpanzee). We partitioned SNPs into subsets, including those that are derived in both archaic lineages, those that are ancestral in both archaic lineages and those that are only derived in one archaic lineage. By doing this, we have conducted separate examinations of subsets of mutations with higher probabilities of divergent phylogenetic origins. While previous investigations have excluded SNPs from common ancestors in principal component analyses, we included common ancestral SNPs in our analyses to visualize the relative placement of the Neanderthal and Denisova among human populations. To assess the genetic similarities among the various hominin lineages, we performed genetic structure analyses to provide a comparison of genetic patterns found within contemporary human genomes that may have archaic or common ancestral roots. Our results indicate that 3.6% of the Neanderthal genome is shared with roughly 65.4% of the average European gene pool, which clinally diminishes with distance from Europe. Our results suggest that Neanderthal genetic associations with contemporary non-Sub-Saharan African populations, as well as the genetic affinities observed between Denisovans and Melanesians most likely result from the retention of ancient mutations in these populations.     

Neanderthal genomics suggests a pleistocene time frame for the first epidemiologic transition

High quality Altai Neanderthal and Denisovan genomes are revealing which regions of archaic hominin DNA have persisted in the modern human genome. A number of these regions are associated with response to infection and immunity, with a suggestion that derived Neanderthal alleles found in modern Europeans and East Asians may be associated with autoimmunity. As such Neanderthal genomes are an independent line of evidence of which infectious diseases Neanderthals were genetically adapted to. Sympathetically, human genome adaptive introgression is an independent line of evidence of which infectious diseases were important for AMH coming in to Eurasia and interacting with Neanderthals. The Neanderthals and Denisovans present interesting cases of hominin hunter‐gatherers adapted to a Eurasian rather than African infectious disease package. Independent sources of DNA‐based evidence allow a re‐evaluation of the first epidemiologic transition and how infectious disease affected Pleistocene hominins. By combining skeletal, archaeological and genetic evidence from modern humans and extinct Eurasian hominins, we question whether the first epidemiologic transition in Eurasia featured a new package of infectious diseases or a change in the impact of existing pathogens. Coupled with pathogen genomics, this approach supports the view that many infectious diseases are pre‐Neolithic, and the list continues to expand. The transfer of pathogens between hominin populations, including the expansion of pathogens from Africa, may also have played a role in the extinction of the Neanderthals and offers an important mechanism to understand hominin–hominin interactions well back beyond the current limits for aDNA extraction from fossils alone. Am J Phys Anthropol 160:379–388, 2016. © 2016 Wiley Periodicals, Inc.     

Loss of Olfactory Receptor Function in Hominin Evolution

The mammalian sense of smell is governed by the largest gene family, which encodes the olfactory receptors (ORs). The gain and loss of OR genes is typically correlated with adaptations to various ecological niches. Modern humans have 853 OR genes but 55% of these have lost their function. Here we show evidence of additional OR loss of function in the Neanderthal and Denisovan hominin genomes using comparative genomic methodologies. Ten Neanderthal and 8 Denisovan ORs show evidence of loss of function that differ from the reference modern human OR genome. Some of these losses are also present in a subset of modern humans, while some are unique to each lineage. Morphological changes in the cranium of Neanderthals suggest different sensory arrangements to that of modern humans. We identify differences in functional olfactory receptor genes among modern humans, Neanderthals and Denisovans, suggesting varied loss of function across all three taxa and we highlight the utility of using genomic information to elucidate the sensory niches of extinct species.     

Neanderthal Extinction by Competitive Exclusion

Background

Despite a long history of investigation, considerable debate revolves around whether Neanderthals became extinct because of climate change or competition with anatomically modern humans (AMH).

Methodology/Principal Findings

We apply a new methodology integrating archaeological and chronological data with high-resolution paleoclimatic simulations to define eco-cultural niches associated with Neanderthal and AMH adaptive systems during alternating cold and mild phases of Marine Isotope Stage 3. Our results indicate that Neanderthals and AMH exploited similar niches, and may have continued to do so in the absence of contact.

Conclusions/Significance

The southerly contraction of Neanderthal range in southwestern Europe during Greenland Interstadial 8 was not due to climate change or a change in adaptation, but rather concurrent AMH geographic expansion appears to have produced competition that led to Neanderthal extinction.     

Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania

It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a "Negrito" group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.     

Early hominin speciation at the Plio/Pleistocene transition

Over the last half-decade or so, there has been an explosion in the recognition of hominin genera and species. We now have the late Miocene genera Orrorin and Sahelanthropus, the mid Pliocene genus Kenyanthropus, three new Pliocene species of Australopithecus (A. anamensis, A. garhi and A. bahrelghazali) and a sub species of Ardipithecus (Ar. r. kadabba) to contend with. Excepting also the more traditional species allocated to Paranthropus, Australopithecus and early Homo we are approaching around 15 species over 5 million years (excluding hominin evolution over the last one million years). Can such a large number of hominin species be justified? An examination of extant hominid (Gorilla gorilla, Pan troglodytes, and Pan paniscus) anatomical variability indicates that the range of fossil hominin variability supports the recognition of this large number of fossil species. It is also shown that not all hominins are directly related to the emergence of early Homo and as such have become extinct. Indeed the traditional australopithecine species 'A'. anamensis, 'A'. afarensis and 'A'. garhi are considered here to belong to a distinct genus Praeanthropus. They are also argued not be hominins, but rather an as yet undefined hominid group from which the more derived hominins evolved. The first hominin is represented by A. africanus or a hominin very much like it. The Paranthropus clade is defined by a derived heterochronic condition of peramorphosis, associated with sequential progenesis (contraction of successive growth stages) in brain and dental development, but a mixture of peramorphic and paedomorphic features in its craniofacial anatomy. Conversely, Kenyanthropus and Homo both share a pattern of peramorphosis, associated with sequential hypermorphosis (prolongation of successive growth stages) in brain development, and paedomorphosis processes in cranial, facial and dental development. This suggests, that these two clades share an important synapomorphy not recognised in the parsimony analyses, suggesting that they may form a sister group relationship to the exclusion of Paranthropus. This highlights the need to re-interpret phylogenetic results in terms of function and development. The rapid speciation and extinction as argued here is in keeping with other fossil groups in Africa at the Plio/Pleistocene transition. This emphasises that we must approach the pre-australopithecines and hominins as part of the endemic African fauna, and not in isolation to the evolutionary and climatic processes that were operating all around them.     

Genome digging: insight into the mitochondrial genome of Homo

Background

A fraction of the Neanderthal mitochondrial genome sequence has a similarity with a 5,839-bp nuclear DNA sequence of mitochondrial origin (numt) on the human chromosome 1. This fact has never been interpreted. Although this phenomenon may be attributed to contamination and mosaic assembly of Neanderthal mtDNA from short sequencing reads, we explain the mysterious similarity by integration of this numt (mtAncestor-1) into the nuclear genome of the common ancestor of Neanderthals and modern humans not long before their reproductive split.

Principal Findings

Exploiting bioinformatics, we uncovered an additional numt (mtAncestor-2) with a high similarity to the Neanderthal mtDNA and indicated that both numts represent almost identical replicas of the mtDNA sequences ancestral to the mitochondrial genomes of Neanderthals and modern humans. In the proteins, encoded by mtDNA, the majority of amino acids distinguishing chimpanzees from humans and Neanderthals were acquired by the ancestral hominins. The overall rate of nonsynonymous evolution in Neanderthal mitochondrial protein-coding genes is not higher than in other lineages. The model incorporating the ancestral hominin mtDNA sequences estimates the average divergence age of the mtDNAs of Neanderthals and modern humans to be 450,000–485,000 years. The mtAncestor-1 and mtAncestor-2 sequences were incorporated into the nuclear genome approximately 620,000 years and 2,885,000 years ago, respectively.

Conclusions

This study provides the first insight into the evolution of the mitochondrial DNA in hominins ancestral to Neanderthals and humans. We hypothesize that mtAncestor-1 and mtAncestor-2 are likely to be molecular fossils of the mtDNAs of Homo heidelbergensis and a stem Homo lineage. The d_N/d_S dynamics suggests that the effective population size of extinct hominins was low. However, the hominin lineage ancestral to humans, Neanderthals and H. heidelbergensis, had a larger effective population size and possessed genetic diversity comparable with those of chimpanzee and gorilla.     

The Omo-Turkana Basin fossil hominins and their contribution to our understanding of human evolution in Africa

The Omo-Turkana Basin, including the hominin fossil sites around Lake Turkana and the sites along the lower reaches of the Omo River, has made and continues to make an important contribution to improving our murky understanding of human evolution. This review highlights the various ways the Omo-Turkana Basin fossil record has contributed to, and continues to challenge, interpretations of human evolution. Despite many diagrams that look suspiciously like comprehensive hypotheses about human evolutionary history, any sensible paleoanthropologist knows that the early hominin fossil record is too meager to do anything other than offer very provisional statements about hominin taxonomy and phylogeny. If history tells us anything, it is that we still have much to learn about the hominin clade. Thus, we summarize the current state of knowledge of the hominin species represented at the Omo-Turkana Basin sites. We then focus on three specific topics for which the fossil evidence is especially relevant: the origin and nature of Paranthropus; the origin and nature of early Homo; and the ongoing debate about whether the pattern of human evolution is more consistent with speciation by cladogenesis, with greater taxonomic diversity or with speciation by anagenetic transformation, resulting in less taxonomic diversity and a more linear interpretation of human evolutionary history.     

Genotyping of Capreolus pygargus fossil DNA from Denisova cave reveals phylogenetic relationships between ancient and modern populations

Background

The extant roe deer (Capreolus Gray, 1821) includes two species: the European roe deer (C. capreolus) and the Siberian roe deer (C. pygargus) that are distinguished by morphological and karyotypical differences. The Siberian roe deer occupies a vast area of Asia and is considerably less studied than the European roe deer. Modern systematics of the Siberian roe deer remain controversial with 4 morphological subspecies. Roe deer fossilized bones are quite abundant in Denisova cave (Altai Mountains, South Siberia), where dozens of both extant and extinct mammalian species from modern Holocene to Middle Pleistocene have been retrieved.

Methodology/Principal Findings

We analyzed a 629 bp fragment of the mitochondrial control region from ancient bones of 10 Holocene and four Pleistocene Siberian roe deer from Denisova cave as well as 37 modern specimen belonging to populations from Altai, Tian Shan (Kyrgyzstan), Yakutia, Novosibirsk region and the Russian Far East. Genealogical reconstructions indicated that most Holocene haplotypes were probably ancestral for modern roe deer populations of Western Siberia and Tian Shan. One of the Pleistocene haplotypes was possibly ancestral for modern Yakutian populations, and two extinct Pleistocene haplotypes were close to modern roe deer from Tian Shan and Yakutia. Most modern geographical populations (except for West Siberian Plains) are heterogeneous and there is some tentative evidence for structure. However, we did not find any distinct phylogenetic signal characterizing particular subspecies in either modern or ancient samples.

Conclusion/Significance

Analysis of mitochondrial DNA from both ancient and modern samples of Siberian roe deer shed new light on understanding the evolutionary history of roe deer. Our data indicate that during the last 50,000 years multiple replacements of populations of the Siberian roe deer took place in the Altai Mountains correlating with climatic changes. The Siberian roe deer represent a complex and heterogeneous species with high migration rates and without evident subspecies structure. Low genetic diversity of the West Siberian Plain population indicates a recent bottleneck or founder effect.     

Reconstructing the Diet of an Extinct Hominin Taxon: The Role of Extant Primate Models

Modern humans represent the only surviving species of an otherwise extinct clade of primates, the hominins. As the closest living relatives to extinct hominins, extant primates are an important source of comparative information for the reconstruction of the diets of extinct hominins. Methods such as comparative and functional morphology, finite element analysis, dental wear, dental topographic analysis, and stable isotope biogeochemistry must be validated and tested within extant populations before they can be applied to extinct taxa. Here we review how these methods have and might be used to reconstruct the diet of a particular extinct hominin, Paranthropus boisei, which has no extant analogue for its highly derived masticatory morphology. Our review emphasizes the potential and limitations of using extant primates as models for the reconstruction of extinct hominin diets. We encourage paleoanthropologists and those who study the feeding behaviors of extant primates to work together to investigate and validate methods for interpreting the diets of all extinct primates, including hominins.     

Using genetic evidence to evaluate four palaeoanthropological hypotheses for the timing of Neanderthal and modern human origins

A better understanding of the evolutionary relationship between modern humans and Neanderthals is essential for improving the resolution of hominin phylogenetic hypotheses. Currently, four distinct chronologies for the timing of population divergence are available, ranging from the late Middle Pleistocene to the late Early Pleistocene, each based on different interpretations of hominin taxonomy. Genetic data can present an independent estimate of the evolutionary timescale involved, making it possible to distinguish between these competing models of hominin evolution. We analysed five dated Neanderthal mitochondrial genomes, together with those of 54 modern humans, and inferred a genetic chronology using multiple age calibrations. Our mean date estimates are consistent with a process of genetic divergence within an ancestral population, commencing approximately 410-440 ka. These results suggest that a reappraisal of key elements in the Pleistocene hominin fossil record may now be required.     

ESTIMATING SPECIATION AND EXTINCTION RATES FROM DIVERSITY DATA AND THE FOSSIL RECORD

Understanding the processes that underlie biodiversity requires insight into the evolutionary history of the taxa involved. Accurate estimation of speciation, extinction, and diversification rates is a prerequisite for gaining this insight. Here, we develop a stochastic birth–death model of speciation and extinction that predicts the probability distribution of both extinct and extant numbers of species in a clade. We present two estimation methods based on this model given data on the number of extinct species (from the fossil record) and extant species (from diversity assessments): a multivariate method of moments approach and a maximum-likelihood approach. We show that, except for some special cases, the two estimation methods produce very similar estimates. This is convenient, because the usually preferred maximum-likelihood approach is much more computationally demanding, so the method of moments can serve as a proxy. Furthermore, we introduce a correction for possible bias that can arise by the mere fact that we will normally only consider extant clades. We find that in some cases the bias correction affects the estimates profoundly. Finally, we show how our model can be extended to incorporate incomplete preservation. Preservation rates can, however, not be reliably estimated on the basis of numbers of extant and extinct species alone.     

A geometric morphometric analysis of hominin upper second and third molars, with particular emphasis on European Pleistocene populations

The study of dental morphology by means of geometric morphometric methods allows for a detailed and quantitative comparison of hominin species that is useful for taxonomic assignment and phylogenetic reconstruction. Upper second and third molars have been studied in a comprehensive sample of Plio- and Pleistocene hominins from African, Asian and European sites in order to complete our analysis of the upper postcanine dentition. Intraspecific variation in these two molars is high, but some interspecific trends can be identified. Both molars exhibit a strong reduction of the distal cusps in recent hominin species, namely European Homo heidelbergensis, Homo neanderthalensis and Homo sapiens, but this reduction shows specific patterns and proportions in the three groups. Second molars tend to show four well developed cusps in earlier hominin species and their morphology is only marginally affected by allometric effects. Third molars can be incipiently reduced in earlier species and they evince a significant allometric component, identified both inter- and intraspecifically. European Middle Pleistocene fossils from Sima de los Huesos (SH) show a very strong reduction of these two molars, even more marked than the reduction observed in Neanderthals and in modern human populations. The highly derived shape of SH molars points to an early acquisition of typical Neanderthal dental traits by pre-Neanderthal populations and to a deviation of this population from mean morphologies of other European Middle Pleistocene groups.     

The single species hypothesis: truly dead and pushing up bushes, or still twitching and ripe for resuscitation?

Frank Livingstone proclaims himself to be the last living proponent of the single species hypothesis. In sharp contrast, a species-rich, bushy phylogeny is favored by most human paleontologists. Is Livingstone's proclamation merely contrarian posturing, or does closer inspection warrant reconsideration of just how speciose the hominin lineage is? The high-speciation perspective draws on evidence of speciosity in the Cercopithecoidea and punctuated equilibria theory for support. If blue monkeys and redtail monkeys are indistinguishable skeletally, this reasoning goes, or if red colobus and black and white colobus are likewise indistinguishable, should we not expect that there are more species of hominin than is apparent from skeletal evidence alone? A contrarian perspective notes that not all monkey taxa are speciose. Importantly, two broadly distributed, partly terrestrial monkeys have not speciated at all: vervets and baboons. Nor are monkeys the first choice as a hominin speciation model. If expectations of species numbers are based on the Hominoidea, a taxon more closely related to hominins, more similar in body size, and found in more hominin-like habitats than monkeys, a single-species perspective is more appealing. No great ape genus has even two sympatric species. Moreover, despite a separation of 1.6 Ma, West African chimpanzees have not speciated from Pt. troglodytes nor Pt. schweinfurthii. It is notable that no two contemporaneous species of hominin were separated by significantly more than this interval. A biological--as opposed to an ecological or geographical--species definition would place all hominins in a single, phenotypically diverse species. Since divergence from the chimpanzee, "species" distinctness in hominins may have been maintained by temporary allopatry and centripetal niche separation. The hominin lineage may have evolved as a single, phenotypically diverse, reticulately evolving species.     

The hominoid proximal radius: re-interpreting locomotor behaviors in early hominins

Studies of fossil hominins are traditionally taxonomically narrow and often exclude comparisons with hylobatids. Hence, results of functional analyses of postcrania, interpreted as indicating that early hominins are "African-ape-like" in their postcranial skeletons and positional behaviors, may reflect an artifact of inadequate taxonomic and morphological breadth of the comparative sample. To address this problem and better understand early hominin positional behaviors, this study included hylobatids in a comparative analysis, focusing on the hominoid elbow joint. Specifically, morphometric variables of the proximal radius were derived from measurements from a sample of all genera of extant hominoids and casts of extinct hominin species. Univariate and multivariate analyses were performed on these data. Results show that early hominins are morphologically diverse and are not, as a group, similar to any one extant group. Instead, the fossils resemble Pan, Gorilla, and Hylobates, and are not like modern Homo sapiens or Pongo. This suggests that the morphology of Hylobates may reflect a morphotype for all later hominoids, thus complicating the functional interpretations of fossil hominins. The implications of these results are that the proximal radius is not a sensitive indicator of locomotor behavior among hominoids since the morphology in hylobatids and Gorilla and Pan is similar despite widely varying positional repertoires. Furthermore, inferences of function from form in extinct hominins can be drastically affected by the comparative outgroup selection. A re-evaluation of the functional morphology of the proximal radius in early hominins is addressed.     

A Haplotype at STAT2 Introgressed from Neanderthals and Serves as a Candidate of Positive Selection in Papua New Guinea

Signals of archaic admixture have been identified through comparisons of the draft Neanderthal and Denisova genomes with those of living humans. Studies of individual loci contributing to these genome-wide average signals are required for characterization of the introgression process and investigation of whether archaic variants conferred an adaptive advantage to the ancestors of contemporary human populations. However, no definitive case of adaptive introgression has yet been described. Here we provide a DNA sequence analysis of the innate immune gene STAT2 and show that a haplotype carried by many Eurasians (but not sub-Saharan Africans) has a sequence that closely matches that of the Neanderthal STAT2. This haplotype, referred to as N, was discovered through a resequencing survey of the entire coding region of STAT2 in a global sample of 90 individuals. Analyses of publicly available complete genome sequence data show that haplotype N shares a recent common ancestor with the Neanderthal sequence (∼80 thousand years ago) and is found throughout Eurasia at an average frequency of ∼5%. Interestingly, N is found in Melanesian populations at ∼10-fold higher frequency (∼54%) than in Eurasian populations. A neutrality test that controls for demography rejects the hypothesis that a variant of N rose to high frequency in Melanesia by genetic drift alone. Although we are not able to pinpoint the precise target of positive selection, we identify nonsynonymous mutations in ERBB3, ESYT1, and STAT2—all of which are part of the same 250 kb introgressive haplotype—as good candidates.     

When should we save the most endangered species?

At the heart of our efforts to protect threatened species, there is a controversial debate about whether to give priority to cost-effective actions or whether focusing solely on the most endangered species will ultimately lead to preservation of the greatest number of species. By framing this debate within a decision-analytic framework, we show that allocating resources solely to the most endangered species will typically not minimise the number of extinctions in the long-term, as this does not account for the risk of less endangered species going extinct in the future. It is only favoured when our planning timeframe is short or we have a long-term view and we are optimistic about future conditions. Conservation funding tends to be short-term in nature, which biases allocations to more endangered species. Our work highlights the need to consider resource allocation for biodiversity over the long-term; 'preventive conservation', rather than just short-term fire-fighting.     

Evidence of recent and continuous speciation in a biodiversity hotspot: a population genetic approach in southern African gladioli (Gladiolus; Iridaceae)

There has been much debate over the origin of species diversity in biodiversity hotspots, particularly the rate of speciation over extinction and the geographic mode of speciation. Here, we looked at speciation with varying degrees of sympatry in a biodiversity hotspot, focusing on a distinct morphological clade in the Cape Floristic Region in southern Africa, the Gladiolus carinatus species complex (Iridaceae). We investigate the mechanisms involved in population and species differentiation through a combination of ecological and genomic approaches. We estimated spatial and phenological overlap, differences in floral morphology, genetic isolation and genomic selection. A genetic coalescent analysis estimated that the time of divergence between lineages followed the establishment of available habitat in the Cape littoral plain where these species currently overlap geographically. Marked shifts in flowering time and morphology, which act as barriers to gene flow, have developed to varying degrees over the last 0.3–1.4 million years. An amplified fragment length polymorphism genome scan revealed signatures of divergent and balancing selection, although half of the loci consistently behaved neutrally. Divergent species outliers (1%) and floral morph outliers (3%) represent a small proportion of the genome, but these loci produced clear genetic clusters of species and significant associations with floral traits. These results indicate that the G. carinatus complex represents a continuum of recent speciation. We provide further evidence for ecological adaptation in the face of gene flow.     

A deterministic model of admixture and genetic introgression: the case of Neanderthal and Cro-Magnon

There is an ongoing debate in the field of human evolution about the possible contribution of Neanderthals to the modern human gene pool. To study how the Neanderthal private alleles may have spread over the genes of Homo sapiens, we propose a deterministic model based on recursive equations and ordinary differential equations. If the Neanderthal population was large compared to the Homo sapiens population at the beginning of the contact period, we show that genetic introgression should have been fast and complete meaning that most of the Neanderthal private alleles should be found in the modern human gene pool in case of ancient admixture. In order to test/reject ancient admixture from genome-wide data, we incorporate the model of genetic introgression into a statistical hypothesis-testing framework. We show that the power to reject ancient admixture increases as the ratio, at the time of putative admixture, of the population size of Homo sapiens over that of Neanderthal decreases. We find that the power to reject ancient admixture might be particularly low if the population size of Homo sapiens was comparable to the Neanderthal population size.     

Modern humans did not admix with Neanderthals during their range expansion into Europe

The process by which the Neanderthals were replaced by modern humans between 42,000 and 30,000 before present is still intriguing. Although no Neanderthal mitochondrial DNA (mtDNA) lineage is found to date among several thousands of Europeans and in seven early modern Europeans, interbreeding rates as high as 25% could not be excluded between the two subspecies. In this study, we introduce a realistic model of the range expansion of early modern humans into Europe, and of their competition and potential admixture with local Neanderthals. Under this scenario, which explicitly models the dynamics of Neanderthals' replacement, we estimate that maximum interbreeding rates between the two populations should have been smaller than 0.1%. We indeed show that the absence of Neanderthal mtDNA sequences in Europe is compatible with at most 120 admixture events between the two populations despite a likely cohabitation time of more than 12,000 y. This extremely low number strongly suggests an almost complete sterility between Neanderthal females and modern human males, implying that the two populations were probably distinct biological species.