Publications

palaeoproteomic evidence identifies archaic hominins associated with the châtelperronian at the grotte du renne.	in western europe, the middle to upper paleolithic transition is associated with the disappearance of neandertals and the spread of anatomically modern humans (amhs). current chronological, behavioral, and biological models of this transitional period hinge on the châtelperronian technocomplex. at the site of the grotte du renne, arcy-sur-cure, morphological neandertal specimens are not directly dated but are contextually associated with the châtelperronian, which contains bone points and beads. ...	2016	27638212
statistical methods for analyzing ancient dna from hominins.	in the past few years, the number of autosomal dna sequences from human fossils has grown explosively and numerous partial or complete sequences are available from our closest relatives, neanderthal and denisovans. i review commonly used statistical methods applied to these sequences. these methods fall into three broad classes: methods for estimating levels of contamination, descriptive methods, and methods based on population genetic models. the latter two classes are largely methods developed ...	2016	27606907
ancestral origins and genetic history of tibetan highlanders.	the origin of tibetans remains one of the most contentious puzzles in history, anthropology, and genetics. analyses of deeply sequenced (30×-60×) genomes of 38 tibetan highlanders and 39 han chinese lowlanders, together with available data on archaic and modern humans, allow us to comprehensively characterize the ancestral makeup of tibetans and uncover their origins. non-modern human sequences compose ∼6% of the tibetan gene pool and form unique haplotypes in some genomic regions, where denisov ...	2016	27569548
the mitogenome of a 35,000-year-old homo sapiens from europe supports a palaeolithic back-migration to africa.	after the dispersal of modern humans (homo sapiens) out of africa, hominins with a similar morphology to that of present-day humans initiated the gradual demographic expansion into eurasia. the mitogenome (33-fold coverage) of the peştera muierii 1 individual (pm1) from romania (35 ky cal bp) we present in this article corresponds fully to homo sapiens, whilst exhibiting a mosaic of morphological features related to both modern humans and neandertals. we have identified the pm1 mitogenome as a b ...	2016	27195518
hla class i variation in iranian lur and kurd populations: high haplotype and allotype diversity with an abundance of kir ligands.	hla-a, -b and -c alleles of 285 individuals, representing three iranian lur populations and one iranian kurd population were sequenced completely, yielding human leukocyte antigen (hla) class i genotypes at high resolution and filling four fields of the official hla nomenclature. each population has 87-99 alleles, evenly distributed between the three hla class i genes, 145 alleles being identified in total. these alleles were already known, named and deposited in the hla database. the alleles fo ...	2016	27558013
the acheulian and early middle paleolithic in latium (italy): stability and innovation.	we present here the results of a technological and typological analysis of the acheulian and early middle paleolithic assemblages from torre in pietra (latium, italy) together with comparisons with the acheulian small tools of castel di guido. the assemblages were never chronometrically dated before. we have now 40ar/39ar dates and esr-u-series dates, within a geomorphological framework, which support correlations to marine isotope stages. the acheulian (previously correlated to mis 9) is now da ...	2016	27525705
divergent ah receptor ligand selectivity during hominin evolution.	we have identified a fixed nonsynonymous sequence difference between humans (val381; derived variant) and neandertals (ala381; ancestral variant) in the ligand-binding domain of the aryl hydrocarbon receptor (ahr) gene. in an exome sequence analysis of four neandertal and denisovan individuals compared with nine modern humans, there are only 90 total nucleotide sites genome-wide for which archaic hominins are fixed for the ancestral nonsynonymous variant and the modern humans are fixed for the d ...	2016	27486223
opsin gene repertoires in northern archaic hominids.	the neanderthals' northern distribution, hunting techniques, and orbit breadths suggest that they were more active in dim light than modern humans. we surveyed visual opsin genes from four neanderthals and two other archaic hominids to see if they provided additional support for this hypothesis. this analysis was motivated by the observation that alleles responsible for anomalous trichromacy in humans are more common in northern latitudes, by data suggesting that these variants might enhance vis ...	2016	27463216
genomic insights into the origin of farming in the ancient near east.	we report genome-wide ancient dna from 44 ancient near easterners ranging in time between ~12,000 and 1,400 bc, from natufian hunter-gatherers to bronze age farmers. we show that the earliest populations of the near east derived around half their ancestry from a 'basal eurasian' lineage that had little if any neanderthal admixture and that separated from other non-african lineages before their separation from each other. the first farmers of the southern levant (israel and jordan) and zagros mou ...	2016	27459054
brain development is similar in neanderthals and modern humans.	while the braincase of adult neanderthals had a similar volume to that of modern humans from the same period, differences in endocranial shape suggest that brain morphology differed between modern humans and neanderthals. when and how these differences arose during evolution and development is a topic of ongoing research, with potential implications for species-specific differences in brain and cognitive development, and in life history [1,2]. earlier research suggested that neanderthals followe ...	2016	27458909
ibd sharing between africans, neandertals, and denisovans.	interbreeding between ancestors of humans and other hominins outside of africa has been studied intensively, while their common history within africa still lacks proper attention. however, shedding light on human evolution in this time period about which little is known, is essential for understanding subsequent events outside of africa. we investigate the genetic relationships of humans, neandertals, and denisovans by identifying very short dna segments in the 1000 genomes phase 3 data that the ...	2016	28158547
recent positive selection in genes of the mammalian epidermal differentiation complex locus.	the epidermal differentiation complex (edc) is the most rapidly evolving locus in the human genome compared to that of the chimpanzee. yet the edc genes that are undergoing positive selection across mammals and in humans are not known. we sought to identify the positively selected genetic variants and determine the evolutionary events of the edc using mammalian-wide and clade-specific branch- and branch-site likelihood ratio tests and a genetic algorithm (ga) branch test. significant non-synonym ...	2016	28119736
identifying major transitions in the evolution of lithic cutting edge production rates.	the notion that the evolution of core reduction strategies involved increasing efficiency in cutting edge production is prevalent in narratives of hominin technological evolution. yet a number of studies comparing two different knapping technologies have found no significant differences in edge production. using digital analysis methods we present an investigation of raw material efficiency in eight core technologies broadly representative of the long-term evolution of lithic technology. these a ...	2016	27936135
the psoriasis-associated deletion of late cornified envelope genes lce3b and lce3c has been maintained under balancing selection since human denisovan divergence.	a common, 32kb deletion of lce3b and lce3c genes is strongly associated with psoriasis. we recently found that this deletion is ancient, predating human-denisovan divergence. however, it was not clear why negative selection has not removed this deletion from the population.	2016	27919236
a gradualist scenario for language evolution: precise linguistic reconstruction of early human (and neandertal) grammars.	in making an argument for the antiquity of language, based on comparative evidence, dediu and levinson (2013) express hope that some combinations of structural features will prove so conservative that they will allow deep linguistic reconstruction. i propose that the earliest stages of syntax/grammar as reconstructed in progovac (2015a), based on a theoretical and data-driven linguistic analysis, provide just such a conservative platform, which would have been commanded also by neandertals and t ...	2016	27877146
selective sweep on human amylase genes postdates the split with neanderthals.	humans have more copies of amylase genes than other primates. it is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in african and non-african populations. analysis of genetic variation in these regions supports the model of an early selecti ...	2016	27853181
evidence for the paleoethnobotany of the neanderthal: a review of the literature.	our perception of our closest human relatives, the neanderthals, has evolved in the last few decades from brutish ape-men to intelligent archaic human peoples. our understanding and appreciation of their cultural sophistication has only recently extended to their diet. only within the last few years, with new techniques and a shift in focus, have we begun to truly investigate and understand the role of plants in their diet and culture. the more we learn about neanderthals, the more we realize th ...	2016	27843675
archaic hominin admixture facilitated adaptation to out-of-africa environments.	as modern humans dispersed from africa throughout the world, they encountered and interbred with archaic hominins, including neanderthals and denisovans [1, 2]. although genome-scale maps of introgressed sequences have been constructed [3-6], considerable gaps in knowledge remain about the functional, phenotypic, and evolutionary significance of archaic hominin dna that persists in present-day individuals. here, we describe a comprehensive set of analyses that identified 126 high-frequency archa ...	2016	27839976
the strength of selection against neanderthal introgression.	hybridization between humans and neanderthals has resulted in a low level of neanderthal ancestry scattered across the genomes of many modern-day humans. after hybridization, on average, selection appears to have removed neanderthal alleles from the human population. quantifying the strength and causes of this selection against neanderthal ancestry is key to understanding our relationship to neanderthals and, more broadly, how populations remain distinct after secondary contact. here, we develop ...	2016	27824859
timing and causes of north african wet phases during the last glacial period and implications for modern human migration.	we present the first speleothem-derived central north africa rainfall record for the last glacial period. the record reveals three main wet periods at 65-61 ka, 52.5-50.5 ka and 37.5-33 ka that lead obliquity maxima and precession minima. we find additional minor wet episodes that are synchronous with greenland interstadials. our results demonstrate that sub-tropical hydrology is forced by both orbital cyclicity and north atlantic moisture sources. the record shows that after the end of a sahara ...	2016	27808237
[innate immunity and human diseases: from archaic introgression to natural selection].	throughout evolution, humans have had to face strong variation in environmental conditions, with pathogens being among the strongest threats that our species has encountered. the use of population genetic approaches provides novel insights into how natural selection imposed by pathogen pressures, in its different forms and intensities, has shaped the patterns of diversity of the human genome at the population level. these studies help to distinguish genes playing essential, non-redundant functio ...	2016	28044971
middle paleolithic human deciduous incisor from grotta del cavallo, italy.	in this contribution, we present a morphological description and comparative morphometric analysis of cavallo d, a human tooth unearthed from the mousterian fiii sublayer of grotta del cavallo (apulia, italy).	2016	27365292
genetic ancestry and natural selection drive population differences in immune responses to pathogens.	individuals from different populations vary considerably in their susceptibility to immune-related diseases. to understand how genetic variation and natural selection contribute to these differences, we tested for the effects of african versus european ancestry on the transcriptional response of primary macrophages to live bacterial pathogens. a total of 9.3% of macrophage-expressed genes show ancestry-associated differences in the gene regulatory response to infection, and african ancestry spec ...	2016	27768889
genetic adaptation and neandertal admixture shaped the immune system of human populations.	humans differ in the outcome that follows exposure to life-threatening pathogens, yet the extent of population differences in immune responses and their genetic and evolutionary determinants remain undefined. here, we characterized, using rna sequencing, the transcriptional response of primary monocytes from africans and europeans to bacterial and viral stimuli-ligands activating toll-like receptor pathways (tlr1/2, tlr4, and tlr7/8) and influenza virus-and mapped expression quantitative trait l ...	2016	27768888
oh-65: the earliest evidence for right-handedness in the fossil record.	labial striations on the anterior teeth have been documented in numerous european pre-neandertal and neandertal fossils and serve as evidence for handedness. oh-65, dated at 1.8 mya, shows a concentration of oblique striations on, especially, the left i(1) and right i(1), i(2) and c(1), which signal that it was right-handed. from these patterns we contend that oh-65 was habitually using the right hand, over the left, in manipulating objects during some kind of oral processing. in living humans r ...	2016	27765150
paranasal sinuses: a problematic proxy for climate adaptation in neanderthals.		2016	27405260
direct radiocarbon dating and genetic analyses on the purported neanderthal mandible from the monti lessini (italy).	anatomically modern humans replaced neanderthals in europe around 40,000 years ago. the demise of the neanderthals and the nature of the possible relationship with anatomically modern humans has captured our imagination and stimulated research for more than a century now. recent chronological studies suggest a possible overlap between neanderthals and anatomically modern humans of more than 5,000 years. analyses of ancient genome sequences from both groups have shown that they interbred multiple ...	2016	27389305
neandertal cannibalism and neandertal bones used as tools in northern europe.	almost 150 years after the first identification of neandertal skeletal material, the cognitive and symbolic abilities of these populations remain a subject of intense debate. we present 99 new neandertal remains from the troisième caverne of goyet (belgium) dated to 40,500-45,500 calbp. the remains were identified through a multidisciplinary study that combines morphometrics, taphonomy, stable isotopes, radiocarbon dating and genetic analyses. the goyet neandertal bones show distinctive anthropo ...	2016	27381450
genetic demographic networks: mathematical model and applications.	recent improvement in the quality of genetic data obtained from extinct human populations and their ancestors encourages searching for answers to basic questions regarding human population history. the most common and successful are model-based approaches, in which genetic data are compared to the data obtained from the assumed demography model. using such approach, it is possible to either validate or adjust assumed demography. model fit to data can be obtained based on reverse-time coalescent ...	2016	27378746
spatial determinants of the mandibular curve of spee in modern and archaic homo.	the curve of spee (cos) is a mesio-distally curved alignment of the canine through distal molar cusp tips in certain mammals including modern humans and some fossil hominins. in humans, the alignment varies from concave to flat, and previous studies have suggested that this difference reflects craniofacial morphology, including the degree of alveolar prognathism. however, the relationship between prognathism and concavity of the cos has not been tested in craniofacially variant populations. we t ...	2016	27346254
home-range size in large-bodied carnivores as a model for predicting neandertal territory size.	adult human foragers expend roughly 30-60 kcal per km in unburdened walking at optimal speeds.(1,2) in the context of foraging rounds and residential moves, they may routinely travel distances of 50-70 km per week, often while carrying loads.(3) movement on the landscape, then, is arguably the single most expensive item in the activity budgets of hunter-gatherers. mobility costs may have been greater still for neandertals. they had stocky, short-limbed physiques that were energetically costly to ...	2016	27312183
the origin and evolution of homo sapiens.	if we restrict the use of homo sapiens in the fossil record to specimens which share a significant number of derived features in the skeleton with extant h. sapiens, the origin of our species would be placed in the african late middle pleistocene, based on fossils such as omo kibish 1, herto 1 and 2, and the levantine material from skhul and qafzeh. however, genetic data suggest that we and our sister species homo neanderthalensis shared a last common ancestor in the middle pleistocene approxima ...	2016	27298468
morphological variation in homo erectus and the origins of developmental plasticity.	homo erectus was the first hominin to exhibit extensive range expansion. this extraordinary departure from africa, especially into more temperate climates of eurasia, has been variously related to technological, energetic and foraging shifts. the temporal and regional anatomical variation in h. erectus suggests that a high level of developmental plasticity, a key factor in the ability of h. sapiens to occupy a variety of habitats, may also have been present in h. erectus. developmental plasticit ...	2016	27298467
ancient dna and human history.	we review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient dna (adna) can provide about the demographic history of humans and our closest relatives. we concentrate on nuclear genomic sequences that have been published in the past few years. in many cases, particularly in the arctic, the americas, and europe, adna has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day g ...	2016	27274045
neandertals revised.	the last decade has seen a significant growth of our knowledge of the neandertals, a population of pleistocene hunter-gatherers who lived in (western) eurasia between ∼400,000 and 40,000 y ago. starting from a source population deep in the middle pleistocene, the hundreds of thousands of years of relative separation between african and eurasian groups led to the emergence of different phenotypes in late pleistocene europe and africa. both recently obtained genetic evidence and archeological data ...	2016	27274044
the age of three middle palaeolithic sites: single-grain optically stimulated luminescence chronologies for pech de l'azé i, ii and iv in france.	optically stimulated luminescence (osl) measurements were made on individual, sand-sized grains of quartz from middle palaeolithic deposits at three sites (pech de l'azé i, ii and iv) located close to one another in the dordogne region of southwest france. we were able to calculate osl ages for 69 samples collected from these three sites. these ages reveal periods of occupation between about 180 and 50 thousand years ago. our single-grain osl chronologies largely support previous age estimates o ...	2016	27260176
adult neandertal clavicles from the el sidrón site (asturias, spain) in the context of homo pectoral girdle evolution.	we undertook a three-dimensional geometric morphometric (3dgm) analysis on 12 new neandertal clavicle specimens from the el sidrón site (spain), dated to 49,000 years ago. the 3dgm methods were applied in a comparative framework in order to improve our understanding of trait polarity in features related to homo pectoral girdle evolution, using other neandertals, homo sapiens, pan, atd6-50 (homo antecessor), and knm-wt 15000 (homo ergaster/erectus) in the reference collection. twenty-nine homolog ...	2016	27260174
the châtelperronian conundrum: blade and bladelet lithic technologies from quinçay, france.	the discovery of an almost complete neanderthal skeleton in a châtelperronian context at saint-césaire 35 years ago changed our perspective on the beginning of the upper paleolithic in western europe. since then, the châtelperronian has generally been considered a "transitional" industry rather than an upper or a middle paleolithic industry because of its chronological position, and the association of neanderthal remains with blades, bone tools and personal ornaments. several competing hypothese ...	2016	27260172
early neanderthal constructions deep in bruniquel cave in southwestern france.	very little is known about neanderthal cultures, particularly early ones. other than lithic implements and exceptional bone tools, very few artefacts have been preserved. while those that do remain include red and black pigments and burial sites, these indications of modernity are extremely sparse and few have been precisely dated, thus greatly limiting our knowledge of these predecessors of modern humans. here we report the dating of annular constructions made of broken stalagmites found deep i ...	2016	27251286
archaeology: neanderthals built underground.		2016	27251273
neonatal postcrania from mezmaiskaya, russia, and le moustier, france, and the development of neandertal body form.	neandertal and modern human adults differ in skeletal features of the cranium and postcranium, and it is clear that many of the cranial differences-although not all of them-are already present at the time of birth. we know less, however, about the developmental origins of the postcranial differences. here, we address this deficiency with morphometric analyses of the postcrania of the two most complete neandertal neonates-mezmaiskaya 1 (from russia) and le moustier 2 (from france)-and a recent hu ...	2016	27217565
variation in the nasal cavity of baboon hybrids with implications for late pleistocene hominins.	hybridization is increasingly proving to be an important force shaping human evolution. comparisons of both ancient and modern genomes have provided support for a complex evolutionary scenario over the past million years, with evidence for multiple incidents of gene exchange. however, to date, genetic evidence is still limited in its ability to pinpoint the precise time and place of ancient admixture. for that we must rely on evidence of admixture from the skeleton. the research presented here b ...	2016	27178465
a genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years.	the study of human evolution has been revolutionized by inferences from ancient dna analyses. key to these studies is the reliable estimation of the age of ancient specimens. high-resolution age estimates can often be obtained using radiocarbon dating, and, while precise and powerful, this method has some biases, making it of interest to directly use genetic data to infer a date for samples that have been sequenced. here, we report a genetic method that uses the recombination clock. the idea is ...	2016	27140627
the genetic history of ice age europe.	modern humans arrived in europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. here we analyse genome-wide data from 51 eurasians from ~45,000-7,000 years ago. over this time, the proportion of neanderthal dna decreased from 3-6% to around 2%, consistent with natural selection against neanderthal variants in modern humans. whereas there is no evidence of the earliest modern humans in europe contributing to the genetic composit ...	2016	27135931
[not available].	medicine owes many to hippocrate, but pneumology traces its origin back to antiquity, from mesopotamia to ancient rome. regarding prehistory: if viscera of this period have not been kept, some bones were. since neanderthals, it is then possible to study osteoarticular pathologies (often chronic arthrosis). but no evidence of tuberculosis was found (all thoracic kyphosis are not tuberculosis). tuberculosis probably appears during the neolithic age, because of high concentration of population. in ...	2016	27120938
neandertal versus modern human dietary responses to climatic fluctuations.	the neandertal lineage developed successfully throughout western eurasia and effectively survived the harsh and severely changing environments of the alternating glacial/interglacial cycles from the middle of the pleistocene until marine isotope stage 3. yet, towards the end of this stage, at the time of deteriorating climatic conditions that eventually led to the last glacial maximum, and soon after modern humans entered western eurasia, the neandertals disappeared. western eurasia was by then ...	2016	27119336
direct u-series analysis of the lezetxiki humerus reveals a middle pleistocene age for human remains in the basque country (northern iberia).	in 1964, a human humerus was found in a sedimentary deposit in lezetxiki cave (basque country, northern iberia). the first studies on the stratigraphy, associated mammal faunal remains and lithic implements placed the deposits containing the humerus into the riss glacial stage. direct chronometric evidence has so far been missing, and the previous chronostratigraphic framework and faunal dating gave inconsistent results. here we report laser ablation u-series analyses on the humerus yielding a m ...	2016	27086059
ecological niche of neanderthals from spy cave revealed by nitrogen isotopes of individual amino acids in collagen.	this study provides a refined view on the diet and ecological niche of neanderthals. the traditional view is that neanderthals obtained most of their dietary protein from terrestrial animals, especially from large herbivores that roamed the open landscapes. evidence based on the conventional carbon and nitrogen isotopic composition of bulk collagen has supported this view, although recent findings based on plant remains in the tooth calculus, microwear analyses, and small game and marine animal ...	2016	27086057
a dental perspective on the taxonomic affinity of the balanica mandible (bh-1).	the middle pleistocene represents a period of critical importance in human evolution, marked by encephalisation and dental reduction, and increasing diversification of temporally and spatially distributed hominin lineages in africa, asia and europe. new specimens, especially from areas less well represented in the fossil record, can inform the debate on morphological changes to the skeleton and teeth and the phylogenetic course of human evolution during this period. the mandible from the cave of ...	2016	27086056
what do cranial bones of lb1 tell us about homo floresiensis?	cranial vault thickness (cvt) of liang bua 1, the specimen that is proposed to be the holotype of homo floresiensis, has not yet been described in detail and compared with samples of fossil hominins, anatomically modern humans or microcephalic skulls. in addition, a complete description from a forensic and pathological point of view has not yet been carried out. it is important to evaluate scientifically if features related to cvt bring new information concerning the possible pathological status ...	2016	27086053
neanderthal genomics suggests a pleistocene time frame for the first epidemiologic transition.	high quality altai neanderthal and denisovan genomes are revealing which regions of archaic hominin dna have persisted in the modern human genome. a number of these regions are associated with response to infection and immunity, with a suggestion that derived neanderthal alleles found in modern europeans and east asians may be associated with autoimmunity. as such neanderthal genomes are an independent line of evidence of which infectious diseases neanderthals were genetically adapted to. sympat ...	2016	27063929
the divergence of neandertal and modern human y chromosomes.	sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. here, we analyze ∼120 kb of exome-captured y-chromosome dna from a neandertal individual from el sidrón, spain. we investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the neandertal lineage as an outgroup to modern human y chromosomes-including a00, the highly divergent basal haplogroup. we estimate that the time to the m ...	2016	27058445
joint estimation of contamination, error and demography for nuclear dna from ancient humans.	when sequencing an ancient dna sample from a hominin fossil, dna from present-day humans involved in excavation and extraction will be sequenced along with the endogenous material. this type of contamination is problematic for downstream analyses as it will introduce a bias towards the population of the contaminating individual(s). quantifying the extent of contamination is a crucial step as it allows researchers to account for possible biases that may arise in downstream genetic analyses. here, ...	2016	27049965
why are there no persisting hybrids of humans with denisovans, neanderthals, or anyone else?		2016	27044111
the genetic cost of neanderthal introgression.	approximately 2-4% of genetic material in human populations outside africa is derived from neanderthals who interbred with anatomically modern humans. recent studies have shown that this neanderthal dna is depleted around functional genomic regions; this has been suggested to be a consequence of harmful epistatic interactions between human and neanderthal alleles. however, using published estimates of neanderthal inbreeding and the distribution of mutational fitness effects, we infer that neande ...	2016	27038113
the combined landscape of denisovan and neanderthal ancestry in present-day humans.	some present-day humans derive up to ∼5% [1] of their ancestry from archaic denisovans, an even larger proportion than the ∼2% from neanderthals [2]. we developed methods that can disambiguate the locations of segments of denisovan and neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual oceanians with high denisovan ancestry [3]. in oceanians, the average size of denisovan fragments is larger than n ...	2016	27032491
identification of a new hominin bone from denisova cave, siberia using collagen fingerprinting and mitochondrial dna analysis.	dna sequencing has revolutionised our understanding of archaic humans during the middle and upper palaeolithic. unfortunately, while many palaeolithic sites contain large numbers of bones, the majority of these lack the diagnostic features necessary for traditional morphological identification. as a result the recovery of pleistocene-age human remains is extremely rare. to circumvent this problem we have applied a method of collagen fingerprinting to more than 2000 fragmented bones from the site ...	2016	27020421
the out of africa hypothesis and the ancestry of recent humans: cherchez la femme (et l'homme).	the out of africa hypothesis (ooah) has been a mainstay in the discussion of human evolution since its presentation in the 1980's. however, recent advances in palaeontology and molecular genetics have made it possible to examine the hypothesis in a manner that was inconceivable at the time of its proposal. the palaeontological progress relates to early homo finds in the caucasus, denisova finds in the altai mountains and neanderthal finds in a wide range of localities from the altai mountains, t ...	2016	26995655
human evolution. five matings for moderns, neandertals.		2016	26989228
excavating neandertal and denisovan dna from the genomes of melanesian individuals.	although neandertal sequences that persist in the genomes of modern humans have been identified in eurasians, comparable studies in people whose ancestors hybridized with both neandertals and denisovans are lacking. we developed an approach to identify dna inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown island melanesian genomes. in aggregate, we recovered 1.34 gigabases and 3 ...	2016	26989198
comparative perspective on antemortem tooth loss in neandertals.	neandertal specimens with severe antemortem (before death) tooth loss (amtl) are sometimes interpreted as evidence for human-like behaviors in neandertals, such as conspecific care or cooking, although it is uncertain whether amtl frequencies in neandertals are similar to those in modern humans and exceed those in non-human primates. this study characterizes amtl (all tooth types) in neandertals relative to recent human hunter-gatherers and several non-human primate taxa using binomial-normal re ...	2016	26989018
brain, calvarium, cladistics: a new approach to an old question, who are modern humans and neandertals?	the evolutionary history of the genus homo is the focus of major research efforts in palaeoanthropology. however, the use of palaeoneurology to infer phylogenies of our genus is rare. here we use cladistics to test the importance of the brain in differentiating and defining neandertals and modern humans. the analysis is based on morphological data from the calvarium and endocast of pleistocene fossils and results in a single most parsimonious cladogram. we demonstrate that the joint use of endoc ...	2016	26989014
oldest ancient-human dna details dawn of neanderthals.		2016	26983523
a reassessment of the presumed torrener bärenhöhle's paleolithic human tooth.		2016	26976744
nuclear dna sequences from the middle pleistocene sima de los huesos hominins.	a unique assemblage of 28 hominin individuals, found in sima de los huesos in the sierra de atapuerca in spain, has recently been dated to approximately 430,000 years ago. an interesting question is how these middle pleistocene hominins were related to those who lived in the late pleistocene epoch, in particular to neanderthals in western eurasia and to denisovans, a sister group of neanderthals so far known only from southern siberia. while the sima de los huesos hominins share some derived mor ...	2016	26976447
neandertals' large lower thorax may represent adaptation to high protein diet.	humans are limited in their capacity to convert protein into energy. we present a hypothesis that a "bell" shaped thorax and a wide pelvis evolved in neandertals, at least in part, as an adaptation to a high protein diet. a high protein diet created a need to house an enlarged liver and urinary system in a wider lower trunk. to test the hypothesis, we applied a model developed to identify points of nutritional stress. a ratio of obligatory dietary fat to total animal fat and protein sourced calo ...	2016	26973080
the uromodulin gene locus shows evidence of pathogen adaptation through human evolution.	common variants in the umod gene encoding uromodulin, associated with risk of hypertension and ckd in the general population, increase umod expression and urinary excretion of uromodulin, causing salt-sensitive hypertension and renal lesions. to determine the effect of selective pressure on variant frequency, we investigated the allelic frequency of the lead umod variant rs4293393 in 156 human populations, in eight ancient human genomes, and in primate genomes. the t allele of rs4293393, associa ...	2016	26966016
genomic signatures of selective pressures and introgression from archaic hominins at human innate immunity genes.	human genes governing innate immunity provide a valuable tool for the study of the selective pressure imposed by microorganisms on host genomes. a comprehensive, genome-wide study of how selective constraints and adaptations have driven the evolution of innate immunity genes is missing. using full-genome sequence variation from the 1000 genomes project, we first show that innate immunity genes have globally evolved under stronger purifying selection than the remainder of protein-coding genes. we ...	2016	26748513
the evolution of language and thought.	language primarily evolved as a vocal medium that transmits the attributes of human culture and the necessities of daily communication. human language has a long, complex evolutionary history. language also serves as an instrument of thought since it has become evident that in the course of this process neural circuits that initially evolved to regulate motor control, motor responses to external events, and ultimately talking were recycled to serve tasks such as working memory, cognitive flexibi ...	2016	26963222
what constitutes homo sapiens? morphology versus received wisdom.	although linnaeus coined homo sapiens in 1735, it was blumenbach forty years later who provided the first morphological definition of the species. since humans were not then allowed to be ante-diluvian, his effort applied to the genus, as well. after the feldhofer grotto neanderthal disproved this creationist notion, and human-fossil hunting became legitimate, new specimens were allocated either to sapiens or new species within homo, or even to new species within new genera. yet as these taxonom ...	2016	26963221
evolutionary genetics: haunted by the past--modern consequences of neanderthal dna.		2016	26948814
ancient hybridization and genomic stabilization in a swordtail fish.	a rapidly increasing body of work is revealing that the genomes of distinct species often exhibit hybrid ancestry, presumably due to postspeciation hybridization between closely related species. despite the growing number of documented cases, we still know relatively little about how genomes evolve and stabilize following hybridization, and to what extent hybridization is functionally relevant. here, we examine the case of xiphophorus nezahualcoyotl, a teleost fish whose genome exhibits signific ...	2016	26937625
selection and use of manganese dioxide by neanderthals.	several mousterian sites in france have yielded large numbers of small black blocs. the usual interpretation is that these 'manganese oxides' were collected for their colouring properties and used in body decoration, potentially for symbolic expression. neanderthals habitually used fire and if they needed black material for decoration, soot and charcoal were readily available, whereas obtaining manganese oxides would have incurred considerably higher costs. compositional analyses lead us to infe ...	2016	26922901
erratum for the report "ancient ethiopian genome reveals extensive eurasian admixture in eastern africa" (previously titled "ancient ethiopian genome reveals extensive eurasian admixture throughout the african continent") by m. gallego llorente, e. r. jones, a. eriksson, v. siska, k. w. arthur, j. w. arthur, m. c. curtis, j. t. stock, m. coltorti, p. pieruccini, s. stretton, f. brock, t. higham, y. park, m. hofreiter, d. g. bradley, j. bhak, r. pinhasi, a. manica.	in the report “ancient ethiopian genome reveals extensive eurasian admixture in eastern africa,” the results were affected by a bioinformatics error. a script necessary to convert the input produced by samtools v0.1.19 to be compatible with plink was not run when merging the ancient genome, mota, with the contemporary populations snp panel, leading to homozygote positions to the human reference genome being dropped as missing data (the analysis of admixture with neandertals and denisovans was no ...	2016	26912899
the phenotypic legacy of admixture between modern humans and neandertals.	many modern human genomes retain dna inherited from interbreeding with archaic hominins, such as neandertals, yet the influence of this admixture on human traits is largely unknown. we analyzed the contribution of common neandertal variants to over 1000 electronic health record (ehr)-derived phenotypes in ~28,000 adults of european ancestry. we discovered and replicated associations of neandertal alleles with neurological, psychiatric, immunological, and dermatological phenotypes. neandertal all ...	2016	26912863
human evolution. neandertal genes linked to modern diseases.		2016	26912836
the evolutionary history of genes involved in spoken and written language: beyond foxp2.	humans possess a communication system based on spoken and written language. other animals can learn vocalization by imitation, but this is not equivalent to human language. many genes were described to be implicated in language impairment (li) and developmental dyslexia (dd), but their evolutionary history has not been thoroughly analyzed. herein we analyzed the evolution of ten genes involved in dd and li. results show that the evolutionary history of li genes for mammals and aves was comparabl ...	2016	26912479
epigenetics: it's getting old. past meets future in paleoepigenetics.	recent years have witnessed the rise of ancient dna (adna) technology, allowing comparative genomics to be carried out at unprecedented time resolution. while it is relatively straightforward to use adna to identify recent genomic changes, it is much less clear how to utilize it to study changes in epigenetic regulation. here we review recent works demonstrating that highly degraded adna still contains sufficient information to allow reconstruction of epigenetic signals, including dna methylatio ...	2016	26898827
model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in central african pygmies.	comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-africans and now extinct hominids such as neanderthals and denisovans. one implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in eurasia. within africa, fossil evidence suggests that anatomically modern humans (am ...	2016	26888264
ancient gene flow from early modern humans into eastern neanderthals.	it has been shown that neanderthals contributed genetically to modern humans outside africa 47,000-65,000 years ago. here we analyse the genomes of a neanderthal and a denisovan from the altai mountains in siberia together with the sequences of chromosome 21 of two neanderthals from spain and croatia. we find that a population that diverged early from other modern humans in africa contributed genetically to the ancestors of neanderthals from the altai mountains roughly 100,000 years ago. by cont ...	2016	26886800
tlrs of our fathers.	two new studies published in the american journal of human genetics (dannemann et al., 2016; deschamps et al., 2016) show that introgression of innate immune genes from neandertals and denisovans contributed to the modern genome of european and asian, but not african, populations, and this might partly explain differences in susceptibility to immune-mediated diseases.	2016	26885854
reconstructing the plinian and co-ignimbrite sources of large volcanic eruptions: a novel approach for the campanian ignimbrite.	the 39 ka campanian ignimbrite (ci) super-eruption was the largest volcanic eruption of the past 200 ka in europe. tephra deposits indicate two distinct plume forming phases, plinian and co-ignimbrite, characteristic of many caldera-forming eruptions. previous numerical studies have characterized the eruption as a single-phase event, potentially leading to inaccurate assessment of eruption dynamics. to reconstruct the volume, intensity, and duration of the tephra dispersal, we applied a computat ...	2016	26883449
a burden of rare variants associated with extremes of gene expression in human peripheral blood.	in order to evaluate whether rare regulatory variants in the vicinity of promoters are likely to impact gene expression, we conducted a novel burden test for enrichment of rare variants at the extremes of expression. after sequencing 2-kb promoter regions of 472 genes in 410 healthy adults, we performed a quadratic regression of rare variant count on bins of peripheral blood transcript abundance from microarrays, summing over ranks of all genes. after adjusting for common eqtls and the major axe ...	2016	26849112
an ecocultural model predicts neanderthal extinction through competition with modern humans.	archaeologists argue that the replacement of neanderthals by modern humans was driven by interspecific competition due to a difference in culture level. to assess the cogency of this argument, we construct and analyze an interspecific cultural competition model based on the lotka-volterra model, which is widely used in ecology, but which incorporates the culture level of a species as a variable interacting with population size. we investigate the conditions under which a difference in culture le ...	2016	26831111
mapping the genomic architecture of adaptive traits with interspecific introgressive origin: a coalescent-based approach.	recent studies of eukaryotes including human and neandertal, mice, and butterflies have highlighted the major role that interspecific introgression has played in adaptive trait evolution. a common question arises in each case: what is the genomic architecture of the introgressed traits? one common approach that can be used to address this question is association mapping, which looks for genotypic markers that have significant statistical association with a trait. it is well understood that sampl ...	2016	26819241
genes with monoallelic expression contribute disproportionately to genetic diversity in humans.	an unexpectedly large number of human autosomal genes are subject to monoallelic expression (mae). our analysis of 4,227 such genes uncovers surprisingly high genetic variation across human populations. this increased diversity is unlikely to reflect relaxed purifying selection. remarkably, mae genes exhibit an elevated recombination rate and an increased density of hypermutable sequence contexts. however, these factors do not fully account for the increased diversity. we find that the elevated ...	2016	26808112
inner ear morphology of the cioclovina early modern european calvaria from romania.	the morphology of the human bony labyrinth is thought to preserve a strong phylogenetic signal and to be minimally, if at all, affected by postnatal processes. the form of the semicircular canals is considered a derived feature of neanderthals and different from the modern human anatomy. among other hominins, european middle pleistocene humans have been found to be most similar to neanderthals. early modern humans have been proposed to show a pattern that is distinct, but most similar to that of ...	2016	26806095
analysis of ancient dna in microbial ecology.	the development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as neandertals and denisovans. moreover, it has also yielded novel insights into the evolution of ancient pathogens. the ana ...	2016	26791510
fossil hominin radii from the sima de los huesos middle pleistocene site (sierra de atapuerca, spain).	complete radii in the fossil record preceding recent humans and neandertals are very scarce. here we introduce the radial remains recovered from the sima de los huesos (sh) site in the sierra de atapuerca between 1976 and 2011 and which have been dated in excess of 430 ky (thousands of years) ago. the sample comprises 89 specimens, 49 of which are attributed to adults representing a minimum of seven individuals. all elements are described anatomically and metrically, and compared with other foss ...	2016	26767960
the bony labyrinth of the middle pleistocene sima de los huesos hominins (sierra de atapuerca, spain).	we performed 3d virtual reconstructions based on ct scans to study the bony labyrinth morphology in 14 individuals from the large middle pleistocene hominin sample from the site of the sima de los huesos (sh) in the sierra de atapuerca in northern spain. the atapuerca (sh) hominins represent early members of the neandertal clade and provide an opportunity to compare the data with the later in time neandertals, as well as pleistocene and recent humans more broadly. the atapuerca (sh) hominins do ...	2016	26767955
postnatal craniofacial ontogeny in neandertals and modern humans.	neandertals and humans are closely related but differ noticeably in adult morphology. previous work has been equivocal as to the contribution of postnatal growth and development to these differences. due to disparate preservation, most analyses focus on specific anatomies, reconstructed fossils, or limited sample sizes. the objective of this research is to highlight the importance of postnatal growth in expressing neandertal-human distinctions in the craniofacial skeleton, using a large and unre ...	2016	26748764
introgression of neandertal- and denisovan-like haplotypes contributes to adaptive variation in human toll-like receptors.	pathogens and the diseases they cause have been among the most important selective forces experienced by humans during their evolutionary history. although adaptive alleles generally arise by mutation, introgression can also be a valuable source of beneficial alleles. archaic humans, who lived in europe and western asia for more than 200,000 years, were probably well adapted to this environment and its local pathogens. it is therefore conceivable that modern humans entering europe and western as ...	2016	26748514
climate-mediated shifts in neandertal subsistence behaviors at pech de l'azé iv and roc de marsal (dordogne valley, france).	neandertals disappeared from europe just after 40,000 years ago. some hypotheses ascribe this to numerous population crashes associated with glacial cycles in the late pleistocene. the goal of this paper is to test the hypothesis that glacial periods stressed neandertal populations. if cold climates stressed neandertals, their subsistence behaviors may have changed-requiring intensified use of prey through more extensive nutrient extraction from faunal carcasses. to test this, an analysis of nea ...	2016	27343769
one pedigree we all may have come from - did adam and eve have the chromosome 2 fusion?	in contrast to great apes, who have 48 chromosomes, modern humans and likely neandertals and denisovans have and had, respectively, 46 chromosomes. the reduction in chromosome number was caused by the head-to-head fusion of two ancestral chromosomes to form human chromosome 2 (hsa2) and may have contributed to the reproductive barrier with great apes.	2016	27708712
denisovans, melanesians, europeans, and neandertals: the confusion of dna assumptions and the biological species concept.	a number of recent articles have appeared on the denisova fossil remains and attempts to produce dna sequences from them. one of these recently appeared in science by vernot et al. (science 352:235-239, 2016). we would like to advance an alternative interpretation of the data presented. one concerns the problem of contamination/degradation of the determined dna sequenced. just as the publication of the first neandertal sequence included an interpretation that argued that neandertals had not cont ...	2016	27517578
hominin interbreeding and the evolution of human variation.	mitochondrial eve confirms the "out of africa" theory, but the evidence also supports interbreeding between homo sapiens and other hominins: neanderthals, denisovans, and homo heidelbergensis. this article explains how interbreeding between early h. sapiens and archaic hominins occurred. the availability of edible insects in east asia aided the spread of the unaggressive, highly cooperative neanderthals, who interbred with h. sapiens in asia, resulting in a higher admixture of neanderthal dna in ...	2016	27429943
the endocranial anatomy of maba 1.	maba 1, a partial cranium from guandong province (china) tentatively dated between 300 and 130 ka, has been suggested to display a mosaic of archaic and derived features, including facial affinities with neandertals. this study aims to evaluate whether maba 1 shows a derived endocranial phenotype, or if it displays a plesiomorphic braincase morphology.	2016	26972814
virtual ancestor reconstruction: revealing the ancestor of modern humans and neandertals.	the timing and geographic origin of the common ancestor of modern humans and neandertals remain controversial. a poor pleistocene hominin fossil record and the evolutionary complexities introduced by dispersals and regionalisation of lineages have fuelled taxonomic uncertainty, while new ancient genomic data have raised completely new questions. here, we use maximum likelihood and 3d geometric morphometric methods to predict possible morphologies of the last common ancestor of modern humans and ...	2016	26852813
trinucleotide's quadruplet symmetries and natural symmetry law of dna creation ensuing chargaff's second parity rule.	for almost 50 years the conclusive explanation of chargaff's second parity rule (cspr), the equality of frequencies of nucleotides a=t and c=g or the equality of direct and reverse complement trinucleotides in the same dna strand, has not been determined yet. here, we relate cspr to the interstrand mirror symmetry in 20 symbolic quadruplets of trinucleotides (direct, reverse complement, complement, and reverse) mapped to double-stranded genome. the symmetries of q-box corresponding to quadruplet ...	2016	26524490
antimicrobial functions of lactoferrin promote genetic conflicts in ancient primates and modern humans.	lactoferrin is a multifunctional mammalian immunity protein that limits microbial growth through sequestration of nutrient iron. additionally, lactoferrin possesses cationic protein domains that directly bind and inhibit diverse microbes. the implications for these dual functions on lactoferrin evolution and genetic conflicts with microbes remain unclear. here we show that lactoferrin has been subject to recurrent episodes of positive selection during primate divergence predominately at antimicr ...	2016	27203426