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Bibliography on: Neanderthals

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ESP: PubMed Auto Bibliography 26 Jun 2019 at 01:34 Created: 


Wikipedia: Neanderthals or Neandertals — named for the Neandertal region in Germany — were a species or subspecies of archaic human, in the genus Homo. Neanderthals became extinct around 40,000 years ago. They were closely related to modern humans, sharing 99.7% of DNA. Remains left by Neanderthals include bone and stone tools, which are found in Eurasia, from Western Europe to Central and Northern Asia. Neanderthals are generally classified by paleontologists as the species Homo neanderthalensis, having separated from the Homo sapiens lineage 600,000 years ago, but a minority consider them to be a subspecies of Homo sapiens (Homo sapiens neanderthalensis). Several cultural assemblages have been linked to the Neanderthals in Europe. The earliest, the Mousterian stone tool culture, dates to about 160,000 years ago. Late Mousterian artifacts were found in Gorham's Cave on the south-facing coast of Gibraltar. Compared to Homo sapiens, Neanderthals had a lower surface-to-volume ratio, with shorter legs and a bigger body, in conformance with Bergmann's rule, as an energy-loss reduction adaptation to life in a high-latitude (i.e. seasonally cold) climate. Their average cranial capacity was notably larger than typical for modern humans: 1600 cm3 vs. 1250-1400 cm3. The Neanderthal genome project published papers in 2010 and 2014 stating that Neanderthals contributed to the DNA of modern humans, including most humans outside sub-Saharan Africa, as well as a few populations in sub-Saharan Africa, through interbreeding, likely between 50,000 and 60,000 years ago.

Created with PubMed® Query: Neanderthal OR Neandertal NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2019-06-21

Ackermann RR, Arnold ML, Baiz MD, et al (2019)

Hybridization in human evolution: Insights from other organisms.

Evolutionary anthropology [Epub ahead of print].

During the late Pleistocene, isolated lineages of hominins exchanged genes thus influencing genomic variation in humans in both the past and present. However, the dynamics of this genetic exchange and associated phenotypic consequences through time remain poorly understood. Gene exchange across divergent lineages can result in myriad outcomes arising from these dynamics and the environmental conditions under which it occurs. Here we draw from our collective research across various organisms, illustrating some of the ways in which gene exchange can structure genomic/phenotypic diversity within/among species. We present a range of examples relevant to questions about the evolution of hominins. These examples are not meant to be exhaustive, but rather illustrative of the diverse evolutionary causes/consequences of hybridization, highlighting potential drivers of human evolution in the context of hybridization including: influences on adaptive evolution, climate change, developmental systems, sex-differences in behavior, Haldane's rule and the large X-effect, and transgressive phenotypic variation.

RevDate: 2019-06-20
CmpDate: 2019-06-20

Gibbons A (2019)

Moderns said to mate with late-surviving Denisovans.

Science (New York, N.Y.), 364(6435):12-13.

RevDate: 2019-06-20
CmpDate: 2019-06-20

Ioannidou M, Falcucci A, Röding C, et al (2019)

Eighth Annual Meeting of the European Society for the Study of Human Evolution.

Evolutionary anthropology, 28(2):52-54.

RevDate: 2019-06-20
CmpDate: 2019-06-20

Chiang CWK, Mangul S, Robles C, et al (2018)

A Comprehensive Map of Genetic Variation in the World's Largest Ethnic Group-Han Chinese.

Molecular biology and evolution, 35(11):2736-2750.

As are most non-European populations, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we present a catalog of 25,057,223 variants, including 548,401 novel variants that are seen at least 10 times in our data set. Individuals from this data set came from 24 out of 33 administrative divisions across China (including 19 provinces, 4 municipalities, and 1 autonomous region), thus allowing us to study population structure, genetic ancestry, and local adaptation in Han Chinese. We identified previously unrecognized population structure along the East-West axis of China, demonstrated a general pattern of isolation-by-distance among Han Chinese, and reported unique regional signals of admixture, such as European influences among the Northwestern provinces of China. Furthermore, we identified a number of highly differentiated, putatively adaptive, loci (e.g., MTHFR, ADH7, and FADS, among others) that may be driven by immune response, climate, and diet in the Han Chinese. Finally, we have made available allele frequency estimates stratified by administrative divisions across China in the Geography of Genetic Variant browser for the broader community. By leveraging the largest currently available genetic data set for Han Chinese, we have gained insights into the history and population structure of the world's largest ethnic group.

RevDate: 2019-06-17

Fiorenza L, Benazzi S, Kullmer O, et al (2019)

Dental macrowear and cortical bone distribution of the Neanderthal mandible from Regourdou (Dordogne, Southwestern France).

Journal of human evolution, 132:174-188.

Tooth wear is an important feature for reconstructing diet, food processing and cultural habits of past human populations. In particular, occlusal wear facets can be extremely useful for detecting information about diet and non-masticatory behaviors. The aim of this study is to reconstruct the diet and cultural behavior of the Neanderthal specimen Regourdou 1 (Dordogne, Southern France) from the analysis of the macrowear pattern, using the occlusal fingerprint analysis method. In addition, we have also examined whether there is any association between the observed dental macrowear and mandibular bone distribution and root dentine thickness. The posterior dentition of Regourdou 1 is characterized by an asymmetric wear pattern, with the right side significantly more worn than the left. In contrast, the left lower P3 shows a more advanced wear than the right premolar, with unusual semicircular enamel wear facets. The results from occlusal fingerprint analysis of this unique pattern suggest tooth-tool uses for daily task activities. Moreover, the left buccal aspect of the mandibular cortical bone is thicker than its right counterpart, and the left P3 has a thicker radicular dentine layer than its antimere. These results show a certain degree of asymmetry in cortical bone topography and dentine tissue that could be associated with the observed dental macrowear pattern. The molar macrowear pattern also suggests that Regourdou 1 had a mixed diet typical of those populations living in temperate deciduous woodlands and Mediterranean habitats, including animal and plant foods. Although this study is limited to one Neanderthal individual, future analyses based on a larger sample may further assist us to better understand the existing relationship between mandibular architecture, occlusal wear and the masticatory apparatus in humans.

RevDate: 2019-06-17

Galletta L, Stephens NB, Bardo A, et al (2019)

Three-dimensional geometric morphometric analysis of the first metacarpal distal articular surface in humans, great apes and fossil hominins.

Journal of human evolution, 132:119-136.

Understanding the manual abilities of fossil hominins has been a focus of palaeoanthropological research for decades. Of interest are the morphological characteristics of the thumb due to its fundamental role in manipulation, particularly that of the trapeziometacarpal joint. Considerably less attention has been given to the thumb metacarpophalangeal (MCP) joint, which plays a role in stabilizing the thumb during forceful grasps and precision pinching. In this study we use a three-dimensional geometric morphometric approach to quantify the shape of the first metacarpal head in extant hominids (Homo, Pan, Gorilla and Pongo) and six fossil hominin species (Homo neanderthalensis Tabun C1 and La Chappelle-aux-Saints, Homo naledi U.W. 101-1282, Australopithecus sediba MH2, Paranthropus robustus/early Homo SK84, Australopithecus africanus StW 418, Australopithecus afarensis A.L. 333w-39), with the aims of identifying shapes that may be correlated with human-like forceful opposition and determining if similar morphologies are present in fossil hominins. Results show that humans differ from extant great apes by having a distally flatter articular surface, larger epicondyle surface area, and a larger radial palmar condyle. We suggest that this suite of features is correlated with a lower range of motion at the MCP joint, which would enhance the thumbs ability to resist the elevated loads associated with the forceful precision grips typical of humans. Great ape genera are each differentiated by distinctive morphological features, each of which is consistently correlated with the predicted biomechanical demands of their particular locomotor and/or manipulatory habits. Neanderthals and U.W. 101-1282 fall within the modern human range of variation, StW 418, SK 84 and U.W. 88-119 fall in between humans and great apes, and A.L. 333w-39 falls within Pan variation. These results agree with those of traditional linear analyses while providing a more comprehensive quantitative basis from which to interpret the hand functional morphology of extinct hominins.

RevDate: 2019-06-14

Haber M, Jones AL, Connell BA, et al (2019)

A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans out of Africa.

Genetics pii:genetics.119.302368 [Epub ahead of print].

Present-day humans outside Africa descend mainly from a single expansion out ∼50,000-70,000 years ago, but many details of this expansion remain unclear, including the history of the male-specific Y chromosome at this time. Here, we re-investigate a rare deep-rooting African Y-chromosomal lineage by sequencing the whole genomes of three Nigerian men described in 2003 as carrying haplogroup DE* Y-chromosomes, and analyzing them in the context of a calibrated worldwide Y-chromosomal phylogeny. We confirm that these three chromosomes do represent a deep-rooting DE lineage, branching close to the DE bifurcation, but place them on the D branch as an outgroup to all other known D chromosomes, and designate the new lineage D0. We consider three models for the expansion of Y lineages out of Africa ∼50,000-100,000 years ago, incorporating migration back to Africa where necessary to explain present-day Y-lineage distributions. Considering both the Y-chromosomal phylogenetic structure incorporating the D0 lineage, and published evidence for modern humans outside Africa, the most favored model involves an origin of the DE lineage within Africa with D0 and E remaining there, and migration out of the three lineages (C, D and FT) that now form the vast majority of non-African Y chromosomes. The exit took place 50,300-81,000 years ago (latest date for FT lineage expansion outside Africa - earliest date for the D/D0 lineage split inside Africa), and most likely 50,300-59,400 years ago (considering Neanderthal admixture). This work resolves a long-running debate about Y-chromosomal out-of-Africa/back-to-Africa migrations, and provides insights into the out-of-Africa expansion more generally.

RevDate: 2019-06-12

Kuhlwilm M, C Boeckx (2019)

A catalog of single nucleotide changes distinguishing modern humans from archaic hominins.

Scientific reports, 9(1):8463 pii:10.1038/s41598-019-44877-x.

Throughout the past decade, studying ancient genomes has provided unique insights into human prehistory, and differences between modern humans and other branches like Neanderthals can enrich our understanding of the molecular basis of unique modern human traits. Modern human variation and the interactions between different hominin lineages are now well studied, making it reasonable to go beyond fixed genetic changes and explore changes that are observed at high frequency in present-day humans. Here, we identify 571 genes with non-synonymous changes at high frequency. We suggest that molecular mechanisms in cell division and networks affecting cellular features of neurons were prominently modified by these changes. Complex phenotypes in brain growth trajectory and cognitive traits are likely influenced by these networks and other non-coding changes presented here. We propose that at least some of these changes contributed to uniquely human traits, and should be prioritized for experimental validation.

RevDate: 2019-06-12

Shultz DR, Montrey M, TR Shultz (2019)

Comparing fitness and drift explanations of Neanderthal replacement.

Proceedings. Biological sciences, 286(1904):20190907.

There is a general consensus among archaeologists that replacement of Neanderthals by anatomically modern humans in Europe occurred around 40-35 ka. However, the causal mechanism for this replacement continues to be debated. Proposed models have featured either fitness advantages in favour of anatomically modern humans or invoked neutral drift under various preconditions. Searching for specific fitness advantages in the archaeological record has proven difficult, as these may be obscured, absent or subject to interpretation. To bridge this gap, we rigorously compare the system-level properties of fitness- and drift-based explanations of Neanderthal replacement. Our stochastic simulations and analytical predictions show that, although both fitness and drift can produce replacement, they present important differences in (i) required initial conditions, (ii) reliability, (iii) time to replacement, and (iv) path to replacement (population histories). These results present useful opportunities for comparison with archaeological and genetic data. We find greater agreement between the available empirical evidence and the system-level properties of replacement by differential fitness, rather than by neutral drift.

RevDate: 2019-06-11

Demuro M, Arnold LJ, Aranburu A, et al (2019)

New bracketing luminescence ages constrain the Sima de los Huesos hominin fossils (Atapuerca, Spain) to MIS 12.

Journal of human evolution, 131:76-95.

Recent chronological studies of the Sima de los Huesos (SH) hominin fossil site, Atapuerca, Spain, have established a close minimum age of at least 430 ka for sedimentary material immediately overlying the human remains. However, a firm maximum age limit still needs to be established for the SH fossils in order to better constrain the timing for the onset of Neandertal speciation. In the present study, we address this important chronological gap at SH by providing direct ages for the sediment deposits that host, and immediately underlie, the hominin fossils. Depositional ages were obtained using single-grain thermally-transferred optically stimulated luminescence (TT-OSL), a technique that has yielded reliable 'extended-range' luminescence chronologies at several independently dated Atapuerca sites. Four single-grain TT-OSL depositional ages of 453 ± 56 ka, 437 ± 38 ka, 457 ± 41 ka and 460 ± 39 ka were obtained for the red clay lithostratigraphic units (LU-5 and LU-6) found underlying and encasing the SH hominin bones. A Bayesian age-depth model was constructed using previously published chronologies, as well as the new single-grain TT-OSL ages for LU-5 and LU-6, in order to derive combined age estimates for individual lithostratigraphic units preserved at SH. The combined modeled ranges reveal that the hominin-bearing layer (LU-6) was deposited between 455 ± 17 ka and 440 ± 15 ka (mean lower and upper boundary 68.2% probability range ± 1σ uncertainty, respectively), with a mean age of 448 ± 15 ka. These new bracketing ages suggest that the hominin fossils at SH were most likely deposited within Marine Isotope Stage (MIS) 12, enabling more precise temporal constraint on the early evolution of the Neandertal lineage. The SH fossils represent the oldest reliably dated hominin remains displaying Neandertal features across Eurasia. These Neandertal features are first observed in the facial skeleton, including the mandible and teeth, as well as the temporomandibular joint, and appear consistently across the SH collection. Our chronological findings suggest that the appearance of these Neandertal traits may have been associated with the climatic demise of MIS 12 and the ecological changes that occurred in Iberia during this period. Other Middle Pleistocene hominin fossils from Europe dated to MIS 12-11, or later, show different morphological trends, with some lacking Neandertal specializations. The latest SH dating results enable improved temporal correlations with these contrasting hominin records from Europe, and suggest a complex picture for hominin evolution during the Middle Pleistocene.

RevDate: 2019-06-11

Radović P, Lindal J, Mihailović D, et al (2019)

The first Neanderthal specimen from Serbia: Maxillary first molar from the Late Pleistocene of Pešturina Cave.

Journal of human evolution, 131:139-151.

Neanderthals were the only human group in Europe throughout the Late Pleistocene until the arrival of modern humans, and while their presence has been confirmed in the surrounding regions, no Neanderthal fossils are known to date from the Central Balkans. Systematic excavations of Pešturina Cave (Serbia) resulted in the discovery of a permanent right M1 (Pes-3). The specimen was recovered from stratigraphic Layer 4b with an estimated age of 102.4 ± 3.2 ka, associated with Mousterian artifacts. The exceptional state of preservation and minimal wear of the molar enabled a detailed description and comparative analysis of the inner and outer dental structure, including non-metric dental traits and morphometric features of the crown, roots, and dental tissues. The results of this study strongly support the identification of Pes-3 as Neanderthal. Non-metric traits of the occlusal surface of the crown, enamel-dentine junction, and roots are consistent with Neanderthal morphology. The crown shows morphometric features typical for Neanderthal M1, such as a buccolingually skewed crown shape, internally compressed cusps, and a relatively large hypocone. The specimen also shows Neanderthal-like dental tissue proportions, characterized by relatively thin enamel and large coronal dentine and coronal pulp volumes. The discovery of the Pes-3 molar therefore confirms the presence of Neanderthals in the territory of Serbia and the Central Balkans at the end of Marine Isotope Stage (MIS) 5c.

RevDate: 2019-06-10

Shebanits K, Günther T, Johansson ACV, et al (2019)

Copy number determination of the gene for the human pancreatic polypeptide receptor NPY4R using read depth analysis and droplet digital PCR.

BMC biotechnology, 19(1):31 pii:10.1186/s12896-019-0523-9.

BACKGROUND: Copy number variation (CNV) plays an important role in human genetic diversity and has been associated with multiple complex disorders. Here we investigate a CNV on chromosome 10q11.22 that spans NPY4R, the gene for the appetite-regulating pancreatic polypeptide receptor Y4. This genomic region has been challenging to map due to multiple repeated elements and its precise organization has not yet been resolved. Previous studies using microarrays were interpreted to show that the most common copy number was 2 per genome.

RESULTS: We have investigated 18 individuals from the 1000 Genomes project using the well-established method of read depth analysis and the new droplet digital PCR (ddPCR) method. We find that the most common copy number for NPY4R is 4. The estimated number of copies ranged from three to seven based on read depth analyses with Control-FREEC and CNVnator, and from four to seven based on ddPCR. We suggest that the difference between our results and those published previously can be explained by methodological differences such as reference gene choice, data normalization and method reliability. Three high-quality archaic human genomes (two Neanderthal and one Denisova) display four copies of the NPY4R gene indicating that a duplication occurred prior to the human-Neanderthal/Denisova split.

CONCLUSIONS: We conclude that ddPCR is a sensitive and reliable method for CNV determination, that it can be used for read depth calibration in CNV studies based on already available whole-genome sequencing data, and that further investigation of NPY4R copy number variation and its consequences are necessary due to the role of Y4 receptor in food intake regulation.

RevDate: 2019-06-05

Santander C, Montinaro F, C Capelli (2019)

Searching for archaic contribution in Africa.

Annals of human biology [Epub ahead of print].

Context: Africa's role in the narrative of human evolution is indisputably emphasised in the emergence Homo sapiens. However, once humans disperse beyond Africa, the history of those who stayed remains vastly understudied lacking the proper attention it deserves as the birthplace of both modern and archaic humans. The sequencing of Neanderthal and Denisovan genomes has elucidated evidence of admixture between archaic and modern humans outside of Africa but has not aided efforts in answering whether archaic admixture happened within Africa. Objectives: We review here the state of research for archaic introgression in African populations and discuss recent insights into this topic. Methods: Gathering published sources and recently released preprints, this review reports on the different methods developed for detecting archaic introgression. Particularly we discuss how relevant these are when implemented on African populations and what findings these studies have shown so far. Results: Methods for detecting archaic introgression have been predominantly developed and implemented on non-African populations. Recent preprints present new methods considering African populations. While a number of studies using these methods suggest archaic introgression in Africa, without an African archaic genome to validate these results, such findings remain as putative archaic introgression. Conclusion: In light of the caveats with implementing current archaic introgression detection methods in Africa, we recommend future studies to concentrate on unravelling the complicated demographic history of Africa through means of ancient DNA where possible and through more focused efforts to sequence modern DNA from more representative populations across the African continent.

RevDate: 2019-06-07

Silvert M, Quintana-Murci L, M Rotival (2019)

Impact and Evolutionary Determinants of Neanderthal Introgression on Transcriptional and Post-Transcriptional Regulation.

American journal of human genetics, 104(6):1241-1250.

Archaic admixture is increasingly recognized as an important source of diversity in modern humans, and Neanderthal haplotypes cover 1%-3% of the genome of present-day Eurasians. Recent work has shown that archaic introgression has contributed to human phenotypic diversity, mostly through the regulation of gene expression. Yet the mechanisms through which archaic variants alter gene expression and the forces driving the introgression landscape at regulatory regions remain elusive. Here, we explored the impact of archaic introgression on transcriptional and post-transcriptional regulation. We focused on promoters and enhancers across 127 different tissues as well as on microRNA (miRNA)-mediated regulation. Although miRNAs themselves harbor few archaic variants, we found that some of these variants may have a strong impact on miRNA-mediated gene regulation. Enhancers were by far the regulatory elements most affected by archaic introgression: up to one-third of the tissues we tested presented significant enrichments. Specifically, we found strong enrichments of archaic variants in adipose-related tissues and primary T cells, even after accounting for various genomic and evolutionary confounders such as recombination rate and background selection. Interestingly, we identified signatures of adaptive introgression at enhancers of some key regulators of adipogenesis, raising the interesting hypothesis of a possible adaptation of early Eurasians to colder climates. Collectively, this study sheds new light on the mechanisms through which archaic admixture has impacted gene regulation in Eurasians and, more generally, increases our understanding of the contribution of Neanderthals to the regulation of acquired immunity and adipose homeostasis in modern humans.

RevDate: 2019-06-10

Degioanni A, Bonenfant C, Cabut S, et al (2019)

Living on the edge: Was demographic weakness the cause of Neanderthal demise?.

PloS one, 14(5):e0216742 pii:PONE-D-19-00615.

The causes of disappearance of the Neanderthals, the only human population living in Europe before the arrival of Homo sapiens, have been debated for decades by the scientific community. Different hypotheses have been advanced to explain this demise, such as cognitive, adaptive and cultural inferiority of Neanderthals. Here, we investigate the disappearance of Neanderthals by examining the extent of demographic changes needed over a period of 10,000 years (yrs) to lead to their extinction. In regard to such fossil populations, we inferred demographic parameters from present day and past hunter-gatherer populations, and from bio-anthropological rules. We used demographic modeling and simulations to identify the set of plausible demographic parameters of the Neanderthal population compatible with the observed dynamics, and to explore the circumstances under which they might have led to the disappearance of Neanderthals. A slight (<4%) but continuous decrease in the fertility rate of younger Neanderthal women could have had a significant impact on these dynamics, and could have precipitated their demise. Our results open the way to non-catastrophic events as plausible explanations for Neanderthal extinction.

RevDate: 2019-06-07

Durvasula A, S Sankararaman (2019)

A statistical model for reference-free inference of archaic local ancestry.

PLoS genetics, 15(5):e1008175 pii:PGENETICS-D-18-01534.

Statistical analyses of genomic data from diverse human populations have demonstrated that archaic hominins, such as Neanderthals and Denisovans, interbred or admixed with the ancestors of present-day humans. Central to these analyses are methods for inferring archaic ancestry along the genomes of present-day individuals (archaic local ancestry). Methods for archaic local ancestry inference rely on the availability of reference genomes from the ancestral archaic populations for accurate inference. However, several instances of archaic admixture lack reference archaic genomes, making it difficult to characterize these events. We present a statistical method that combines diverse population genetic summary statistics to infer archaic local ancestry without access to an archaic reference genome. We validate the accuracy and robustness of our method in simulations. When applied to genomes of European individuals, our method recovers segments that are substantially enriched for Neanderthal ancestry, even though our method did not have access to any Neanderthal reference genomes.

RevDate: 2019-06-10

Liu C, Everall I, Pantelis C, et al (2019)

Interrogating the Evolutionary Paradox of Schizophrenia: A Novel Framework and Evidence Supporting Recent Negative Selection of Schizophrenia Risk Alleles.

Frontiers in genetics, 10:389.

Schizophrenia is a psychiatric disorder with a worldwide prevalence of ∼1%. The high heritability and reduced fertility among schizophrenia patients have raised an evolutionary paradox: why has negative selection not eliminated schizophrenia associated alleles during evolution? To address this question, we examined evolutionary markers, known as modern-human-specific (MD) sites and archaic-human-specific sites, using existing genome-wide association study (GWAS) data from 34,241 individuals with schizophrenia and 45,604 healthy controls included in the Psychiatric Genomics Consortium (PGC). By testing the distribution of schizophrenia single nucleotide polymorphisms (SNPs) with risk and protective effects in the human-specific sites, we observed a negative selection of risk alleles for schizophrenia in modern humans relative to archaic humans (e.g., Neanderthal and Denisovans). Such findings indicate that risk alleles of schizophrenia have been gradually removed from the modern human genome due to negative selection pressure. This novel evidence contributes to our understanding of the genetic origins of schizophrenia.

RevDate: 2019-05-22

Ham E, Underdown SJ, CJ Houldcroft (2019)

The relative roles of maternal survival and inter-personal violence as selection pressures on the persistence of Neanderthal hypercoagulability alleles in modern Europeans.

Annals of human biology [Epub ahead of print].

BACKGROUND: Simoni et al (2016) reported variation in the frequency of Neanderthal alleles found in modern humans and argued that they may have provided an evolutionary advantage. One such allele is SNP rs3917862, associated with hypercoagulability. rs3917862 can be deleterious but can also help prevent blood loss.

AIM: To investigate two possible selective pressure hypotheses for rs3917862 surviving to higher frequencies: deaths from interpersonal violent trauma and childbirth.

SUBJECTS AND METHODS: Mortality data from modern hunter-gatherers models the living conditions and causes of death of humans and Neanderthals at the point of admixture.

RESULTS: National census data indicates a positive correlation between presence of rs3917862 and decreased maternal mortality ratios. When maternal mortality ratio is modelled using GDP, births attended by skilled assistants and the presence of rs3917862, women are 0.1% more likely to die in childbirth in populations lacking rs3917862. Deaths due to violence show no correlation with rs3917862.

CONCLUSION: These findings challenge the idea that Neanderthal admixture has negatively impacted the overall health of modern humans. Maternal survival may have acted as a selective pressure for the persistence of hypercoagulability alleles in modern Europeans. Understanding the role of hypercoagulability in childbirth, and the role of rs3917862, could help to reduce maternal mortality ratios.

RevDate: 2019-05-22

Gómez-Robles A (2019)

Dental evolutionary rates and its implications for the Neanderthal-modern human divergence.

Science advances, 5(5):eaaw1268 pii:aaw1268.

The origin of Neanderthal and modern human lineages is a matter of intense debate. DNA analyses have generally indicated that both lineages diverged during the middle period of the Middle Pleistocene, an inferred time that has strongly influenced interpretations of the hominin fossil record. This divergence time, however, is not compatible with the anatomical and genetic Neanderthal affinities observed in Middle Pleistocene hominins from Sima de los Huesos (Spain), which are dated to 430 thousand years (ka) ago. Drawing on quantitative analyses of dental evolutionary rates and Bayesian analyses of hominin phylogenetic relationships, I show that any divergence time between Neanderthals and modern humans younger than 800 ka ago would have entailed unexpectedly rapid dental evolution in early Neanderthals from Sima de los Huesos. These results support a pre-800 ka last common ancestor for Neanderthals and modern humans unless hitherto unexplained mechanisms sped up dental evolution in early Neanderthals.

RevDate: 2019-06-10

Morales JI, Cebrià A, Burguet-Coca A, et al (2019)

The Middle-to-Upper Paleolithic transition occupations from Cova Foradada (Calafell, NE Iberia).

PloS one, 14(5):e0215832 pii:PONE-D-18-31331.

The Middle-to-Upper Paleolithic transition in Europe covers the last millennia of Neanderthal life together with the appearance and expansion of Modern Human populations. Culturally, it is defined by the Late Middle Paleolithic succession, and by Early Upper Paleolithic complexes like the Châtelperronian (southwestern Europe), the Protoaurignacian, and the Early Aurignacian. Up to now, the southern boundary for the transition has been established as being situated between France and Iberia, in the Cantabrian façade and Pyrenees. According to this, the central and southern territories of Iberia are claimed to have been the refuge of the last Neanderthals for some additional millennia after they were replaced by anatomically Modern Humans on the rest of the continent. In this paper, we present the Middle-to-Upper Paleolithic transition sequence from Cova Foradada (Tarragona), a cave on the Catalan Mediterranean coastline. Archaeological research has documented a stratigraphic sequence containing a succession of very short-term occupations pertaining to the Châtelperronian, Early Aurignacian, and Gravettian. Cova Foradada therefore represents the southernmost Châtelperronian-Early Aurignacian sequence ever documented in Europe, significantly enlarging the territorial distribution of both cultures and providing an important geographical and chronological reference for understanding Neanderthal disappearance and the complete expansion of anatomically Modern Humans.

RevDate: 2019-05-15

Vangenot C, Gagneux P, de Groot NG, et al (2019)

Humans and Chimpanzees Display Opposite Patterns of Diversity in arylamineN-acetyltranferase Genes.

G3 (Bethesda, Md.) pii:g3.119.400223 [Epub ahead of print].

Among the many genes involved in the metabolism of therapeutic drugs, human arylamine N-acetyltransferases (NATs) genes have been extensively studied, due to their medical importance both in pharmacogenetics and disease epidemiology. One member of this small gene family, NAT2, is established as the locus of the classic human acetylation polymorphism in drug metabolism. Current hypotheses hold that selective processes favoring haplotypes conferring lower NAT2 activity have been operating in modern humans' recent history as an adaptation to local chemical and dietary environments. To shed new light on such hypotheses, we investigated the genetic diversity of the three members of the NAT gene family in seven hominid species, including modern humans, Neanderthals and Denisovans. Little polymorphism sharing was found among hominids, yet all species displayed high NAT diversity, but distributed in an opposite fashion in chimpanzees and bonobos (Pan genus) compared to modern humans, with higher diversity in Pan species at NAT1 and lower at NAT2, while the reverse is observed in humans. This pattern was also reflected in the results returned by selective neutrality tests, which suggest, in agreement with the predicted functional impact of mutations detected in non-human primates, stronger directional selection, presumably purifying selection, at NAT1 in modern humans, and at NAT2 in chimpanzees. Overall, the results point to the evolution of divergent functions of these highly homologous genes in the different primate species, possibly related to their specific chemical/dietary environment (exposome) and we hypothesize that this is likely linked to the emergence of controlled fire use in the human lineage.

RevDate: 2019-05-19

Rhodes SE, Starkovich BM, NJ Conard (2019)

Did climate determine Late Pleistocene settlement dynamics in the Ach Valley, SW Germany?.

PloS one, 14(5):e0215172 pii:PONE-D-18-34440.

The loss of Neanderthal groups across Western and Central Europe during Oxygen Isotope Stage (OIS) 3 has held the attention of archaeologists for decades. The role that climatic change, genetic interbreeding, and interspecies competition played in the extinction of Neanderthal groups is still debated. Hohle Fels is one of several important Middle and Upper Paleolithic sites from the Ach Valley in southwestern Germany which documents the presence of Neanderthals and modern humans in the region. Chronological and stratigraphic records indicate that these two groups occupied the site with little to no overlap or interaction. This provides the opportunity to examine the behavioural variability of Swabian Neanderthal populations without the complication of cross-cultural influence. In this study we contribute a terrestrial paleoenvironmental record derived from the small mammal material from Hohle Fels Cave to the ever-growing archaeological record of this period. By reconstructing the climate and landscape of the Ach Valley during this time we can identify the effect that the OIS 3 environment had on the presence of Neanderthals in the region. Based on indicator taxa and the habitat weighing method, the small mammal record, which includes rodents, insectivores, and bats, from Hohle Fels shows that the earliest Neanderthal occupation took place on a landscape characterized by substantial woodland and forest, rivers and ponds, as well as moist meadows and grasslands. A gradual increase in cold tundra and arctic environments is clear towards the end of the Middle Paleolithic, extending to the end of the early Aurignacian which may correlate with the onset of the Heinrich 4 event (~42,000 kya). Our taphonomic analysis indicates the material was accumulated primarily by opportunistic predators such as the great grey owl, snowy owl, and European eagle owl, and therefore reflects the diversity of landscapes present around the site in the past. Importantly, at the time Neanderthals abandoned the Ach Valley we find no indication for dramatic climatic deterioration. Rather, we find evidence of a gradual cooling of the Swabian landscape which may have pushed Neanderthal groups out of the Ach Valley prior to the arrival of modern human Aurignacian groups.

RevDate: 2019-05-19

Letsinger AC, Granados JZ, Little SE, et al (2019)

Alleles associated with physical activity levels are estimated to be older than anatomically modern humans.

PloS one, 14(4):e0216155 pii:PONE-D-18-32514.

The purpose of this study was to determine the estimated mutation age and conservation of single-nucleotide polymorphisms (SNPs) associated with physical activity (PA) in humans. All human SNPs found to be significantly associated with PA levels in the literature were cross-referenced with the National Heart, Lung, and Blood Institute's Grand Opportunity Exome Sequencing Project to find estimated African-American (AA) and European-American (EA) mutation age. As a secondary measure of mutation age, SNPs were searched for in Hawk's mutation age prediction database which utilizes linkage equilibrium. To determine conservation among hominids, all SNPs were searched in the University of California, Santa Cruz Genome Browser, which contains Neanderthal and chimpanzee reference genomes. Six of the 104 SNPs associated with PA regulation were exon-located missense variants found in IFNAR2, PPARGC1A, PML, CTBP2, IL5RA, and APOE genes. The remaining 98 SNPs were located in non-protein coding regions. Average AA and EA estimated mutation age of the exon-located SNPs were 478.4 ± 327.5 kya and 542.1 ± 369.4 kya, respectively. There were four selective sweeps (suggestive of strong positive selection) of SNPs in humans when compared to Neanderthal or chimpanzee genomes. Exon-located PA candidate SNPs are older than the hypothesized emergence of anatomically modern humans. However, 95% of PA associated SNPs are found in intron and intergenic location. Across all SNPs, there seems to be a high level of conservation of alleles between humans, Neanderthals, and chimpanzees. However, the presence of four selective sweeps suggests there were selection pressures or drift unique to Homo sapiens that influenced the development of mutations associated with PA regulation.

RevDate: 2019-04-26

Bosman AM, K Harvati (2019)

A virtual assessment of the proposed suprainiac fossa on the early modern European calvaria from Cioclovina, Romania.

American journal of physical anthropology [Epub ahead of print].

OBJECTIVES: The calvaria from Cioclovina (Romania) has been argued to possess some traits commonly ascribed to individuals belonging to the Neanderthal lineage, including a suprainiac fossa. However, its supranuchal morphology has only been evaluated with a qualitative analysis of the ectocranial surface. We evaluate whether the morphology of the supranuchal area of this specimen is homologous to the Neanderthal condition.

MATERIALS AND METHODS: We described in detail the external morphology, and, using computed tomography, investigated the internal morphology of the Cioclovina supranuchal area. We took measurements of the internal structures and calculated their relative contributions to total cranial vault thickness, which were compared to published data and evaluated with a principal component analysis (PCA).

RESULTS: The Cioclovina supranuchal region is characterized by superficial resorption present on the outer layer of the external table. Neither the diploic layer nor the external table decrease in relative thickness in the area above inion. In the PCA, Cioclovina falls within the convex hulls of recent modern Homo sapiens.

DISCUSSION: Our results show that the morphology of the Cioclovina supranuchal region does not correspond to the external and internal morphology of the typical Neanderthal suprainiac fossa. It cannot be characterized as a depression but rather as an area presenting superficial bone turnover. Together with earlier results, there is little phenotypic evidence that Cioclovina has high levels of Neanderthal ancestry. Our study demonstrates the usefulness of this quantitative method in assessing proposed Neanderthal-like suprainiac depressions in Upper Paleolithic and other fossil specimens.

RevDate: 2019-05-08

Leierer L, Jambrina-Enríquez M, Herrera-Herrera AV, et al (2019)

Insights into the timing, intensity and natural setting of Neanderthal occupation from the geoarchaeological study of combustion structures: A micromorphological and biomarker investigation of El Salt, unit Xb, Alcoy, Spain.

PloS one, 14(4):e0214955 pii:PONE-D-18-34439.

Middle Paleolithic lithic and faunal assemblages throughout Eurasia reflect short-term Neanderthal occupations, which suggest high group mobility. However, the timing of these short-term occupations, a key factor to assess group mobility and territorial range, remains unresolved. Anthropogenic combustion structures are prominent in the Middle Paleolithic record and conceal information on the timing and intensity and natural setting of their associated human occupations. This paper examines a concentration of eleven combustion structures from unit Xb of El Salt, a Middle Paleolithic site in Spain through a geoarchaeological approach, in search of temporal, human impact and paleoenvironmental indicators to assess the timing, intensity and natural setting of the associated human occupations. The study was conducted using micromorphology, lipid biomarker analysis and compound specific isotope analysis. Results show in situ hearths built on different diachronic topsoils rich in herbivore excrements and angiosperm plant residues with rare anthropogenic remains. These data are suggestive of low impact, short-term human occupations separated by relatively long periods of time, with possible indicators of seasonality. Results also show an absence of conifer biomarkers in the mentioned topsoils and presence of conifer charcoal among the fuel residues (ash), indicating that fire wood was brought to the site from elsewhere. A microscopic and molecular approach in the study of combustion structures allows us to narrow down the timescale of archaeological analysis and contributes valuable information towards an understanding of Neanderthal group mobility and settlement patterns.

RevDate: 2019-06-03
CmpDate: 2019-06-03

Pfeifer B, DD Kapan (2019)

Estimates of introgression as a function of pairwise distances.

BMC bioinformatics, 20(1):207 pii:10.1186/s12859-019-2747-z.

BACKGROUND: Research over the last 10 years highlights the increasing importance of hybridization between species as a major force structuring the evolution of genomes and potentially providing raw material for adaptation by natural and/or sexual selection. Fueled by research in a few model systems where phenotypic hybrids are easily identified, research into hybridization and introgression (the flow of genes between species) has exploded with the advent of whole-genome sequencing and emerging methods to detect the signature of hybridization at the whole-genome or chromosome level. Amongst these are a general class of methods that utilize patterns of single-nucleotide polymorphisms (SNPs) across a tree as markers of hybridization. These methods have been applied to a variety of genomic systems ranging from butterflies to Neanderthals to detect introgression, however, when employed at a fine genomic scale these methods do not perform well to quantify introgression in small sample windows.

RESULTS: We introduce a novel method to detect introgression by combining two widely used statistics: pairwise nucleotide diversity dxy and Patterson's D. The resulting statistic, the distance fraction (df), accounts for genetic distance across possible topologies and is designed to simultaneously detect and quantify introgression. We also relate our new method to the recently published fd and incorporate these statistics into the powerful genomics R-package PopGenome, freely available on GitHub (pievos101/PopGenome) and the Comprehensive R Archive Network (CRAN). The supplemental material contains a wide range of simulation studies and a detailed manual how to perform the statistics within the PopGenome framework.

CONCLUSION: We present a new distance based statistic df that avoids the pitfalls of Patterson's D when applied to small genomic regions and accurately quantifies the fraction of introgression (f) for a wide range of simulation scenarios.

RevDate: 2019-05-03

Jacobs GS, Hudjashov G, Saag L, et al (2019)

Multiple Deeply Divergent Denisovan Ancestries in Papuans.

Cell, 177(4):1010-1021.e32.

Genome sequences are known for two archaic hominins-Neanderthals and Denisovans-which interbred with anatomically modern humans as they dispersed out of Africa. We identified high-confidence archaic haplotypes in 161 new genomes spanning 14 island groups in Island Southeast Asia and New Guinea and found large stretches of DNA that are inconsistent with a single introgressing Denisovan origin. Instead, modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages that separated over 350 thousand years ago. Spatial and temporal structure among these lineages suggest that introgression from one of these Denisovan groups predominantly took place east of the Wallace line and continued until near the end of the Pleistocene. A third Denisovan lineage occurs in modern East Asians. This regional mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with multiple Denisovan groups that were geographically isolated from each other over deep evolutionary time.

RevDate: 2019-05-08
CmpDate: 2019-05-08

Rotival M, Quach H, L Quintana-Murci (2019)

Defining the genetic and evolutionary architecture of alternative splicing in response to infection.

Nature communications, 10(1):1671 pii:10.1038/s41467-019-09689-7.

Host and environmental factors contribute to variation in human immune responses, yet the genetic and evolutionary drivers of alternative splicing in response to infection remain largely uncharacterised. Leveraging 970 RNA-sequencing profiles of resting and stimulated monocytes from 200 individuals of African- and European-descent, we show that immune activation elicits a marked remodelling of the isoform repertoire, while increasing the levels of erroneous splicing. We identify 1,464 loci associated with variation in isoform usage (sQTLs), 9% of them being stimulation-specific, which are enriched in disease-related loci. Furthermore, we detect a longstanding increased plasticity of immune gene splicing, and show that positive selection and Neanderthal introgression have both contributed to diversify the splicing landscape of human populations. Together, these findings suggest that differential isoform usage has been an important substrate of innovation in the long-term evolution of immune responses and a more recent vehicle of population local adaptation.

RevDate: 2019-04-18

Moncel MH, Fernandes P, Willmes M, et al (2019)

Rocks, teeth, and tools: New insights into early Neanderthal mobility strategies in South-Eastern France from lithic reconstructions and strontium isotope analysis.

PloS one, 14(4):e0214925 pii:PONE-D-18-22928.

Neanderthals had complex land use patterns, adapting to diversified landscapes and climates. Over the past decade, considerable progress has been made in reconstructing the chronology, land use and subsistence patterns, and occupation types of sites in the Rhône Valley, southeast France. In this study, Neanderthal mobility at the site of Payre is investigated by combining information from lithic procurement analysis ("chaîne evolutive" and "chaîne opératoire" concepts) and strontium isotope analysis of teeth (childhood foraging area), from two units (F and G). Both units date to the transition from Marine Isotope Stage (MIS) 8 to MIS 7, and show similar environmental conditions, but represent contrasting occupation durations. Level Gb (unit G) represents a long-term year-round use, in contrast to short-term seasonal use of the cave in level Fb (unit F). For both levels, lithic material and food were generally collected from a local to semi-local region. However, in level Gb, lithic materials were mainly collected from colluviums and food collected in the valley, whereas in level Fb, lithic procurement focused primarily on alluvial deposits and food was collected from higher elevation plateaus. These procurement or exchange patterns might be related to flint availability, knapping advantages of alluvial flint or occupation duration. The site of Payre is located in a flint rich circulation corridor and the movement of groups or exchanges between groups were organized along a north-south axis on the plateaus or towards the east following the river. The ridges were widely used as they are rich in flint, whereas the Rhône Valley is not an important source of lithic raw materials. Compared to other western European Middle Palaeolithic sites, these results indicate that procurement strategies have a moderate link with occupation types and duration, and with lithic technology. The Sr isotope ratios broadly match the proposed foraging areas, with the Rhône Valley being predominantly used in unit G and the ridges and limestone plateaus in unit F. While lithic reconstructions and childhood foraging are not directly related this suggests that the three analysed Neanderthals spend their childhood in the same general area and supports the idea of mobile Neanderthals in the Rhône Valley and neighbouring higher elevation plateaus. The combination of reconstructing lithic raw material sources, provisioning strategies, and strontium isotope analyses provides new details on how Neanderthals at Payre practised land use and mobility in the Early Middle Palaeolithic.

RevDate: 2019-06-10

Harris DN, Ruczinski I, Yanek LR, et al (2019)

Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World.

Genome biology and evolution, 11(5):1417-1430.

The metabolic conversion of dietary omega-3 and omega-6 18 carbon (18C) to long chain (>20 carbon) polyunsaturated fatty acids (LC-PUFAs) is vital for human life. The rate-limiting steps of this process are catalyzed by fatty acid desaturase (FADS) 1 and 2. Therefore, understanding the evolutionary history of the FADS genes is essential to our understanding of hominin evolution. The FADS genes have two haplogroups, ancestral and derived, with the derived haplogroup being associated with more efficient LC-PUFA biosynthesis than the ancestral haplogroup. In addition, there is a complex global distribution of these haplogroups that is suggestive of Neanderthal introgression. We confirm that Native American ancestry is nearly fixed for the ancestral haplogroup, and replicate a positive selection signal in Native Americans. This positive selection potentially continued after the founding of the Americas, although simulations suggest that the timing is dependent on the allele frequency of the ancestral Beringian population. We also find that the Neanderthal FADS haplotype is more closely related to the derived haplogroup and the Denisovan clusters closer to the ancestral haplogroup. Furthermore, the derived haplogroup has a time to the most recent common ancestor of 688,474 years before present. These results support an ancient polymorphism, as opposed to Neanderthal introgression, forming in the FADS region during the Pleistocene with possibly differential selection pressures on both haplogroups. The near fixation of the ancestral haplogroup in Native American ancestry calls for future studies to explore the potential health risk of associated low LC-PUFA levels in these populations.

RevDate: 2019-03-24

Poza-Rey EM, Gómez-Robles A, JL Arsuaga (2019)

Brain size and organization in the Middle Pleistocene hominins from Sima de los Huesos. Inferences from endocranial variation.

Journal of human evolution, 129:67-90.

The Sima de los Huesos (SH) endocranial sample includes 16 complete or partial endocasts corresponding to European Middle Pleistocene hominins. Different anatomical and molecular studies have demonstrated that these hominins are phylogenetically related to Neanderthals, thus making them the earliest unquestionable representatives of the Neanderthal lineage. The description of endocranial variation in this population is fundamental to shedding light on the evolution of the Neanderthal brain. In this contribution, we analyze and describe endocranial variation in this sample, including aspects related to brain size (endocranial volume and encephalization) and brain organization (through qualitative descriptions and quantitative analyses). Our results indicate that the SH hominins show a transitional state between a primitive hominin endocranial configuration (which is found in Homo erectus and non-SH Middle Pleistocene Homo) and the derived configurations found in Neanderthals and modern humans, without a clear anticipation of classic Neanderthal endocranial traits. In comparison with other cranial and postcranial traits that show a fully Neanderthal or clear pre-Neanderthal condition in the SH collection, endocranial variation in these hominins is surprisingly primitive and shows no Neanderthal affinity. These results and the comparison with other cranial traits confirm that Neanderthals evolved in a mosaic fashion. Traits related to mastication (dental, facial and mandibular anatomy) led the Neanderthalization process, whereas neurocranial anatomy must have acquired a fully Neanderthal condition considerably later.

RevDate: 2019-04-02

Di Maida G, Mannino MA, Krause-Kyora B, et al (2019)

Radiocarbon dating and isotope analysis on the purported Aurignacian skeletal remains from Fontana Nuova (Ragusa, Italy).

PloS one, 14(3):e0213173 pii:PONE-D-18-23492.

Proving voyaging at sea by Palaeolithic humans is a difficult archaeological task, even for short distances. In the Mediterranean, a commonly accepted sea crossing is that from the Italian Peninsula to Sicily by anatomically modern humans, purportedly of the Aurignacian culture. This claim, however, was only supported by the typological attribution to the Aurignacian of the lithic industries from the insular site of Fontana Nuova. AMS radiocarbon dating undertaken as part of our research shows that the faunal remains, previously considered Aurignacian, actually date to the Holocene. Absolute dating on dentinal collagen also attributes the human teeth from the site to the early Holocene, although we were unable to obtain ancient DNA to evaluate their ancestry. Ten radiocarbon dates on human and other taxa are comprised between 9910-9700 cal. BP and 8600-8480 cal. BP, indicating that Fontana Nuova was occupied by Mesolithic and not Aurignacian hunter-gatherers. Only a new study of the lithic assemblage could establish if the material from Fontana Nuova is a mixed collection that includes both late Upper Palaeolithic (Epigravettian) and Mesolithic artefacts, as can be suggested by taking into account both the results of our study and of the most recent reinterpretation of the lithics. Nevertheless, this research suggests that the notion that Aurignacian groups were present in Sicily should now be revised. Another outcome of our study is that we found that three specimens, attributed on grounds both of morphological and ZooMS identifications to Cervus elaphus, had δ13C values significantly higher than any available for such species in Europe.

RevDate: 2019-05-10

Vyas DN, CJ Mulligan (2019)

Analyses of Neanderthal introgression suggest that Levantine and southern Arabian populations have a shared population history.

American journal of physical anthropology, 169(2):227-239.

OBJECTIVES: Modern humans are thought to have interbred with Neanderthals in the Near East soon after modern humans dispersed out of Africa. This introgression event likely took place in either the Levant or southern Arabia depending on the dispersal route out of Africa that was followed. In this study, we compare Neanderthal introgression in contemporary Levantine and southern Arabian populations to investigate Neanderthal introgression and to study Near Eastern population history.

MATERIALS AND METHODS: We analyzed genotyping data on >400,000 autosomal SNPs from seven Levantine and five southern Arabian populations and compared these data to those from populations from around the world including Neanderthal and Denisovan genomes. We used f4 and D statistics to estimate and compare levels of Neanderthal introgression between Levantine, southern Arabian, and comparative global populations. We also identified 1,581 putative Neanderthal-introgressed SNPs within our dataset and analyzed their allele frequencies as a means to compare introgression patterns in Levantine and southern Arabian genomes.

RESULTS: We find that Levantine and southern Arabian populations have similar levels of Neanderthal introgression to each other but lower levels than other non-Africans. Furthermore, we find that introgressed SNPs have very similar allele frequencies in the Levant and southern Arabia, which indicates that Neanderthal introgression is similarly distributed in Levantine and southern Arabian genomes.

DISCUSSION: We infer that the ancestors of contemporary Levantine and southern Arabian populations received Neanderthal introgression prior to separating from each other and that there has been extensive gene flow between these populations.

RevDate: 2019-03-29

Wißing C, Rougier H, Baumann C, et al (2019)

Stable isotopes reveal patterns of diet and mobility in the last Neandertals and first modern humans in Europe.

Scientific reports, 9(1):4433 pii:10.1038/s41598-019-41033-3.

Correlating cultural, technological and ecological aspects of both Upper Pleistocene modern humans (UPMHs) and Neandertals provides a useful approach for achieving robust predictions about what makes us human. Here we present ecological information for a period of special relevance in human evolution, the time of replacement of Neandertals by modern humans during the Late Pleistocene in Europe. Using the stable isotopic approach, we shed light on aspects of diet and mobility of the late Neandertals and UPMHs from the cave sites of the Troisième caverne of Goyet and Spy in Belgium. We demonstrate that their diet was essentially similar, relying on the same terrestrial herbivores, whereas mobility strategies indicate considerable differences between Neandertal groups, as well as in comparison to UPMHs. Our results indicate that UPMHs exploited their environment to a greater extent than Neandertals and support the hypothesis that UPMHs had a substantial impact not only on the population dynamics of large mammals but also on the whole structure of the ecosystem since their initial arrival in Europe.

RevDate: 2019-04-02

Nowaczewska W, Binkowski M, Kubicka AM, et al (2019)

Neandertal-like traits visible in the internal structure of non-supranuchal fossae of some recent Homo sapiens: The problem of their identification in hominins and phylogenetic implications.

PloS one, 14(3):e0213687 pii:PONE-D-18-33383.

Although recently the internal structure of the non-supranuchal fossa of Homo sapiens has been described and compared to that observed in the Neandertal suprainiac fossa, until now it has not been examined in any modern human children. In this study, the internal structure of this fossa in the occipital bones of three children (two aged 3‒4 years and one aged 5 years ± 16 months) and one adult individual representing recent Homo sapiens from Australia was analysed and compared to that of the Neandertal suprainiac fossa. In order to analyse the internal composition of the fossae of the examined specimens, initially, high-resolution micro-CT datasets were obtained for their occipital bones; next, 3D topographic maps of the variation in thickness of structural layers of the occipital bones were made and 2D virtual sections in the median region of these fossae were prepared. In the fossa of one immature individual, the thinning of the diploic layer characteristic of a Neandertal suprainiac fossa was firmly diagnosed. The other Neandertal-like trait, concerning the lack of substantial thinning of the external table of the bone in the region of the fossa, was established in two individuals (one child and one adult) due to the observation of an irregular pattern of the thickness of this table in the other specimens, suggesting the presence of an inflammatory process. Our study presents, for the first time, Neandertal-like traits (but not the whole set of features that justifies the autapomorphic status of the Neandertal supraniac fossa) in the internal structure of non-supranuchal fossae of some recent Homo sapiens. We discuss the phylogenetic implications of the results of our analysis and stress the reasons that use of the 3D topographic mapping method is important for the correct diagnosis of Neandertal traits of the internal structure of occipital fossae.

RevDate: 2019-03-29

Morin E, Meier J, El Guennouni K, et al (2019)

New evidence of broader diets for archaic Homo populations in the northwestern Mediterranean.

Science advances, 5(3):eaav9106 pii:aav9106.

Investigating diet breadth is critical for understanding how archaic Homo populations, including Neanderthals, competed for seasonally scarce resources. The current consensus in Western Europe is that ungulates formed the bulk of the human diet during the Lower and Middle Paleolithic, while small fast prey taxa were virtually ignored. Here, we present a multisite taphonomic study of leporid assemblages from Southern France that supports frequent exploitation of small fast game during marine isotope stages 11 to 3. Along with recent evidence from Iberia, our results indicate that the consumption of small fast game was more common prior to the Upper Paleolithic than previously thought and that archaic hominins from the northwestern Mediterranean had broader diets than those from adjacent regions. Although likely of secondary importance relative to ungulates, the frequent exploitation of leporids documented here implies that human diet breadths were substantially more variable within Europe than assumed by current evolutionary models.

RevDate: 2019-03-29

Rogers J, Raveendran M, Harris RA, et al (2019)

The comparative genomics and complex population history of Papio baboons.

Science advances, 5(1):eaau6947 pii:aau6947.

Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus Papio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of Papio baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.

RevDate: 2019-05-21

Gunz P, Tilot AK, Wittfeld K, et al (2019)

Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity.

Current biology : CB, 29(5):895.

RevDate: 2019-03-03

Pablos A, Gómez-Olivencia A, Maureille B, et al (2019)

Neandertal foot remains from Regourdou 1 (Montignac-sur-Vézère, Dordogne, France).

Journal of human evolution, 128:17-44.

Regourdou is a well-known Middle Paleolithic site which has yielded the fossil remains of a minimum of two Neandertal individuals. The first individual (Regourdou 1) is represented by a partial skeleton while the second one is represented by a calcaneus. The foot remains of Regourdou 1 have been used in a number of comparative studies, but to date a full description and comparison of all the foot remains from the Regourdou 1 Neandertal, coming from the old excavations and from the recent reanalysis of the faunal remains, does not exist. Here, we describe and comparatively assess the Regourdou 1 tarsals, metatarsals and phalanges. They display traits observed in other Neandertal feet, which are different from some traits of the Sima de los Huesos (Atapuerca) hominins and of Middle Paleolithic, Upper Paleolithic and recent modern humans. These Neandertal features are: a rectangular talar trochlea with a large lateral malleolar facet, a broad talar head, a broad calcaneus with a projecting sustentaculum tali, a wide and wedged navicular with a projecting medial tubercle, large and wide bases of the lateral metatarsals, and mediolaterally expanded and robust phalanges that also show hallux valgus in a strongly built hallux.

RevDate: 2019-05-06
CmpDate: 2019-05-06

Haeusler M, Trinkaus E, Fornai C, et al (2019)

Morphology, pathology, and the vertebral posture of the La Chapelle-aux-Saints Neandertal.

Proceedings of the National Academy of Sciences of the United States of America, 116(11):4923-4927.

Although the early postural reconstructions of the Neandertals as incompletely erect were rejected half a century ago, recent studies of Neandertal vertebral remains have inferred a hypolordotic, flat lower back and spinal imbalance for them, including the La Chapelle-aux-Saints 1 skeleton. These studies form part of a persistent trend to view the Neandertals as less "human" than ourselves despite growing evidence for little if any differences in basic functional anatomy and behavioral capabilities. We have therefore reassessed the spinal posture of La Chapelle-aux-Saints 1 using a new pelvic reconstruction to infer lumbar lordosis, interarticulation of lower lumbar (L4-S1) and cervical (C4-T2) vertebrae, and consideration of his widespread age-related osteoarthritis. La Chapelle-aux-Saints 1 exhibits a pelvic incidence (and hence lumbar lordosis) similar to modern humans, articulation of lumbar and cervical vertebrae indicating pronounced lordosis, and Baastrup disease as a product of his advanced age, osteoarthritis, and lordosis. Our findings challenge the view of generally small spinal curvatures in Neandertals. Setting aside the developmentally abnormal Kebara 2 vertebral column, La Chapelle-aux-Saints 1 is joined by other Neandertals with sufficient vertebral remains in providing them with a fully upright (and human) axial posture.

RevDate: 2019-05-06
CmpDate: 2019-05-06

Jaouen K, Richards MP, Le Cabec A, et al (2019)

Exceptionally high δ15N values in collagen single amino acids confirm Neandertals as high-trophic level carnivores.

Proceedings of the National Academy of Sciences of the United States of America, 116(11):4928-4933.

Isotope and archeological analyses of Paleolithic food webs have suggested that Neandertal subsistence relied mainly on the consumption of large herbivores. This conclusion was primarily based on elevated nitrogen isotope ratios in Neandertal bone collagen and has been significantly debated. This discussion relies on the observation that similar high nitrogen isotopes values could also be the result of the consumption of mammoths, young animals, putrid meat, cooked food, freshwater fish, carnivores, or mushrooms. Recently, compound-specific C and N isotope analyses of bone collagen amino acids have been demonstrated to add significantly more information about trophic levels and aquatic food consumption. We undertook single amino acid C and N isotope analysis on two Neandertals, which were characterized by exceptionally high N isotope ratios in their bulk bone or tooth collagen. We report here both C and N isotope ratios on single amino acids of collagen samples for these two Neandertals and associated fauna. The samples come from two sites dating to the Middle to Upper Paleolithic transition period (Les Cottés and Grotte du Renne, France). Our results reinforce the interpretation of Neandertal dietary adaptations as successful top-level carnivores, even after the arrival of modern humans in Europe. They also demonstrate that high δ15N values of bone collagen can solely be explained by mammal meat consumption, as supported by archeological and zooarcheological evidence, without necessarily invoking explanations including the processing of food (cooking, fermenting), the consumption of mammoths or young mammals, or additional (freshwater fish, mushrooms) dietary protein sources.

RevDate: 2019-02-19

Martinón-Torres M, Bermúdez de Castro JM, Martínez de Pinillos M, et al (2019)

New permanent teeth from Gran Dolina-TD6 (Sierra de Atapuerca). The bearing of Homo antecessor on the evolutionary scenario of Early and Middle Pleistocene Europe.

Journal of human evolution, 127:93-117.

Here we analyze the unpublished hominin dental remains recovered from the late Early Pleistocene Gran Dolina-TD6.2 level of the Sierra de Atapuerca (northern Spain), as well as provide a reassessment of the whole TD6.2 hominin dental sample. Comparative descriptions of the outer enamel surface (OES) and the enamel-dentine junction (EDJ) are provided. Overall, the data presented here support the taxonomic validity of Homo antecessor, since this species presents a unique mosaic of traits. Homo antecessor displays several primitive features for the genus Homo as well as some traits exclusively shared with Early and Middle Pleistocene Eurasian hominins. Some of these Eurasian traits were retained by the Middle Pleistocene hominins of Europe, and subsequently became the typical condition of the Neanderthal lineage. Although other skeletal parts present resemblances with Homo sapiens, TD6.2 teeth do not show any synapomorphy with modern humans. In addition, TD6.2 teeth can be well differentiated from those of Asian Homo erectus. The dental evidence is compatible with previous hypothesis about H. antecessor belonging to the basal population from which H. sapiens, Homo neanderthalensis, and Denisovans emerged. Future findings and additional research may help to elucidate the precise phylogenetic link among them.

RevDate: 2019-02-19

Dinnis R, Bessudnov A, Reynolds N, et al (2019)

New data for the Early Upper Paleolithic of Kostenki (Russia).

Journal of human evolution, 127:21-40.

Several questions remain regarding the timing and nature of the Neanderthal-anatomically modern human (AMH) transition in Europe. The situation in Eastern Europe is generally less clear due to the relatively few sites and a dearth of reliable radiocarbon dates. Claims have been made for both notably early AMH and notably late Neanderthal presence, as well as for early AMH (Aurignacian) dispersal into the region from Central/Western Europe. The Kostenki-Borshchevo complex (European Russia) of Early Upper Paleolithic (EUP) sites offers high-quality data to address these questions. Here we revise the chronology and cultural status of the key sites of Kostenki 17 and Kostenki 14. The Kostenki 17/II lithic assemblage shares important features with Proto-Aurignacian material, strengthening an association with AMHs. New radiocarbon dates for Kostenki 17/II of ∼41-40 ka cal BP agree with new dates for the recently excavated Kostenki 14/IVw, which shows some similarities to Kostenki 17/II. Dates of ≥41 ka cal BP from other Kostenki sites cannot be linked to diagnostic archaeological material, and therefore cannot be argued to date AMH occupation. Kostenki 14's Layer in Volcanic Ash assemblage, on the other hand, compares to Early Aurignacian material. New radiocarbon dates targeting diagnostic lithics date to 39-37 ka cal BP. Overall, Kostenki's early EUP is in good agreement with the archaeological record further west. Our results are therefore consistent with models predicting interregional penecontemporaneity of diagnostic EUP assemblages. Most importantly, our work highlights ongoing challenges for reliably radiocarbon dating the period. Dates for Kostenki 14 agreed with the samples' chronostratigraphic positions, but standard pre-treatment methods consistently produced incorrect ages for Kostenki 17/II. Extraction of hydroxyproline from bone collagen using preparative high-performance liquid chromatography, however, yielded results consistent with the samples' chronostratigraphic position and with the layer's archaeological contents. This suggests that for some sites compound-specific techniques are required to build reliable radiocarbon chronologies.

RevDate: 2019-02-19

Ekshtain R, CA Tryon (2019)

Lithic raw material acquisition and use by early Homo sapiens at Skhul, Israel.

Journal of human evolution, 127:149-170.

The site of Skhul in Israel has featured prominently in discussions about the early presence of Homo sapiens outside of Africa since its excavation in the 1930s. Until now, attention has been primarily focused on the site's fossil hominins and evidence for symbolic behavior in the form of burials and rare artifacts such as pierced shells and pigment objects. We present here the results of renewed analysis of the lithic artifacts from Skhul drawn from archival collections in the United States, United Kingdom, and Israel. Although lithic artifacts form the majority of the archaeological record from the site, they have rarely been the subject of comprehensive study. Our analyses of raw material selection, use and transport combined with technological analyses of artifact production methods (1) indicate selective transport to the site of large flakes, retouched pieces, and particularly Levallois points from non-local sources, and (2) demonstrate substantial variability in raw material procurement that fails to indicate clear differences in landscape use between H. sapiens and Neanderthals.

RevDate: 2019-02-18

Buttura RV, Ramalho J, Lima THA, et al (2019)

HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levels.

Human immunology, 80(2):112-119.

HLA-F is one of the most conserved loci among the HLA gene family. The exact function of HLA-F is still under investigation. HLA-F might present tolerogenic features, participate in the stabilization of HLA molecules in open conformation, and also participate in the recycling of HLA molecules. Here we evaluate the variability and haplotype structure of the HLA-F distal promoter segment (from -1893 to -943) and how this segment is correlated with the coding region. Variability at the promoter segment was surveyed in 196 Brazilian samples using second-generation sequencing. The HLA-F promoter region presents two major haplotype lineages. Most of the variable sites are in perfect linkage and associated with a single promoter haplotype, here named F∗distal-C. This haplotype is associated with F∗01:01:02 alleles, while alleles from the F∗01:01:01 or F∗01:03 groups present closely related promoter sequences. F∗distal-C is quite frequent in Brazil and in worldwide populations, with frequencies ranging from 8.41% at the Iberian Population in Spain to 34.34% in Vietnam. F∗distal-C is also present in Neanderthal and Denisovan samples. In silico analyses demonstrated that F∗distal-C presents a different transcription factor binding profile compared with other HLA-F promoters. Moreover, individuals carrying this haplotype present higher HLA-F mRNA expression levels. Functional studies are required to define the exact mechanism underlying this higher HLA-F mRNA expression level associated with F∗distal-C and F∗01:01:02 alleles.

RevDate: 2019-05-02

James WPT, Johnson RJ, Speakman JR, et al (2019)

Nutrition and its role in human evolution.

Journal of internal medicine, 285(5):533-549.

Our understanding of human evolution has improved rapidly over recent decades, facilitated by large-scale cataloguing of genomic variability amongst both modern and archaic humans. It seems clear that the evolution of the ancestors of chimpanzees and hominins separated 7-9 million years ago with some migration out of Africa by the earlier hominins; Homo sapiens slowly emerged as climate change resulted in drier, less forested African conditions. The African populations expanded and evolved in many different conditions with slow mutation and selection rates in the human genome, but with much more rapid mutation occurring in mitochondrial DNA. We now have evidence stretching back 300 000 years of humans in their current form, but there are clearly four very different large African language groups that correlate with population DNA differences. Then, about 50 000-100 000 years ago a small subset of modern humans also migrated out of Africa resulting in a persistent signature of more limited genetic diversity amongst non-African populations. Hybridization with archaic hominins occurred around this time such that all non-African modern humans possess some Neanderthal ancestry and Melanesian populations additionally possess some Denisovan ancestry. Human populations both within and outside Africa also adapted to diverse aspects of their local environment including altitude, climate, UV exposure, diet and pathogens, in some cases leaving clear signatures of patterns of genetic variation. Notable examples include haemoglobin changes conferring resistance to malaria, other immune changes and the skin adaptations favouring the synthesis of vitamin D. As humans migrated across Eurasia, further major mitochondrial changes occurred with some interbreeding with ancient hominins and the development of alcohol intolerance. More recently, an ability to retain lactase persistence into adulthood has evolved rapidly under the environmental stimulus of pastoralism with the ability to husband lactating ruminants. Increased amylase copy numbers seem to relate to the availability of starchy foods, whereas the capacity to desaturase and elongate monounsaturated fatty acids in different societies seems to be influenced by whether there is a lack of supply of readily available dietary sources of long-chain polyunsaturated fatty acids. The process of human evolution includes genetic drift and adaptation to local environments, in part through changes in mitochondrial and nuclear DNA. These genetic changes may underlie susceptibilities to some modern human pathologies including folate-responsive neural tube defects, diabetes, other age-related pathologies and mental health disorders.

RevDate: 2019-04-01

Becam G, Verna C, Gómez-Robles A, et al (2019)

Isolated teeth from La Ferrassie: Reassessment of the old collections, new remains, and their implications.

American journal of physical anthropology, 169(1):132-142.

OBJECTIVES: We provide the description and comparative analysis of six new teeth from the site of La Ferrassie. Our goal is to discuss their taxonomic attribution, and to provide an updated inventory of Neandertal and modern human remains from La Ferrassie in their associated archeological context.

MATERIALS AND METHODS: We use external and internal anatomy, classic morphometrics, and geometric morphometrics. The teeth from La Ferrassie are compared to several samples of contemporary Neandertals and upper Paleolithic modern humans and to recent modern humans.

RESULTS: Three specimens are classified as Neandertals, two as modern humans, and one remains unclassified.

DISCUSSION: Based on the previously known fossil samples and the new teeth reported here, there are currently a minimum of four adult and five immature Neandertal individuals coming from the "Grand Abri" and a minimum of two modern human adult individuals: one from "Grand Abri" and one from "Grotte." It is noteworthy that the spatial distribution of the recovered Neandertal remains is not restricted to the area where the LF1-LF 8 were found but now covers the full extension of the excavated area. Moreover, while both Neandertal and modern human occupations have yielded isolated human remains, the partial-to-complete skeletons only belong to Neandertals. These considerations open new perspectives for the understanding of the occupation and use of the La Ferrassie site.

RevDate: 2019-03-03

Ríos L, Kivell TL, Lalueza-Fox C, et al (2019)

Skeletal Anomalies in The Neandertal Family of El Sidrón (Spain) Support A Role of Inbreeding in Neandertal Extinction.

Scientific reports, 9(1):1697 pii:10.1038/s41598-019-38571-1.

Neandertals disappeared from the fossil record around 40,000 bp, after a demographic history of small and isolated groups with high but variable levels of inbreeding, and episodes of interbreeding with other Paleolithic hominins. It is reasonable to expect that high levels of endogamy could be expressed in the skeleton of at least some Neandertal groups. Genetic studies indicate that the 13 individuals from the site of El Sidrón, Spain, dated around 49,000 bp, constituted a closely related kin group, making these Neandertals an appropriate case study for the observation of skeletal signs of inbreeding. We present the complete study of the 1674 identified skeletal specimens from El Sidrón. Altogether, 17 congenital anomalies were observed (narrowing of the internal nasal fossa, retained deciduous canine, clefts of the first cervical vertebra, unilateral hypoplasia of the second cervical vertebra, clefting of the twelfth thoracic vertebra, diminutive thoracic or lumbar rib, os centrale carpi and bipartite scaphoid, tripartite patella, left foot anomaly and cuboid-navicular coalition), with at least four individuals presenting congenital conditions (clefts of the first cervical vertebra). At 49,000 years ago, the Neandertals from El Sidrón, with genetic and skeletal evidence of inbreeding, could be representative of the beginning of the demographic collapse of this hominin phenotype.

RevDate: 2019-02-05

Sherwood CC, BJ Bradley (2019)

Brain Evolution: Mapping the Inner Neandertal.

Current biology : CB, 29(3):R95-R97.

Human populations that migrated out of Africa interbred with Neandertals. A new study assesses the effects of Neandertal gene variants on brain shape in modern humans, providing insights into the genomic basis of the uniquely globular human brain.

RevDate: 2019-02-22

Miller IF, Barton RA, CL Nunn (2019)

Quantitative uniqueness of human brain evolution revealed through phylogenetic comparative analysis.

eLife, 8: pii:41250.

While the human brain is clearly large relative to body size, less is known about the timing of brain and brain component expansion within primates and the relative magnitude of volumetric increases. Using Bayesian phylogenetic comparative methods and data for both extant and fossil species, we identified that a distinct shift in brain-body scaling occurred as hominins diverged from other primates, and again as humans and Neanderthals diverged from other hominins. Within hominins, we detected a pattern of directional and accelerating evolution towards larger brains, consistent with a positive feedback process in the evolution of the human brain. Contrary to widespread assumptions, we found that the human neocortex is not exceptionally large relative to other brain structures. Instead, our analyses revealed a single increase in relative neocortex volume at the origin of haplorrhines, and an increase in relative cerebellar volume in apes.

RevDate: 2019-02-11

Douka K, Slon V, Jacobs Z, et al (2019)

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

Nature, 565(7741):640-644.

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.

RevDate: 2019-02-11

Jacobs Z, Li B, Shunkov MV, et al (2019)

Timing of archaic hominin occupation of Denisova Cave in southern Siberia.

Nature, 565(7741):594-599.

The Altai region of Siberia was inhabited for parts of the Pleistocene by at least two groups of archaic hominins-Denisovans and Neanderthals. Denisova Cave, uniquely, contains stratified deposits that preserve skeletal and genetic evidence of both hominins, artefacts made from stone and other materials, and a range of animal and plant remains. The previous site chronology is based largely on radiocarbon ages for fragments of bone and charcoal that are up to 50,000 years old; older ages of equivocal reliability have been estimated from thermoluminescence and palaeomagnetic analyses of sediments, and genetic analyses of hominin DNA. Here we describe the stratigraphic sequences in Denisova Cave, establish a chronology for the Pleistocene deposits and associated remains from optical dating of the cave sediments, and reconstruct the environmental context of hominin occupation of the site from around 300,000 to 20,000 years ago.

RevDate: 2019-02-12

Pan L, C Zanolli (2019)

Comparative observations on the premolar root and pulp canal configurations of Middle Pleistocene Homo in China.

American journal of physical anthropology, 168(3):637-646.

OBJECTIVES: The aim of this study is to explore the root and root canal morphology of Homo fossil occupying China during the Middle Pleistocene period. Human occupation and evolutionary dynamics in East Asia during the Middle Pleistocene period is one of the most intriguing issues in paleoanthropology, with the coexistence of multiple lineages and regional morphs suggesting a complex population interaction scenario. Although premolar root and canal morphology has certain phylogenetic, taxonomic, and functional implications, its morphological diversity, possible evolutionary trend and characteristics regarding Middle Pleistocene hominins inhabiting East Asia are still insufficiently understood; where these populations fits within the Homo lineage (with respect to root and pulp canal structure) needs to be explored.

MATERIALS AND METHODS: Using microtomography, we directly observed and assessed the nonmetric variability of root and canal forms in maxillary and mandibular premolars of Chinese Middle Pleistocene Homo (N = 19), and compared our observed variations with Eurasian Early Pleistocene specimens from the Asia continent (N = 1) and Java (N = 2), as well as with Neanderthals (N = 28) and recent modern humans (N = 67).

RESULTS: A total number of nine types of root-canal forms were recorded. As a whole, the Chinese Middle Pleistocene record shows an evolutionary trend toward a modern human-like condition (a reduction of root/canal number and a simplification of root surface structure). We documented primitive signals like high percentage of Tomes' root in lower premolars. A considerable occurrence of incompletely separated root branches and bifid root and canal apices, representing evolutionary transformation from multi-root to single-root condition was also noticed. The results were compared with previous publications on Early and Middle Pleistocene Homo in East Africa, North Africa, and Eurasia.

CONCLUSION: This work provides new original data, incorporates the latest human fossil discoveries and suggests that analyzing the variation of premolar root structural organization, notably integrating together root/canal form and number, could possibly contribute to taxonomic and phylogenetic assessments. The mid-Middle Pleistocene populations, or "classic" Homo erectus, in our study show closer affinity to Early and Middle Pleistocene hominins in Eurasia, than to East African early Homo, which supports the suggestion that at least some of the Early Pleistocene hominin groups in Eurasia contribute to the later population; on the other hand, it is still difficult to clearly trace the evolutionary fate of those late Middle Pleistocene populations (roughly assigned as archaic Homo sapiens through a craniodental perspective). More comparable materials from the Early to Middle Pleistocene period as well as precise chronological framework is needed to further explore the evolutionary trends of archaic hominins in the Asian continent before the arrival of modern humans.

RevDate: 2019-01-30

Milks A, Parker D, M Pope (2019)

External ballistics of Pleistocene hand-thrown spears: experimental performance data and implications for human evolution.

Scientific reports, 9(1):820 pii:10.1038/s41598-018-37904-w.

The appearance of weaponry - technology designed to kill - is a critical but poorly established threshold in human evolution. It is an important behavioural marker representing evolutionary changes in ecology, cognition, language and social behaviours. While the earliest weapons are often considered to be hand-held and consequently short-ranged, the subsequent appearance of distance weapons is a crucial development. Projectiles are seen as an improvement over contact weapons, and are considered by some to have originated only with our own species in the Middle Stone Age and Upper Palaeolithic. Despite the importance of distance weapons in the emergence of full behavioral modernity, systematic experimentation using trained throwers to evaluate the ballistics of thrown spears during flight and at impact is lacking. This paper addresses this by presenting results from a trial of trained javelin athletes, providing new estimates for key performance parameters. Overlaps in distances and impact energies between hand-thrown spears and spearthrowers are evidenced, and skill emerges as a significant factor in successful use. The results show that distance hunting was likely within the repertoire of hunting strategies of Neanderthals, and the resulting behavioural flexibility closely mirrors that of our own species.

RevDate: 2019-05-13
CmpDate: 2019-05-13

Henry JP (2019)

[Genetics and origin of Homo sapiens].

Medecine sciences : M/S, 35(1):39-45.

Usually, paleoanthropology studies remains and artefacts. However, more recently, genetics offer new avenues. Information on humanisation mechanisms has been obtained from comparison with primate or archaic Homo DNA sequences. Likewise, the 1 000 Genomes Project has characterized the geographic spectrum of human genetic variation offering a basis for a genomic study of Homo sapiens phylogeny. From these studies, a model, Out of Africa, was derived. His origin is Africa, where he lived 200 000 years ago. A small fraction of the population left Africa between 50 and 100 000 years ago that have populated the rest of the world, to Europe, coastal Asia to Australia and mainland Asia to Behring Land Bridge and America. The model is supported by the decrease of genetic diversity with the distance to Eastern Africa (serial founder effect). In Europe and Asia, Homo sapiens met archaic Homo neanderthalis and H denisova. The presence of 1-3% neanderthalis sequences in modern Homo ADN indicates admixtures between these groups. Some archaic sequences are on positive selection pressure, thus suggesting that the extinct hominins might have facilitated the adaptation of H sapiens to new environments.

RevDate: 2019-05-29
CmpDate: 2019-05-29

Cortés-Sánchez M, Jiménez-Espejo FJ, Simón-Vallejo MD, et al (2019)

An early Aurignacian arrival in southwestern Europe.

Nature ecology & evolution, 3(2):207-212.

Westernmost Europe constitutes a key location in determining the timing of the replacement of Neanderthals by anatomically modern humans (AMHs). In this study, the replacement of late Mousterian industries by Aurignacian ones at the site of Bajondillo Cave (Málaga, southern Spain) is reported. On the basis of Bayesian analyses, a total of 26 radiocarbon dates, including 17 new ones, show that replacement at Bajondillo took place in the millennia centring on ~45-43 calibrated thousand years before the present (cal ka BP)-well before the onset of Heinrich event 4 (~40.2-38.3 cal ka BP). These dates indicate that the arrival of AMHs at the southernmost tip of Iberia was essentially synchronous with that recorded in other regions of Europe, and significantly increases the areal expansion reached by early AMHs at that time. In agreement with human dispersal scenarios on other continents, such rapid expansion points to coastal corridors as favoured routes for early AMH. The new radiocarbon dates align Iberian chronologies with AMH dispersal patterns in Eurasia.

RevDate: 2019-02-15
CmpDate: 2019-02-01

Mondal M, Bertranpetit J, O Lao (2019)

Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania.

Nature communications, 10(1):246 pii:10.1038/s41467-018-08089-7.

Since anatomically modern humans dispersed Out of Africa, the evolutionary history of Eurasian populations has been marked by introgressions from presently extinct hominins. Some of these introgressions have been identified using sequenced ancient genomes (Neanderthal and Denisova). Other introgressions have been proposed for still unidentified groups using the genetic diversity present in current human populations. We built a demographic model based on deep learning in an Approximate Bayesian Computation framework to infer the evolutionary history of Eurasian populations including past introgression events in Out of Africa populations fitting the current genetic evidence. In addition to the reported Neanderthal and Denisovan introgressions, our results support a third introgression in all Asian and Oceanian populations from an archaic population. This population is either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage. We propose the use of deep learning methods for clarifying situations with high complexity in evolutionary genomics.

RevDate: 2019-04-01
CmpDate: 2019-03-22

Petr M, Pääbo S, Kelso J, et al (2019)

Limits of long-term selection against Neandertal introgression.

Proceedings of the National Academy of Sciences of the United States of America, 116(5):1639-1644.

Several studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45,000 years. Here, we show that this decline is an artifact likely caused by gene flow between modern human populations, which is not taken into account by statistics previously used to estimate Neandertal ancestry. When we apply a statistic that avoids assumptions about modern human demography by taking advantage of two high-coverage Neandertal genomes, we find no evidence for a change in Neandertal ancestry in Europe over the past 45,000 years. We use whole-genome simulations of selection and introgression to investigate a wide range of model parameters and find that negative selection is not expected to cause a significant long-term decline in genome-wide Neandertal ancestry. Nevertheless, these models recapitulate previously observed signals of selection against Neandertal alleles, in particular the depletion of Neandertal ancestry in conserved genomic regions. Surprisingly, we find that this depletion is strongest in regulatory and conserved noncoding regions and in the most conserved portion of protein-coding sequences.

RevDate: 2019-04-01

Taylor ME, Snelling T, Smith DF, et al (2019)

Absence of a human ortholog of rodent Kupffer cell galactose-binding receptor encoded by the CLEC4f gene.

Glycobiology, 29(4):332-345.

The murine CLEC4f gene encodes the Kupffer cell receptor, a galactose-binding receptor containing a C-type carbohydrate-recognition domain. Orthologs have been identified in nearly 100 species. The receptors from rat and mouse have previously been characterized and data presented here show that functional CLEC4f protein is expressed in domestic cattle (Bos taurus). However, the human CLEC4f gene does not encode a functional receptor because a mutation in the splice acceptor site of the final exon prevents appropriate splicing and a missense mutation disrupts the sugar-binding site. Transcriptomic and PCR analysis of transcripts confirms the absence of a spliced transcript containing the final exon and only background levels of transcripts are detected in human tissues. These mutations are also present in the CLEC4f gene in Neanderthals. In contrast to humans, closely related species, including chimpanzees, do have CLEC4f genes that encode full-length receptors. Affinity chromatography and glycan array results demonstrate that the chimpanzee, bovine and murine proteins all bind to galactose, but they show preferences for different subsets of galactose-containing glycans. In non-human primates, the receptor is expressed in spleen rather than in liver. The results indicate that the CLEC4f protein probably has distinct functions in different species. Absence of the receptor precludes using it for targeting of glycoconjugates to cells in human liver. The fact that CLEC4f protein is expressed in spleen in non-human primates and the close evolutionary relationship of the CLEC4f protein to langerin (CD207) suggest that it may function in the immune system, possibly as a pathogen receptor.

RevDate: 2019-05-20
CmpDate: 2019-05-20

Velliky EC, Porr M, NJ Conard (2018)

Ochre and pigment use at Hohle Fels cave: Results of the first systematic review of ochre and ochre-related artefacts from the Upper Palaeolithic in Germany.

PloS one, 13(12):e0209874 pii:PONE-D-18-31621.

Though many European Upper Palaeolithic sites document early examples of symbolic material expressions (e.g., cave art, personal ornaments, figurines), there exist few reports on the use of earth pigments outside of cave art-and occasionally Neanderthal-contexts. Here, we present the first in-depth study of the diachronic changes in ochre use throughout an entire Upper Palaeolithic sequence at Hohle Fels cave, Germany, spanning from ca. 44,000-14,500 cal. yr. BP. A reassessment of the assemblage has yielded 869 individual ochre artefacts, of which 27 show traces of anthropogenic modification. The ochre artefacts are from all Upper Palaeolithic layers, stemming from the earliest Aurignacian horizons to the Holocene. This wide temporal spread demonstrates the long-term presence and continuity of ochre use in a part of Europe where it has not been systematically reported before. The anthropogenic modifications present on the ochre artefacts from the Gravettian and Magdalenian are consistent with pigment powder production, whereas the only modified piece from the Aurignacian displays a possible engraved motif. The non-modified artefacts show that more hematite-rich specular ochres as well as fine-grained deep red iron oxide clays were preferred during the Gravettian and Magdalenian, while the Aurignacian layers contain a broader array of colours and textures. Furthermore, numerous other artefacts such as faunal elements, personal ornaments, shells, and an ochre grindstone further strengthen the conclusion that ochre behaviours were well established during the onset of the Aurignacian and subsequently flourished throughout the Upper Palaeolithic at Hohle Fels cave.

RevDate: 2018-12-25

Lague MR, Chirchir H, Green DJ, et al (2019)

Cross-sectional properties of the humeral diaphysis of Paranthropus boisei: Implications for upper limb function.

Journal of human evolution, 126:51-70.

A ∼1.52 Ma adult upper limb skeleton of Paranthropus boisei (KNM-ER 47000) recovered from the Koobi Fora Formation, Kenya (FwJj14E, Area 1A) includes most of the distal half of a right humerus (designated KNM-ER 47000B). Natural transverse fractures through the diaphysis of KNM-ER 470000B provide unobstructed views of cortical bone at two sections typically used for analyzing cross-sectional properties of hominids (i.e., 35% and 50% of humerus length from the distal end). Here we assess cross-sectional properties of KNM-ER 47000B and two other P. boisei humeri (OH 80-10, KNM-ER 739). Cross-sectional properties for P. boisei associated with bending/torsional strength (section moduli) and relative cortical thickness (%CA; percent cortical area) are compared to those reported for nonhuman hominids, AL 288-1 (Australopithecus afarensis), and multiple species of fossil and modern Homo. Polar section moduli (Zp) are assessed relative to a mechanically relevant measure of body size (i.e., the product of mass [M] and humerus length [HL]). At both diaphyseal sections, P. boisei exhibits %CA that is high among extant hominids (both human and nonhuman) and similar to that observed among specimens of Pleistocene Homo. High values for Zp relative to size (M × HL) indicate that P. boisei had humeral bending strength greater than that of modern humans and Neanderthals and similar to that of great apes, A. afarensis, and Homo habilis. Such high humeral strength is consistent with other skeletal features of P. boisei (reviewed here) that suggest routine use of powerful upper limbs for arboreal climbing.

RevDate: 2018-12-27

Van Laer B, Kapp U, Soler-Lopez M, et al (2018)

Molecular comparison of Neanderthal and Modern Human adenylosuccinate lyase.

Scientific reports, 8(1):18008 pii:10.1038/s41598-018-36195-5.

The availability of genomic data from extinct homini such as Neanderthals has caused a revolution in palaeontology allowing the identification of modern human-specific protein substitutions. Currently, little is known as to how these substitutions alter the proteins on a molecular level. Here, we investigate adenylosuccinate lyase, a conserved enzyme involved in purine metabolism for which several substitutions in the modern human protein (hADSL) have been described to affect intelligence and behaviour. During evolution, modern humans acquired a specific substitution (Ala429Val) in ADSL distinguishing it from the ancestral variant present in Neanderthals (nADSL). We show here that despite this conservative substitution being solvent exposed and located distant from the active site, there is a difference in thermal stability, but not enzymology or ligand binding between nADSL and hADSL. Substitutions near residue 429 which do not profoundly affect enzymology were previously reported to cause neurological symptoms in humans. This study also reveals that ADSL undergoes conformational changes during catalysis which, together with the crystal structure of a hitherto undetermined product bound conformation, explains the molecular origin of disease for several modern human ADSL mutants.

RevDate: 2019-04-12
CmpDate: 2019-04-12

Reher D, Key FM, Andrés AM, et al (2019)

Immune Gene Diversity in Archaic and Present-day Humans.

Genome biology and evolution, 11(1):232-241 pii:5253179.

Genome-wide analyses of two Neandertals and a Denisovan have shown that these archaic humans had lower genetic heterozygosity than present-day people. A similar reduction in genetic diversity of protein-coding genes (gene diversity) was found in exome sequences of three Neandertals. Reduced gene diversity, particularly in genes involved in immunity, may have important functional consequences. In fact, it has been suggested that reduced diversity in immune genes may have contributed to Neandertal extinction. We therefore explored gene diversity in different human groups, and at different time points on the Neandertal lineage, with a particular focus on the diversity of genes involved in innate immunity and genes of the Major Histocompatibility Complex (MHC).We find that the two Neandertals and a Denisovan have similar gene diversity, all significantly lower than any present-day human. This is true across gene categories, with no gene set showing an excess decrease in diversity compared with the genome-wide average. Innate immune-related genes show a similar reduction in diversity to other genes, both in present-day and archaic humans. There is also no observable decrease in gene diversity over time in Neandertals, suggesting that there may have been no ongoing reduction in gene diversity in later Neandertals, although this needs confirmation with a larger sample size. In both archaic and present-day humans, genes with the highest levels of diversity are enriched for MHC-related functions. In fact, in archaic humans the MHC genes show evidence of having retained more diversity than genes involved only in the innate immune system.

RevDate: 2019-05-06
CmpDate: 2019-05-06

Mohammed Ismail W, Pagel KA, Pejaver V, et al (2018)

The sequencing and interpretation of the genome obtained from a Serbian individual.

PloS one, 13(12):e0208901 pii:PONE-D-18-12238.

Recent genetic studies and whole-genome sequencing projects have greatly improved our understanding of human variation and clinically actionable genetic information. Smaller ethnic populations, however, remain underrepresented in both individual and large-scale sequencing efforts and hence present an opportunity to discover new variants of biomedical and demographic significance. This report describes the sequencing and analysis of a genome obtained from an individual of Serbian origin, introducing tens of thousands of previously unknown variants to the currently available pool. Ancestry analysis places this individual in close proximity to Central and Eastern European populations; i.e., closest to Croatian, Bulgarian and Hungarian individuals and, in terms of other Europeans, furthest from Ashkenazi Jewish, Spanish, Sicilian and Baltic individuals. Our analysis confirmed gene flow between Neanderthal and ancestral pan-European populations, with similar contributions to the Serbian genome as those observed in other European groups. Finally, to assess the burden of potentially disease-causing/clinically relevant variation in the sequenced genome, we utilized manually curated genotype-phenotype association databases and variant-effect predictors. We identified several variants that have previously been associated with severe early-onset disease that is not evident in the proband, as well as putatively impactful variants that could yet prove to be clinically relevant to the proband over the next decades. The presence of numerous private and low-frequency variants, along with the observed and predicted disease-causing mutations in this genome, exemplify some of the global challenges of genome interpretation, especially in the context of under-studied ethnic groups.

RevDate: 2019-03-01
CmpDate: 2019-03-01

Murphy E, A Benítez-Burraco (2018)

Paleo-oscillomics: inferring aspects of Neanderthal language abilities from gene regulation of neural oscillations.

Journal of anthropological sciences = Rivista di antropologia : JASS, 96:111-124.

Language seemingly evolved from changes in brain anatomy and wiring. We argue that language evolution can be better understood if particular changes in phasal and cross-frequency coupling properties of neural oscillations, resulting in core features of language, are considered. Because we cannot track the oscillatory activity of the brain from extinct hominins, we used our current understanding of the language oscillogenome (that is, the set of genes responsible for basic aspects of the oscillatory activity relevant for language) to infer some properties of the Neanderthal oscillome. We have found that several candidates for the language oscillogenome show differences in their methylation patterns between Neanderthals and humans. We argue that differences in their expression levels could be informative of differences in cognitive functions important for language.

RevDate: 2018-12-21

Savriama Y, Valtonen M, Kammonen JI, et al (2018)

Bracketing phenogenotypic limits of mammalian hybridization.

Royal Society open science, 5(11):180903 pii:rsos180903.

An increasing number of mammalian species have been shown to have a history of hybridization and introgression based on genetic analyses. Only relatively few fossils, however, preserve genetic material, and morphology must be used to identify the species and determine whether morphologically intermediate fossils could represent hybrids. Because dental and cranial fossils are typically the key body parts studied in mammalian palaeontology, here we bracket the potential for phenotypically extreme hybridizations by examining uniquely preserved cranio-dental material of a captive hybrid between grey and ringed seals. We analysed how distinct these species are genetically and morphologically, how easy it is to identify the hybrids using morphology and whether comparable hybridizations happen in the wild. We show that the genetic distance between these species is more than twice the modern human-Neanderthal distance, but still within that of morphologically similar species pairs known to hybridize. By contrast, morphological and developmental analyses show grey and ringed seals to be highly disparate, and that the hybrid is a predictable intermediate. Genetic analyses of the parent populations reveal introgression in the wild, suggesting that grey-ringed seal hybridization is not limited to captivity. Taken together, we postulate that there is considerable potential for mammalian hybridization between phenotypically disparate taxa.

RevDate: 2019-01-10
CmpDate: 2019-01-10

Benítez-Burraco A (2018)

Differences in the Neanderthal BRCA2 gene might be related to their distinctive cognitive profile.

Hereditas, 155:38 pii:76.

The unique divergence of the BRCA2 gene in Neanderthals compared to modern humans has been hypothesized to account for a differential susceptibility to cancer. However, the role of the gene in brain development and its connection with autism suggest that these differences might be (also) related to the more encapsulated nature of the Neanderthal cognition and their (inferred) autistic-like features.

RevDate: 2019-06-06
CmpDate: 2019-06-06

Gibney E, Callaway E, Cyranoski D, et al (2018)

Nature's 10: Ten people who mattered in science in 2018.

Nature, 564(7736):325-335.

RevDate: 2019-02-22

Gunz P, Tilot AK, Wittfeld K, et al (2019)

Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity.

Current biology : CB, 29(1):120-127.e5.

One of the features that distinguishes modern humans from our extinct relatives and ancestors is a globular shape of the braincase [1-4]. As the endocranium closely mirrors the outer shape of the brain, these differences might reflect altered neural architecture [4, 5]. However, in the absence of fossil brain tissue, the underlying neuroanatomical changes as well as their genetic bases remain elusive. To better understand the biological foundations of modern human endocranial shape, we turn to our closest extinct relatives: the Neandertals. Interbreeding between modern humans and Neandertals has resulted in introgressed fragments of Neandertal DNA in the genomes of present-day non-Africans [6, 7]. Based on shape analyses of fossil skull endocasts, we derive a measure of endocranial globularity from structural MRI scans of thousands of modern humans and study the effects of introgressed fragments of Neandertal DNA on this phenotype. We find that Neandertal alleles on chromosomes 1 and 18 are associated with reduced endocranial globularity. These alleles influence expression of two nearby genes, UBR4 and PHLPP1, which are involved in neurogenesis and myelination, respectively. Our findings show how integration of fossil skull data with archaic genomics and neuroimaging can suggest developmental mechanisms that may contribute to the unique modern human endocranial shape.

RevDate: 2019-01-14
CmpDate: 2019-01-14

Gibbons A (2018)

Why modern humans have round heads.

Science (New York, N.Y.), 362(6420):1229.

RevDate: 2019-05-18

Banerjee N, Polushina T, Bettella F, et al (2019)

Analysis of differentially methylated regions in great apes and extinct hominids provides support for the evolutionary hypothesis of schizophrenia.

Schizophrenia research, 206:209-216.

INTRODUCTION: The persistence of schizophrenia in human populations separated by geography and time led to the evolutionary hypothesis that proposes schizophrenia as a by-product of the higher cognitive abilities of modern humans. To explore this hypothesis, we used here an evolutionary epigenetics approach building on differentially methylated regions (DMRs) of the genome.

METHODS: We implemented a polygenic enrichment testing pipeline using the summary statistics of genome-wide association studies (GWAS) of schizophrenia and 12 other phenotypes. We investigated the enrichment of association of these traits across genomic regions with variable methylation between modern humans and great apes (orangutans, chimpanzees and gorillas; great ape DMRs) and between modern humans and recently extinct hominids (Neanderthals and Denisovans; hominid DMRs).

RESULTS: Regions that are hypo-methylated in humans compared to great apes show enrichment of association with schizophrenia only if the major histocompatibility complex (MHC) region is included. With the MHC region removed from the analysis, only a modest enrichment for SNPs of low effect persists. The INRICH pipeline confirms this finding after rigorous permutation and bootstrapping procedures.

CONCLUSION: The analyses of regions with differential methylation changes in humans and great apes do not provide compelling evidence of enrichment of association with schizophrenia, in contrast to our previous findings on more recent methylation differences between modern humans, Neanderthals and Denisovans. Our results further support the evolutionary hypothesis of schizophrenia and indicate that the origin of some of the genetic susceptibility factors of schizophrenia may lie in recent human evolution.

RevDate: 2019-05-08
CmpDate: 2019-05-08

Caricola I, Zupancich A, Moscone D, et al (2018)

An integrated method for understanding the function of macro-lithic tools. Use wear, 3D and spatial analyses of an Early Upper Palaeolithic assemblage from North Eastern Italy.

PloS one, 13(12):e0207773 pii:PONE-D-18-21873.

The article presents an original analysis which combines use-wear, 3D modelling and spatial analyses to experimental archaeology in order to investigate Early Upper Palaeolithic flint-knapping gestures and techniques involving the use of macro-lithic tools. In particular, the methodological framework proposed in this paper was applied to the study of Protoaurignacian and Aurignacian macro-tools from Fumane Cave (Verona, Italy). Combining spatial analysis and use wear investigation, both at low and high magnifications, permitted the identification and detailed description of the use-related traces affecting both the hammerstones and retouchers which, at Fumane Cave, were used at different stages during flint tool production. Several experimental activities were performed including core reduction, maintenance, and blank production together with different types of edge retouching. From a methodological perspective, the protocol of analysis permitted to codify specific traces and to produce quantitative data related to their geometry and distribution over the tool's surface, according to the activities and gestures performed. The results obtained allowed a careful investigation of the function and the gestures associated to the use of the macro-lithic tools coming from the Protoaurignacian and Aurignacian levels of Fumane Cave while providing a methodological tool for interpreting different archaeological samples.

RevDate: 2019-04-15

Bruner E (2019)

Human paleoneurology: Shaping cortical evolution in fossil hominids.

The Journal of comparative neurology, 527(10):1753-1765.

Evolutionary neuroanatomy must integrate two different sources of information, namely from fossil and from living species. Fossils supply information concerning the process of evolution, whereas living species supply information on the product of evolution. Unfortunately, the fossil record is partial and fragmented, and often cannot support validations for specific evolutionary hypotheses. Living species can provide more comprehensive indications, but they do not represent ancestral groups or primitive forms. Macaques or chimpanzees are frequently used as proxy for human ancestral conditions, despite the fact they are divergent and specialized lineages, with their own biological features. Similarly, in paleoanthropology independent lineages (such as Neanderthals) should not be confused with ancestral modern human stages. In this comparative framework, paleoneurology deals with the analysis of the endocranial cavity in extinct species, in order to make inferences on brain evolution. A main target of this field is to distinguish the endocranial variations due to brain changes, from those due to cranial constraints. Digital anatomy and computed morphometrics have provided major advances in this field. However, brains and endocasts can be hard to analyze with geometrical models, because of uncertainties due to the localization of cortical landmarks and boundaries. The study of the evolution of the parietal cortex supplies an interesting case-study in which paleontological and neontological data can integrate and test evolutionary hypotheses based on multiple sources of evidence. The relationships with visuospatial functions and brain-body-tool integration stress further that the analysis of the cognitive system should go beyond the neural boundaries of the brain.

RevDate: 2019-01-07
CmpDate: 2019-01-07

Mirazón Lahr M (2018)

The not-so-dangerous lives of Neanderthals.

Nature, 563(7733):634-636.

RevDate: 2019-06-10
CmpDate: 2019-05-23

Villanea FA, JG Schraiber (2019)

Multiple episodes of interbreeding between Neanderthal and modern humans.

Nature ecology & evolution, 3(1):39-44.

Neanderthals and anatomically modern humans overlapped geographically for a period of over 30,000 years following human migration out of Africa. During this period, Neanderthals and humans interbred, as evidenced by Neanderthal portions of the genome carried by non-African individuals today. A key observation is that the proportion of Neanderthal ancestry is ~12-20% higher in East Asian individuals relative to European individuals. Here, we explore various demographic models that could explain this observation. These include distinguishing between a single admixture event and multiple Neanderthal contributions to either population, and the hypothesis that reduced Neanderthal ancestry in modern Europeans resulted from more recent admixture with a ghost population that lacked a Neanderthal ancestry component (the 'dilution' hypothesis). To summarize the asymmetric pattern of Neanderthal allele frequencies, we compiled the joint fragment frequency spectrum of European and East Asian Neanderthal fragments and compared it with both analytical theory and data simulated under various models of admixture. Using maximum-likelihood and machine learning, we found that a simple model of a single admixture did not fit the empirical data, and instead favour a model of multiple episodes of gene flow into both European and East Asian populations. These findings indicate a longer-term, more complex interaction between humans and Neanderthals than was previously appreciated.

RevDate: 2019-04-15
CmpDate: 2019-04-15

Mafessoni F (2019)

Encounters with archaic hominins.

Nature ecology & evolution, 3(1):14-15.

RevDate: 2018-12-05

Becam G, T Chevalier (2019)

Neandertal features of the deciduous and permanent teeth from Portel-Ouest Cave (Ariège, France).

American journal of physical anthropology, 168(1):45-69.

OBJECTIVES: We describe 14 unpublished and nine published teeth from the Mousterian level of Portel-Ouest (Ariège, France), dated to 44 ka. In a comparative context, we explore the taxonomical affinities of those teeth with Neandertals and modern humans which are both known to exist at that time. We further make some paleobiological inferences about this human group.

METHODS: The comparative analysis of Neandertals and modern humans is based on nonmetric traits at the outer enamel surface and the enamel-dentine junction, crown diameters and three-dimensional (3D) enamel thickness measurements of lower permanent teeth. The crown and roots are explored in detail based on the μCT-scan data to identify the multiple criteria involved in the paleobiological approach.

RESULTS: Nonmetric traits and 3D enamel thickness tend to be more similar to Neandertals than modern humans, notably for C1 , P4 , and M2 (included in all analyses) as well as volume of the pulp cavity in roots of the anterior permanent teeth. The Portel-Ouest sample corresponds to a minimum of seven juveniles, one or two adolescents and one adult, which exhibit recurrent linear enamel hypoplasia (up to five events for one individual), the torsiversion of one anterior tooth and irregular oblique wear in some anterior deciduous teeth.

DISCUSSION: This morphological study confirms that the remains from Portel-Ouest are Neandertals, associated with a Mousterian complex. Furthermore, we found the expected pattern of mortality and stress for a Neandertal group, that is, various age categories and developmental defects (nonexclusive to Neandertals), while adults are underrepresented and juveniles are overrepresented. Further excavations would contribute finding new remains and maybe complete this demographic profile.

RevDate: 2019-06-05
CmpDate: 2019-06-05

Beier J, Anthes N, Wahl J, et al (2018)

Similar cranial trauma prevalence among Neanderthals and Upper Palaeolithic modern humans.

Nature, 563(7733):686-690.

Neanderthals are commonly depicted as leading dangerous lives and permanently struggling for survival. This view largely relies on the high incidences of trauma that have been reported1,2 and have variously been attributed to violent social behaviour3,4, highly mobile hunter-gatherer lifestyles2 or attacks by carnivores5. The described Neanderthal pattern of predominantly cranial injuries is further thought to reflect violent encounters with large prey mammals, resulting from the use of close-range hunting weapons1. These interpretations directly shape our understanding of Neanderthal lifestyles, health and hunting abilities, yet mainly rest on descriptive, case-based evidence. Quantitative, population-level studies of traumatic injuries are rare. Here we reassess the hypothesis of higher cranial trauma prevalence among Neanderthals using a population-level approach-accounting for preservation bias and other contextual data-and an exhaustive fossil database. We show that Neanderthals and early Upper Palaeolithic anatomically modern humans exhibit similar overall incidences of cranial trauma, which are higher for males in both taxa, consistent with patterns shown by later populations of modern humans. Beyond these similarities, we observed species-specific, age-related variation in trauma prevalence, suggesting that there were differences in the timing of injuries during life or that there was a differential mortality risk of trauma survivors in the two groups. Finally, our results highlight the importance of preservation bias in studies of trauma prevalence.

RevDate: 2018-11-26
CmpDate: 2018-11-26

Michalak P, L Kang (2018)

Unique divergence of the breast cancer 2 (BRCA2) gene in Neanderthals.

Hereditas, 155:34.

Unique divergence of the BRCA2, a tumor suppressor gene, in Neanderthals relative to other primates, including modern humans, is highlighted. This divergence with potentially pathogenic consequences raises a question about cancer susceptibility in the archaic species that was replaced by modern humans about 40,000 years ago.

RevDate: 2019-06-10

Smith TM, Austin C, Green DR, et al (2018)

Wintertime stress, nursing, and lead exposure in Neanderthal children.

Science advances, 4(10):eaau9483.

Scholars endeavor to understand the relationship between human evolution and climate change. This is particularly germane for Neanderthals, who survived extreme Eurasian environmental variation and glaciations, mysteriously going extinct during a cool interglacial stage. Here, we integrate weekly records of climate, tooth growth, and metal exposure in two Neanderthals and one modern human from southeastern France. The Neanderthals inhabited cooler and more seasonal periods than the modern human, evincing childhood developmental stress during wintertime. In one instance, this stress may have included skeletal mobilization of elemental stores and weight loss; this individual was born in the spring and appears to have weaned 2.5 years later. Both Neanderthals were exposed to lead at least twice during the deep winter and/or early spring. This multidisciplinary approach elucidates direct relationships between ancient environments and hominin paleobiology.

RevDate: 2019-02-25
CmpDate: 2019-02-25

Kamnikar KR, Herrmann NP, AM Plemons (2018)

New Approaches to Juvenile Age Estimation in Forensics: Application of Transition Analysis via the Shackelford et al. Method to a Diverse Modern Subadult Sample.

Human biology, 90(1):11-30.

Dental development is one of the most widely utilized and accurate methods available for estimating age in subadult skeletal remains. The timing of tooth growth and development is regulated by genetics and less affected by external factors, allowing reliable estimates of chronological age. Traditional methodology focuses on comparing tooth developmental scores to corresponding age charts. Using the Moorrees, Fanning, and Hunt (MFH) developmental scores, Shackelford and colleagues embed the dental development method in a statistical framework based on transition analysis. They generated numerical parameters underlining each "stage" and age-at-death distribution and applied them to fossil hominins and Neanderthals with limited application to modern humans. We use this same method on a subadult test sample (n = 201), representing modern individuals that may become part of the forensic record. We assess the probability coverage of the Shackelford et al. method derived from MFH standards as it applies to all available dentition. Results indicate promise: the age range at 90% and 95% confidence levels includes the chronological age of almost every individual tested. The maximum likelihood age estimates underestimate age by 0.5-2.5 years for individuals 0-15 years of age and by >2.5 years for individuals 16-18 years of age, as previously shown. In an attempt to refine the method, we adjusted the numerical parameters underlying the stages for developing teeth based on a combined modern reference sample (n = 1,964) and tested these revised parameters using the same test sample. The estimated ages from the modified method differ from the original Shackelford et al. methodology by underestimating age to a lesser degree. The modified method does include mean age-at-attainment values for earlier stages of several teeth, allowing for the calculation of narrower confidence intervals. While this study highlights areas of future research in refining dental developmental aging by transition analysis, it also demonstrates that the Shackelford et al. method is applicable and accurate when aging modern subadults in forensic work.

RevDate: 2019-02-13

Akhtari FS, Havener TM, Fukudo M, et al (2018)

The influence of Neanderthal alleles on cytotoxic response.

PeerJ, 6:e5691.

Various studies have shown that people of Eurasian origin contain traces of DNA inherited from interbreeding with Neanderthals. Recent studies have demonstrated that these Neanderthal variants influence a range of clinically important traits and diseases. Thus, understanding the genetic factors responsible for the variability in individual response to drug or chemical exposure is a key goal of pharmacogenomics and toxicogenomics, as dose responses are clinically and epidemiologically important traits. It is well established that ethnic and racial differences are important in dose response traits, but to our knowledge the influence of Neanderthal ancestry on response to xenobiotics is unknown. Towards this aim, we examined if Neanderthal ancestry plays a role in cytotoxic response to anti-cancer drugs and toxic environmental chemicals. We identified common Neanderthal variants in lymphoblastoid cell lines (LCLs) derived from the globally diverse 1000 Genomes Project and Caucasian cell lines from the Children's Hospital of Oakland Research Institute. We analyzed the effects of these Neanderthal alleles on cytotoxic response to 29 anti-cancer drugs and 179 environmental chemicals at varying concentrations using genome-wide data. We identified and replicated single nucleotide polymorphisms (SNPs) from these association results, including a SNP in the SNORD-113 cluster. Our results also show that the Neanderthal alleles cumulatively lead to increased sensitivity to both the anti-cancer drugs and the environmental chemicals. Our results demonstrate the influence of Neanderthal ancestry-informative markers on cytotoxic response. These results could be important in identifying biomarkers for personalized medicine or in dissecting the underlying etiology of dose response traits.

RevDate: 2019-03-20
CmpDate: 2019-02-19

Chen Z, DeSalle R, Schiffman M, et al (2018)

Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans.

PLoS pathogens, 14(11):e1007352.

Recent discoveries on the origins of modern humans from multiple archaic hominin populations and the diversity of human papillomaviruses (HPVs) suggest a complex scenario of virus-host evolution. To evaluate the origin of HPV pathogenesis, we estimated the phylogeny, timing, and dispersal of HPV16 variants using a Bayesian Markov Chain Monte Carlo framework. To increase precision, we identified and characterized non-human primate papillomaviruses from New and Old World monkeys to set molecular clock models. We demonstrate specific host niche adaptation of primate papillomaviruses with subsequent coevolution with their primate hosts for at least 40 million years. Analyses of 212 HPV16 complete genomes and 3582 partial sequences estimated ancient divergence of HPV16 variants (between A and BCD lineages) from their most recent common ancestors around half a million years ago, roughly coinciding with the timing of the split between archaic Neanderthals and modern Homo sapiens, and nearly three times longer than divergence times of modern Homo sapiens. HPV16 A lineage variants were significantly underrepresented in present African populations, whereas the A sublineages were highly prevalent in European (A1-3) and Asian (A4) populations, indicative of viral sexual transmission from Neanderthals to modern non-African humans through multiple interbreeding events in the past 80 thousand years. Remarkably, the human leukocyte antigen B*07:02 and C*07:02 alleles associated with increased risk in cervix cancer represent introgressed regions from Neanderthals in present-day Eurasians. The archaic hominin-host-switch model was also supported by other HPV variants. Niche adaptation and virus-host codivergence appear to influence the pathogenesis of papillomaviruses.

RevDate: 2019-01-07
CmpDate: 2019-01-07

Gómez-Olivencia A, Barash A, García-Martínez D, et al (2018)

3D virtual reconstruction of the Kebara 2 Neandertal thorax.

Nature communications, 9(1):4387.

The size and shape of the Neandertal thorax has been debated since the first discovery of Neandertal ribs more than 150 years ago, with workers proposing different interpretations ranging from a Neandertal thoracic morphology that is indistinguishable from modern humans, to one that was significantly different from them. Here, we provide a virtual 3D reconstruction of the thorax of the adult male Kebara 2 Neandertal. Our analyses reveal that the Kebara 2 thorax is significantly different but not larger from that of modern humans, wider in its lower segment, which parallels his wide bi-iliac breadth, and with a more invaginated vertebral column. Kinematic analyses show that rib cages that are wider in their lower segment produce greater overall size increments (respiratory capacity) during inspiration. We hypothesize that Neandertals may have had a subtle, but somewhat different breathing mechanism compared to modern humans.

RevDate: 2019-05-03
CmpDate: 2019-05-03

de Filippo C, Meyer M, K Prüfer (2018)

Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences.

BMC biology, 16(1):121.

BACKGROUND: The study of ancient DNA is hampered by degradation, resulting in short DNA fragments. Advances in laboratory methods have made it possible to retrieve short DNA fragments, thereby improving access to DNA preserved in highly degraded, ancient material. However, such material contains large amounts of microbial contamination in addition to DNA fragments from the ancient organism. The resulting mixture of sequences constitutes a challenge for computational analysis, since microbial sequences are hard to distinguish from the ancient sequences of interest, especially when they are short.

RESULTS: Here, we develop a method to quantify spurious alignments based on the presence or absence of rare variants. We find that spurious alignments are enriched for mismatches and insertion/deletion differences and lack substitution patterns typical of ancient DNA. The impact of spurious alignments can be reduced by filtering on these features and by imposing a sample-specific minimum length cutoff. We apply this approach to sequences from four ~ 430,000-year-old Sima de los Huesos hominin remains, which contain particularly short DNA fragments, and increase the amount of usable sequence data by 17-150%. This allows us to place a third specimen from the site on the Neandertal lineage.

CONCLUSIONS: Our method maximizes the sequence data amenable to genetic analysis from highly degraded ancient material and avoids pitfalls that are associated with the analysis of ultra-short DNA sequences.

RevDate: 2018-12-05

Pablos A, Gómez-Olivencia A, JL Arsuaga (2019)

A Neandertal foot phalanx from the Galería de las Estatuas site (Sierra de Atapuerca, Spain).

American journal of physical anthropology, 168(1):222-228.

OBJECTIVES: The Galería de las Estatuas site (GE), a new Mousterian site at the Sierra de Atapuerca site complex (Spain), has revealed a Late Pleistocene detrital sequence with at least five lithostratigraphic units. These units have yielded evidence of Mousterian occupations with sporadic carnivore activity, and have provided datings of 80-112 ka BP using single-grain optically stimulated luminescence. This places the sequence at the end of MIS5 and beginning of the MIS4. We described here a complete adult human distal foot phalanx (GE-1573) recovered during the 2017 field season in the interface between lithostratigraphic units 3 and 4 (107-112 ka BP) in the GE-I test pit.

MATERIALS AND METHOD: This phalanx (GE-1573) probably corresponds to the fifth toe from the right side due to the medial deviation of the distal tuberosity. We compared the metric variables of this phalanx to several fossil and recent Homo samples.

RESULTS: Neandertals display foot phalanges that are broader and more robust than those of recent humans. Despite the scarcity of well-identified distal phalanges in the Homo fossil record, the GE-1573 phalanx is broad, long and robust when compared with recent and Upper Paleolithic modern humans.

DISCUSSION: These traits, which align the GE-1573 foot phalanx with the Neandertal morphology, are consistent with the stratigraphic context, likely corresponding to one of the oldest Late Neandertals found inland on the Iberian Peninsula. Additionally, it provides the first evidence of a Neandertal human fossil in a stratigraphic context in the Sierra de Atapuerca.

RevDate: 2018-12-05

Stelzer S, Neubauer S, Hublin JJ, et al (2019)

Morphological trends in arcade shape and size in Middle Pleistocene Homo.

American journal of physical anthropology, 168(1):70-91.

OBJECTIVES: Middle Pleistocene fossil hominins, often summarized as Homo heidelbergensis sensu lato, are difficult to interpret due to a fragmentary fossil record and ambiguous combinations of primitive and derived characters. Here, we focus on one aspect of facial shape and analyze shape variation of the dental arcades of these fossils together with other Homo individuals.

MATERIALS AND METHODS: Three-dimensional landmark data were collected on computed tomographic scans and surface scans of Middle Pleistocene fossil hominins (n = 8), Homo erectus s.l. (n = 4), Homo antecessor (n = 1), Homo neanderthalensis (n = 13), recent (n = 52) and fossil (n = 19) Homo sapiens. To increase sample size, we used multiple multivariate regression to reconstruct complementary arches for isolated mandibles, and explored size and shape differences among maxillary arcades.

RESULTS: The shape of the dental arcade in H. erectus s.l. and H. antecessor differs markedly from both Neanderthals and H. sapiens. The latter two show subtle but consistent differences in arcade length and width. Shape variation among Middle Pleistocene fossil hominins does not exceed the amount of variation of other species, but includes individuals with more primitive and more derived morphology, all more similar to Neanderthals and H. sapiens than to H. erectus s.l.

DISCUSSION: Although our results cannot reject the hypothesis that the Middle Pleistocene fossil hominins belong to a single species, their shape variation comprises a more primitive morph that represents a likely candidate for the shape of the last common ancestor of Neanderthals and H. sapiens, and a more derived morph resembling Neanderthals. The arcade shape difference between Neanderthals and H. sapiens might be related to different ways to withstand mechanical stress.

RevDate: 2019-03-14
CmpDate: 2019-03-14

Cortés-Sánchez M, Riquelme-Cantal JA, Simón-Vallejo MD, et al (2018)

Pre-Solutrean rock art in southernmost Europe: Evidence from Las Ventanas Cave (Andalusia, Spain).

PloS one, 13(10):e0204651.

The south of Iberia conserves an important group of Palaeolithic rock art sites. The graphisms have been mostly attributed to the Solutrean and Magdalenian periods, while the possibility that older remains exist has provoked extensive debate. This circumstance has been linked to both the cited periods, until recently, due to the transition from the Middle to Upper Palaeolithic in the extreme southwest of Europe as well as the non-existence of some of the early periods of Palaeolithic art documented in northern Iberia. This study presents the results of interdisciplinary research conducted in Las Ventanas Cave. These results enabled us to identify a new Palaeolithic rock art site. The technical, stylistic and temporal traits point to certain similarities with the range of exterior deep engravings in Cantabrian Palaeolithic rock art. Ventanas appears to corroborate the age attributed to those kinds of graphic expression and points to the early arrival of the Upper Palaeolithic in the south of Iberia. Importantly, the results provide information on the pre-Solutrean date attributed to trilinear hind figures. These findings challenge the supposed Neanderthal survival idea at one of the main late Middle Palaeolithic southern Iberian sites (Carigüela) and, due to the parallels between them and an engraving attributed to this period in Gibraltar, it raises the possibility of interaction between modern humans and Neanderthals in the extreme southwest of Europe.

RevDate: 2019-02-05

Williams AC, LJ Hill (2018)

Nicotinamide's Ups and Downs: Consequences for Fertility, Development, Longevity and Diseases of Poverty and Affluence.

International journal of tryptophan research : IJTR, 11:1178646918802289.

To further explore the role of dietary nicotinamide in both brain development and diseases, particularly those of ageing. Articles cover neurodegenerative disease and cancer. Also discussed are the effects of nicotinamide, contained in meat and supplements and derived from symbionts, on the major transitions of disease and fertility from ancient times up to the present day. A key role for the tryptophan - NAD 'de novo' and immune tolerance pathway are discussed at length in the context of fertility and longevity and the transitions from immune paresis to Treg-mediated immune tolerance and then finally to intolerance and their associated diseases. Abstract: Nicotinamide in human evolution increased cognitive power in a positive feedback loop originally involving hunting. As the precursor to metabolic master molecule NAD it is, as vitamin B3, vital for health. Paradoxically, a lower dose on a diverse plant then cereal-based diet fuelled population booms from the Mesolithic onwards, by upping immune tolerance of the foetus. Increased tolerance of risky symbionts, whether in the gut or TB, that excrete nicotinamide co-evolved as buffers for when diet was inadequate. High biological fertility, despite disease trade-offs, avoided the extinction of Homo sapiens and heralded the dawn of a conscious, creative, and pro-fertility culture. Nicotinamide equity now would stabilise populations and prevent NAD-based diseases of poverty and affluence.

RevDate: 2018-12-11
CmpDate: 2018-12-11

Hardy K, Buckley S, L Copeland (2018)

Pleistocene dental calculus: Recovering information on Paleolithic food items, medicines, paleoenvironment and microbes.

Evolutionary anthropology, 27(5):234-246.

Dental calculus is now widely used to recover information on items ingested in the past. It is particularly valuable in the earlier Paleolithic, where recovered data may represent the only evidence for plant use. Several recovery methods are used and each one produces different results. Biomolecular markers and genetic material recovered from dental calculus is providing new data on identifiable dietary and medicinal items and human microbial communities. The recovery of microfossils, in particular, starch granules, has triggered a new awareness of the role of plants in the diet throughout the Paleolithic. However, the minute amount of material recovered has little relationship with food eaten during a person's life, while salivary amylase breaks down cooked starch. Therefore, broader dietary interpretations and detection of cooked food are problematic. The study of ancient dental calculus holds great potential to recover information about past lives, within realistic parameters.

RevDate: 2018-11-14

Gravina B, Bachellerie F, Caux S, et al (2018)

No Reliable Evidence for a Neanderthal-Châtelperronian Association at La Roche-à-Pierrot, Saint-Césaire.

Scientific reports, 8(1):15134.

The demise of Neanderthals and their interaction with dispersing anatomically modern human populations remain some of the most contentious issues in palaeoanthropology. The Châtelperronian, now generally recognized as the first genuine Upper Palaeolithic industry in Western Europe and commonly attributed to the Neanderthals, plays a pivotal role in these debates. The Neanderthal authorship of this techno-complex is based on reported associations of Neanderthal skeletal material with Châtelperronian assemblages at only two sites, La Roche-à-Pierrot (Saint-Césaire) and the Grotte du Renne (Arcy-sur-Cure). The reliability of such an association has, however, been the subject of heated controversy. Here we present a detailed taphonomic, spatial and typo-technological reassessment of the level (EJOP sup) containing the Neanderthal skeletal material at Saint-Césaire. Our assessment of a new larger sample of lithic artifacts, combined with a systematic refitting program and spatial projections of diagnostic artifacts, produced no reliable evidence for a Neanderthal-Châtelperronian association at the site. These results significantly impact current models concerning the Middle-to-Upper Palaeolithic transition in Western Europe and force a critical reappraisal of who exactly were the makers of the Châtelperronian.

RevDate: 2018-10-16
CmpDate: 2018-10-16

Hoffmann DL, Standish CD, García-Diez M, et al (2018)

Response to Comment on "U-Th dating of carbonate crusts reveals Neandertal origin of Iberian cave art".

Science (New York, N.Y.), 362(6411):.

Slimak et al challenge the reliability of our oldest (>65,000 years) U-Th dates on carbonates associated with cave paintings in Spain. They cite a supposed lack of parietal art for the 25,000 years following this date, along with potential methodological issues relating to open-system behavior and corrections to detrital or source water 230Th. We show that their criticisms are unfounded.

RevDate: 2019-02-15
CmpDate: 2019-02-06

Bamford CGG, Aranday-Cortes E, Filipe IC, et al (2018)

A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages.

PLoS pathogens, 14(10):e1007307.

As antimicrobial signalling molecules, type III or lambda interferons (IFNλs) are critical for defence against infection by diverse pathogens, including bacteria, fungi and viruses. Counter-intuitively, expression of one member of the family, IFNλ4, is associated with decreased clearance of hepatitis C virus (HCV) in the human population; by contrast, a natural frameshift mutation that abrogates IFNλ4 production improves HCV clearance. To further understand how genetic variation between and within species affects IFNλ4 function, we screened a panel of all known extant coding variants of human IFNλ4 for their antiviral potential and identify three that substantially affect activity: P70S, L79F and K154E. The most notable variant was K154E, which was found in African Congo rainforest 'Pygmy' hunter-gatherers. K154E greatly enhanced in vitro activity in a range of antiviral (HCV, Zika virus, influenza virus and encephalomyocarditis virus) and gene expression assays. Remarkably, E154 is the ancestral residue in mammalian IFNλ4s and is extremely well conserved, yet K154 has been fixed throughout evolution of the hominid genus Homo, including Neanderthals. Compared to chimpanzee IFNλ4, the human orthologue had reduced activity due to amino acid K154. Comparison of published gene expression data from humans and chimpanzees showed that this difference in activity between K154 and E154 in IFNλ4 correlates with differences in antiviral gene expression in vivo during HCV infection. Mechanistically, our data show that the human-specific K154 negatively affects IFNλ4 activity through a novel means by reducing its secretion and potency. We thus demonstrate that attenuated activity of IFNλ4 is conserved among humans and postulate that differences in IFNλ4 activity between species contribute to distinct host-specific responses to-and outcomes of-infection, such as HCV infection. The driver of reduced IFNλ4 antiviral activity in humans remains unknown but likely arose between 6 million and 360,000 years ago in Africa.

RevDate: 2019-03-25
CmpDate: 2019-03-25

Anonymous (2018)

Neanderthal liaisons bestowed virus-fighting genes on humans.

Nature, 562(7726):166.

RevDate: 2019-04-13

Rodríguez W, Mazet O, Grusea S, et al (2018)

The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure.

Heredity, 121(6):663-678.

In the last years, a wide range of methods allowing to reconstruct past population size changes from genome-wide data have been developed. At the same time, there has been an increasing recognition that population structure can generate genetic data similar to those produced under models of population size change. Recently, Mazet et al. (Heredity 116:362-371, 2016) showed that, for any model of population structure, it is always possible to find a panmictic model with a particular function of population size changes, having exactly the same distribution of T2 (the coalescence time for a sample of size two) as that of the structured model. They called this function IICR (Inverse Instantaneous Coalescence Rate) and showed that it does not necessarily correspond to population size changes under non-panmictic models. Besides, most of the methods used to analyse data under models of population structure tend to arbitrarily fix that structure and to minimise or neglect population size changes. Here, we extend the seminal work of Herbots (PhD thesis, University of London, 1994) on the structured coalescent and propose a new framework, the Non-Stationary Structured Coalescent (NSSC) that incorporates demographic events (changes in gene flow and/or deme sizes) to models of nearly any complexity. We show how to compute the IICR under a wide family of stationary and non-stationary models. As an example we address the question of human and Neanderthal evolution and discuss how the NSSC framework allows to interpret genomic data under this new perspective.

RevDate: 2019-06-03

Enard D, DA Petrov (2018)

Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans.

Cell, 175(2):360-371.e13.

Neanderthals and modern humans interbred at least twice in the past 100,000 years. While there is evidence that most introgressed DNA segments from Neanderthals to modern humans were removed by purifying selection, less is known about the adaptive nature of introgressed sequences that were retained. We hypothesized that interbreeding between Neanderthals and modern humans led to (1) the exposure of each species to novel viruses and (2) the exchange of adaptive alleles that provided resistance against these viruses. Here, we find that long, frequent-and more likely adaptive-segments of Neanderthal ancestry in modern humans are enriched for proteins that interact with viruses (VIPs). We found that VIPs that interact specifically with RNA viruses were more likely to belong to introgressed segments in modern Europeans. Our results show that retained segments of Neanderthal ancestry can be used to detect ancient epidemics.

RevDate: 2019-06-05
CmpDate: 2019-06-05

Huerta-Sánchez E, FP Casey (2018)

Simultaneous Viral Exposure and Protection from Neanderthal Introgression.

Cell, 175(2):306-307.

In this issue, Enard and Petrov present intriguing results on the possibility of genetic traces left behind in our genomes from adaptation to past viral epidemics that may have been initiated by interaction with Neanderthal archaic hominins. The work highlights how powerful infectious agents can act as a selective force to shape our genetic makeup.

RevDate: 2018-11-14

Jones JR, Richards MP, Straus LG, et al (2018)

Changing environments during the Middle-Upper Palaeolithic transition in the eastern Cantabrian Region (Spain): direct evidence from stable isotope studies on ungulate bones.

Scientific reports, 8(1):14842.

Environmental change has been proposed as a factor that contributed to the extinction of the Neanderthals in Europe during MIS3. Currently, the different local environmental conditions experienced at the time when Anatomically Modern Humans (AMH) met Neanderthals are not well known. In the Western Pyrenees, particularly, in the eastern end of the Cantabrian coast of the Iberian Peninsula, extensive evidence of Neanderthal and subsequent AMH activity exists, making it an ideal area in which to explore the palaeoenvironments experienced and resources exploited by both human species during the Middle to Upper Palaeolithic transition. Red deer and horse were analysed using bone collagen stable isotope analysis to reconstruct environmental conditions across the transition. A shift in the ecological niche of horses after the Mousterian demonstrates a change in environment, towards more open vegetation, linked to wider climatic change. In the Mousterian, Aurignacian and Gravettian, high inter-individual nitrogen ranges were observed in both herbivores. This could indicate that these individuals were procured from areas isotopically different in nitrogen. Differences in sulphur values between sites suggest some variability in the hunting locations exploited, reflecting the human use of different parts of the landscape. An alternative and complementary explanation proposed is that there were climatic fluctuations within the time of formation of these archaeological levels, as observed in pollen, marine and ice cores.

RevDate: 2019-03-13
CmpDate: 2019-03-13

Zanolli C, Martinón-Torres M, Bernardini F, et al (2018)

The Middle Pleistocene (MIS 12) human dental remains from Fontana Ranuccio (Latium) and Visogliano (Friuli-Venezia Giulia), Italy. A comparative high resolution endostructural assessment.

PloS one, 13(10):e0189773.

The penecontemporaneous Middle Pleistocene sites of Fontana Ranuccio (Latium) and Visogliano (Friuli-Venezia Giulia), set c. 450 km apart in central and northeastern Italy, respectively, have yielded some among the oldest human fossil remains testifying to a peopling phase of the Italian Peninsula broadly during the glacial MIS 12, a stage associated with one among the harshest climatic conditions in the Northern hemisphere during the entire Quaternary period. Together with the large samples from Atapuerca Sima de los Huesos, Spain, and Caune de l'Arago at Tautavel, France, the remains from Fontana Ranuccio and Visogliano are among the few mid-Middle Pleistocene dental assemblages from Western Europe available for investigating the presence of an early Neanderthal signature in their inner structure. We applied two- three-dimensional techniques of virtual imaging and geometric morphometrics to the high-resolution X-ray microtomography record of the dental remains from these two Italian sites and compared the results to the evidence from a selected number of Pleistocene and extant human specimens/samples from Europe and North Africa. Depending on their preservation quality and on the degree of occlusal wear, we comparatively assessed: (i) the crown enamel and radicular dentine thickness topographic variation of a uniquely represented lower incisor; (ii) the lateral crown tissue proportions of premolars and molars; (iii) the enamel-dentine junction, and (iv) the pulp cavity morphology of all available specimens. Our analyses reveal in both samples a Neanderthal-like inner structural signal, for some aspects also resembling the condition shown by the contemporary assemblage from Atapuerca SH, and clearly distinct from the recent human figures. This study provides additional evidence indicating that an overall Neanderthal morphological dental template was preconfigured in Western Europe at least 430 to 450 ka ago.

RevDate: 2019-03-06
CmpDate: 2019-03-06

Martín-Francés L, Martinón-Torres M, Martínez de Pinillos M, et al (2018)

Tooth crown tissue proportions and enamel thickness in Early Pleistocene Homo antecessor molars (Atapuerca, Spain).

PloS one, 13(10):e0203334.

Tooth crown tissue proportions and enamel thickness distribution are considered reliable characters for inferring taxonomic identity, phylogenetic relationships, dietary and behavioural adaptations in fossil and extant hominids. While most Pleistocene hominins display variations from thick to hyper-thick enamel, Neanderthals exhibit relatively thinner. However, the chronological and geographical origin for the appearance of this typical Neanderthal condition is still unknown. The European late Early Pleistocene species Homo antecessor (Gran Dolina-TD6 site, Sierra de Atapuerca) represents an opportunity to investigate the appearance of the thin condition in the fossil record. In this study, we aim to test the hypothesis if H. antecessor molars approximates the Neanderthal condition for tissue proportions and enamel thickness. To do so, for the first time we characterised the molar inner structural organization in this Early Pleistocene hominin taxon (n = 17) and compared it to extinct and extant populations of the genus Homo from African, Asian and European origin (n = 355). The comparative sample includes maxillary and mandibular molars belonging to H. erectus, East and North African Homo, European Middle Pleistocene Homo, Neanderthals, and fossil and extant H. sapiens. We used high-resolution images to investigate the endostructural configuration of TD6 molars (tissue proportions, enamel thickness and distribution). TD6 permanent molars tend to exhibit on average thick absolute and relative enamel in 2D and 3D estimates, both in the complete crown and the lateral enamel. This condition is shared with the majority of extinct and extant hominin sample, except for Neanderthals and some isolated specimens. However, while the total crown percentage of dentine in TD6 globally resembles the low modern values, the lateral crown percentage of dentine tends to be much higher, closer to the Neanderthal signal. Similarly, the H. antecessor molar enamel distribution maps reveal a relative distribution pattern that is more similar to the Neanderthal condition (with the thickest enamel more spread at the periphery of the occlusal basin) rather than that of other fossil specimens and modern humans (with thicker cuspal enamel). Future studies on European Middle Pleistocene populations will provide more insights into the evolutionary trajectory of the typical Neanderthal dental structural organization.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

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The first fossil recognized to be an ancestral human was found in the Neander Valley (thal in German) in 1856. William King suggested Homo neanderthalensis (human from the Neander Valley) as the scientific name for the specimen — hence Neanderthal became the common name by which this early human became known. Now Neanderthal genomes have been sequenced, more is known about their path to extinction, and the existence of Neanderthal culture, including music, has been established. To understand the evolutionary path of the hominid line, one must be familiar with Homo neanderthalensis. These books are highly recommended. R. Robbins

Electronic Scholarly Publishing
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E-mail: RJR8222 @

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )