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Bibliography on: Neanderthals

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ESP: PubMed Auto Bibliography 06 Aug 2020 at 01:49 Created: 

Neanderthals

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®)

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RevDate: 2020-08-04

Course MM, Gudsnuk K, Smukowski SN, et al (2020)

Evolution of a Human-Specific Tandem Repeat Associated with ALS.

American journal of human genetics pii:S0002-9297(20)30234-2 [Epub ahead of print].

Tandem repeats are proposed to contribute to human-specific traits, and more than 40 tandem repeat expansions are known to cause neurological disease. Here, we characterize a human-specific 69 bp variable number tandem repeat (VNTR) in the last intron of WDR7, which exhibits striking variability in both copy number and nucleotide composition, as revealed by long-read sequencing. In addition, greater repeat copy number is significantly enriched in three independent cohorts of individuals with sporadic amyotrophic lateral sclerosis (ALS). Each unit of the repeat forms a stem-loop structure with the potential to produce microRNAs, and the repeat RNA can aggregate when expressed in cells. We leveraged its remarkable sequence variability to align the repeat in 288 samples and uncover its mechanism of expansion. We found that the repeat expands in the 3'-5' direction, in groups of repeat units divisible by two. The expansion patterns we observed were consistent with duplication events, and a replication error called template switching. We also observed that the VNTR is expanded in both Denisovan and Neanderthal genomes but is fixed at one copy or fewer in non-human primates. Evaluating the repeat in 1000 Genomes Project samples reveals that some repeat segments are solely present or absent in certain geographic populations. The large size of the repeat unit in this VNTR, along with our multiplexed sequencing strategy, provides an unprecedented opportunity to study mechanisms of repeat expansion, and a framework for evaluating the roles of VNTRs in human evolution and disease.

RevDate: 2020-08-03

Örd T, Puurand T, Örd D, et al (2020)

A human-specific VNTR in the TRIB3 promoter causes gene expression variation between individuals.

PLoS genetics, 16(8):e1008981 pii:PGENETICS-D-20-00244 [Epub ahead of print].

Tribbles homolog 3 (TRIB3) is pseudokinase involved in intracellular regulatory processes and has been implicated in several diseases. In this article, we report that human TRIB3 promoter contains a 33-bp variable number tandem repeat (VNTR) and characterize the heterogeneity and function of this genetic element. Analysis of human populations around the world uncovered the existence of alleles ranging from 1 to 5 copies of the repeat, with 2-, 3- and 5-copy alleles being the most common but displaying considerable geographical differences in frequency. The repeated sequence overlaps a C/EBP-ATF transcriptional regulatory element and is highly conserved, but not repeated, in various mammalian species, including great apes. The repeat is however evident in Neanderthal and Denisovan genomes. Reporter plasmid experiments in human cell culture reveal that an increased copy number of the TRIB3 promoter 33-bp repeat results in increased transcriptional activity. In line with this, analysis of whole genome sequencing and RNA-Seq data from human cohorts demonstrates that the copy number of TRIB3 promoter 33-bp repeats is positively correlated with TRIB3 mRNA expression level in many tissues throughout the body. Moreover, the copy number of the TRIB3 33-bp repeat appears to be linked to known TRIB3 eQTL SNPs as well as TRIB3 SNPs reported in genetic association studies. Taken together, the results indicate that the promoter 33-bp VNTR constitutes a causal variant for TRIB3 expression variation between individuals and could underlie the results of SNP-based genetic studies.

RevDate: 2020-07-31

Ríos L, HFV Cardoso (2020)

Comment on 'Krapina atlases suggest a high prevalence of anatomical variations in the first cervical vertebra of Neanderthals'.

Journal of anatomy [Epub ahead of print].

A review of the observation of an anterior cleft on the atlas of a Neanderthal from Krapina.

RevDate: 2020-07-30

Anonymous (2020)

Dinosaur retraction, Neanderthal pain and EU budget woe.

Nature, 583(7818):665.

RevDate: 2020-07-29

Grine FE, Mongle CS, Smith SL, et al (2020)

Human manual distal phalanges from the Middle Stone Age deposits of Klasies River Main Site , Western Cape Province, South Africa.

Journal of human evolution, 146:102849 pii:S0047-2484(20)30110-X [Epub ahead of print].

Two new distal manual phalanges from the Middle Stone Age deposits of Klasies River Main Site are described. One (SAM-AP 6387) likely derives from ray II or ray III, whereas the other (SAM-AP 6388) is from the thumb. Both derive from a late adolescent or fully adult individual. They were recovered by H. Deacon from the same stratigraphic unit (submember W or possibly submember R) of the Shell and Sand Member of Cave 1, which places them between 100 and 90 ka. Both are comparatively small elements, and the possibility that they came from the same hand cannot be discounted at this time. These bones add to the meager and all too fragmentary postcranial human fossil sample from the Late Pleistocene of South Africa. These two specimens provide some additional evidence pertaining to the morphological attributes of the distal phalanges of the Middle Stone Age inhabitants of South Africa. Together with the distal pollical phalanx from Die Kelders (SAM-AP 6402), they are relatively small in comparison with homologs from recent human samples as well as Late Pleistocene specimens from Eurasia. Given their small sizes, the distal pollical phalanges from Klasies and Die Kelders are not dissimilar to Holocene Khoesan homologs. As expected, the Klasies elements differ noticeably from Neandertal homologs, especially in the narrowness of their shafts and distal tuberosities.

RevDate: 2020-07-28

Rinker DC, Simonti CN, McArthur E, et al (2020)

Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations.

Nature ecology & evolution pii:10.1038/s41559-020-1261-z [Epub ahead of print].

Neanderthal ancestry remains across modern Eurasian genomes and introgressed sequences influence diverse phenotypes. Here, we demonstrate that introgressed sequences reintroduced thousands of ancestral alleles that were lost in Eurasian populations before introgression. Our simulations and variant effect predictions argue that these reintroduced alleles (RAs) are more likely to be tolerated by modern humans than are introgressed Neanderthal-derived alleles (NDAs) due to their distinct evolutionary histories. Consistent with this, we show enrichment for RAs and depletion for NDAs on introgressed haplotypes with expression quantitative trait loci (eQTL) and phenotype associations. Analysis of available cross-population eQTLs and massively parallel reporter assay data show that RAs commonly influence gene expression independent of linked NDAs. We further validate these independent effects for one RA in vitro. Finally, we demonstrate that NDAs are depleted for regulatory activity compared to RAs, while RAs have activity levels similar to non-introgressed variants. In summary, our study reveals that Neanderthal introgression reintroduced thousands of lost ancestral variants with gene regulatory activity and that these RAs were more tolerated than NDAs. Thus, RAs and their distinct evolutionary histories must be considered when evaluating the effects of introgression.

RevDate: 2020-07-24

Zeberg H, Dannemann M, Sahlholm K, et al (2020)

A Neanderthal Sodium Channel Increases Pain Sensitivity in Present-Day Humans.

Current biology : CB pii:S0960-9822(20)30861-7 [Epub ahead of print].

The sodium channel Nav1.7 is crucial for impulse generation and conduction in peripheral pain pathways [1]. In Neanderthals, the Nav1.7 protein carried three amino acid substitutions (M932L, V991L, and D1908G) relative to modern humans. We expressed Nav1.7 proteins carrying all combinations of these substitutions and studied their electrophysiological effects. Whereas the single amino acid substitutions do not affect the function of the ion channel, the full Neanderthal variant carrying all three substitutions, as well as the combination of V991L with D1908G, shows reduced inactivation, suggesting that peripheral nerves were more sensitive to painful stimuli in Neanderthals than in modern humans. We show that, due to gene flow from Neanderthals, the three Neanderthal substitutions are found in ∼0.4% of present-day Britons, where they are associated with heightened pain sensitivity.

RevDate: 2020-07-25

Callaway E (2020)

Neanderthal gene linked to increased pain sensitivity.

RevDate: 2020-07-23

Sánchez-Romero L, Benito-Calvo A, Marín-Arroyo AB, et al (2020)

Author Correction: New insights for understanding spatial patterning and formation processes of the Neanderthal occupation in the Amalda I cave (Gipuzkoa, Spain).

Scientific reports, 10(1):12456 pii:10.1038/s41598-020-68761-1.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

RevDate: 2020-07-22

Baumann C, Bocherens H, Drucker DG, et al (2020)

Fox dietary ecology as a tracer of human impact on Pleistocene ecosystems.

PloS one, 15(7):e0235692 pii:PONE-D-20-05722.

Nowadays, opportunistic small predators, such as foxes (Vulpes vulpes and Vulpes lagopus), are well known to be very adaptable to human modified ecosystems. However, the timing of the start of this phenomenon in terms of human impact on ecosystems and of the implications for foxes has hardly been studied. We hypothesize that foxes can be used as an indicator of past human impact on ecosystems, as a reflection of population densities and consequently to track back the influence of humans on the Pleistocene environment. To test this hypothesis, we used stable isotope analysis (δ13C, δ15N) of bone collagen extracted from faunal remains from several archaeological sites located in the Swabian Jura (southwest Germany) and covering a time range over three important cultural periods, namely the Middle Palaeolithic (older than 42,000 years ago) attributed to Neanderthals, and the early Upper Palaeolithic periods Aurignacian and Gravettian (42,000 to 30,000 years ago) attributed to modern humans. We then ran Bayesian statistic systems (SIBER, mixSIAR) to reconstruct the trophic niches and diets of Pleistocene foxes. We observed that during the Middle Palaeolithic period, when Neanderthals sparsely populated the Swabian Jura, the niches occupied by foxes suggest a natural trophic behavior. In contrast, during the early Upper Palaeolithic periods, a new trophic fox niche appeared, characterized by a restricted diet on reindeer. This trophic niche could be due to the consumption of human subsidies related to a higher human population density and the resulting higher impact on the Pleistocene environment by modern humans compared to Neanderthals. Furthermore, our study suggests that, a synanthropic commensal behavior of foxes started already in the Aurignacian, around 42,000 years ago.

RevDate: 2020-07-22

Peeters S, H Zwart (2020)

Neanderthals as familiar strangers and the human spark: How the 'golden years' of Neanderthal research reopen the question of human uniqueness.

History and philosophy of the life sciences, 42(3):33 pii:10.1007/s40656-020-00327-w.

During the past decades, our image of Homo neanderthalensis has changed dramatically. Initially, Neanderthals were seen as primitive brutes. Increasingly, however, Neanderthals are regarded as basically human. New discoveries and technologies have led to an avalanche of data, and as a result of that it becomes increasingly difficult to pinpoint what the difference between modern humans and Neanderthals really is. And yet, the persistent quest for a minimal difference which separates them from us is still noticeable in Neanderthal research. Neanderthal discourse is a vantage point from which the logic of 'us' versus 'other' is critically reconsidered. Studying contemporary academic literature and science autobiographies from an oblique perspective, focusing not on Neanderthals as objects, but on the dynamics of interaction between Neanderthal researchers and their finds, basic convictions at work in this type of research are retrieved. What is at issue is not the actual distinction between modern humans and Neanderthals (which is continuously being redefined), but rather the dualistic construction of human and nonhuman. Neanderthal understanding is affected by the desire to safeguard human uniqueness. The overall trend is to identify the human mark or spark, which defines us as favoured 'winners'. The paradoxes emerging in contemporary Neanderthal discourse are symptomatic of the fact that a dualistic style of thinking is no longer tenable.

RevDate: 2020-07-21

Montinaro F, C Capelli (2020)

A Worldwide Map of Human Structural Variants.

Trends in genetics : TIG pii:S0168-9525(20)30168-2 [Epub ahead of print].

Genomic variation extends from single nucleotide variants to large chromosomal rearrangements, but the extent of structural variation in Homo sapiens is still unclear. Almarri et al. provide a worldwide catalogue of structural variants present in human populations. Most of the reported variation is novel, with some variants being inherited from Neanderthals and Denisovans. Drift and selection shaped the distribution of these variants with some suggested to have functional implications.

RevDate: 2020-07-18

Marra F, Rolfo MF, Gaeta M, et al (2020)

Anomalous Last Interglacial Tyrrhenian sea levels and Neanderthal settling at Guattari and Moscerini caves (central Italy).

Scientific reports, 10(1):11929 pii:10.1038/s41598-020-68604-z.

We present a geological-stratigraphical study aimed to provide chronologic constraints to the sea-level markers occurring at two coastal caves of central Italy (Grotta Guattari and Grotta dei Moscerini) and to the Neanderthal frequentation of these caves, in the light of recent archaeological and geomorphological-geochronological studies suggesting similar sea levels during MIS 5.5 and MIS 5.3, and only few m below the Present during MIS 5.1 in this region. Based on the review of previous literature data, combined with new stratigraphic observations at Grotta Guattari and re-analysis of archive material including unpublished field notes from Grotta dei Moscerini, we reconstruct a plausible sea-level history accounting for the lithological and paleoenvironmental features of their sedimentary fillings. In particular, we outline the abundant occurrence of well-rounded pumice clasts within the sedimentary deposits of Moscerini Cave, attesting for the proximity to the beach where this pumice was gathered by wave action. Through the petrographic and geochemical analysis of this pumice we evidence provenance from Phlegraean Fields and Ischia Island volcanic districts, framing their chronology in the time span 118-40 ka, consistent with literature ESR-U/Th dates providing ages ranging 101 ± 5-74 ± 7 ka for the sedimentary filling of both Moscerini and Guattari caves.

RevDate: 2020-07-15

Hallast P, Agdzhoyan A, Balanovsky O, et al (2020)

A Southeast Asian origin for present-day non-African human Y chromosomes.

Human genetics pii:10.1007/s00439-020-02204-9 [Epub ahead of print].

The genomes of present-day humans outside Africa originated almost entirely from a single out-migration ~ 50,000-70,000 years ago, followed by mixture with Neanderthals contributing ~ 2% to all non-Africans. However, the details of this initial migration remain poorly understood because no ancient DNA analyses are available from this key time period, and interpretation of present-day autosomal data is complicated due to subsequent population movements/reshaping. One locus, however, does retain male-specific information from this early period: the Y chromosome, where a detailed calibrated phylogeny has been constructed. Three present-day Y lineages were carried by the initial migration: the rare haplogroup D, the moderately rare C, and the very common FT lineage which now dominates most non-African populations. Here, we show that phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y chromosomes, all point to East/Southeast Asia as the origin 50,000-55,000 years ago of all known surviving non-African male lineages (apart from recent migrants). This observation contrasts with the expectation of a West Eurasian origin predicted by a simple model of expansion from a source near Africa, and can be interpreted as resulting from extensive genetic drift in the initial population or replacement of early western Y lineages from the east, thus informing and constraining models of the initial expansion.

RevDate: 2020-07-14

Columbu A, Chiarini V, Spötl C, et al (2020)

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

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

RevDate: 2020-07-14
CmpDate: 2020-07-14

Bailey SE, Brophy JK, Moggi-Cecchi J, et al (2019)

The deciduous dentition of Homo naledi: A comparative study.

Journal of human evolution, 136:102655.

In 2013, 2014 new hominin remains were uncovered in the Dinaledi chamber of the Rising Star cave system in South Africa. In 2015 Berger and colleagues identified these remains as belonging to a new species Homo naledi (Berger et al., 2015). Subsequent comparative studies of the skull, postcrania and permanent dentition have supported this taxonomic affiliation (Harcourt-Smith et al., 2015; Kivell et al., 2015; Irish et al., 2018). The deciduous teeth can offer unique insights into hominin evolution. Due to their early onset and rapid development their morphology is thought to be under stronger genetic control and less influenced by environment than are the permanent teeth. In this study we compared the H. naledi deciduous teeth from the 2013-2014 excavations to samples representing much of the hominin clade including Australopithecus afarensis, Australopithecus africanus, Paranthropus boisei, Paranthropus robustus, early Homo, Homo antecessor, Homo erectus s.l., Homo floresiensis, Middle Pleistocene Homo, Homo neanderthalensis, early Homo sapiens and recent H. sapiens from Sub-Saharan Africa. By making such a broad morphological comparison, we aimed to contextualize the Dinaledi hominins and to further assess the validity of their taxonomic assignment. Our analysis of the deciduous teeth revealed a unique combination of features that mirror (but also expand) that found in the permanent teeth. This mosaic includes an asymmetrical lower canine with a distal tubercle, an upper first molar with a large hypocone and epicrista associated with a mesial cuspule, a molarized lower first molar resembling Paranthropus, and upper and lower second molars that resemble later Homo in their lack of accessory cusps. The unique combination of deciduous dental characters supports previous studies assigning H. naledi to a new species, although its phylogenetic position vis-à-vis other Homo species remains ambiguous.

RevDate: 2020-07-11

Pomeroy E, Hunt CO, Reynolds T, et al (2020)

Issues of theory and method in the analysis of Paleolithic mortuary behavior: A view from Shanidar Cave.

Evolutionary anthropology [Epub ahead of print].

Mortuary behavior (activities concerning dead conspecifics) is one of many traits that were previously widely considered to have been uniquely human, but on which perspectives have changed markedly in recent years. Theoretical approaches to hominin mortuary activity and its evolution have undergone major revision, and advances in diverse archeological and paleoanthropological methods have brought new ways of identifying behaviors such as intentional burial. Despite these advances, debates concerning the nature of hominin mortuary activity, particularly among the Neanderthals, rely heavily on the rereading of old excavations as new finds are relatively rare, limiting the extent to which such debates can benefit from advances in the field. The recent discovery of in situ articulated Neanderthal remains at Shanidar Cave offers a rare opportunity to take full advantage of these methodological and theoretical developments to understand Neanderthal mortuary activity, making a review of these advances relevant and timely.

RevDate: 2020-07-07

Andrea C, Veronica C, Christoph S, et al (2020)

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

Nature ecology & evolution pii:10.1038/s41559-020-1243-1 [Epub ahead of print].

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

RevDate: 2020-07-07

Bastir M, García-Martínez D, Torres-Tamayo N, et al (2020)

Rib cage anatomy in Homo erectus suggests a recent evolutionary origin of modern human body shape.

Nature ecology & evolution pii:10.1038/s41559-020-1240-4 [Epub ahead of print].

The tall and narrow body shape of anatomically modern humans (Homo sapiens) evolved via changes in the thorax, pelvis and limbs. It is debated, however, whether these modifications first evolved together in African Homo erectus, or whether H. erectus had a more primitive body shape that was distinct from both the more ape-like Australopithecus species and H. sapiens. Here we present the first quantitative three-dimensional reconstruction of the thorax of the juvenile H. erectus skeleton, KNM-WT 15000, from Nariokotome, Kenya, along with its estimated adult rib cage, for comparison with H. sapiens and the Kebara 2 Neanderthal. Our three-dimensional reconstruction demonstrates a short, mediolaterally wide and anteroposteriorly deep thorax in KNM-WT 15000 that differs considerably from the much shallower thorax of H. sapiens, pointing to a recent evolutionary origin of fully modern human body shape. The large respiratory capacity of KNM-WT 15000 is compatible with the relatively stocky, more primitive, body shape of H. erectus.

RevDate: 2020-07-07
CmpDate: 2020-07-07

Conde-Valverde M, Rosa M, Martínez I, et al (2019)

A revision of the conductive hearing loss in Cranium 4 from the Middle Pleistocene site of Sima de los Huesos (Burgos, Spain).

Journal of human evolution, 135:102663.

Pathological conditions have been previously documented in the Middle Pleistocene Sima de los Huesos hominins from northern Spain, and several of these have clear behavioral implications. Within this fossil assemblage, Cranium 4 shows bilateral external auditory exostoses which have been preliminarily interpreted as causing a significant hearing loss in this individual. If confirmed, this would be the oldest recorded case of deafness in human history and could have important implications for the antiquity of this condition, as well as social interactions. To further investigate this case, the current study presents 3D reconstructions of the entire outer and middle ear, based on computed tomography scans of both temporal bones in Cranium 4. We established the degree of stenosis in both external auditory canals, showing that in both cases the degree of stenosis is less than 52% of the original cross-sectional area of each canal. Based on clinical studies in living humans, the buildup of wax due to the degree of stenosis in Cranium 4 is unlikely to have caused frequent external ear infections. In addition, we estimated the pattern of sound power transmission up to 5 kHz in both ears relying on a comprehensive model developed in the bioengineering literature and which has been applied previously to the Sima de los Huesos hominins. The model was modified to account for the peculiar shape of the pathological external ear canals in Cranium 4. The results show that this pathology had little to no influence on the sound power transmission in this individual. Thus, we conclude that the exostoses present in both ears of Cranium 4 did not significantly affect their hearing.

RevDate: 2020-07-07
CmpDate: 2020-07-07

Barsky D, Moigne AM, V Pois (2019)

The shift from typical Western European Late Acheulian to microproduction in unit 'D' of the late Middle Pleistocene deposits of the Caune de l'Arago (Pyrénées-Orientales, France).

Journal of human evolution, 135:102650.

Stratigraphic Unit D levels of the Caune de l'Arago (Pyrénées-Orientales, France), situated in the upper part of the depositional sequence of Ensemble Stratigraphique III (ES III), has yielded a rich Acheulian archeopaleontological record dated to the Middle Pleistocene. The site's infill, dated from 690 to 90 ka, encloses a thick cultural sequence comprising some of the oldest evidence of Acheulian documented so far in Western Europe (Unit P levels). The deposits contain successive occupation layers with abundant faunal remains, stone artifacts, and sometimes hominin remains attributed to Homo erectus tautavelensis. The Unit D levels are chronostratigraphically positioned at the top of the ES III sequence, accumulated at the end of Marine Isotope Stage (MIS) 12. The Unit D lithic assemblage shows no evidence of Levallois knapping strategies. Rather, its features indicate a trend towards microproduction that continues into subsequent occupational phases, apparently marking a local expression of the transition from the Lower to the Middle Paleolithic. Remarkably, tiny discoid and multidirectional type cores, predominantly knapped from small-sized quartz pebbles, characterize the Unit D lithic assemblage. Experimental work presented here demonstrates the likelihood that, despite the small size of the cores and the recalcitrant crystalline materials from which they were knapped, flake production can be carried out with free-hand hard hammer techniques. We explore behavioral aspects gleaned from Unit D cultural material, contrasting them with microlithic praxis observed elsewhere in Europe and the Near East in a similar timeframe.

RevDate: 2020-07-02

Yan SM, RC McCoy (2020)

Archaic hominin genomics provides a window into gene expression evolution.

Current opinion in genetics & development, 62:44-49 pii:S0959-437X(20)30065-4 [Epub ahead of print].

Differences in gene expression are thought to account for most phenotypic differences within and between species. Consequently, gene expression is a powerful lens through which to study divergence between modern humans and our closest evolutionary relatives, the Neanderthals and Denisovans. Such insights complement biological knowledge gleaned from the fossil record, while also revealing general features of the mode and tempo of regulatory evolution. Because of the degradation of ancient RNA, gene expression profiles of archaic hominins must be studied by indirect means. As such, conclusions drawn from these studies are often laden with assumptions about the genetic architecture of gene expression, the complexity of which is increasingly apparent. Despite these challenges, rapid technical and conceptual advances in the fields of ancient genomics, functional genomics, statistical genomics, and genome engineering are revolutionizing understanding of hominin gene expression evolution.

RevDate: 2020-07-02

Senturk N, MC Ergoren (2020)

Developing an Online Portal for Determining the Genomic Signature of Archaic DNA that are Associated to Modern Human Genetic Diseases: A Meta-Analysis Study.

The Eurasian journal of medicine, 52(2):153-160.

Objective: Mutations or introgression can cause and rise adaptive alleles of which some can be beneficial. Archaic humans lived more than 200,000 years ago in Europe and Western Asia. They were adapted to the environment and pathogens that prevailed in these locations. It can therefore be thought that modern humans obtained significant immune advantage from the archaic alleles.

Materials and Methods: First, data were collected by meta-analysis from previously identified genetic diseases caused by alleles that were introgressed from archaics. Second, the in silico model portal (http://www.archaics2phenotype.xxx.edu.tr) was designed to trace the history of the Neanderthal allele. The portal also shows the current distribution of the genotypes of the selected alleles within different populations and correlates with the individuals phenotype.

Results: Our developed model provides a better understanding for the origin of genetic diseases or traits that are associated with the Neanderthal genome.

Conclusion: The developed medicine model will help individuals and their populations to receive the best treatment. It also clarifies why there are differences in disease phenotypes in modern humans.

RevDate: 2020-06-29

Nielsen M, Langley MC, Shipton C, et al (2020)

Homo neanderthalensis and the evolutionary origins of ritual in Homo sapiens.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 375(1805):20190424.

There is a large, if disparate, body of archaeological literature discussing specific instantiations of symbolic material culture and the possibility of ritual practices in Neanderthal populations. Despite this attention, however, no single synthesis exists that draws upon cognitive, psychological and cultural evolutionary theories of ritual. Here, we review the evidence for ritual-practice among now-extinct Homo neanderthalensis, as well as the necessary cognitive pre-conditions for such behaviour, in order to explore the evolution of ritual in Homo sapiens. We suggest that the currently available archaeological evidence indicates that Neanderthals may have used 'ritualization' to increase the successful transmission of technical knowledge across generations-providing an explanation for the technological stability of the Middle Palaeolithic and attesting to a survival strategy differing from near-contemporary H. sapiens. This article is part of the theme issue 'Ritual renaissance: new insights into the most human of behaviours'.

RevDate: 2020-06-28

Martínez de Pinillos M, Martín-Francés L, de Castro JMB, et al (2020)

Inner morphological and metric characterization of the molar remains from the Montmaurin-La Niche mandible: The Neanderthal signal.

Journal of human evolution, 145:102739 pii:S0047-2484(19)30370-7 [Epub ahead of print].

Here, we present a metric and morphological study of the molar remains from the Montmaurin-La Niche mandible by means of microcomputed tomography. According to the last analysis, based on the combination of geomorphological and paleontological data, the level bearing this human mandible probably corresponds to the marine isotope stages (MIS) 7. These data place the Montmaurin-La Niche in a chronologically intermediate position between the Neanderthals and the Middle Pleistocene fossils (e.g., Sima de los Huesos, la Caune de l'Arago). A recent study has revealed that while the mandible is more closely related to the Early and Middle Pleistocene African and Eurasian populations, the morphology of the outer enamel surfaces of its molars is typical of the Neanderthal linage. The data presented here are in line with this finding because the morphology of the enamel-dentine junction of the molars is similar to that of Neanderthals, whereas the absolute and relative enamel thickness values (2D and 3D) are closer to those exhibited by some Early Pleistocene hominins. Moreover, the pulp cavity morphology and proportions are in concordance with the Neanderthal populations. Our results strengthen the hypothesis that the settlement of Europe could be the result of several migrations, at different times, originated from a common source population. Thus, the variability in the European Middle Pleistocene populations (e.g., Montmaurin, Sima de los Huesos, Arago, Mala Balanica) could indicate different migrations at different times and/or population fragmentation, without excluding the possible hybridization between residents and new settlers.

RevDate: 2020-06-26

Weiß CL, Gansauge MT, Aximu-Petri A, et al (2020)

Mining ancient microbiomes using selective enrichment of damaged DNA molecules.

BMC genomics, 21(1):432 pii:10.1186/s12864-020-06820-7.

BACKGROUND: The identification of bona fide microbial taxa in microbiomes derived from ancient and historical samples is complicated by the unavoidable mixture between DNA from ante- and post-mortem microbial colonizers. One possibility to distinguish between these sources of microbial DNA is querying for the presence of age-associated degradation patterns typical of ancient DNA (aDNA). The presence of uracils, resulting from cytosine deamination, has been detected ubiquitously in aDNA retrieved from diverse sources, and used as an authentication criterion. Here, we employ a library preparation method that separates molecules that carry uracils from those that do not for a set of samples that includes Neandertal remains, herbarium specimens and archaeological plant remains.

RESULTS: We show that sequencing DNA libraries enriched in molecules carrying uracils effectively amplifies age associated degradation patterns in microbial mixtures of ancient and historical origin. This facilitates the discovery of authentic ancient microbial taxa in cases where degradation patterns are difficult to detect due to large sequence divergence in microbial mixtures. Additionally, the relative enrichment of taxa in the uracil enriched fraction can help to identify bona fide ancient microbial taxa that could be missed using a more targeted approach.

CONCLUSIONS: Our experiments show, that in addition to its use in enriching authentic endogenous DNA of organisms of interest, the selective enrichment of damaged DNA molecules can be a valuable tool in the discovery of ancient microbial taxa.

RevDate: 2020-06-24

Bosman AM, Reyes-Centeno H, K Harvati (2020)

A virtual assessment of the suprainiac depressions on the Eyasi I (Tanzania) and Aduma ADU-VP-1/3 (Ethiopia) Pleistocene hominin crania.

Journal of human evolution, 145:102815 pii:S0047-2484(20)30076-2 [Epub ahead of print].

Despite a steady increase in our understanding of the phenotypic variation of Pleistocene Homo, debate continues over phylogenetically informative features. One such trait is the suprainiac fossa, a depression on the occipital bone above inion that is commonly considered an autapomorphy of the Neanderthal lineage. Challenging this convention, depressions in the suprainiac region have also been described for two Pleistocene hominin crania from sub-Saharan Africa: Eyasi I (Tanzania) and ADU-VP-1/3 (Ethiopia). Here, we use a combined quantitative and qualitative approach, using μCT imaging, to investigate the occipital depressions on these specimens. The results show that neither the external nor the internal morphologies of these depressions bear any resemblance to the Neanderthal condition. A principal component analysis based on multiple thickness measurements along the occipital squama demonstrates that the relative thickness values for the internal structures in Eyasi I and ADU-VP-1/3 are within the range of Homo sapiens. Thus, our results support the autapomorphic status of the Neanderthal suprainiac fossa and highlight the need to use nuanced approaches and multiple lines of evidence.

RevDate: 2020-06-23

Mathov Y, Batyrev D, Meshorer E, et al (2020)

Harnessing epigenetics to study human evolution.

Current opinion in genetics & development, 62:23-29 pii:S0959-437X(20)30074-5 [Epub ahead of print].

Recent advances in ancient DNA extraction and high-throughput sequencing technologies enabled the high-quality sequencing of archaic genomes, including the Neanderthal and the Denisovan. While comparisons with modern humans revealed both archaic-specific and human-specific sequence changes, in the absence of gene expression information, understanding the functional implications of such genetic variations remains a major challenge. To study gene regulation in archaic humans, epigenetic research comes to our aid. DNA methylation, which is highly correlated with transcription, can be directly measured in modern samples, as well as reconstructed in ancient samples. This puts DNA methylation as a natural basis for comparative epigenetics between modern humans, archaic humans and nonhuman primates.

RevDate: 2020-06-19

Dannemann M, He Z, Heide C, et al (2020)

Human Stem Cell Resources Are an Inroad to Neandertal DNA Functions.

Stem cell reports pii:S2213-6711(20)30190-9 [Epub ahead of print].

Induced pluripotent stem cells (iPSCs) from diverse humans offer the potential to study human functional variation in controlled culture environments. A portion of this variation originates from an ancient admixture between modern humans and Neandertals, which introduced alleles that left a phenotypic legacy on individual humans today. Here, we show that a large iPSC repository harbors extensive Neandertal DNA, including alleles that contribute to human phenotypes and diseases, encode hundreds of amino acid changes, and alter gene expression in specific tissues. We provide a database of the inferred introgressed Neandertal alleles for each individual iPSC line, together with the annotation of the predicted functional variants. We also show that transcriptomic data from organoids generated from iPSCs can be used to track Neandertal-derived RNA over developmental processes. Human iPSC resources provide an opportunity to experimentally explore Neandertal DNA function and its contribution to present-day phenotypes, and potentially study Neandertal traits.

RevDate: 2020-06-19

Khan N, de Manuel M, Peyregne S, et al (2020)

Multiple Genomic Events Altering Hominin SIGLEC Biology and Innate Immunity Predated the Common Ancestor of Humans and Archaic Hominins.

Genome biology and evolution pii:5859627 [Epub ahead of print].

Human-specific pseudogenization of the CMAH gene eliminated the mammalian sialic acid (Sia) Neu5Gc (generating an excess of its precursor Neu5Ac), thus changing ubiquitous cell surface "self-associated molecular patterns" (SAMPs) that modulate innate immunity via engagement of CD33-related-Siglec receptors. The Alu-fusion-mediated loss-of-function of CMAH fixed ∼2-3 million years ago (Mya), possibly contributing to the origins of the genus Homo. The mutation likely altered human SAMPs, triggering multiple events, including emergence of human-adapted pathogens with strong preference for Neu5Ac recognition and/or presenting Neu5Ac-containing molecular mimics of human glycans, which can suppress immune responses via CD33-related-Siglec engagement. Human-specific alterations reported in some genes encoding Sia-sensing proteins suggested a "hotspot" in hominin evolution. The availability of more hominid genomes including those of two extinct hominins now allows full reanalysis and evolutionary timing. Functional changes occur in 8/13 members of the human genomic cluster encoding CD33-related-Siglecs, all predating the human common ancestor. Comparisons with great ape genomes indicate that these changes are unique to hominins. We found no evidence for strong selection after the Human-Neanderthal/Denisovan common ancestor, and these extinct hominin genomes include almost all major changes found in humans, indicating that these changes in hominin sialobiology predate the Neanderthal-human divergence ∼0.6Mya. Multiple changes in this genomic cluster may also explain human-specific expression of CD33rSiglecs in unexpected locations such as amnion, placental trophoblast, pancreatic islets, ovarian fibroblasts, microglia, NK cells and epithelia. Taken together, our data suggest that innate immune interactions with pathogens markedly altered hominin Siglec biology between 0.6-2 Mya, potentially affecting human evolution.

RevDate: 2020-06-17

Mafessoni F, Grote S, de Filippo C, et al (2020)

A high-coverage Neandertal genome from Chagyrskaya Cave.

Proceedings of the National Academy of Sciences of the United States of America pii:2004944117 [Epub ahead of print].

We sequenced the genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, to 27-fold genomic coverage. We show that this Neandertal was a female and that she was more related to Neandertals in western Eurasia [Prüfer et al., Science 358, 655-658 (2017); Hajdinjak et al., Nature 555, 652-656 (2018)] than to Neandertals who lived earlier in Denisova Cave [Prüfer et al., Nature 505, 43-49 (2014)], which is located about 100 km away. About 12.9% of the Chagyrskaya genome is spanned by homozygous regions that are between 2.5 and 10 centiMorgans (cM) long. This is consistent with the fact that Siberian Neandertals lived in relatively isolated populations of less than 60 individuals. In contrast, a Neandertal from Europe, a Denisovan from the Altai Mountains, and ancient modern humans seem to have lived in populations of larger sizes. The availability of three Neandertal genomes of high quality allows a view of genetic features that were unique to Neandertals and that are likely to have been at high frequency among them. We find that genes highly expressed in the striatum in the basal ganglia of the brain carry more amino-acid-changing substitutions than genes expressed elsewhere in the brain, suggesting that the striatum may have evolved unique functions in Neandertals.

RevDate: 2020-06-17
CmpDate: 2020-06-17

Schmidt P, Rageot M, Blessing M, et al (2020)

The Zandmotor data do not resolve the question whether Middle Paleolithic birch tar making was complex or not.

Proceedings of the National Academy of Sciences of the United States of America, 117(9):4456-4457.

RevDate: 2020-06-17
CmpDate: 2020-06-17

Kozowyk PRB, Langejans GHJ, Dusseldorp GL, et al (2020)

Reply to Schmidt et al.: Interpretation of Paleolithic adhesive production: Combining experimental and paleoenvironmental information.

Proceedings of the National Academy of Sciences of the United States of America, 117(9):4458-4459.

RevDate: 2020-06-12

Almarri MA, Bergström A, Prado-Martinez J, et al (2020)

Population Structure, Stratification, and Introgression of Human Structural Variation.

Cell pii:S0092-8674(20)30619-X [Epub ahead of print].

Structural variants contribute substantially to genetic diversity and are important evolutionarily and medically, but they are still understudied. Here we present a comprehensive analysis of structural variation in the Human Genome Diversity panel, a high-coverage dataset of 911 samples from 54 diverse worldwide populations. We identify, in total, 126,018 variants, 78% of which were not identified in previous global sequencing projects. Some reach high frequency and are private to continental groups or even individual populations, including regionally restricted runaway duplications and putatively introgressed variants from archaic hominins. By de novo assembly of 25 genomes using linked-read sequencing, we discover 1,643 breakpoint-resolved unique insertions, in aggregate accounting for 1.9 Mb of sequence absent from the GRCh38 reference. Our results illustrate the limitation of a single human reference and the need for high-quality genomes from diverse populations to fully discover and understand human genetic variation.

RevDate: 2020-06-11
CmpDate: 2020-06-11

Gibbons A (2020)

Oldest Homo sapiens bones found in Europe.

Science (New York, N.Y.), 368(6492):697.

RevDate: 2020-06-08

Martín-Francés L, Martinón-Torres M, Martínez de Pinillos M, et al (2020)

Crown tissue proportions and enamel thickness distribution in the Middle Pleistocene hominin molars from Sima de los Huesos (SH) population (Atapuerca, Spain).

PloS one, 15(6):e0233281 pii:PONE-D-19-24814.

Dental enamel thickness, topography, growth and development vary among hominins. In Homo, the thickness of dental enamel in most Pleistocene hominins display variations from thick to hyper-thick, while Neanderthals exhibit proportionally thinner enamel. The origin of the thin trait remains unclear. In this context, the Middle Pleistocene human dental assemblage from Atapuerca-Sima de los Huesos (SH) provides a unique opportunity to trace the evolution of enamel thickness in European hominins. In this study, we aim to test the hypothesis if the SH molar sample approximates the Neanderthal condition for enamel thickness and/or distribution. This study includes 626 molars, both original and comparative data. We analysed the molar inner structural organization of the original collections (n = 124), belonging to SH(n = 72) and modern humans from Spanish origin (n = 52). We compared the SH estimates to those of extinct and extant populations of the genus Homo from African, Asian and European origin (estimates extracted from literature n = 502). The comparative sample included 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 SH molars (tissue proportions, enamel thickness and distribution). The SH molars exhibit on average thick absolute and relative enamel in 2D and 3D estimates, both in the complete crown and the lateral enamel. This primitive condition is shared with the majority of extinct and extant hominin sample, except for Neanderthals and some isolated specimens. On the contrary, the SH molar enamel distribution maps reveal a distribution pattern similar to the Neanderthal signal (with thicker enamel on the lingual cusps and more peripherally distributed), compared to H. antecessor and modern humans. Due to the phylogenetic position of the SH population, the thick condition in molars could represent the persistence of the plesiomorphic condition in this group. Still, more data is needed on other Early and Middle Pleistocene populations to fully understand the evolutionary meaning of this trait.

RevDate: 2020-06-04

Skov L, Coll Macià M, Sveinbjörnsson G, et al (2020)

The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes.

Nature, 582(7810):78-83.

Human evolutionary history is rich with the interbreeding of divergent populations. Most humans outside of Africa trace about 2% of their genomes to admixture from Neanderthals, which occurred 50-60 thousand years ago1. Here we examine the effect of this event using 14.4 million putative archaic chromosome fragments that were detected in fully phased whole-genome sequences from 27,566 Icelanders, corresponding to a range of 56,388-112,709 unique archaic fragments that cover 38.0-48.2% of the callable genome. On the basis of the similarity with known archaic genomes, we assign 84.5% of fragments to an Altai or Vindija Neanderthal origin and 3.3% to Denisovan origin; 12.2% of fragments are of unknown origin. We find that Icelanders have more Denisovan-like fragments than expected through incomplete lineage sorting. This is best explained by Denisovan gene flow, either into ancestors of the introgressing Neanderthals or directly into humans. A within-individual, paired comparison of archaic fragments with syntenic non-archaic fragments revealed that, although the overall rate of mutation was similar in humans and Neanderthals during the 500 thousand years that their lineages were separate, there were differences in the relative frequencies of mutation types-perhaps due to different generation intervals for males and females. Finally, we assessed 271 phenotypes, report 5 associations driven by variants in archaic fragments and show that the majority of previously reported associations are better explained by non-archaic variants.

RevDate: 2020-06-03

Kolendrianou M, Ligkovanlis S, Maniakas I, et al (2020)

The Palaeolithic cave of Kalamakia (Mani Peninsula), Greece: new insights on the palaeoenvironment using microvertebrates and mesowear analysis of ruminant teeth.

Heliyon, 6(5):e03958 pii:e03958.

In the present study, results from the examination of mammalian teeth from the cave of Kalamakia with modern techniques, as well as a qualitative overview of the microvertebrate and lithic material, are presented together with a revision of previous related work done for the site, in order to assess the palaeoenvironmental conditions in the area and the role they played in the Neanderthal's repeated occupation of the cave. Geometric morphometrics analyses performed on the first lower molars of Microtus spp. individuals revealed persistent populations of the subgenus Terricola, in which the presence of Microtus thomasi and Microtus subterraneus are continuous through the stratigraphic units. Mesowear analyses performed on ruminant teeth showed no significant variation in toothwear through time, except for relatively elevated levels of dietary abrasion for the more recent samples. The study of the lithics revealed that Neanderthals visited the cave in alternating short and more permanent episodes of occupation, with the human occupants exhibiting special concern for raw material economy, while exploiting poor raw materials for the construction of their tools. The overview of the microvertebrate remains showed a growing trend towards the upper stratigraphic units, where taxa typical of temperate climate, open woodland and shrubland become more dominant. These results, along with observations derived from previous studies, suggest that temperate climate and open environment were the factors that mainly contributed to making the cave of Kalamakia attractive as a habitation site to the humans of the area.

RevDate: 2020-05-27

Sánchez-Romero L, Benito-Calvo A, Marín-Arroyo AB, et al (2020)

New insights for understanding spatial patterning and formation processes of the Neanderthal occupation in theAmalda I cave (Gipuzkoa, Spain).

Scientific reports, 10(1):8733 pii:10.1038/s41598-020-65364-8.

The Level VII of Amalda I cave (Gipuzkoa, Spain) represents one of the latest Middle Palaeolithic occupations in the Cantabrian Region. It is characterized by the presence of Middle Palaeolithic lithic industry and animal remains, with clear evidences of anthropic and carnivore manipulation. At this site, the Neanderthal presence has been questioned in relation to the role of carnivores in the accumulation of large, medium-sized and small mammals. It has also been proposed that the Neanderthal occupation could have consisted of short-term occupations, where different activities took place in a structured space within the cave. However, all hypotheses lacked any integrative analysis of the site formation processes. With the aim of understanding these processes, a combination of spatial techniques, based on GIS and inferential statistics (density analysis, hotspots tools and palaeotopographic reconstruction), along with the taphonomic study of identifiable and non-identifiable macromammals remains, were employed. This study has revealed distinct use of the cave space by Neanderthals and carnivores. The major concentrations of lithics and medium-size mammal remains were clearly accumulated by humans at the cave entrance, while the small-size mammals were gathered by carnivores in an inner zone. The activities of the Neanderthals seem to be distinctly structured, suggesting a parallel exploitation of resources.

RevDate: 2020-05-26

Natri HM, Bobowik KS, Kusuma P, et al (2020)

Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago.

PLoS genetics, 16(5):e1008749 pii:PGENETICS-D-19-01376 [Epub ahead of print].

Indonesia is the world's fourth most populous country, host to striking levels of human diversity, regional patterns of admixture, and varying degrees of introgression from both Neanderthals and Denisovans. However, it has been largely excluded from the human genomics sequencing boom of the last decade. To serve as a benchmark dataset of molecular phenotypes across the region, we generated genome-wide CpG methylation and gene expression measurements in over 100 individuals from three locations that capture the major genomic and geographical axes of diversity across the Indonesian archipelago. Investigating between- and within-island differences, we find up to 10.55% of tested genes are differentially expressed between the islands of Sumba and New Guinea. Variation in gene expression is closely associated with DNA methylation, with expression levels of 9.80% of genes correlating with nearby promoter CpG methylation, and many of these genes being differentially expressed between islands. Genes identified in our differential expression and methylation analyses are enriched in pathways involved in immunity, highlighting Indonesia's tropical role as a source of infectious disease diversity and the strong selective pressures these diseases have exerted on humans. Finally, we identify robust within-island variation in DNA methylation and gene expression, likely driven by fine-scale environmental differences across sampling sites. Together, these results strongly suggest complex relationships between DNA methylation, transcription, archaic hominin introgression and immunity, all jointly shaped by the environment. This has implications for the application of genomic medicine, both in critically understudied Indonesia and globally, and will allow a better understanding of the interacting roles of genomic and environmental factors shaping molecular and complex phenotypes.

RevDate: 2020-05-26

Esteller-Cucala P, Maceda I, Børglum AD, et al (2020)

Genomic analysis of the natural history of attention-deficit/hyperactivity disorder using Neanderthal and ancient Homo sapiens samples.

Scientific reports, 10(1):8622 pii:10.1038/s41598-020-65322-4.

Attention-deficit/hyperactivity disorder (ADHD) is an impairing neurodevelopmental condition highly prevalent in current populations. Several hypotheses have been proposed to explain this paradox, mainly in the context of the Paleolithic versus Neolithic cultural shift but especially within the framework of the mismatch theory. This theory elaborates on how a particular trait once favoured in an ancient environment might become maladaptive upon environmental changes. However, given the lack of genomic data available for ADHD, these theories have not been empirically tested. We took advantage of the largest GWAS meta-analysis available for this disorder consisting of over 20,000 individuals diagnosed with ADHD and 35,000 controls, to assess the evolution of ADHD-associated alleles in European populations using archaic, ancient and modern human samples. We also included Approximate Bayesian computation coupled with deep learning analyses and singleton density scores to detect human adaptation. Our analyses indicate that ADHD-associated alleles are enriched in loss of function intolerant genes, supporting the role of selective pressures in this early-onset phenotype. Furthermore, we observed that the frequency of variants associated with ADHD has steadily decreased since Paleolithic times, particularly in Paleolithic European populations compared to samples from the Neolithic Fertile Crescent. We demonstrate this trend cannot be explained by African admixture nor Neanderthal introgression, since introgressed Neanderthal alleles are enriched in ADHD risk variants. All analyses performed support the presence of long-standing selective pressures acting against ADHD-associated alleles until recent times. Overall, our results are compatible with the mismatch theory for ADHD but suggest a much older time frame for the evolution of ADHD-associated alleles compared to previous hypotheses.

RevDate: 2020-05-26

Hoffmann DL, Standish CD, García-Diez M, et al (2020)

Response to White et al.'s reply: 'Still no archaeological evidence that Neanderthals created Iberian cave art' [J. Hum. Evol. (2020) 102640].

Journal of human evolution pii:S0047-2484(20)30071-3 [Epub ahead of print].

RevDate: 2020-05-21

Zeberg H, Kelso J, S Pääbo (2020)

The Neandertal Progesterone Receptor.

Molecular biology and evolution pii:5841671 [Epub ahead of print].

The hormone progesterone is important for preparing the uterine lining for egg implantation and in maintaining the early stages of pregnancy. The gene encoding the progesterone receptor (PGR) carries introgressed Neandertal haplotypes with two non-synonymous substitutions and a mobile Alu element. They have reached nearly 20% frequency in non-Africans and have been associated with preterm birth. Here we show that whereas one of the missense substitutions appears fixed among Neandertals, the other substitution as well as the Alu insertion were polymorphic among Neandertals. We show that two Neandertal haplotypes carrying the PGR gene entered the modern human population and that present-day carriers of the Neandertal haplotypes express higher levels of the receptor. In a cohort of present-day Britons, these carriers have more siblings, fewer miscarriages and less bleeding during early pregnancy suggesting that it promotes fertility. This may explain the high frequency of the Neandertal progesterone receptor alleles in modern human populations.

RevDate: 2020-05-21

Palancar CA, García-Martínez D, Radovčić D, et al (2020)

Krapina atlases suggest a high prevalence of anatomical variations in the first cervical vertebra of Neanderthals.

Journal of anatomy [Epub ahead of print].

The first cervical vertebra, atlas, and its anatomical variants have been widely studied in Homo sapiens. However, in Neanderthals, the presence of anatomical variants of the atlas has been very little studied until very recently. Only the Neanderthal group from the El Sidrón site (Spain) has been analysed with regard to the anatomical variants of the atlas. A high prevalence of anatomical variants has been described in this sample, which points to low genetic diversity in this Neanderthal group. Even so, the high prevalence of anatomical variations detected in El Sidrón Neanderthal atlases needs to be confirmed by analysing more Neanderthal remains. In this context, we analysed the possible presence of anatomical variants in the three Neanderthal atlases recovered from the Krapina site (Croatia) within the Neanderthal lineage. Two of the three Krapina atlases presented anatomical variations. One atlas (Krapina 98) had an unclosed transverse foramen and the other (Krapina 99) presented a non-fused anterior atlas arch. Moreover, an extended review of the bibliography also showed these anatomical variations in other Middle and Upper Pleistocene hominins, leading us to hypothesise that anatomical variations of the atlas had a higher prevalence in extinct hominins than in modern humans.

RevDate: 2020-05-21

Ricci C, Kakularam KR, Marzocchi C, et al (2020)

Thr92Ala polymorphism in the type 2 deiodinase gene: an evolutionary perspective.

Journal of endocrinological investigation pii:10.1007/s40618-020-01287-5 [Epub ahead of print].

PURPOSE: In the past, a role of thyroid hormones in human evolution has been hypothesized. T3, the metabolically active form, derives from extrathyroidal conversion of T4 by deionidase 2 (D2) enzyme encoded by DIO2 gene. In thyroid-deficient patients, decreased levels of free T3 have been associated with the polymorphism rs225014 A/G in DIO2, which causes the substitution of Threonine with Alanine (p.Thr92Ala) at protein level.

METHODS: We compared DNA and protein sequences of D2 from archaic human subspecies with those of contemporary humans.

RESULTS: Neanderthals and Denisovans displayed only the G allele at the rs225014 polymorphism, which encodes for an Alanine on the amino acid level. These data suggest that these hominines were homozygous for the Ala amino acid. These arcaic humans often lived in condition of iodine deficiency and thus, defective mechanisms of T3 biosynthesis could be life threatining. A reduced D2 activity is likely to cause decreased T3 levels, which could be critical for those individuals. Neanderthals and Denisovans were hunters/gatherers, and their diet was mainly based on the consumption of meat, with a low intake of carbohydrates. The need for circulating T3 is reduced at such alimentary conditions. On the basis of our genome comparisons the A allele, corresponding to Threonine and associated with higher levels of circulating T3 in thyroid-deficient patients, appeared for the first time during evolution in Anatomically Modern Humans during the Upper Pleistocene and has been conserved during the Neolithic age. With the advent of agriculture and herding, individuals carrying A allele might have a higher probability for surviving and reproducing. Thus, the variant was positively selected during the evolution.

CONCLUSION: Here we present an evolutionary perspective for p.Thr92Ala variant of D2 from Neanderthals to Anatomically Modern Humans.

RevDate: 2020-05-20

Hublin JJ, Sirakov N, Aldeias V, et al (2020)

Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria.

Nature, 581(7808):299-302.

The Middle to Upper Palaeolithic transition in Europe witnessed the replacement and partial absorption of local Neanderthal populations by Homo sapiens populations of African origin1. However, this process probably varied across regions and its details remain largely unknown. In particular, the duration of chronological overlap between the two groups is much debated, as are the implications of this overlap for the nature of the biological and cultural interactions between Neanderthals and H. sapiens. Here we report the discovery and direct dating of human remains found in association with Initial Upper Palaeolithic artefacts2, from excavations at Bacho Kiro Cave (Bulgaria). Morphological analysis of a tooth and mitochondrial DNA from several hominin bone fragments, identified through proteomic screening, assign these finds to H. sapiens and link the expansion of Initial Upper Palaeolithic technologies with the spread of H. sapiens into the mid-latitudes of Eurasia before 45 thousand years ago3. The excavations yielded a wealth of bone artefacts, including pendants manufactured from cave bear teeth that are reminiscent of those later produced by the last Neanderthals of western Europe4-6. These finds are consistent with models based on the arrival of multiple waves of H. sapiens into Europe coming into contact with declining Neanderthal populations7,8.

RevDate: 2020-05-13

Hardy BL, Moncel MH, Kerfant C, et al (2020)

Author Correction: Direct evidence of Neanderthal fibre technology and its cognitive and behavioral implications.

Scientific reports, 10(1):8167 pii:10.1038/s41598-020-65143-5.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

RevDate: 2020-05-07

Verna C, Détroit F, Kupczik K, et al (2020)

The Middle Pleistocene hominin mandible from Payre (Ardèche, France).

Journal of human evolution, 144:102775 pii:S0047-2484(20)30036-1 [Epub ahead of print].

Although Neandertals are the best-known fossil hominins, the tempo and evolutionary processes in their lineage are strongly debated. This is in part due to the scarcity of the fossil record, in particular before the marine isotopic stage (MIS) 5. In 2010, a partial hominin mandible was discovered at the Middle Paleolithic site of Payre (France) in a layer that is dated to the end of MIS 8/beginning of MIS 7, a time period for which very few fossils are known in Europe. The Payre 15 mandible retains the complete symphyseal region and right lateral corpus with heavily worn P4, M1, and M2 in situ. Taphonomic modifications in the form of three notches suggest that this individual was chewed by a carnivore. We provide here the first detailed description of this specimen and a comparative analysis that includes morphological features, linear mandibular dimensions, an elliptic Fourier analysis of the symphysis, and a morphometric analysis of the M1 roots (based on segmented CT scan data). Our comparative sample encompasses European Middle and Upper Pleistocene specimens attributed to Homo heidelbergensis and Homo neanderthalensis, Upper Pleistocene Homo sapiens, and Holocene Homo sapiens. The Payre 15 mandible shows a combination of primitive and Neandertal-like features, with a receding symphyseal profile without any element of the mentum osseum, a posterior location of the mental foramen and lateral prominence. Its mandibular body is tall and thick anteriorly. Payre 15 has mesotaurodont M1 roots and a three-rooted M2. By its dimensions and combination of features, Payre 15 aligns better with Middle Pleistocene European hominins than with MIS 6-3 Neandertals. Noteworthy, it falls well within the range of variation of the Sima de los Huesos sample. Our results underscore that the total pattern of Neandertal-derived morphology was not achieved at the beginning of the MIS 7 and suggest a low level of mandibular diachronic changes for the period MIS 11-7.

RevDate: 2020-05-06

Yeshurun R, Malkinson D, Crater Gershtein KM, et al (2020)

Site occupation dynamics of early modern humans at Misliya Cave (Mount Carmel, Israel): Evidence from the spatial taphonomy of faunal remains.

Journal of human evolution, 143:102797 pii:S0047-2484(20)30058-0 [Epub ahead of print].

Space use in Middle Paleolithic (MP) camps has been suggested as a source of information on the intensity and repetition of occupations and, by extension, of demographics. In the Levant, clear evidence for differential intrasite use and maintenance was important in viewing the late MP Neanderthal sites as base camps inhabited for a significant duration, relative to the Early MP (EMP). We test this model with the rich faunal assemblage from the EMP (>140 ka) site of Misliya Cave, Mount Carmel, Israel. Excavations in Misliya yielded a large and diverse lithic assemblage, combustion features, and a modern human maxilla, together with a large archaeofaunal assemblage that we use as a spatial marker. We analyzed the distribution of bone items with variable taphonomic properties (anthropogenic, biogenic, and abiotic bone-surface modifications) in a hearth-related context, both by comparing grid squares and point patterns. Both analyses are largely congruent. They indicate repeated and consistent use of the site's space that includes hearth-related consumption activities and peripheral activities further away, albeit with little evidence for site maintenance. Thus, the Misliya results display a mixed signal of clear around-the-fire pattern and differential space use in the EMP that is reminiscent of the much later MP sites in the Levant, but without the more elaborate camp maintenance. More case studies and detailed proxies are needed before we can fine-tune our understanding of camp structure in the Levantine MP and its bearing to site occupation dynamics.

RevDate: 2020-05-01

Jordan B (2020)

[Neandertal DNA in Africans].

Medecine sciences : M/S, 36(4):421-423.

Sophisticated analyses of current human populations compared to a high-coverage Neandertal genome sequence indicate that, contrary to the previous consensus, African genomes carry a small but significant amount of Neandertal-specific DNA. This indicates back-migration into Africa of modern humans (carrying some Neandertal sequences) and underlines the complexity of ancient human migrations.

RevDate: 2020-04-30
CmpDate: 2020-04-30

Peyrégne S, Slon V, Mafessoni F, et al (2019)

Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe.

Science advances, 5(6):eaaw5873.

Little is known about the population history of Neandertals over the hundreds of thousands of years of their existence. We retrieved nuclear genomic sequences from two Neandertals, one from Hohlenstein-Stadel Cave in Germany and the other from Scladina Cave in Belgium, who lived around 120,000 years ago. Despite the deeply divergent mitochondrial lineage present in the former individual, both Neandertals are genetically closer to later Neandertals from Europe than to a roughly contemporaneous individual from Siberia. That the Hohlenstein-Stadel and Scladina individuals lived around the time of their most recent common ancestor with later Neandertals suggests that all later Neandertals trace at least part of their ancestry back to these early European Neandertals.

RevDate: 2020-04-24

Lodewijk GA, Fernandes DP, Vretzakis I, et al (2020)

Evolution of human brain-size associated NOTCH2NL genes proceeds towards reduced protein levels.

Molecular biology and evolution pii:5824797 [Epub ahead of print].

Ever since the availability of genomes from Neanderthals, Denisovans and ancient humans, the field of evolutionary genomics has been searching for protein coding variants that may hold clues to how our species evolved over the last ∼ 400,000 years. In this study, we identify such variants in the human-specific NOTCH2NL gene family, which were recently identified as possible contributors to the evolutionary expansion of the human brain. We find evidence for the existence of unique protein-coding NOTCH2NL variants in Neanderthals and Denisovans which could affect their ability to activate Notch signaling. Furthermore, in the Neanderthal and Denisovan genomes, we find unusual NOTCH2NL configurations, not found in any of the modern human genomes analyzed. Finally, genetic analysis of archaic and modern humans reveals ongoing adaptive evolution of modern human NOTCH2NL genes, identifying three structural variants acting complementary to drive our genome to produce a lower dosage of NOTCH2NL protein. Because copy-number variations of the 1q21.1 locus, encompassing NOTCH2NL genes, are associated with severe neurological disorders, this seemingly contradicting drive towards low levels of NOTCH2NL protein indicates that the optimal dosage of NOTCH2NL may have not yet been settled in the human population.

RevDate: 2020-04-24

Gouy A, L Excoffier (2020)

Polygenic Patterns of Adaptive Introgression in Modern Humans Are Mainly Shaped by Response to Pathogens.

Molecular biology and evolution, 37(5):1420-1433.

Anatomically modern humans carry many introgressed variants from other hominins in their genomes. Some of them affect their phenotype and can thus be negatively or positively selected. Several individual genes have been proposed to be the subject of adaptive introgression, but the possibility of polygenic adaptive introgression has not been extensively investigated yet. In this study, we analyze archaic introgression maps with refined functional enrichment methods to find signals of polygenic adaptation of introgressed variants. We first apply a method to detect sets of connected genes (subnetworks) within biological pathways that present higher-than-expected levels of archaic introgression. We then introduce and apply a new statistical test to distinguish between epistatic and independent selection in gene sets of present-day humans. We identify several known targets of adaptive introgression, and we show that they belong to larger networks of introgressed genes. After correction for genetic linkage, we find that signals of polygenic adaptation are mostly explained by independent and potentially sequential selection episodes. However, we also find some gene sets where introgressed variants present significant signals of epistatic selection. Our results confirm that archaic introgression has facilitated local adaptation, especially in immunity related and metabolic functions and highlight its involvement in a coordinated response to pathogens out of Africa.

RevDate: 2020-04-23
CmpDate: 2020-04-23

Willson J (2020)

There and back again - ancient genes reveal early migrations.

Nature reviews. Genetics, 21(4):205.

RevDate: 2020-04-22

Zeng Y, Pu X, Du J, et al (2020)

Molecular Mechanism of Functional Ingredients in Barley to Combat Human Chronic Diseases.

Oxidative medicine and cellular longevity, 2020:3836172.

Barley plays an important role in health and civilization of human migration from Africa to Asia, later to Eurasia. We demonstrated the systematic mechanism of functional ingredients in barley to combat chronic diseases, based on PubMed, CNKI, and ISI Web of Science databases from 2004 to 2020. Barley and its extracts are rich in 30 ingredients to combat more than 20 chronic diseases, which include the 14 similar and 9 different chronic diseases between grains and grass, due to the major molecular mechanism of six functional ingredients of barley grass (GABA, flavonoids, SOD, K-Ca, vitamins, and tryptophan) and grains (β-glucans, polyphenols, arabinoxylan, phytosterols, tocols, and resistant starch). The antioxidant activity of barley grass and grain has the same and different functional components. These results support findings that barley grain and its grass are the best functional food, promoting ancient Babylonian and Egyptian civilizations, and further show the depending functional ingredients for diet from Pliocene hominids in Africa and Neanderthals in Europe to modern humans in the world. This review paper not only reveals the formation and action mechanism of barley diet overcoming human chronic diseases, but also provides scientific basis for the development of health products and drugs for the prevention and treatment of human chronic diseases.

RevDate: 2020-04-17

Moriano J, C Boeckx (2020)

Modern human changes in regulatory regions implicated in cortical development.

BMC genomics, 21(1):304 pii:10.1186/s12864-020-6706-x.

BACKGROUND: Recent paleogenomic studies have highlighted a very small set of proteins carrying modern human-specific missense changes in comparison to our closest extinct relatives. Despite being frequently alluded to as highly relevant, species-specific differences in regulatory regions remain understudied. Here, we integrate data from paleogenomics, chromatin modification and physical interaction, and single-cell gene expression of neural progenitor cells to identify derived regulatory changes in the modern human lineage in comparison to Neanderthals/Denisovans. We report a set of genes whose enhancers and/or promoters harbor modern human single nucleotide changes and are active at early stages of cortical development.

RESULTS: We identified 212 genes controlled by regulatory regions harboring modern human changes where Neanderthals/Denisovans carry the ancestral allele. These regulatory regions significantly overlap with putative modern human positively-selected regions and schizophrenia-related genetic loci. Among the 212 genes, we identified a substantial proportion of genes related to transcriptional regulation and, specifically, an enrichment for the SETD1A histone methyltransferase complex, known to regulate WNT signaling for the generation and proliferation of intermediate progenitor cells.

CONCLUSIONS: This study complements previous research focused on protein-coding changes distinguishing our species from Neanderthals/Denisovans and highlights chromatin regulation as a functional category so far overlooked in modern human evolution studies. We present a set of candidates that will help to illuminate the investigation of modern human-specific ontogenetic trajectories.

RevDate: 2020-04-14

Barreiro LB, L Quintana-Murci (2020)

Evolutionary and population (epi)genetics of immunity to infection.

Human genetics pii:10.1007/s00439-020-02167-x [Epub ahead of print].

Immune response is one of the functions that have been more strongly targeted by natural selection during human evolution. The evolutionary genetic dissection of the immune system has greatly helped to distinguish genes and functions that are essential, redundant or advantageous for human survival. It is also becoming increasingly clear that admixture between early Eurasians with now-extinct hominins such as Neanderthals or Denisovans, or admixture between modern human populations, can be beneficial for human adaptation to pathogen pressures. In this review, we discuss how the integration of population genetics with functional genomics in diverse human populations can inform about the changes in immune functions related to major lifestyle transitions (e.g., from hunting and gathering to farming), the action of natural selection to the evolution of the immune system, and the history of past epidemics. We also highlight the need of expanding the characterization of the immune system to a larger array of human populations-particularly neglected human groups historically exposed to different pathogen pressures-to fully capture the relative contribution of genetic, epigenetic, and environmental factors to immune response variation in humans.

RevDate: 2020-04-10

Hardy BL, Moncel MH, Kerfant C, et al (2020)

Direct evidence of Neanderthal fibre technology and its cognitive and behavioral implications.

Scientific reports, 10(1):4889 pii:10.1038/s41598-020-61839-w.

Neanderthals are often considered as less technologically advanced than modern humans. However, we typically only find faunal remains or stone tools at Paleolithic sites. Perishable materials, comprising the vast majority of material culture items, are typically missing. Individual twisted fibres on stone tools from the Abri du Maras led to the hypothesis of Neanderthal string production in the past, but conclusive evidence was lacking. Here we show direct evidence of fibre technology in the form of a 3-ply cord fragment made from inner bark fibres on a stone tool recovered in situ from the same site. Twisted fibres provide the basis for clothing, rope, bags, nets, mats, boats, etc. which, once discovered, would have become an indispensable part of daily life. Understanding and use of twisted fibres implies the use of complex multi-component technology as well as a mathematical understanding of pairs, sets, and numbers. Added to recent evidence of birch bark tar, art, and shell beads, the idea that Neanderthals were cognitively inferior to modern humans is becoming increasingly untenable.

RevDate: 2020-04-09

Welker F, Ramos-Madrigal J, Gutenbrunner P, et al (2020)

The dental proteome of Homo antecessor.

Nature, 580(7802):235-238.

The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated1-5. For the oldest remains, the molecular study of these relationships is hindered by the degradation of ancient DNA. However, recent research has demonstrated that the analysis of ancient proteins can address this challenge6-8. Here we present the dental enamel proteomes of H. antecessor from Atapuerca (Spain)9,10 and Homo erectus from Dmanisi (Georgia)1, two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal and divergence. We provide evidence that H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans. This placement implies that the modern-like face of H. antecessor-that is, similar to that of modern humans-may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form. By recovering AMELY-specific peptide sequences, we also conclude that the H. antecessor molar fragment from Atapuerca that we analysed belonged to a male individual. Finally, these H. antecessor and H. erectus fossils preserve evidence of enamel proteome phosphorylation and proteolytic digestion that occurred in vivo during tooth formation. Our results provide important insights into the evolutionary relationships between H. antecessor and other hominin groups, and pave the way for future studies using enamel proteomes to investigate hominin biology across the existence of the genus Homo.

RevDate: 2020-04-08

Merseburger AS, Rüssel C, Belz H, et al (2020)

[Early- vs. late-onset treatment using abiraterone acetate plus prednisone in chemo-naïve, asymptomatic or mildly symptomatic patients with metastatic CRPC after androgen deprivation therapy].

Aktuelle Urologie [Epub ahead of print].

BACKGROUND: Abiraterone acetate (AA) is a prodrug of abiraterone, which is an irreversible inhibitor of 17α-hydroxylase/C17, 20-lyase. Since 2011, abiraterone acetate has been available in combination with prednisone/prednisolone (AA + P) for the treatment of metastatic castration-resistant prostate cancer (mCRPC) after pre-treatment with docetaxel, and since 2012 for the treatment of chemotherapy-naïve asymptomatic or mildly symptomatic mCRPC patients. A revision of the guidelines of the European Association of Urology in 2014 redefining castration resistance gave rise to the question of when the treatment of mCRPC with abiraterone acetate plus prednisone should be initiated after prior hormone treatment and how successful it would be. This led us to observe an early-onset AA + P therapy cohort (EC) and a late-onset therapy cohort (LC) of patients.

PATIENTS AND METHODS: We designed a combined retrospective and prospective, multicentre, non-interventional two-cohort study to obtain data on the effectiveness and safety of an early-onset AA + P therapy in mCRPC patients in the clinical routine compared to a late therapy onset. The EC comprised patients who received AA + P immediately after castration resistance without a prior first-generation antiandrogen such as bicalutamide or flutamide. The LC included patients who, after castration resistance had occurred, started treatment with AA + P only after unsuccessful treatment with a first-generation antiandrogen. Patients with mCRPC who received AA + P therapy according to the physician's routine clinical practice decision were considered. The patients were consecutively included in the study on the basis of their medical records, with the treatment decision having been made independently of and before patient enrolment. Patients were documented or followed from the beginning of AA + P therapy until the start of a carcinoma-specific systemic follow-up therapy (retrospectively if before and prospectively if after start of data collection). Effectiveness analyses were done for all patients with at least two AA + P administrations and safety analyses for all treated patients.

RESULTS: Of the 159 patients included, 44 received early therapy and 105 received later therapy with AA + P. 10 patients could not be clearly assigned and were summarised in a third cohort (missed early-onset therapy assignment; MEC). 56/159 patients (35.2 %) were still alive at study start and 103/159 patients (64.8 %) had already deceased (31/44 [70.5 %] in EC, 64/105 [61.0 %] in LC, and 8/10 [80.0 %] in MEC). 24/159 patients (15.1 %) were documented both retrospectively and prospectively. The median duration of AA + P treatment was 11.3 months for EC, 12.0 months for LC, and 8.3 months for MEC patients. The median time to next systemic cancer therapy or death was 12.3 months for EC and 12.8 months for LC patients (p = 0.2820). The median time to the next systemic cancer therapy alone (i. e. without the event 'death') was 22.7 months for EC and 23.3 months for LC patients (p = 0.5995). Median overall survival (OS) was 22.3 months for EC and 39.2 months for LC patients (p = 0.0232). The incidence of serious adverse events (SAEs) was low. SAEs occurred in 3/44 EC (6.8 %), 4/105 LC (3.8 %), and 1/10 MEC patients (10.0 %). One SAE in EC and one in LC resulted in death.

CONCLUSIONS: In contrast to the new definition of castration resistance, AA + P was still more frequently used in daily clinical practice during the study observation period in patients treated with antiandrogens of the first generation after occurrence of castration resistance. Nevertheless, AA + P therapy appears to be effective and well tolerated during clinical routine in mCRPC patients. A comparison of the study results with earlier 'real-world' studies, however, has to take limiting factors into account. The observed difference in median overall survival might be explained by the imbalance of baseline characteristics between both cohorts with regard to number of patients, patients already deceased at start of documentation, patients with visceral metastases and patients with opioids at start of AA + P. For these reasons, patients in the EC initially might have had a poorer prognosis. A prospective randomised and controlled clinical trial would therefore be necessary to assess a possible difference in overall survival and response of the AA + P treatment with respect to therapy onset.

RevDate: 2020-04-05

Grimaud-Hervé D, Albessard-Ball L, Pokhojaev A, et al (2020)

The endocast of the late Middle Paleolithic Manot 1 specimen, Western Galilee, Israel.

Journal of human evolution pii:S0047-2484(19)30365-3 [Epub ahead of print].

Studying endocasts has long allowed anthropologists to examine changes in the external topography and the overall size of the brain throughout the evolutionary history of hominins. The nearly complete calvaria of Manot 1 presents an opportunity to gain insights into the external brain morphology, vascular system, and dimensions of the brain of this late Middle Paleolithic hominin. Detailed size and shape analyses of the Manot 1 endocast indicate a modern Homo sapiens anatomy, despite the presence of some primitive features of the calvaria. Traits considered to be derived endocranial features for H. sapiens are present in Manot 1, including an elongated parietal sagittal chord with an elevated superior part of the hemisphere, a widened posterior part of the frontal lobes, a considerable development of the parietal reliefs such as the supramarginal lobules, and a slight posterior projection of the occipital lobes. These findings, together with data presented in previous studies, rule out the possibility of a direct Neanderthal ancestry for the Manot 1 hominin and instead confirm its affiliation with H. sapiens. The Manot 1 calvaria is more similar to that of later Upper Paleolithic H. sapiens than it is to the earlier Levantine populations of Skhul and Qafzeh. The late Middle Paleolithic date of Manot 1 provides an opportunity to analyze the recent developments in human cerebral morphology and organization.

RevDate: 2020-04-04

Pereira-Pedro AS, Bruner E, Gunz P, et al (2020)

A morphometric comparison of the parietal lobe in modern humans and Neanderthals.

Journal of human evolution, 142:102770 pii:S0047-2484(20)30031-2 [Epub ahead of print].

The modern human brain and braincase have a characteristic globular shape including parietal and cerebellar bulging. In contrast, Neanderthals, although having similar endocranial volume, displayed more elongated endocrania with flatter parietal and cerebellar regions. Based on endocranial imprints, we compare the parietal lobe morphology of modern humans and Neanderthals, as this brain region is central to several cognitive functions including tool use and visual imaging. In paleoneurology, shape analyses of endocasts are based either on anatomical landmarks that represent endocranial surface features homologous to cortical convolutions (impressions of brain gyri and sulci) or on dense meshes of semilandmarks that capture overall endocranial shape. Previous analyses using the former suggested that modern humans have relatively longer and taller parietal lobes than extinct human species, while the latter emphasized parietal bulging without a significant size difference of parietal regions. In the present study, we combine both anatomical landmarks and surface semilandmarks to investigate the morphological differences of the parietal lobes between modern humans and Neanderthals. Despite limitations by landmark uncertainty, our analyses were able to detect and confirm average different parietal shapes, with modern humans displaying taller and anteroposteriorly extended parietal lobes. We also show mean size differences, with modern humans displaying slightly larger surface areas on the dorsal posterior parietal region, and on a lateral region comprising the supramarginal gyrus, angular gyrus, and intraparietal sulcus. While we observed average differences in the parietal form between the two species, their ranges of distribution overlap, indicating the differences could be a matter of degree. Thus, further analyses on intraspecific variation in parietal lobe morphology within modern human brains should help understand the differences between globular and elongated endocrania. This is crucial because changes to the parietal cortex might affect associative and integrative functions between somatic and visual primary inputs.

RevDate: 2020-04-02

Taskent O, Lin YL, Patramanis I, et al (2020)

Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage.

Genetics pii:genetics.120.303167 [Epub ahead of print].

The time, extent, and genomic impact of the introgressions from archaic humans into ancestors of extant human populations remain one of the most exciting venues of population genetics research in the last decade. Several studies have shown population-specific signatures of introgression events from Neanderthals, Denisovans, and potentially other unknown hominin populations in different human groups. Moreover, it was shown that these introgression events may have contributed to phenotypic variation in extant humans, with biomedical and evolutionary consequences. In this study, we present a comprehensive analysis of the unusually divergent haplotypes in the Eurasian genomes and showed that they can be traced back to multiple introgression events. In parallel, we document hundreds of deletion polymorphisms shared with Neanderthals. A locus-specific analysis of one such shared deletion suggests the existence of a direct introgression event from the Altai Neanderthal lineage into the ancestors of extant East Asian populations. Overall, our study is in agreement with the emergent notion that various Neanderthal populations contributed to extant human genetic variation in a population-specific manner.

RevDate: 2020-03-28

Will M (2020)

Neanderthal surf and turf.

Science (New York, N.Y.), 367(6485):1422-1423.

RevDate: 2020-03-28

Zilhão J, Angelucci DE, Igreja MA, et al (2020)

Last Interglacial Iberian Neandertals as fisher-hunter-gatherers.

Science (New York, N.Y.), 367(6485):.

Marine food-reliant subsistence systems such as those in the African Middle Stone Age (MSA) were not thought to exist in Europe until the much later Mesolithic. Whether this apparent lag reflects taphonomic biases or behavioral distinctions between archaic and modern humans remains much debated. Figueira Brava cave, in the Arrábida range (Portugal), provides an exceptionally well preserved record of Neandertal coastal resource exploitation on a comparable scale to the MSA and dated to ~86 to 106 thousand years ago. The breadth of the subsistence base-pine nuts, marine invertebrates, fish, marine birds and mammals, tortoises, waterfowl, and hoofed game-exceeds that of regional early Holocene sites. Fisher-hunter-gatherer economies are not the preserve of anatomically modern people; by the Last Interglacial, they were in place across the Old World in the appropriate settings.

RevDate: 2020-03-27
CmpDate: 2020-03-27

Price M (2019)

Face of the mysterious Denisovans emerges.

Science (New York, N.Y.), 365(6459):1232.

RevDate: 2020-03-24
CmpDate: 2020-03-24

Zilhão J (2019)

Tar adhesives, Neandertals, and the tyranny of the discontinuous mind.

Proceedings of the National Academy of Sciences of the United States of America, 116(44):21966-21968.

RevDate: 2020-03-23
CmpDate: 2020-03-23

Wade L (2019)

Was our species in Europe 210,000 years ago?.

Science (New York, N.Y.), 365(6449):111.

RevDate: 2020-03-21

Hunt KD (2020)

Obituary of Charles Loring Brace, IV (1930-2019).

Journal of human evolution, 142:102743 pii:S0047-2484(20)30004-X [Epub ahead of print].

RevDate: 2020-03-20

Bergström A, McCarthy SA, Hui R, et al (2020)

Insights into human genetic variation and population history from 929 diverse genomes.

Science (New York, N.Y.), 367(6484):.

Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.

RevDate: 2020-03-14

Modesto-Mata M, Dean MC, Lacruz RS, et al (2020)

Short and long period growth markers of enamel formation distinguish European Pleistocene hominins.

Scientific reports, 10(1):4665 pii:10.1038/s41598-020-61659-y.

Characterizing dental development in fossil hominins is important for distinguishing between them and for establishing where and when the slow overall growth and development of modern humans appeared. Dental development of australopiths and early Homo was faster than modern humans. The Atapuerca fossils (Spain) fill a barely known gap in human evolution, spanning ~1.2 to ~0.4 million years (Ma), during which H. sapiens and Neandertal dental growth characteristics may have developed. We report here perikymata counts, perikymata distributions and periodicities of all teeth belonging to the TE9 level of Sima del Elefante, level TD6.2 of Gran Dolina (H. antecessor) and Sima de los Huesos. We found some components of dental growth in the Atapuerca fossils resembled more recent H. sapiens. Mosaic evolution of perikymata counts and distribution generate three distinct clusters: H. antecessor, Sima de los Huesos and H. sapiens.

RevDate: 2020-03-12

Belcastro MG, Mariotti V, Pietrobelli A, et al (2020)

The study of the lower limb entheses in the Neanderthal sample from El Sidrón (Asturias, Spain): How much musculoskeletal variability did Neanderthals accumulate?.

Journal of human evolution, 141:102746 pii:S0047-2484(20)30007-5 [Epub ahead of print].

Entheses have rarely been systematically studied in the field of human evolution. However, the investigation of their morphological variability (e.g., robusticity) could provide new insight into their evolutionary significance in the European Neanderthal populations. The aim of this work is to study the entheses and joint features of the lower limbs of El Sidrón Neanderthals (Spain; 49 ka), using standardized scoring methods developed on modern samples. Paleobiology, growth, and development of both juveniles and adults from El Sidrón are studied and compared with those of Krapina Neanderthals (Croatia, 130 ka) and extant humans. The morphological patterns of the gluteus maximus and vastus intermedius entheses in El Sidrón, Krapina, and modern humans differ from one another. Both Neanderthal groups show a definite enthesis design for the gluteus maximus, with little intrapopulation variability with respect to modern humans, who are characterized by a wider range of morphological variability. The gluteus maximus enthesis in the El Sidrón sample shows the osseous features of fibrous entheses, as in modern humans, whereas the Krapina sample shows the aspects of fibrocartilaginous ones. The morphology and anatomical pattern of this enthesis has already been established during growth in all three human groups. One of two and three of five adult femurs from El Sidrón and from Krapina, respectively, show the imprint of the vastus intermedius, which is absent among juveniles from those Neanderthal samples and in modern samples. The scant intrapopulation and the high interpopulation variability in the two Neanderthal samples is likely due to a long-term history of small, isolated populations with high levels of inbreeding, who also lived in different ecological conditions. The comparison of different anatomical entheseal patterns (fibrous vs. fibrocartilaginous) in the Neanderthals and modern humans provides additional elements in the discussion of their functional and genetic origin.

RevDate: 2020-03-08

Rosas A, Losada Agustina B, García-Martínez D, et al (2020)

Analyses of the neandertal patellae from El Sidrón (Asturias, Spain) with implications for the evolution of body form in Homo.

Journal of human evolution, 141:102738 pii:S0047-2484(19)30369-0 [Epub ahead of print].

The evolution of the body form in Homo and its potential morphological connection to the arrangement of different skeletal systems is of major interest in human evolution. Patella morphology as part of the knee is potentially influenced by body form. Here, we describe for the first time the patellae remains recovered at El Sidrón Neandertal site and analyze them in a comparative evolutionary framework. We aim to clarify whether morphometric features frequently observed in Neandertal and modern human patellae are retained from a primitive anatomical arrangement or whether they represent derived features (apomorphies). For this purpose, we combine analyses of discrete features, classic anthropological measurements, and 3D geometric morphometrics based on generalized Procrustes analysis, mean size and shape comparisons, and principal components analysis. We found a size increment of the patella in hominin evolution, with large species showing a larger patella. Modern humans and Neandertals exhibit overall larger patellae, with maximum values observed in the latter, likely as a consequence of their broader body shape. Also, some Neandertals display a thicker patella, which has been linked to larger quadriceps muscles. However, Neandertals retain a primitive morphology in their patellar articular surfaces, with similar-sized lateral and medial articular facets, leading to a more symmetrical internal face. This feature is inherited from a primitive Homo ancestor and suggests a different configuration of the knee in Neandertals. Conversely, Homo sapiens exhibits an autoapomorphic patellar anatomy with expanded lateral articular facets. We propose that these distinct configurations of the patella within Homo may be a consequence of different body forms rather than specific functional adaptations of the knee. Thus, the slender body form of modern humans may entail a medial reorientation of the tibial tuberosity (patellar ligament), allowing lateral surface expansion. These anatomical evolutionary variations may involve subtle secondary differences in bipedalism within Homo.

RevDate: 2020-03-05

Gokhman D, Nissim-Rafinia M, Agranat-Tamir L, et al (2020)

Differential DNA methylation of vocal and facial anatomy genes in modern humans.

Nature communications, 11(1):1189 pii:10.1038/s41467-020-15020-6.

Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that likely emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes associated with face and vocal tract anatomy went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-associated genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.

RevDate: 2020-03-04

Rogers AR, Harris NS, AA Achenbach (2020)

Neanderthal-Denisovan ancestors interbred with a distantly related hominin.

Science advances, 6(8):eaay5483 pii:aay5483.

Previous research has shown that modern Eurasians interbred with their Neanderthal and Denisovan predecessors. We show here that hundreds of thousands of years earlier, the ancestors of Neanderthals and Denisovans interbred with their own Eurasian predecessors-members of a "superarchaic" population that separated from other humans about 2 million years ago. The superarchaic population was large, with an effective size between 20 and 50 thousand individuals. We confirm previous findings that (i) Denisovans also interbred with superarchaics, (ii) Neanderthals and Denisovans separated early in the middle Pleistocene, (iii) their ancestors endured a bottleneck of population size, and (iv) the Neanderthal population was large at first but then declined in size. We provide qualified support for the view that (v) Neanderthals interbred with the ancestors of modern humans.

RevDate: 2020-03-02
CmpDate: 2020-03-02

Fox K, J Hawks (2019)

Use ancient remains more wisely.

Nature, 572(7771):581-583.

RevDate: 2020-02-25

Durvasula A, S Sankararaman (2020)

Recovering signals of ghost archaic introgression in African populations.

Science advances, 6(7):eaax5097 pii:aax5097.

While introgression from Neanderthals and Denisovans has been documented in modern humans outside Africa, the contribution of archaic hominins to the genetic variation of present-day Africans remains poorly understood. We provide complementary lines of evidence for archaic introgression into four West African populations. Our analyses of site frequency spectra indicate that these populations derive 2 to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans. Using a method that can identify segments of archaic ancestry without the need for reference archaic genomes, we built genome-wide maps of archaic ancestry in the Yoruba and the Mende populations. Analyses of these maps reveal segments of archaic ancestry at high frequency in these populations that represent potential targets of adaptive introgression. Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day West African populations.

RevDate: 2020-02-24
CmpDate: 2020-02-24

Centi L, Groman-Yaroslavski I, Friedman N, et al (2019)

The bulb retouchers in the Levant: New insights into Middle Palaeolithic retouching techniques and mobile tool-kit composition.

PloS one, 14(7):e0218859 pii:PONE-D-18-33465.

In this paper we describe two assemblages of flint retouchers or "bulb retouchers" retrieved from Nesher Ramla and Quneitra, two Middle Palaeolithic, open-air sites in the Levant. The site of Nesher Ramla yielded the largest assemblage of bulb retouchers (n = 159) currently known, allowing a detailed investigation of this poorly known phenomenon. An extensive experimental program and use-wear analysis enabled us to characterize the different sets of traces related to the retouching activity and to identify different motions applied by the knappers in the course of this action. In both sites, blanks used as bulb retouchers were almost exclusively retouched items, with a special emphasis on convergent morphotypes in Nesher Ramla. The use of retouched items as bulb retouchers is a common trait over different time spans and geographical areas. Our data suggests that bulb retouchers were versatile, multi-purpose tools with a long use-life, transported over long distances as components of the hunter-gatherer mobile tool kit. The high frequencies of bulb retouchers within some archaeological units of Nesher Ramla appear to be connected to the highly curated nature of the lithic assemblages, in turn reflecting a high mobility of the human groups that produced them.

RevDate: 2020-02-21

Anonymous (2017)

Ancient encounters of the Neanderthal kind.

Nature, 550(7675):161-162.

RevDate: 2020-02-21

Anonymous (2017)

Neanderthal brains were slow to grow.

Nature, 549(7673):435.

RevDate: 2020-02-20

Moncel MH, Ashton N, Arzarello M, et al (2020)

Early Levallois core technology between Marine Isotope Stage 12 and 9 in Western Europe.

Journal of human evolution, 139:102735 pii:S0047-2484(19)30366-5 [Epub ahead of print].

Early Levallois core technology is usually dated in Europe to the end of Marine Isotope Stage (MIS) 9 and particularly from the beginning of MIS 8 to MIS 6. This technology is considered as one of the markers of the transition from lower to Middle Paleolithic or from Mode 2 to Mode 3. Recent discoveries show that some lithic innovations actually appeared earlier in western Europe, from MIS 12 to MIS 9, contemporaneous with changes in subsistence strategies and the first appearance of early Neanderthal anatomical features. Among these discoveries, there is the iconic Levallois core technology. A selection of well-dated assemblages in the United Kingdom, France, and Italy dated from MIS 12 to 9, which include both cores and flakes with Levallois features, has been described and compared with the aim of characterizing this technology. The conclusion supports the interpretation that several technical features may be attributed to a Levallois technology similar to those observed in younger Middle Paleolithic sites, distinct from the main associated core technologies in each level. Some features in the sample of sites suggest a gradual transformation of existing core technologies. The small evidence of Levallois could indicate occasional local innovations from different technological backgrounds and would explain the diversity of Levallois methods that is observed from MIS 12. The technological roots of Levallois technology in the Middle Pleistocene would suggest a multiregional origin and diffusion in Europe and early evidence of regionalization of local traditions through Europe from MIS 12 to 9. The relationships of Levallois technology with new needs and behaviors are discussed, such as flake preference, functional reasons related to hunting and hafting, an increase in the use of mental templates in European populations, and changes in the structure of hominin groups adapting to climatic and environmental changes.

RevDate: 2020-02-18

Weissbrod L, M Weinstein-Evron (2020)

Climate variability in early expansions of Homo sapiens in light of the new record of micromammals in Misliya Cave, Israel.

Journal of human evolution, 139:102741 pii:S0047-2484(20)30002-6 [Epub ahead of print].

In this study, we provide the first taphonomic and taxonomic descriptions of the micromammals from Misliya Cave, where recently a Homo sapiens hemimaxilla has been reported. This finding significantly extends the time frame for the out-of-Africa presence of anatomically modern humans. It also provides an opportunity to reassess variation in early modern human population responses to climate change in the Levantine sequence. Information on species ranking and diversity estimations (Shannon functions) is obtained from quantitative data across 31 Levantine assemblages and investigated in a broad comparative frame using multivariate analyses. Recent models of human-climate interactions in the late Early-Middle Paleolithic of the southern Levant have drawn heavily on on-site associations of human fossils with remains of micromammals. However, there has been little, if any, attempt to examine the long-term picture of how paleocommunities of micromammals responded qualitatively and quantitatively to climatic oscillations of the region by altering their compositional complexity. Consequently, our understanding is vastly limited in regard to the paleoecosystem functions that linked past precipitation shifts to changes in primary producers and consumers or as to the background climatic conditions that allowed for the development of highly nonanalog ancient communities in the region. Although previous studies argued for a correspondence between alternations in H. sapiens and Neanderthal occupations of the Levant and faunal shifts in key biostratigraphic indicator taxa (such as Euro-Siberian Ellobius versus Saharo-Arabian Mastomys and Arvicanthis), our data indicate the likelihood that early H. sapiens populations (Misliya and Qafzeh hominins) persisted through high amplitudes of paleoecological and climatic oscillations. It is unlikely, given these results, that climate functioned as a significant filter of early modern human persistence and genetic interactions with Neanderthals in the Levant.

RevDate: 2020-02-14
CmpDate: 2020-02-14

Rotival M, L Quintana-Murci (2020)

Functional consequences of archaic introgression and their impact on fitness.

Genome biology, 21(1):3.

RevDate: 2020-02-07

Le Tortorec A, Matusali G, Mahé D, et al (2020)

From Ancient to Emerging Infections: The Odyssey of Viruses in the Male Genital Tract.

Physiological reviews [Epub ahead of print].

The male genital tract (MGT) is the target of a number of viral infections that can have deleterious consequences at the individual, offspring and population levels. These consequences include infertility, cancers of male organs, transmission to the embryo/fetal development abnormalities and sexual dissemination of major viral pathogens such as human immunodeficiency virus (HIV) and hepatitis B virus (HBV). Lately, two emerging viruses, Zika and Ebola, have additionally revealed that the human MGT can constitute a reservoir for viruses cleared from peripheral circulation by the immune system, leading to their sexual transmission by cured men. This represents a concern for future epidemics and further underlines the need for a better understanding of the interplay between viruses and the MGT. We review here how viruses, from ancient viruses that integrated the germ line during evolution through old viruses (e.g. papillomaviruses originating from Neanderthals) and more modern sexually-transmitted infections (e.g. simian zoonotic HIV) to emerging viruses (e.g. Ebola and Zika) take advantage of genital tract colonization for horizontal dissemination, viral persistence, vertical transmission and endogenization. The MGT immune responses to viruses and the impact of these infections are discussed. We summarize the latest data regarding the sources of viruses in semen and the complex role of this body fluid in sexual transmission. Finally, we introduce key animal findings that are relevant for our understanding of viral infection and persistence in the human MGT and suggest future research directions.

RevDate: 2020-01-31

Chen L, Wolf AB, Fu W, et al (2020)

Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals.

Cell pii:S0092-8674(20)30059-3 [Epub ahead of print].

Admixture has played a prominent role in shaping patterns of human genomic variation, including gene flow with now-extinct hominins like Neanderthals and Denisovans. Here, we describe a novel probabilistic method called IBDmix to identify introgressed hominin sequences, which, unlike existing approaches, does not use a modern reference population. We applied IBDmix to 2,504 individuals from geographically diverse populations to identify and analyze Neanderthal sequences segregating in modern humans. Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date.

RevDate: 2020-01-31

Price M (2020)

Africans, too, carry Neanderthal genetic legacy.

Science (New York, N.Y.), 367(6477):497.

RevDate: 2020-01-28

Kolobova KA, Roberts RG, Chabai VP, et al (2020)

Archaeological evidence for two separate dispersals of Neanderthals into southern Siberia.

Proceedings of the National Academy of Sciences of the United States of America pii:1918047117 [Epub ahead of print].

Neanderthals were once widespread across Europe and western Asia. They also penetrated into the Altai Mountains of southern Siberia, but the geographical origin of these populations and the timing of their dispersal have remained elusive. Here we describe an archaeological assemblage from Chagyrskaya Cave, situated in the Altai foothills, where around 90,000 Middle Paleolithic artifacts and 74 Neanderthal remains have been recovered from deposits dating to between 59 and 49 thousand years ago (age range at 95.4% probability). Environmental reconstructions suggest that the Chagyrskaya hominins were adapted to the dry steppe and hunted bison. Their distinctive toolkit closely resembles Micoquian assemblages from central and eastern Europe, including the northern Caucasus, more than 3,000 kilometers to the west of Chagyrskaya Cave. At other Altai sites, evidence of earlier Neanderthal populations lacking associated Micoquian-like artifacts implies two or more Neanderthal incursions into this region. We identify eastern Europe as the most probable ancestral source region for the Chagyrskaya toolmakers, supported by DNA results linking the Neanderthal remains with populations in northern Croatia and the northern Caucasus, and providing a rare example of a long-distance, intercontinental population movement associated with a distinctive Paleolithic toolkit.

RevDate: 2020-01-24

Hubisz M, A Siepel (2020)

Inference of Ancestral Recombination Graphs Using ARGweaver.

Methods in molecular biology (Clifton, N.J.), 2090:231-266.

This chapter describes the usage of the program ARGweaver, which estimates the ancestral recombination graph for as many as about 100 genome sequences. The ancestral recombination graph is a detailed description of the coalescence and recombination events that define the relationships among the sampled sequences. This rich description is useful for a wide variety of population genetic analyses. We describe the preparation of data and major considerations for running ARGweaver, as well as the interpretation of results. We then demonstrate an analysis using the DARC (Duffy) gene as an example, and show how ARGweaver can be used to detect signatures of natural selection and Neandertal introgression, as well as to estimate the dates of mutation events. This chapter provides sufficient detail to get a new user up and running with this complex but powerful analysis tool.

RevDate: 2020-01-27

Villa P, Soriano S, Pollarolo L, et al (2020)

Neandertals on the beach: Use of marine resources at Grotta dei Moscerini (Latium, Italy).

PloS one, 15(1):e0226690.

Excavated in 1949, Grotta dei Moscerini, dated MIS 5 to early MIS 4, is one of two Italian Neandertal sites with a large assemblage of retouched shells (n = 171) from 21 layers. The other occurrence is from the broadly contemporaneous layer L of Grotta del Cavallo in southern Italy (n = 126). Eight other Mousterian sites in Italy and one in Greece also have shell tools but in a very small number. The shell tools are made on valves of the smooth clam Callista chione. The general idea that the valves of Callista chione were collected by Neandertals on the beach after the death of the mollusk is incomplete. At Moscerini 23.9% of the specimens were gathered directly from the sea floor as live animals by skin diving Neandertals. Archaeological data from sites in Italy, France and Spain confirm that shell fishing and fresh water fishing was a common activity of Neandertals, as indicated by anatomical studies recently published by E. Trinkaus. Lithic analysis provides data to show the relation between stone tools and shell tools. Several layers contain pumices derived from volcanic eruptions in the Ischia Island or the Campi Flegrei (prior to the Campanian Ignimbrite mega-eruption). Their rounded edges indicate that they were transported by sea currents to the beach at the base of the Moscerini sequence. Their presence in the occupation layers above the beach is discussed. The most plausible hypothesis is that they were collected by Neandertals. Incontrovertible evidence that Neandertals collected pumices is provided by a cave in Liguria. Use of pumices as abraders is well documented in the Upper Paleolithic. We prove that the exploitation of submerged aquatic resources and the collection of pumices common in the Upper Paleolithic were part of Neandertal behavior well before the arrival of modern humans in Western Europe.

RevDate: 2019-12-31

Gómez-Olivencia A, López-Onaindia D, Sala N, et al (2019)

The human remains from Axlor (Dima, Biscay, northern Iberian Peninsula).

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

OBJECTIVES: We provide the description and comparative analysis of all the human fossil remains found at Axlor during the excavations carried out by J. M. de Barandiarán from 1967 to 1974: a cranial vault fragment and eight teeth, five of which likely belonged to the same individual, although two are currently lost. Our goal is to describe in detail all these human remains and discuss both their taxonomic attribution and their stratigraphic context.

MATERIALS AND METHODS: We describe external and internal anatomy, and use classic and geometric morphometrics. The teeth from Axlor are compared to Neandertals, Upper Paleolithic, and recent modern humans.

RESULTS: Three teeth (a left dm2 , a left di1 , and a right I1) and the parietal fragment show morphological features consistent with a Neandertal classification, and were found in an undisturbed Mousterian context. The remaining three teeth (plus the two lost ones), initially classified as Neandertals, show morphological features and a general size that are more compatible with their classification as modern humans.

DISCUSSION: The combined anatomical and stratigraphic study suggest that the remains of two different adult Neandertals have been recovered during the old excavations performed by Barandiarán: a left parietal fragment (Level VIII) and a right I1 (Level V). Additionally, two different Neandertal children lost deciduous teeth during the formations of levels V (left di1) and IV (right dm2). In addition, a modern human individual is represented by five remains (two currently lost) from a complex stratigraphic setting. Some of the morphological features of these remains suggest that they may represent one of the scarce examples of Upper Paleolithic modern human remains in the northern Iberian Peninsula, which should be confirmed by direct dating.

RevDate: 2020-01-18

Bücking R, Cox MP, Hudjashov G, et al (2019)

Archaic mitochondrial DNA inserts in modern day nuclear genomes.

BMC genomics, 20(1):1017 pii:10.1186/s12864-019-6392-8.

BACKGROUND: Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs).

RESULTS: We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin, present in 15 analysed genomes; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male.

CONCLUSIONS: Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

RevDate: 2020-01-08

Ottoni C, Guellil M, Ozga AT, et al (2019)

Metagenomic analysis of dental calculus in ancient Egyptian baboons.

Scientific reports, 9(1):19637.

Dental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, ancient metagenomics made it possible to unlock the wealth of microbial and dietary information of dental calculus to reconstruct oral microbiomes and lifestyle of humans from the past. Although most studies have so far focused on ancient humans, dental calculus is known to form in a wide range of animals, potentially informing on how human-animal interactions changed the animals' oral ecology. Here, we characterise the oral microbiome of six ancient Egyptian baboons held in captivity during the late Pharaonic era (9th-6th centuries BC) and of two historical baboons from a zoo via shotgun metagenomics. We demonstrate that these captive baboons possessed a distinctive oral microbiome when compared to ancient and modern humans, Neanderthals and a wild chimpanzee. These results may reflect the omnivorous dietary behaviour of baboons, even though health, food provisioning and other factors associated with human management, may have changed the baboons' oral microbiome. We anticipate our study to be a starting point for more extensive studies on ancient animal oral microbiomes to examine the extent to which domestication and human management in the past affected the diet, health and lifestyle of target animals.

RevDate: 2020-02-06

Wall JD, Ratan A, Stawiski E, et al (2019)

Identification of African-Specific Admixture between Modern and Archaic Humans.

American journal of human genetics, 105(6):1254-1261.

Recent work has demonstrated that two archaic human groups (Neanderthals and Denisovans) interbred with modern humans and contributed to the contemporary human gene pool. These findings relied on the availability of high-coverage genomes from both Neanderthals and Denisovans. Here we search for evidence of archaic admixture from a worldwide panel of 1,667 individuals using an approach that does not require the presence of an archaic human reference genome. We find no evidence for archaic admixture in the Andaman Islands, as previously claimed, or on the island of Flores, where Homo floresiensis fossils have been found. However, we do find evidence for at least one archaic admixture event in sub-Saharan Africa, with the strongest signal in Khoesan and Pygmy individuals from Southern and Central Africa. The locations of these putative archaic admixture tracts are weighted against functional regions of the genome, consistent with the long-term effects of purifying selection against introgressed genetic material.

RevDate: 2020-01-08

Langley MC, Benítez-Burraco A, V Kempe (2019)

Playing with language, creating complexity: Has play contributed to the evolution of complex language?.

Evolutionary anthropology [Epub ahead of print].

We argue that enhanced play may have contributed to the emergence of complex language systems in modern humans (Homo sapiens). To support this idea, we first discuss evidence for an expansion of playing behavior connected to the extended childhood of modern human children, and the potential of this period for the transmission of complex cultural traits, including language. We then link two of the most important functions of play-exploration and innovation-to the potential for cumulative cultural evolution in general and for the emergence of complex language in particular. If correct, the shorter childhood of Neanderthals-involving restrictions on time to experiment and innovate-may have restricted their language (and other symbolic) system/s. Consequently, fully investigating the role that play may have had in the transmission of language and the development of symbolic cultures in both modern humans and Neanderthals provides a new avenue of research for Paleolithic archaeology and related disciplines.

RevDate: 2019-12-18

Weniger GC, de Andrés-Herrero M, Bolin V, et al (2019)

Late Glacial rapid climate change and human response in the Westernmost Mediterranean (Iberia and Morocco).

PloS one, 14(12):e0225049.

This paper investigates the correlation between climate, environment and human land use in the Westernmost Mediterranean on both sides of the Strait of Gibraltar during the Late Glacial. Using a multi-proxy approach on a sample of 300 sites from the Solutrean and Magdalenian of the Iberian Peninsula and from the Iberomaurusian in Morocco, we find evidence for significant changes in settlement patterns and site density after the Last Glacial Maximum. In Southern Iberia, during Heinrich Stadial 1, hyperarid zones expanded drastically from the south-eastern coast to the West through the Interior. This aridification process heavily affected Magdalenian settlement in the South and caused a strong decline of hunter-gatherer population. Southern Iberia during Heinrich Stadial 1 turned out to be a high-risk environment when compared to Northern Iberia. At the same time, the Late Iberomaurusian of Morocco, although considered to be situated in a high-risk environment as well, experiences an increase of sites and expansion of settlement area.

RevDate: 2020-01-08

Mallol C, Hernández C, Mercier N, et al (2019)

Fire and brief human occupations in Iberia during MIS 4: Evidence from Abric del Pastor (Alcoy, Spain).

Scientific reports, 9(1):18281.

There is a relatively low amount of Middle Paleolithic sites in Europe dating to MIS 4. Of the few that exist, several of them lack evidence for anthropogenic fire, raising the question of how this period of global cooling may have affected the Neanderthal population. The Iberian Peninsula is a key area to explore this issue, as it has been considered as a glacial refugium during critical periods of the Neanderthal timeline and might therefore yield archaeological contexts in which we can explore possible changes in the behaviour and settlement patterns of Neanderthal groups during MIS 4. Here we report recent data from Abric del Pastor, a small rock shelter in Alcoy (Alicante, Spain) with a stratified deposit containing Middle Palaeolithic remains. We present absolute dates that frame the sequence within MIS 4 and multi-proxy geoarchaeological evidence of in situ anthropogenic fire, including microscopic evidence of in situ combustion residues and thermally altered sediment. We also present archaeostratigraphic evidence of recurrent, functionally diverse, brief human occupation of the rock shelter. Our results suggest that Neanderthals occupied the Central Mediterranean coast of the Iberian Peninsula during MIS 4, that these Neanderthals were not undergoing climatic stress and they were habitual fire users.

RevDate: 2020-01-08

Karban ME (2019)

Occipital hemi-bun development and shape covariation in a longitudinal extant human growth sample.

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

OBJECTIVES: Although the homology of the Neanderthal occipital bun and anatomically modern human "hemi-bun" has long been debated, little is known about the developmental timing and patterning of these two patterns of prominent occipital squama convexity. In this study, occipital hemi-bun ontogeny and cranial shape covariation are assessed in a comparative extant human sample.

MATERIALS AND METHODS: Two-dimensional geometric morphometric methods were used to investigate hemi-bun development in a longitudinal sample of growth study cephalograms representing extant human subjects predominantly of European ancestry. Subjects were each measured at three distinct age points, ranging from 3.0 to 20.4 years, and two-block partial least squares analysis was used to assess patterns of covariation between midsagittal occipital bone morphology and other aspects of craniofacial shape.

RESULTS: Occipital hemi-bun morphology, when present, was found to develop early in ontogeny, in association with anteroposterior elongation of the frontal and parietal bones. No significant pattern of covariation was found between occipital hemi-bun shape and cranial/basicranial breadth, basicranial length, basicranial angle, or midfacial prognathism.

DISCUSSION: This study suggests that the occipital hemi-bun, at least in this extant human population, should not be considered an independent trait, as its development is closely linked to shape variation in the frontal and parietal bones. Importantly, these results suggest that occipital hemi-bun morphology is not significantly influenced by basicranial morphology during development, but instead covaries with changes in midsagittal neurocranial vault shape.

RevDate: 2019-12-11

Vaesen K, Scherjon F, Hemerik L, et al (2019)

Inbreeding, Allee effects and stochasticity might be sufficient to account for Neanderthal extinction.

PloS one, 14(11):e0225117.

The replacement of Neanderthals by Anatomically Modern Humans has typically been attributed to environmental pressure or a superiority of modern humans with respect to competition for resources. Here we present two independent models that suggest that no such heatedly debated factors might be needed to account for the demise of Neanderthals. Starting from the observation that Neanderthal populations already were small before the arrival of modern humans, the models implement three factors that conservation biology identifies as critical for a small population's persistence, namely inbreeding, Allee effects and stochasticity. Our results indicate that the disappearance of Neanderthals might have resided in the smallness of their population(s) alone: even if they had been identical to modern humans in their cognitive, social and cultural traits, and even in the absence of inter-specific competition, Neanderthals faced a considerable risk of extinction. Furthermore, we suggest that if modern humans contributed to the demise of Neanderthals, that contribution might have had nothing to do with resource competition, but rather with how the incoming populations geographically restructured the resident populations, in a way that reinforced Allee effects, and the effects of inbreeding and stochasticity.

RevDate: 2019-11-27

Krueger KL, Willman JC, Matthews GJ, et al (2019)

Anterior tooth-use behaviors among early modern humans and Neandertals.

PloS one, 14(11):e0224573 pii:PONE-D-19-17387.

Early modern humans (EMH) are often touted as behaviorally advanced to Neandertals, with more sophisticated technologies, expanded resource exploitation, and more complex clothing production. However, recent analyses have indicated that Neandertals were more nuanced in their behavioral adaptations, with the production of the Châtelperronian technocomplex, the processing and cooking of plant foods, and differences in behavioral adaptations according to habitat. This study adds to this debate by addressing the behavioral strategies of EMH (n = 30) within the context of non-dietary anterior tooth-use behaviors to glean possible differences between them and their Neandertal (n = 45) counterparts. High-resolution casts of permanent anterior teeth were used to collect microwear textures of fossil and comparative bioarchaeological samples using a Sensofar white-light confocal profiler with a 100x objective lens. Labial surfaces were scanned, totaling a work envelope of 204 x 276 μm for each individual. The microwear textures were examined for post-mortem damage and uploaded to SSFA software packages for surface characterization. Statistical analyses were performed to examine differences in central tendencies and distributions of anisotropy and textural fill volume variables among the EMH sample itself by habitat, location, and time interval, and between the EMH and Neandertal samples by habitat and location. Descriptive statistics for the EMH sample were compared to seven bioarchaeological samples (n = 156) that utilized different tooth-use behaviors to better elucidate specific activities that may have been performed by EMH. Results show no significant differences between the means within the EMH sample by habitat, location, or time interval. Furthermore, there are no significant differences found here between EMH and Neandertals. Comparisons to the bioarchaeological samples suggest both fossil groups participated in clamping and grasping activities. These results indicate that EMH and Neandertals were similar in their non-dietary anterior tooth-use behaviors and provide additional evidence for overlapping behavioral strategies employed by these two hominins.

RevDate: 2019-12-31

Garralda MD, Maureille B, Le Cabec A, et al (2020)

The Neanderthal teeth from Marillac (Charente, Southwestern France): Morphology, comparisons and paleobiology.

Journal of human evolution, 138:102683.

Few European sites have yielded human dental remains safely dated to the end of MIS 4/beginning of MIS 3. One of those sites is Marillac (Southwestern France), a collapsed karstic cave where archeological excavations (1967-1980) conducted by B. Vandermeersch unearthed numerous faunal and human remains, as well as a few Mousterian Quina tools. The Marillac sinkhole was occasionally used by humans to process the carcasses of different prey, but there is no evidence for a residential use of the site, nor have any hearths been found. Rare carnivore bones were also discovered, demonstrating that the sinkhole was seasonally used, not only by Neanderthals, but also by predators across several millennia. The lithostratigraphic units containing the human remains were dated to ∼60 kyr. The fossils consisted of numerous fragments of skulls and jaws, isolated teeth and several post-cranial bones, many of them with traces of perimortem manipulations. For those already published, their morphological characteristics and chronostratigraphic context allowed their attribution to Neanderthals. This paper analyzes sixteen unpublished human teeth (fourteen permanent and two deciduous) by investigating the external morphology and metrical variation with respect to other Neanderthal remains and a sample from modern populations. We also investigate their enamel thickness distribution in 2D and 3D, the enamel-dentine junction morphology (using geometric morphometrics) of one molar and two premolars, the roots and the possible expression of taurodontism, as well as pathologies and developmental defects. The anterior tooth use and paramasticatory activities are also discussed. Morphological and structural alterations were found on several teeth, and interpreted in light of human behavior (tooth-pick) and carnivores' actions (partial digestion). The data are interpreted in the context of the available information for the Eurasian Neanderthals.

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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.

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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.

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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.

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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.

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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.

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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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Neanderthals

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
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @ gmail.com

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).

Timelines

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

Biographies

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 )