@article {pmid31412053,
year = {2019},
author = {Trinkaus, E and Samsel, M and Villotte, S},
title = {External auditory exostoses among western Eurasian late Middle and Late Pleistocene humans.},
journal = {PloS one},
volume = {14},
number = {8},
pages = {e0220464},
doi = {10.1371/journal.pone.0220464},
pmid = {31412053},
issn = {1932-6203},
abstract = {External auditory exostoses (EAE) have been noted among the Neandertals and a few other Pleistocene humans, but until recently they have been discussed primary as minor pathological lesions with possible auditory consequences. An assessment of available western Eurasian late Middle and Late Pleistocene human temporal bones with sufficiently preserved auditory canals (n = 77) provides modest levels of EAE among late Middle Pleistocene archaic humans (≈20%) and early modern humans (Middle Paleolithic: ≈25%; Early/Mid Upper Paleolithic: 20.8%; Late Upper Paleolithic: 9.5%). The Neandertals, however, exhibit an exceptionally high level of EAE (56.5%; 47.8% if two anomalous cases are considered normal). The levels of EAE for the early modern humans are well within recent human ranges of variation, frequencies which are low for equatorial inland and high latitude samples but occasionally higher elsewhere. The Early/Mid Upper Paleolithic frequency is nonetheless high for a high latitude sample under interpleniglacial conditions. Given the strong etiological and environmental associations of EAE development with exposure to cold water and/or damp wind chill, the high frequency of EAE among the Neandertals implies frequent aquatic resource exploitation, more frequent than the archeological and stable isotopic evidence for Middle Paleolithic/Neandertal littoral and freshwater resource foraging implies. As such, the Neandertal data parallel a similar pattern evident in eastern Eurasian archaic humans. Yet, factors in addition to cold water/wind exposure may well have contributed to their high EAE frequencies.},
}

@article {pmid31409814,
year = {2019},
author = {Zwyns, N and Paine, CH and Tsedendorj, B and Talamo, S and Fitzsimmons, KE and Gantumur, A and Guunii, L and Davakhuu, O and Flas, D and Dogandžić, T and Doerschner, N and Welker, F and Gillam, JC and Noyer, JB and Bakhtiary, RS and Allshouse, AF and Smith, KN and Khatsenovich, AM and Rybin, EP and Byambaa, G and Hublin, JJ},
title = {The Northern Route for Human dispersal in Central and Northeast Asia: New evidence from the site of Tolbor-16, Mongolia.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {11759},
doi = {10.1038/s41598-019-47972-1},
pmid = {31409814},
issn = {2045-2322},
support = {17649//Villum Fonden (Villum Foundation)/ ; },
abstract = {The fossil record suggests that at least two major human dispersals occurred across the Eurasian steppe during the Late Pleistocene. Neanderthals and Modern Humans moved eastward into Central Asia, a region intermittently occupied by the enigmatic Denisovans. Genetic data indicates that the Denisovans interbred with Neanderthals near the Altai Mountains (South Siberia) but where and when they met H. sapiens is yet to be determined. Here we present archaeological evidence that document the timing and environmental context of a third long-distance population movement in Central Asia, during a temperate climatic event around 45,000 years ago. The early occurrence of the Initial Upper Palaeolithic, a techno-complex whose sudden appearance coincides with the first occurrence of H. sapiens in the Eurasian steppes, establishes an essential archaeological link between the Siberian Altai and Northwestern China . Such connection between regions provides empirical ground to discuss contacts between local and exogenous populations in Central and Northeast Asia during the Late Pleistocene.},
}

@article {pmid30814723,
year = {2019},
author = {Callaway, E},
title = {Siberia's ancient ghost clan starts to surrender its secrets.},
journal = {Nature},
volume = {566},
number = {7745},
pages = {444-446},
doi = {10.1038/d41586-019-00672-2},
pmid = {30814723},
issn = {1476-4687},
mesh = {Animals ; *Archaeology ; Caves ; China ; Collagen/analysis/genetics ; Female ; Finger Phalanges/metabolism ; Fossils ; History, Ancient ; Hominidae/*classification/*genetics ; Humans ; Jewelry/history ; Molar/metabolism ; Neanderthals/classification/genetics ; Phylogeny ; Siberia ; Skull/metabolism ; Tool Use Behavior ; },
}

Animals
*Archaeology
Caves
China
Collagen/analysis/genetics
Female
Finger Phalanges/metabolism
Fossils
History, Ancient
Hominidae/*classification/*genetics
Humans
Jewelry/history
Molar/metabolism
Neanderthals/classification/genetics
Phylogeny
Siberia
Skull/metabolism
Tool Use Behavior

@article {pmid29960127,
year = {2018},
author = {Lazaridis, I},
title = {The evolutionary history of human populations in Europe.},
journal = {Current opinion in genetics & development},
volume = {53},
number = {},
pages = {21-27},
doi = {10.1016/j.gde.2018.06.007},
pmid = {29960127},
issn = {1879-0380},
mesh = {Animals ; DNA, Ancient ; Europe ; European Continental Ancestry Group/*genetics ; *Genetics, Population ; Genome, Human/*genetics ; *Genomics ; Human Migration ; Humans ; Neanderthals/genetics ; },
abstract = {I review the evolutionary history of human populations in Europe with an emphasis on what has been learned in recent years through the study of ancient DNA. Human populations in Europe ∼430-39kya (archaic Europeans) included Neandertals and their ancestors, who were genetically differentiated from other archaic Eurasians (such as the Denisovans of Siberia), as well as modern humans. Modern humans arrived to Europe by ∼45kya, and are first genetically attested by ∼39kya when they were still mixing with Neandertals. The first Europeans who were recognizably genetically related to modern ones appeared in the genetic record shortly thereafter at ∼37kya. At ∼15kya a largely homogeneous set of hunter-gatherers became dominant in most of Europe, but with some admixture from Siberian hunter-gatherers in the eastern part of the continent. These hunter-gatherers were joined by migrants from the Near East beginning at ∼8-9kya: Anatolian farmers settled most of mainland Europe, and migrants from the Caucasus reached eastern Europe, forming steppe populations. After ∼5kya there was migration from the steppe into mainland Europe and vice versa. Present-day Europeans (ignoring the long-distance migrations of the modern era) are largely the product of this Bronze Age collision of steppe pastoralists with Neolithic farmers.},
}

Animals
DNA, Ancient
Europe
European Continental Ancestry Group/*genetics
*Genetics, Population
Genome, Human/*genetics
*Genomics
Human Migration
Humans
Neanderthals/genetics

@article {pmid31392716,
year = {2019},
author = {Garralda, MD and Maíllo-Fernández, JM and Higham, T and Neira, A and Bernaldo de Quirós, F},
title = {The Gravettian child mandible from El Castillo Cave (Puente Viesgo, Cantabria, Spain).},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.23906},
pmid = {31392716},
issn = {1096-8644},
support = {HAR2015-70652-P//Spanish Ministry of Research and Science/ ; HAR2012-35214//Spanish Ministry of Research and Science/ ; },
abstract = {OBJECTIVES: This article documents an incomplete child's mandible found in H. Obermaier's excavation campaign (in 1912) in El Castillo Cave, Spain. This fossil was assigned to what was then considered a phase of the "Aurignacian-delta".

MATERIALS AND METHODS: We exhaustively analyzed the original Obermaier documents, with particular attention to those corresponding to the year of the discovery. We extracted a bone sample to radiocarbon date the fossil directly. We also followed established methods to measure, describe and compare the mandible with other human remains.

RESULTS: The analysis of Obermaier's documents and new data derived from modern excavations, show that the mandible was discovered in an interior area of the cave. Direct radiocarbon dating yielded a result of 24,720 ± 210 BP and 29,300 - 28,300 cal BP, a date similar to those known for the Gravettian technocomplex both in the El Castillo site and across Europe. The jaw corresponded to a child aged 4-5 years, with modern morphology, but with a certain robustness, especially in the symphyseal region. Comparisons were made with several modern children (Granada, Spitalfields, and Black series) and with immature fossils (European Aurignacian and Gravettian). The few differences between the modern and the fossil children are related to the symphysis and mandibular corpus thickness and height, and to the symphyseal morphology and larger teeth dimensions. Paleoisotopic data for Castillo C correspond with a varied diet. Numerous cutmarks were identified in the midline internal symphyseal region.

DISCUSSION AND CONCLUSIONS: The results agree with those published for other fossils of similar age and chronology (e.g., the mandible of the Lagar Velho child) and show clear differences from the jaws of the young Neanderthals. The interpretation of the original data on the mandible discovery may indicate the destruction of a burial and the displacement, by percolation or by a den, at least of part of the skeleton. The perimortem manipulations in the child's mandible are the first described in the Gravettian world of Western Europe.},
}

@article {pmid31368158,
year = {2019},
author = {Lieberman, P},
title = {The antiquity and evolution of the neural bases of rhythmic activity.},
journal = {Annals of the New York Academy of Sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/nyas.14199},
pmid = {31368158},
issn = {1749-6632},
abstract = {The evolution of the anatomy and neural circuits that regulate the rhythm of speech can be traced back to the Devonian age, 400 million years ago. Epigenetic processes 100 million years later modified these circuits. Natural selection on similar genetic processes occurred during the evolution of archaic hominins and humans. The lungs and larynx-anatomy that produces the rhythmic fundamental frequency patterns of speech-have a deep evolutionary history. Neural circuits linking the cortex, basal ganglia, and other subcortical structures plan, sequence, and execute motor as well as cognitive acts. These neural circuits generate the rhythm of speech, singing, and chanting. The human form of the transcription factor FOXP2 increased synaptic connectivity and plasticity in basal ganglia circuits, enhancing motor control and cognitive and linguistic capabilities in humans as well as Neanderthals. The archeological record also suggests that Neanderthals passed spoken language. Homologous circuits existed in amphibians. In songbirds, the avian form of FOXP2 acted on similar neural circuits allowing birds to learn and produce new songs. Current studies point to natural selection on genetic events enhancing these and other neural circuits to yield fully human rhythmic speech, and motor, cognitive, and linguistic capabilities, rather than the saltation proposed by Noam Chomsky.},
}

@article {pmid31358183,
year = {2019},
author = {Aranguren, B and Grimaldi, S and Benvenuti, M and Capalbo, C and Cavanna, F and Cavulli, F and Ciani, F and Comencini, G and Giuliani, C and Grandinetti, G and Mariotti Lippi, M and Masini, F and Mazza, PPA and Pallecchi, P and Santaniello, F and Savorelli, A and Revedin, A},
title = {Poggetti Vecchi (Tuscany, Italy): A late Middle Pleistocene case of human-elephant interaction.},
journal = {Journal of human evolution},
volume = {133},
number = {},
pages = {32-60},
doi = {10.1016/j.jhevol.2019.05.013},
pmid = {31358183},
issn = {1095-8606},
abstract = {A paleosurface with a concentration of wooden-, bone-, and stone-tools interspersed among an accumulation of fossil bones, largely belonging to the straight-tusked elephant Palaeoloxodon antiquus, was found at the bottom of a pool, fed by hot springs, that was excavated at Poggetti Vecchi, near Grosseto (Tuscany, Italy). The site is radiometrically dated to the late Middle Pleistocene, around 171,000 years BP. Notable is the association of the artifacts with the elephant bones, and in particular the presence of digging sticks made from boxwood (Buxus sp.). Although stone tools show evidence of use mainly on animal tissues, indicating some form of interaction between hominins and animals, the precise use of the sticks is unclear. Here we discuss about the role played by the hominins at the site: paleobiological and taphonomic evidence indicates that the elephants died by a natural cause and were butchered soon after their death. The associated paleontological and archeological evidence from this site provides fresh insights into the behavior of early Neanderthals in Central Italy. The discovery of Poggetti Vecchi shows how opportunistically flexible Neanderthals were in response to environmental contingencies.},
}

@article {pmid31358180,
year = {2019},
author = {Davies, TW and Delezene, LK and Gunz, P and Hublin, JJ and Skinner, MM},
title = {Endostructural morphology in hominoid mandibular third premolars: Geometric morphometric analysis of dentine crown shape.},
journal = {Journal of human evolution},
volume = {133},
number = {},
pages = {198-213},
doi = {10.1016/j.jhevol.2019.06.004},
pmid = {31358180},
issn = {1095-8606},
abstract = {In apes, the mandibular third premolar (P3) is adapted for a role in honing the large upper canine. The role of honing was lost early in hominin evolution, releasing the tooth from this functional constraint and allowing it to respond to subsequent changes in masticatory demands. This led to substantial morphological changes, and as such the P3 has featured prominently in systematic analyses of the hominin clade. The application of microtomography has also demonstrated that examination of the enamel-dentine junction (EDJ) increases the taxonomic value of variations in crown morphology. Here we use geometric morphometric techniques to analyze the shape of the P3 EDJ in a broad sample of fossil hominins, modern humans, and extant apes (n = 111). We test the utility of P3 EDJ shape for distinguishing among hominoids, address the affinities of a number of hominin specimens of uncertain taxonomic attribution, and characterize the changes in P3 EDJ morphology across our sample, with particular reference to features relating to canine honing and premolar 'molarization'. We find that the morphology of the P3 EDJ is useful in taxonomic identification of individual specimens, with a classification accuracy of up to 88%. The P3 EDJ of canine-honing apes displays a tall protoconid, little metaconid development, and an asymmetrical crown shape. Plio-Pleistocene hominin taxa display derived masticatory adaptations at the EDJ, such as the molarized premolars of Australopithecus africanus and Paranthropus, which have well-developed marginal ridges, an enlarged talonid, and a large metaconid. Modern humans and Neanderthals display a tall dentine body and reduced metaconid development, a morphology shared with premolars from Mauer and the Cave of Hearths. Homo naledi displays a P3 EDJ morphology that is unique among our sample; it is quite unlike Middle Pleistocene and recent Homo samples and most closely resembles Australopithecus, Paranthropus and early Homo specimens.},
}

@article {pmid31358177,
year = {2019},
author = {Richard, M and Falguères, C and Valladas, H and Ghaleb, B and Pons-Branchu, E and Mercier, N and Richter, D and Conard, NJ},
title = {New electron spin resonance (ESR) ages from Geißenklösterle Cave: A chronological study of the Middle and early Upper Paleolithic layers.},
journal = {Journal of human evolution},
volume = {133},
number = {},
pages = {133-145},
doi = {10.1016/j.jhevol.2019.05.014},
pmid = {31358177},
issn = {1095-8606},
abstract = {Geißenklösterle Cave (Germany) is one of the most important Paleolithic sites in Europe, as it is characterized by human occupation during the Middle and early Upper Paleolithic. Aurignacian layers prior to 37-38 ka cal BP feature both musical and figurative art objects that are linked to the early arrival in Europe of Homo sapiens. Middle Paleolithic layers yielded lithic artifacts attributed to Homo neanderthalensis. Since human occupation at the site is attributed to both Neanderthals and modern humans, chronology is essential to clarify the issues of Neanderthal disappearance, modern human expansion in Europe, and the origin of the Aurignacian in Western Europe. Electron spin resonance (ESR) dating was performed on fossil tooth enamel collected from the Middle Paleolithic layers, which are beyond the radiocarbon dating range, and from the nearly sterile 'transitional' geological horizon (GH) 17 and the lower Aurignacian deposits, to cross-check ESR ages with previous radiocarbon, thermoluminescence and ESR age results. The Middle Paleolithic layers were dated between 94 ± 10 ka (GH 21) and 55 ± 6 ka (GH 18) by ESR on tooth enamel. Mean ages for GH 17, at 46 ± 3 ka, and for the lower Aurignacian layers, at 37 ± 3 ka, are in agreement with previous dating results, thus supporting the reliability of ESR chronology for the base of the sequence where dating comparisons are not possible. These results suggest that Neanderthals occupied the site from Marine Isotope Stage (MIS) 5 to the second half of MIS 3 and confirm the antiquity of early Aurignacian deposits. The presence of an almost sterile layer that separates Middle and Upper Paleolithic occupations could be related to the abandonment of the site by Neanderthals, possibly during Heinrich Stadial 5 (ca. 49-47 ka), thus before the arrival of H. sapiens in the area around 42 ka cal BP. These dates for the Middle Paleolithic of the Swabian Jura represent an important contribution to the prehistory of the region, where nearly all of the excavations were conducted decades ago and prior to the development of reliable radiometric dating beyond the range of radiocarbon.},
}

@article {pmid30012742,
year = {2018},
author = {Pettitt, P},
title = {Hominin evolutionary thanatology from the mortuary to funerary realm: the palaeoanthropological bridge between chemistry and culture.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {373},
number = {1754},
pages = {},
pmid = {30012742},
issn = {1471-2970},
mesh = {Animals ; Anthropology, Cultural ; *Archaeology ; Burial ; *Cultural Evolution ; *Funeral Rites ; Humans ; *Mortuary Practice ; Neanderthals/psychology ; *Thanatology ; },
abstract = {Palaeoanthropology, or more precisely Palaeolithic archaeology, offers the possibility of bridging the gap between mortuary activities that can be observed in the wider animal community and which relate to chemistry and emotion; to the often-elaborate systems of rationalization and symbolic contextualisation that are characteristic of recently observable societies. I draw on ethological studies to provide a core set of mortuary behaviours one might expect hominoids to inherit, and on anthropological observations to explore funerary activity represented in the Middle and Upper Palaeolithic, in order to examine how a distinctly human set of funerary behaviours arose from a more widespread set of mortuary behaviours. I suggest that the most profound innovation of the hominins was the incorporation of places into the commemoration of the dead, and propose a falsifiable mechanism for why this came about; and I suggest that the pattern of the earliest burials fits with modern hunter-gatherer belief systems about death, and how these vary by social complexity. Finally, I propose several research questions pertaining to the social context of funerary practices, suggesting how a hominin evolutionary thanatology may contribute not only to our understanding of human behavioural evolution, but to a wider thanatology of the animal kingdom.This article is part of the theme issue 'Evolutionary thanatology: impacts of the dead on the living in humans and other animals'.},
}

Animals
Anthropology, Cultural
*Archaeology
Burial
*Cultural Evolution
*Funeral Rites
Humans
*Mortuary Practice
Neanderthals/psychology
*Thanatology

@article {pmid31341308,
year = {2019},
author = {El-Showk, S},
title = {Neanderthal clues to brain evolution in humans.},
journal = {Nature},
volume = {571},
number = {7766},
pages = {S10-S11},
doi = {10.1038/d41586-019-02210-6},
pmid = {31341308},
issn = {1476-4687},
}

@article {pmid31336034,
year = {2019},
author = {Bräuer, G and Pitsios, T and Säring, D and von Harling, M and Jessen, F and Kroll, A and Groden, C},
title = {Virtual reconstruction and comparative analyses of the Middle Pleistocene Apidima 2 cranium (Greece).},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.24225},
pmid = {31336034},
issn = {1932-8494},
abstract = {The Apidima 2 fossil cranium from South Peloponnese is one of the most important hominin specimens from Southeast Europe. Nevertheless, there has been continuous controversy as to whether it represents a so-called Preneandertal/H. heidelbergensis such as e.g., the Petralona cranium from Northern Greece or a more derived Neandertal. Recent absolute dating evidence alone cannot clarify the issue because both classifications would be possible during the respective Middle Pleistocene time span. Since only limited data were available on the cranium there have been repeated claims for the need of a broader comparative study of the hominin. The present paper presents a CT-based virtual reconstruction including corrections of postmortem fractures and deformation as well as detailed metrical and morphological analyses of the specimen. Endocranial capacity could be estimated for the first time based on virtual reconstruction. Our multivariate analyses of metric data from the face and vault revealed close affinities to early and later Neandertals, especially showing the derived facial morphometrics. In addition, comparative analyses of Apidima 2 were done for many derived Neandertal features. Here again, a significant number of Neandertal features could be found in the Apidima cranium but no conditions common in Preneandertals. In agreement with a later Middle Pleistocene age Apidima is currently the earliest evidence of a hominin in Europe with such a derived Neandertal facial morphology. The place of Apidima in the complex process of Neandertal evolution as well as its taxonomic classification are discussed as well. This article is protected by copyright. All rights reserved.},
}

@article {pmid30606828,
year = {2019},
author = {Gibbons, A},
title = {Spotting evolution among us.},
journal = {Science (New York, N.Y.)},
volume = {363},
number = {6422},
pages = {21-23},
doi = {10.1126/science.363.6422.21},
pmid = {30606828},
issn = {1095-9203},
mesh = {Alleles ; Animals ; *Databases, Genetic ; *Evolution, Molecular ; *Genome, Human ; Genotype ; Humans ; Neanderthals/*genetics ; Selection, Genetic ; United Kingdom ; },
}

Alleles
Animals
*Databases, Genetic
*Evolution, Molecular
*Genome, Human
Genotype
Humans
Neanderthals/*genetics
Selection, Genetic
United Kingdom

@article {pmid31314755,
year = {2019},
author = {Pitarch Martí, A and d'Errico, F and Turq, A and Lebraud, E and Discamps, E and Gravina, B},
title = {Provenance, modification and use of manganese-rich rocks at Le Moustier (Dordogne, France).},
journal = {PloS one},
volume = {14},
number = {7},
pages = {e0218568},
doi = {10.1371/journal.pone.0218568},
pmid = {31314755},
issn = {1932-6203},
abstract = {The use of colouring materials by Neanderthals has attracted a great deal of attention in recent years. Here we present a taphonomic, technological, chemical-mineralogical and functional analysis of fifty-four manganese rich lumps recovered during past and on-going excavations at the lower rockshelter of Le Moustier (Dordogne, France). We compare compositional data for archaeological specimens with the same information for twelve potential geological sources. Morphometric analysis shows that material from Peyrony's excavations before the First World War provides a highly biased picture of the importance of these materials for Mousterian groups. These early excavations almost exclusively recovered large modified pieces, while Mn-rich lumps from the on-going excavations predominantly consist of small pieces, only half of which bear traces of modification. We estimate that at least 168 pieces were not recovered during early work at the site. Neanderthals developed a dedicated technology for processing Mn-rich fragments, which involved a variety of tools and motions. Processing techniques were adapted to the size and density of the raw material, and evidence exists for the successive or alternating use of different techniques. Morphological, textural and chemical differences between geological and archaeological samples suggest that Neanderthals did not collect Mn-rich lumps at the outcrops we sampled. The association and variability in Mn, Ni, As, Ba content, compared to that observed at the sampled outcrops, suggests that either the Le Moustier lumps come from a unique source with a broad variation in composition, associating Mn, Ni, As, Ba, or that they were collected at different sources, characterized either by Mn-Ni-As or Mn-Ba. In the latter case, changes in raw material composition across the stratigraphy support the idea that Neanderthal populations bearing different stone tool technologies collected Mn fragments from different outcrops. Our results favour a use of these materials for multiple utilitarian and symbolic purposes.},
}

@article {pmid31308224,
year = {2019},
author = {Bokelmann, L and Hajdinjak, M and Peyrégne, S and Brace, S and Essel, E and de Filippo, C and Glocke, I and Grote, S and Mafessoni, F and Nagel, S and Kelso, J and Prüfer, K and Vernot, B and Barnes, I and Pääbo, S and Meyer, M and Stringer, C},
title = {A genetic analysis of the Gibraltar Neanderthals.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1903984116},
pmid = {31308224},
issn = {1091-6490},
abstract = {The Forbes' Quarry and Devil's Tower partial crania from Gibraltar are among the first Neanderthal remains ever found. Here, we show that small amounts of ancient DNA are preserved in the petrous bones of the 2 individuals despite unfavorable climatic conditions. However, the endogenous Neanderthal DNA is present among an overwhelming excess of recent human DNA. Using improved DNA library construction methods that enrich for DNA fragments carrying deaminated cytosine residues, we were able to sequence 70 and 0.4 megabase pairs (Mbp) nuclear DNA of the Forbes' Quarry and Devil's Tower specimens, respectively, as well as large parts of the mitochondrial genome of the Forbes' Quarry individual. We confirm that the Forbes' Quarry individual was a female and the Devil's Tower individual a male. We also show that the Forbes' Quarry individual is genetically more similar to the ∼120,000-y-old Neanderthals from Scladina Cave in Belgium (Scladina I-4A) and Hohlenstein-Stadel Cave in Germany, as well as to a ∼60,000- to 70,000-y-old Neanderthal from Russia (Mezmaiskaya 1), than to a ∼49,000-y-old Neanderthal from El Sidrón (El Sidrón 1253) in northern Spain and other younger Neanderthals from Europe and western Asia. This suggests that the Forbes' Quarry fossil predates the latter Neanderthals. The preservation of archaic human DNA in the warm coastal climate of Gibraltar, close to the shores of Africa, raises hopes for the future recovery of archaic human DNA from regions in which climatic conditions are less than optimal for DNA preservation.},
}

@article {pmid31292546,
year = {2019},
author = {Harvati, K and Röding, C and Bosman, AM and Karakostis, FA and Grün, R and Stringer, C and Karkanas, P and Thompson, NC and Koutoulidis, V and Moulopoulos, LA and Gorgoulis, VG and Kouloukoussa, M},
title = {Apidima Cave fossils provide earliest evidence of Homo sapiens in Eurasia.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-019-1376-z},
pmid = {31292546},
issn = {1476-4687},
abstract = {Two fossilized human crania (Apidima 1 and Apidima 2) from Apidima Cave, southern Greece, were discovered in the late 1970s but have remained enigmatic owing to their incomplete nature, taphonomic distortion and lack of archaeological context and chronology. Here we virtually reconstruct both crania, provide detailed comparative descriptions and analyses, and date them using U-series radiometric methods. Apidima 2 dates to more than 170 thousand years ago and has a Neanderthal-like morphological pattern. By contrast, Apidima 1 dates to more than 210 thousand years ago and presents a mixture of modern human and primitive features. These results suggest that two late Middle Pleistocene human groups were present at this site-an early Homo sapiens population, followed by a Neanderthal population. Our findings support multiple dispersals of early modern humans out of Africa, and highlight the complex demographic processes that characterized Pleistocene human evolution and modern human presence in southeast Europe.},
}

@article {pmid29615820,
year = {2018},
author = {Otto, G},
title = {Human evolution: Archaic admixture with Denisovans.},
journal = {Nature reviews. Genetics},
volume = {19},
number = {5},
pages = {251},
pmid = {29615820},
issn = {1471-0064},
mesh = {Base Sequence ; Evolution, Molecular ; Humans ; Neanderthals/*genetics ; },
}

Base Sequence
Evolution, Molecular
Humans
Neanderthals/*genetics

@article {pmid31278514,
year = {2019},
author = {Brzozowska, MM and Havula, E and Allen, RB and Cox, MP},
title = {Genetics, adaptation to environmental changes and archaic admixture in the pathogenesis of diabetes mellitus in Indigenous Australians.},
journal = {Reviews in endocrine & metabolic disorders},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11154-019-09505-z},
pmid = {31278514},
issn = {1573-2606},
abstract = {Indigenous Australians are particularly affected by type 2 diabetes mellitus (T2D) due to both their genetic susceptibility and a range of environmental and lifestyle risk factors. Recent genetic studies link predisposition to some diseases, including T2D, to alleles acquired from archaic hominins, such as Neanderthals and Denisovans, which persist in the genomes of modern humans today. Indo-Pacific human populations, including Indigenous Australians, remain extremely underrepresented in genomic research with a paucity of data examining the impact of Denisovan or Neanderthal lineages on human phenotypes in Oceania. The few genetic studies undertaken emphasize the uniqueness and antiquity of Indigenous Australian genomes, with possibly the largest proportion of Denisovan ancestry of any population in the world. In this review, we focus on the potential contributions of ancient genes/pathways to modern human phenotypes, while also highlighting the evolutionary roles of genetic adaptation to dietary and environmental changes associated with an adopted Western lifestyle. We discuss the role of genetic and epigenetic factors in the pathogenesis of T2D in understudied Indigenous Australians, including the potential impact of archaic gene lineages on this disease. Finally, we propose that greater understanding of the underlying genetic predisposition may contribute to the clinical efficacy of diabetes management in Indigenous Australians. We suggest that improved identification of T2D risk variants in Oceania is needed. Such studies promise to clarify how genetic and phenotypic differences vary between populations and, crucially, provide novel targets for personalised medical therapies in currently marginalized groups.},
}

@article {pmid31265485,
year = {2016},
author = {Dannemann, M and Andrés, AM and Kelso, J},
title = {Erratum: Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors.},
journal = {American journal of human genetics},
volume = {98},
number = {2},
pages = {399},
doi = {10.1016/j.ajhg.2016.01.012},
pmid = {31265485},
issn = {1537-6605},
abstract = {[This corrects the article DOI: 10.1016/j.ajhg.2015.11.015.].},
}

@article {pmid31258332,
year = {2019},
author = {Williams, AC and Hill, LJ},
title = {Nicotinamide as Independent Variable for Intelligence, Fertility, and Health: Origin of Human Creative Explosions?.},
journal = {International journal of tryptophan research : IJTR},
volume = {12},
number = {},
pages = {1178646919855944},
doi = {10.1177/1178646919855944},
pmid = {31258332},
issn = {1178-6469},
abstract = {Meat and nicotinamide acquisition was a defining force during the 2-million-year evolution of the big brains necessary for, anatomically modern, Homo sapiens to survive. Our next move was down the food chain during the Mesolithic 'broad spectrum', then horticultural, followed by the Neolithic agricultural revolutions and progressively lower average 'doses' of nicotinamide. We speculate that a fertility crisis and population bottleneck around 40 000 years ago, at the time of the Last Glacial Maximum, was overcome by Homo (but not the Neanderthals) by concerted dietary change plus profertility genes and intense sexual selection culminating in behaviourally modern Homo sapiens. Increased reliance on the 'de novo' synthesis of nicotinamide from tryptophan conditioned the immune system to welcome symbionts, such as TB (that excrete nicotinamide), and to increase tolerance of the foetus and thereby fertility. The trade-offs during the warmer Holocene were physical and mental stunting and more infectious diseases and population booms and busts. Higher nicotinamide exposure could be responsible for recent demographic and epidemiological transitions to lower fertility and higher longevity, but with more degenerative and auto-immune disease.},
}

@article {pmid31242180,
year = {2019},
author = {Ekshtain, R and Malinsky-Buller, A and Greenbaum, N and Mitki, N and Stahlschmidt, MC and Shahack-Gross, R and Nir, N and Porat, N and Bar-Yosef Mayer, DE and Yeshurun, R and Been, E and Rak, Y and Agha, N and Brailovsky, L and Krakovsky, M and Spivak, P and Ullman, M and Vered, A and Barzilai, O and Hovers, E},
title = {Persistent Neanderthal occupation of the open-air site of 'Ein Qashish, Israel.},
journal = {PloS one},
volume = {14},
number = {6},
pages = {e0215668},
doi = {10.1371/journal.pone.0215668},
pmid = {31242180},
issn = {1932-6203},
abstract = {Over the last two decades, much of the recent efforts dedicated to the Levantine Middle Paleolithic has concentrated on the role of open-air sites in the settlement system in the region. Here focus on the site of 'Ein Qashish as a cases study. Located in present-day northern Israel, the area of this site is estimated to have been >1300 m2, of which ca. 670 were excavated. The site is located at the confluence of the Qishon stream with a small tributary running off the eastern flanks of the Mt. Carmel. At the area of this confluence, water channels and alluvial deposits created a dynamic depositional environment. Four Archaeological Units were identified in a 4.5-m thick stratigraphic sequence were dated by Optically Stimulated Luminescence (OSL) to between-71 and 54 ka, and probably shorter time span-~70-~60 ka. Here we present the diverse material culture remains from the site (lithics, including refitted sequences; modified limestone pieces; molluscs; faunal remains) against their changing paleogeographic backdrop. Skeletal evidence suggests that these remains were associated with Neanderthals. The large-scale repeated accumulation of late Middle Paleolithic remains in the same place on the landscape provides a unique opportunity to address questions of occupation duration and intensity in open-air sites. We find that each occupation was of ephemeral nature, yet presents a range of activities, suggesting that the locale has been used as a generalized residential site rather than specialized task-specific ones. This role of 'Ein Qashish did not change through time, suggesting that during the late Middle Paleolithic settlement system in this part of the southern Levant were stable.},
}

@article {pmid31237235,
year = {2019},
author = {Langley, SA and Miga, KH and Karpen, GH and Langley, CH},
title = {Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
doi = {10.7554/eLife.42989},
pmid = {31237235},
issn = {2050-084X},
support = {R01 GM117420//National Institute of General Medical Sciences/ ; R01 GM119011//National Institute of General Medical Sciences/ ; },
abstract = {Despite critical roles in chromosome segregation and disease, the repetitive structure and vast size of centromeres and their surrounding heterochromatic regions impede studies of genomic variation. Here we report the identification of large-scale haplotypes (cenhaps) in humans that span the centromere-proximal regions of all metacentric chromosomes, including the arrays of highly repeated α-satellites on which centromeres form. Cenhaps reveal deep diversity, including entire introgressed Neanderthal centromeres and equally ancient lineages among Africans. These centromere-spanning haplotypes contain variants, including large differences in α-satellite DNA content, which may influence the fidelity and bias of chromosome transmission. The discovery of cenhaps creates new opportunities to investigate their contribution to phenotypic variation, especially in meiosis and mitosis, as well as to more incisively model the unexpectedly rich evolution of these challenging genomic regions.},
}

@article {pmid31222847,
year = {2019},
author = {Ackermann, RR and Arnold, ML and Baiz, MD and Cahill, JA and Cortés-Ortiz, L and Evans, BJ and Grant, BR and Grant, PR and Hallgrimsson, B and Humphreys, RA and Jolly, CJ and Malukiewicz, J and Percival, CJ and Ritzman, TB and Roos, C and Roseman, CC and Schroeder, L and Smith, FH and Warren, KA and Wayne, RK and Zinner, D},
title = {Hybridization in human evolution: Insights from other organisms.},
journal = {Evolutionary anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/evan.21787},
pmid = {31222847},
issn = {1520-6505},
support = {//National Research Foundation of South Africa/ ; //DST/NRF Centre of Excellence in Palaeosciences (CoE-Pal)/ ; },
abstract = {During the late Pleistocene, isolated lineages of hominins exchanged genes thus influencing genomic variation in humans in both the past and present. However, the dynamics of this genetic exchange and associated phenotypic consequences through time remain poorly understood. Gene exchange across divergent lineages can result in myriad outcomes arising from these dynamics and the environmental conditions under which it occurs. Here we draw from our collective research across various organisms, illustrating some of the ways in which gene exchange can structure genomic/phenotypic diversity within/among species. We present a range of examples relevant to questions about the evolution of hominins. These examples are not meant to be exhaustive, but rather illustrative of the diverse evolutionary causes/consequences of hybridization, highlighting potential drivers of human evolution in the context of hybridization including: influences on adaptive evolution, climate change, developmental systems, sex-differences in behavior, Haldane's rule and the large X-effect, and transgressive phenotypic variation.},
}

@article {pmid30948532,
year = {2019},
author = {Gibbons, A},
title = {Moderns said to mate with late-surviving Denisovans.},
journal = {Science (New York, N.Y.)},
volume = {364},
number = {6435},
pages = {12-13},
doi = {10.1126/science.364.6435.12},
pmid = {30948532},
issn = {1095-9203},
mesh = {Animals ; *Biological Evolution ; *Extinction, Biological ; *Hominidae ; Neanderthals ; New Guinea ; },
}

Animals
*Biological Evolution
*Extinction, Biological
*Hominidae
Neanderthals
New Guinea

@article {pmid30809866,
year = {2019},
author = {Ioannidou, M and Falcucci, A and Röding, C and Kandel, AW},
title = {Eighth Annual Meeting of the European Society for the Study of Human Evolution.},
journal = {Evolutionary anthropology},
volume = {28},
number = {2},
pages = {52-54},
doi = {10.1002/evan.21770},
pmid = {30809866},
issn = {1520-6505},
mesh = {Animals ; Anthropology/*organization & administration ; *Biological Evolution ; Biology/*organization & administration ; Humans ; Models, Biological ; Neanderthals ; Portugal ; },
}

Animals
Anthropology/*organization & administration
*Biological Evolution
Biology/*organization & administration
Humans
Models, Biological
Neanderthals
Portugal

@article {pmid30169787,
year = {2018},
author = {Chiang, CWK and Mangul, S and Robles, C and Sankararaman, S},
title = {A Comprehensive Map of Genetic Variation in the World's Largest Ethnic Group-Han Chinese.},
journal = {Molecular biology and evolution},
volume = {35},
number = {11},
pages = {2736-2750},
doi = {10.1093/molbev/msy170},
pmid = {30169787},
issn = {1537-1719},
support = {R00 GM111744/GM/NIGMS NIH HHS/United States ; T32 NS048004/NS/NINDS NIH HHS/United States ; T32 HG002536/HG/NHGRI NIH HHS/United States ; R35 GM125055/GM/NIGMS NIH HHS/United States ; K25 HL080079/HL/NHLBI NIH HHS/United States ; U01 DA024417/DA/NIDA NIH HHS/United States ; R01 GM083198/GM/NIGMS NIH HHS/United States ; R01 ES021801/ES/NIEHS NIH HHS/United States ; R01 MH101782/MH/NIMH NIH HHS/United States ; R01 ES022282/ES/NIEHS NIH HHS/United States ; },
mesh = {Adaptation, Biological ; Animals ; Asian Continental Ancestry Group/*genetics ; *Biological Evolution ; Case-Control Studies ; China ; Depressive Disorder, Major/genetics ; Female ; Gene Frequency ; *Genetic Variation ; Humans ; Neanderthals/genetics ; Phylogeography ; Selection, Genetic ; },
abstract = {As are most non-European populations, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we present a catalog of 25,057,223 variants, including 548,401 novel variants that are seen at least 10 times in our data set. Individuals from this data set came from 24 out of 33 administrative divisions across China (including 19 provinces, 4 municipalities, and 1 autonomous region), thus allowing us to study population structure, genetic ancestry, and local adaptation in Han Chinese. We identified previously unrecognized population structure along the East-West axis of China, demonstrated a general pattern of isolation-by-distance among Han Chinese, and reported unique regional signals of admixture, such as European influences among the Northwestern provinces of China. Furthermore, we identified a number of highly differentiated, putatively adaptive, loci (e.g., MTHFR, ADH7, and FADS, among others) that may be driven by immune response, climate, and diet in the Han Chinese. Finally, we have made available allele frequency estimates stratified by administrative divisions across China in the Geography of Genetic Variant browser for the broader community. By leveraging the largest currently available genetic data set for Han Chinese, we have gained insights into the history and population structure of the world's largest ethnic group.},
}

Adaptation, Biological
Animals
Asian Continental Ancestry Group/*genetics
*Biological Evolution
Case-Control Studies
China
Depressive Disorder, Major/genetics
Female
Gene Frequency
*Genetic Variation
Humans
Neanderthals/genetics
Phylogeography
Selection, Genetic

@article {pmid31203846,
year = {2019},
author = {Fiorenza, L and Benazzi, S and Kullmer, O and Zampirolo, G and Mazurier, A and Zanolli, C and Macchiarelli, R},
title = {Dental macrowear and cortical bone distribution of the Neanderthal mandible from Regourdou (Dordogne, Southwestern France).},
journal = {Journal of human evolution},
volume = {132},
number = {},
pages = {174-188},
doi = {10.1016/j.jhevol.2019.05.005},
pmid = {31203846},
issn = {1095-8606},
abstract = {Tooth wear is an important feature for reconstructing diet, food processing and cultural habits of past human populations. In particular, occlusal wear facets can be extremely useful for detecting information about diet and non-masticatory behaviors. The aim of this study is to reconstruct the diet and cultural behavior of the Neanderthal specimen Regourdou 1 (Dordogne, Southern France) from the analysis of the macrowear pattern, using the occlusal fingerprint analysis method. In addition, we have also examined whether there is any association between the observed dental macrowear and mandibular bone distribution and root dentine thickness. The posterior dentition of Regourdou 1 is characterized by an asymmetric wear pattern, with the right side significantly more worn than the left. In contrast, the left lower P3 shows a more advanced wear than the right premolar, with unusual semicircular enamel wear facets. The results from occlusal fingerprint analysis of this unique pattern suggest tooth-tool uses for daily task activities. Moreover, the left buccal aspect of the mandibular cortical bone is thicker than its right counterpart, and the left P3 has a thicker radicular dentine layer than its antimere. These results show a certain degree of asymmetry in cortical bone topography and dentine tissue that could be associated with the observed dental macrowear pattern. The molar macrowear pattern also suggests that Regourdou 1 had a mixed diet typical of those populations living in temperate deciduous woodlands and Mediterranean habitats, including animal and plant foods. Although this study is limited to one Neanderthal individual, future analyses based on a larger sample may further assist us to better understand the existing relationship between mandibular architecture, occlusal wear and the masticatory apparatus in humans.},
}

@article {pmid31203843,
year = {2019},
author = {Galletta, L and Stephens, NB and Bardo, A and Kivell, TL and Marchi, D},
title = {Three-dimensional geometric morphometric analysis of the first metacarpal distal articular surface in humans, great apes and fossil hominins.},
journal = {Journal of human evolution},
volume = {132},
number = {},
pages = {119-136},
doi = {10.1016/j.jhevol.2019.04.008},
pmid = {31203843},
issn = {1095-8606},
abstract = {Understanding the manual abilities of fossil hominins has been a focus of palaeoanthropological research for decades. Of interest are the morphological characteristics of the thumb due to its fundamental role in manipulation, particularly that of the trapeziometacarpal joint. Considerably less attention has been given to the thumb metacarpophalangeal (MCP) joint, which plays a role in stabilizing the thumb during forceful grasps and precision pinching. In this study we use a three-dimensional geometric morphometric approach to quantify the shape of the first metacarpal head in extant hominids (Homo, Pan, Gorilla and Pongo) and six fossil hominin species (Homo neanderthalensis Tabun C1 and La Chappelle-aux-Saints, Homo naledi U.W. 101-1282, Australopithecus sediba MH2, Paranthropus robustus/early Homo SK84, Australopithecus africanus StW 418, Australopithecus afarensis A.L. 333w-39), with the aims of identifying shapes that may be correlated with human-like forceful opposition and determining if similar morphologies are present in fossil hominins. Results show that humans differ from extant great apes by having a distally flatter articular surface, larger epicondyle surface area, and a larger radial palmar condyle. We suggest that this suite of features is correlated with a lower range of motion at the MCP joint, which would enhance the thumbs ability to resist the elevated loads associated with the forceful precision grips typical of humans. Great ape genera are each differentiated by distinctive morphological features, each of which is consistently correlated with the predicted biomechanical demands of their particular locomotor and/or manipulatory habits. Neanderthals and U.W. 101-1282 fall within the modern human range of variation, StW 418, SK 84 and U.W. 88-119 fall in between humans and great apes, and A.L. 333w-39 falls within Pan variation. These results agree with those of traditional linear analyses while providing a more comprehensive quantitative basis from which to interpret the hand functional morphology of extinct hominins.},
}

@article {pmid31196864,
year = {2019},
author = {Haber, M and Jones, AL and Connell, BA and Asan, and Arciero, E and Yang, H and Thomas, MG and Xue, Y and Tyler-Smith, C},
title = {A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans out of Africa.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1534/genetics.119.302368},
pmid = {31196864},
issn = {1943-2631},
abstract = {Present-day humans outside Africa descend mainly from a single expansion out ∼50,000-70,000 years ago, but many details of this expansion remain unclear, including the history of the male-specific Y chromosome at this time. Here, we re-investigate a rare deep-rooting African Y-chromosomal lineage by sequencing the whole genomes of three Nigerian men described in 2003 as carrying haplogroup DE* Y-chromosomes, and analyzing them in the context of a calibrated worldwide Y-chromosomal phylogeny. We confirm that these three chromosomes do represent a deep-rooting DE lineage, branching close to the DE bifurcation, but place them on the D branch as an outgroup to all other known D chromosomes, and designate the new lineage D0. We consider three models for the expansion of Y lineages out of Africa ∼50,000-100,000 years ago, incorporating migration back to Africa where necessary to explain present-day Y-lineage distributions. Considering both the Y-chromosomal phylogenetic structure incorporating the D0 lineage, and published evidence for modern humans outside Africa, the most favored model involves an origin of the DE lineage within Africa with D0 and E remaining there, and migration out of the three lineages (C, D and FT) that now form the vast majority of non-African Y chromosomes. The exit took place 50,300-81,000 years ago (latest date for FT lineage expansion outside Africa - earliest date for the D/D0 lineage split inside Africa), and most likely 50,300-59,400 years ago (considering Neanderthal admixture). This work resolves a long-running debate about Y-chromosomal out-of-Africa/back-to-Africa migrations, and provides insights into the out-of-Africa expansion more generally.},
}

@article {pmid31186485,
year = {2019},
author = {Kuhlwilm, M and Boeckx, C},
title = {A catalog of single nucleotide changes distinguishing modern humans from archaic hominins.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {8463},
doi = {10.1038/s41598-019-44877-x},
pmid = {31186485},
issn = {2045-2322},
support = {KU 3467/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; LCF/BQ/PR19/11700002//"la Caixa" Foundation (Caixa Foundation)/ ; PIRG-GA-2009-256413//EC | EC Seventh Framework Programm | FP7 People: Marie-Curie Actions (FP7-PEOPLE - Specific Programme "People" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; JP17H06379//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 2017-SGR-341//Departament d'Innovació, Universitats i Empresa, Generalitat de Catalunya (Department of Innovation, Education and Enterprise, Government of Catalonia)/ ; FFI2016-78034-C2-1-P//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; },
abstract = {Throughout the past decade, studying ancient genomes has provided unique insights into human prehistory, and differences between modern humans and other branches like Neanderthals can enrich our understanding of the molecular basis of unique modern human traits. Modern human variation and the interactions between different hominin lineages are now well studied, making it reasonable to go beyond fixed genetic changes and explore changes that are observed at high frequency in present-day humans. Here, we identify 571 genes with non-synonymous changes at high frequency. We suggest that molecular mechanisms in cell division and networks affecting cellular features of neurons were prominently modified by these changes. Complex phenotypes in brain growth trajectory and cognitive traits are likely influenced by these networks and other non-coding changes presented here. We propose that at least some of these changes contributed to uniquely human traits, and should be prioritized for experimental validation.},
}

@article {pmid31185865,
year = {2019},
author = {Shultz, DR and Montrey, M and Shultz, TR},
title = {Comparing fitness and drift explanations of Neanderthal replacement.},
journal = {Proceedings. Biological sciences},
volume = {286},
number = {1904},
pages = {20190907},
doi = {10.1098/rspb.2019.0907},
pmid = {31185865},
issn = {1471-2954},
abstract = {There is a general consensus among archaeologists that replacement of Neanderthals by anatomically modern humans in Europe occurred around 40-35 ka. However, the causal mechanism for this replacement continues to be debated. Proposed models have featured either fitness advantages in favour of anatomically modern humans or invoked neutral drift under various preconditions. Searching for specific fitness advantages in the archaeological record has proven difficult, as these may be obscured, absent or subject to interpretation. To bridge this gap, we rigorously compare the system-level properties of fitness- and drift-based explanations of Neanderthal replacement. Our stochastic simulations and analytical predictions show that, although both fitness and drift can produce replacement, they present important differences in (i) required initial conditions, (ii) reliability, (iii) time to replacement, and (iv) path to replacement (population histories). These results present useful opportunities for comparison with archaeological and genetic data. We find greater agreement between the available empirical evidence and the system-level properties of replacement by differential fitness, rather than by neutral drift.},
}

@article {pmid31182208,
year = {2019},
author = {Demuro, M and Arnold, LJ and Aranburu, A and Sala, N and Arsuaga, JL},
title = {New bracketing luminescence ages constrain the Sima de los Huesos hominin fossils (Atapuerca, Spain) to MIS 12.},
journal = {Journal of human evolution},
volume = {131},
number = {},
pages = {76-95},
doi = {10.1016/j.jhevol.2018.12.003},
pmid = {31182208},
issn = {1095-8606},
abstract = {Recent chronological studies of the Sima de los Huesos (SH) hominin fossil site, Atapuerca, Spain, have established a close minimum age of at least 430 ka for sedimentary material immediately overlying the human remains. However, a firm maximum age limit still needs to be established for the SH fossils in order to better constrain the timing for the onset of Neandertal speciation. In the present study, we address this important chronological gap at SH by providing direct ages for the sediment deposits that host, and immediately underlie, the hominin fossils. Depositional ages were obtained using single-grain thermally-transferred optically stimulated luminescence (TT-OSL), a technique that has yielded reliable 'extended-range' luminescence chronologies at several independently dated Atapuerca sites. Four single-grain TT-OSL depositional ages of 453 ± 56 ka, 437 ± 38 ka, 457 ± 41 ka and 460 ± 39 ka were obtained for the red clay lithostratigraphic units (LU-5 and LU-6) found underlying and encasing the SH hominin bones. A Bayesian age-depth model was constructed using previously published chronologies, as well as the new single-grain TT-OSL ages for LU-5 and LU-6, in order to derive combined age estimates for individual lithostratigraphic units preserved at SH. The combined modeled ranges reveal that the hominin-bearing layer (LU-6) was deposited between 455 ± 17 ka and 440 ± 15 ka (mean lower and upper boundary 68.2% probability range ± 1σ uncertainty, respectively), with a mean age of 448 ± 15 ka. These new bracketing ages suggest that the hominin fossils at SH were most likely deposited within Marine Isotope Stage (MIS) 12, enabling more precise temporal constraint on the early evolution of the Neandertal lineage. The SH fossils represent the oldest reliably dated hominin remains displaying Neandertal features across Eurasia. These Neandertal features are first observed in the facial skeleton, including the mandible and teeth, as well as the temporomandibular joint, and appear consistently across the SH collection. Our chronological findings suggest that the appearance of these Neandertal traits may have been associated with the climatic demise of MIS 12 and the ecological changes that occurred in Iberia during this period. Other Middle Pleistocene hominin fossils from Europe dated to MIS 12-11, or later, show different morphological trends, with some lacking Neandertal specializations. The latest SH dating results enable improved temporal correlations with these contrasting hominin records from Europe, and suggest a complex picture for hominin evolution during the Middle Pleistocene.},
}

@article {pmid31182199,
year = {2019},
author = {Radović, P and Lindal, J and Mihailović, D and Roksandic, M},
title = {The first Neanderthal specimen from Serbia: Maxillary first molar from the Late Pleistocene of Pešturina Cave.},
journal = {Journal of human evolution},
volume = {131},
number = {},
pages = {139-151},
doi = {10.1016/j.jhevol.2019.03.018},
pmid = {31182199},
issn = {1095-8606},
abstract = {Neanderthals were the only human group in Europe throughout the Late Pleistocene until the arrival of modern humans, and while their presence has been confirmed in the surrounding regions, no Neanderthal fossils are known to date from the Central Balkans. Systematic excavations of Pešturina Cave (Serbia) resulted in the discovery of a permanent right M1 (Pes-3). The specimen was recovered from stratigraphic Layer 4b with an estimated age of 102.4 ± 3.2 ka, associated with Mousterian artifacts. The exceptional state of preservation and minimal wear of the molar enabled a detailed description and comparative analysis of the inner and outer dental structure, including non-metric dental traits and morphometric features of the crown, roots, and dental tissues. The results of this study strongly support the identification of Pes-3 as Neanderthal. Non-metric traits of the occlusal surface of the crown, enamel-dentine junction, and roots are consistent with Neanderthal morphology. The crown shows morphometric features typical for Neanderthal M1, such as a buccolingually skewed crown shape, internally compressed cusps, and a relatively large hypocone. The specimen also shows Neanderthal-like dental tissue proportions, characterized by relatively thin enamel and large coronal dentine and coronal pulp volumes. The discovery of the Pes-3 molar therefore confirms the presence of Neanderthals in the territory of Serbia and the Central Balkans at the end of Marine Isotope Stage (MIS) 5c.},
}

@article {pmid31164119,
year = {2019},
author = {Shebanits, K and Günther, T and Johansson, ACV and Maqbool, K and Feuk, L and Jakobsson, M and Larhammar, D},
title = {Copy number determination of the gene for the human pancreatic polypeptide receptor NPY4R using read depth analysis and droplet digital PCR.},
journal = {BMC biotechnology},
volume = {19},
number = {1},
pages = {31},
doi = {10.1186/s12896-019-0523-9},
pmid = {31164119},
issn = {1472-6750},
support = {K2013-55X-22189-01-2//Vetenskapsrådet/ ; FO2016-0217//Hjärnfonden/ ; },
abstract = {BACKGROUND: Copy number variation (CNV) plays an important role in human genetic diversity and has been associated with multiple complex disorders. Here we investigate a CNV on chromosome 10q11.22 that spans NPY4R, the gene for the appetite-regulating pancreatic polypeptide receptor Y4. This genomic region has been challenging to map due to multiple repeated elements and its precise organization has not yet been resolved. Previous studies using microarrays were interpreted to show that the most common copy number was 2 per genome.

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

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

@article {pmid31163991,
year = {2019},
author = {Santander, C and Montinaro, F and Capelli, C},
title = {Searching for archaic contribution in Africa.},
journal = {Annals of human biology},
volume = {},
number = {},
pages = {1-39},
doi = {10.1080/03014460.2019.1624823},
pmid = {31163991},
issn = {1464-5033},
abstract = {Context: Africa's role in the narrative of human evolution is indisputably emphasised in the emergence Homo sapiens. However, once humans disperse beyond Africa, the history of those who stayed remains vastly understudied lacking the proper attention it deserves as the birthplace of both modern and archaic humans. The sequencing of Neanderthal and Denisovan genomes has elucidated evidence of admixture between archaic and modern humans outside of Africa but has not aided efforts in answering whether archaic admixture happened within Africa. Objectives: We review here the state of research for archaic introgression in African populations and discuss recent insights into this topic. Methods: Gathering published sources and recently released preprints, this review reports on the different methods developed for detecting archaic introgression. Particularly we discuss how relevant these are when implemented on African populations and what findings these studies have shown so far. Results: Methods for detecting archaic introgression have been predominantly developed and implemented on non-African populations. Recent preprints present new methods considering African populations. While a number of studies using these methods suggest archaic introgression in Africa, without an African archaic genome to validate these results, such findings remain as putative archaic introgression. Conclusion: In light of the caveats with implementing current archaic introgression detection methods in Africa, we recommend future studies to concentrate on unravelling the complicated demographic history of Africa through means of ancient DNA where possible and through more focused efforts to sequence modern DNA from more representative populations across the African continent.},
}

@article {pmid31155285,
year = {2019},
author = {Silvert, M and Quintana-Murci, L and Rotival, M},
title = {Impact and Evolutionary Determinants of Neanderthal Introgression on Transcriptional and Post-Transcriptional Regulation.},
journal = {American journal of human genetics},
volume = {104},
number = {6},
pages = {1241-1250},
doi = {10.1016/j.ajhg.2019.04.016},
pmid = {31155285},
issn = {1537-6605},
abstract = {Archaic admixture is increasingly recognized as an important source of diversity in modern humans, and Neanderthal haplotypes cover 1%-3% of the genome of present-day Eurasians. Recent work has shown that archaic introgression has contributed to human phenotypic diversity, mostly through the regulation of gene expression. Yet the mechanisms through which archaic variants alter gene expression and the forces driving the introgression landscape at regulatory regions remain elusive. Here, we explored the impact of archaic introgression on transcriptional and post-transcriptional regulation. We focused on promoters and enhancers across 127 different tissues as well as on microRNA (miRNA)-mediated regulation. Although miRNAs themselves harbor few archaic variants, we found that some of these variants may have a strong impact on miRNA-mediated gene regulation. Enhancers were by far the regulatory elements most affected by archaic introgression: up to one-third of the tissues we tested presented significant enrichments. Specifically, we found strong enrichments of archaic variants in adipose-related tissues and primary T cells, even after accounting for various genomic and evolutionary confounders such as recombination rate and background selection. Interestingly, we identified signatures of adaptive introgression at enhancers of some key regulators of adipogenesis, raising the interesting hypothesis of a possible adaptation of early Eurasians to colder climates. Collectively, this study sheds new light on the mechanisms through which archaic admixture has impacted gene regulation in Eurasians and, more generally, increases our understanding of the contribution of Neanderthals to the regulation of acquired immunity and adipose homeostasis in modern humans.},
}

@article {pmid31141515,
year = {2019},
author = {Degioanni, A and Bonenfant, C and Cabut, S and Condemi, S},
title = {Living on the edge: Was demographic weakness the cause of Neanderthal demise?.},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0216742},
doi = {10.1371/journal.pone.0216742},
pmid = {31141515},
issn = {1932-6203},
abstract = {The causes of disappearance of the Neanderthals, the only human population living in Europe before the arrival of Homo sapiens, have been debated for decades by the scientific community. Different hypotheses have been advanced to explain this demise, such as cognitive, adaptive and cultural inferiority of Neanderthals. Here, we investigate the disappearance of Neanderthals by examining the extent of demographic changes needed over a period of 10,000 years (yrs) to lead to their extinction. In regard to such fossil populations, we inferred demographic parameters from present day and past hunter-gatherer populations, and from bio-anthropological rules. We used demographic modeling and simulations to identify the set of plausible demographic parameters of the Neanderthal population compatible with the observed dynamics, and to explore the circumstances under which they might have led to the disappearance of Neanderthals. A slight (<4%) but continuous decrease in the fertility rate of younger Neanderthal women could have had a significant impact on these dynamics, and could have precipitated their demise. Our results open the way to non-catastrophic events as plausible explanations for Neanderthal extinction.},
}

@article {pmid31136573,
year = {2019},
author = {Durvasula, A and Sankararaman, S},
title = {A statistical model for reference-free inference of archaic local ancestry.},
journal = {PLoS genetics},
volume = {15},
number = {5},
pages = {e1008175},
doi = {10.1371/journal.pgen.1008175},
pmid = {31136573},
issn = {1553-7404},
abstract = {Statistical analyses of genomic data from diverse human populations have demonstrated that archaic hominins, such as Neanderthals and Denisovans, interbred or admixed with the ancestors of present-day humans. Central to these analyses are methods for inferring archaic ancestry along the genomes of present-day individuals (archaic local ancestry). Methods for archaic local ancestry inference rely on the availability of reference genomes from the ancestral archaic populations for accurate inference. However, several instances of archaic admixture lack reference archaic genomes, making it difficult to characterize these events. We present a statistical method that combines diverse population genetic summary statistics to infer archaic local ancestry without access to an archaic reference genome. We validate the accuracy and robustness of our method in simulations. When applied to genomes of European individuals, our method recovers segments that are substantially enriched for Neanderthal ancestry, even though our method did not have access to any Neanderthal reference genomes.},
}

@article {pmid31114607,
year = {2019},
author = {Liu, C and Everall, I and Pantelis, C and Bousman, C},
title = {Interrogating the Evolutionary Paradox of Schizophrenia: A Novel Framework and Evidence Supporting Recent Negative Selection of Schizophrenia Risk Alleles.},
journal = {Frontiers in genetics},
volume = {10},
number = {},
pages = {389},
doi = {10.3389/fgene.2019.00389},
pmid = {31114607},
issn = {1664-8021},
abstract = {Schizophrenia is a psychiatric disorder with a worldwide prevalence of ∼1%. The high heritability and reduced fertility among schizophrenia patients have raised an evolutionary paradox: why has negative selection not eliminated schizophrenia associated alleles during evolution? To address this question, we examined evolutionary markers, known as modern-human-specific (MD) sites and archaic-human-specific sites, using existing genome-wide association study (GWAS) data from 34,241 individuals with schizophrenia and 45,604 healthy controls included in the Psychiatric Genomics Consortium (PGC). By testing the distribution of schizophrenia single nucleotide polymorphisms (SNPs) with risk and protective effects in the human-specific sites, we observed a negative selection of risk alleles for schizophrenia in modern humans relative to archaic humans (e.g., Neanderthal and Denisovans). Such findings indicate that risk alleles of schizophrenia have been gradually removed from the modern human genome due to negative selection pressure. This novel evidence contributes to our understanding of the genetic origins of schizophrenia.},
}

@article {pmid31113254,
year = {2019},
author = {Ham, E and Underdown, SJ and Houldcroft, CJ},
title = {The relative roles of maternal survival and inter-personal violence as selection pressures on the persistence of Neanderthal hypercoagulability alleles in modern Europeans.},
journal = {Annals of human biology},
volume = {},
number = {},
pages = {1-28},
doi = {10.1080/03014460.2019.1622038},
pmid = {31113254},
issn = {1464-5033},
abstract = {BACKGROUND: Simoni et al (2016) reported variation in the frequency of Neanderthal alleles found in modern humans and argued that they may have provided an evolutionary advantage. One such allele is SNP rs3917862, associated with hypercoagulability. rs3917862 can be deleterious but can also help prevent blood loss.

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

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

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

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

@article {pmid31106274,
year = {2019},
author = {Gómez-Robles, A},
title = {Dental evolutionary rates and its implications for the Neanderthal-modern human divergence.},
journal = {Science advances},
volume = {5},
number = {5},
pages = {eaaw1268},
doi = {10.1126/sciadv.aaw1268},
pmid = {31106274},
issn = {2375-2548},
abstract = {The origin of Neanderthal and modern human lineages is a matter of intense debate. DNA analyses have generally indicated that both lineages diverged during the middle period of the Middle Pleistocene, an inferred time that has strongly influenced interpretations of the hominin fossil record. This divergence time, however, is not compatible with the anatomical and genetic Neanderthal affinities observed in Middle Pleistocene hominins from Sima de los Huesos (Spain), which are dated to 430 thousand years (ka) ago. Drawing on quantitative analyses of dental evolutionary rates and Bayesian analyses of hominin phylogenetic relationships, I show that any divergence time between Neanderthals and modern humans younger than 800 ka ago would have entailed unexpectedly rapid dental evolution in early Neanderthals from Sima de los Huesos. These results support a pre-800 ka last common ancestor for Neanderthals and modern humans unless hitherto unexplained mechanisms sped up dental evolution in early Neanderthals.},
}

@article {pmid31095578,
year = {2019},
author = {Morales, JI and Cebrià, A and Burguet-Coca, A and Fernández-Marchena, JL and García-Argudo, G and Rodríguez-Hidalgo, A and Soto, M and Talamo, S and Tejero, JM and Vallverdú, J and Fullola, JM},
title = {The Middle-to-Upper Paleolithic transition occupations from Cova Foradada (Calafell, NE Iberia).},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0215832},
doi = {10.1371/journal.pone.0215832},
pmid = {31095578},
issn = {1932-6203},
abstract = {The Middle-to-Upper Paleolithic transition in Europe covers the last millennia of Neanderthal life together with the appearance and expansion of Modern Human populations. Culturally, it is defined by the Late Middle Paleolithic succession, and by Early Upper Paleolithic complexes like the Châtelperronian (southwestern Europe), the Protoaurignacian, and the Early Aurignacian. Up to now, the southern boundary for the transition has been established as being situated between France and Iberia, in the Cantabrian façade and Pyrenees. According to this, the central and southern territories of Iberia are claimed to have been the refuge of the last Neanderthals for some additional millennia after they were replaced by anatomically Modern Humans on the rest of the continent. In this paper, we present the Middle-to-Upper Paleolithic transition sequence from Cova Foradada (Tarragona), a cave on the Catalan Mediterranean coastline. Archaeological research has documented a stratigraphic sequence containing a succession of very short-term occupations pertaining to the Châtelperronian, Early Aurignacian, and Gravettian. Cova Foradada therefore represents the southernmost Châtelperronian-Early Aurignacian sequence ever documented in Europe, significantly enlarging the territorial distribution of both cultures and providing an important geographical and chronological reference for understanding Neanderthal disappearance and the complete expansion of anatomically Modern Humans.},
}

@article {pmid31068377,
year = {2019},
author = {Vangenot, C and Gagneux, P and de Groot, NG and Baumeyer, A and Mouterde, M and Crouau-Roy, B and Darlu, P and Sanchez-Mazas, A and Sabbagh, A and Poloni, ES},
title = {Humans and Chimpanzees Display Opposite Patterns of Diversity in arylamineN-acetyltranferase Genes.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1534/g3.119.400223},
pmid = {31068377},
issn = {2160-1836},
abstract = {Among the many genes involved in the metabolism of therapeutic drugs, human arylamine N-acetyltransferases (NATs) genes have been extensively studied, due to their medical importance both in pharmacogenetics and disease epidemiology. One member of this small gene family, NAT2, is established as the locus of the classic human acetylation polymorphism in drug metabolism. Current hypotheses hold that selective processes favoring haplotypes conferring lower NAT2 activity have been operating in modern humans' recent history as an adaptation to local chemical and dietary environments. To shed new light on such hypotheses, we investigated the genetic diversity of the three members of the NAT gene family in seven hominid species, including modern humans, Neanderthals and Denisovans. Little polymorphism sharing was found among hominids, yet all species displayed high NAT diversity, but distributed in an opposite fashion in chimpanzees and bonobos (Pan genus) compared to modern humans, with higher diversity in Pan species at NAT1 and lower at NAT2, while the reverse is observed in humans. This pattern was also reflected in the results returned by selective neutrality tests, which suggest, in agreement with the predicted functional impact of mutations detected in non-human primates, stronger directional selection, presumably purifying selection, at NAT1 in modern humans, and at NAT2 in chimpanzees. Overall, the results point to the evolution of divergent functions of these highly homologous genes in the different primate species, possibly related to their specific chemical/dietary environment (exposome) and we hypothesize that this is likely linked to the emergence of controlled fire use in the human lineage.},
}

@article {pmid31048924,
year = {2019},
author = {Rhodes, SE and Starkovich, BM and Conard, NJ},
title = {Did climate determine Late Pleistocene settlement dynamics in the Ach Valley, SW Germany?.},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0215172},
doi = {10.1371/journal.pone.0215172},
pmid = {31048924},
issn = {1932-6203},
abstract = {The loss of Neanderthal groups across Western and Central Europe during Oxygen Isotope Stage (OIS) 3 has held the attention of archaeologists for decades. The role that climatic change, genetic interbreeding, and interspecies competition played in the extinction of Neanderthal groups is still debated. Hohle Fels is one of several important Middle and Upper Paleolithic sites from the Ach Valley in southwestern Germany which documents the presence of Neanderthals and modern humans in the region. Chronological and stratigraphic records indicate that these two groups occupied the site with little to no overlap or interaction. This provides the opportunity to examine the behavioural variability of Swabian Neanderthal populations without the complication of cross-cultural influence. In this study we contribute a terrestrial paleoenvironmental record derived from the small mammal material from Hohle Fels Cave to the ever-growing archaeological record of this period. By reconstructing the climate and landscape of the Ach Valley during this time we can identify the effect that the OIS 3 environment had on the presence of Neanderthals in the region. Based on indicator taxa and the habitat weighing method, the small mammal record, which includes rodents, insectivores, and bats, from Hohle Fels shows that the earliest Neanderthal occupation took place on a landscape characterized by substantial woodland and forest, rivers and ponds, as well as moist meadows and grasslands. A gradual increase in cold tundra and arctic environments is clear towards the end of the Middle Paleolithic, extending to the end of the early Aurignacian which may correlate with the onset of the Heinrich 4 event (~42,000 kya). Our taphonomic analysis indicates the material was accumulated primarily by opportunistic predators such as the great grey owl, snowy owl, and European eagle owl, and therefore reflects the diversity of landscapes present around the site in the past. Importantly, at the time Neanderthals abandoned the Ach Valley we find no indication for dramatic climatic deterioration. Rather, we find evidence of a gradual cooling of the Swabian landscape which may have pushed Neanderthal groups out of the Ach Valley prior to the arrival of modern human Aurignacian groups.},
}

@article {pmid31034533,
year = {2019},
author = {Letsinger, AC and Granados, JZ and Little, SE and Lightfoot, JT},
title = {Alleles associated with physical activity levels are estimated to be older than anatomically modern humans.},
journal = {PloS one},
volume = {14},
number = {4},
pages = {e0216155},
doi = {10.1371/journal.pone.0216155},
pmid = {31034533},
issn = {1932-6203},
abstract = {The purpose of this study was to determine the estimated mutation age and conservation of single-nucleotide polymorphisms (SNPs) associated with physical activity (PA) in humans. All human SNPs found to be significantly associated with PA levels in the literature were cross-referenced with the National Heart, Lung, and Blood Institute's Grand Opportunity Exome Sequencing Project to find estimated African-American (AA) and European-American (EA) mutation age. As a secondary measure of mutation age, SNPs were searched for in Hawk's mutation age prediction database which utilizes linkage equilibrium. To determine conservation among hominids, all SNPs were searched in the University of California, Santa Cruz Genome Browser, which contains Neanderthal and chimpanzee reference genomes. Six of the 104 SNPs associated with PA regulation were exon-located missense variants found in IFNAR2, PPARGC1A, PML, CTBP2, IL5RA, and APOE genes. The remaining 98 SNPs were located in non-protein coding regions. Average AA and EA estimated mutation age of the exon-located SNPs were 478.4 ± 327.5 kya and 542.1 ± 369.4 kya, respectively. There were four selective sweeps (suggestive of strong positive selection) of SNPs in humans when compared to Neanderthal or chimpanzee genomes. Exon-located PA candidate SNPs are older than the hypothesized emergence of anatomically modern humans. However, 95% of PA associated SNPs are found in intron and intergenic location. Across all SNPs, there seems to be a high level of conservation of alleles between humans, Neanderthals, and chimpanzees. However, the presence of four selective sweeps suggests there were selection pressures or drift unique to Homo sapiens that influenced the development of mutations associated with PA regulation.},
}

@article {pmid31025315,
year = {2019},
author = {Bosman, AM and Harvati, K},
title = {A virtual assessment of the proposed suprainiac fossa on the early modern European calvaria from Cioclovina, Romania.},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.23844},
pmid = {31025315},
issn = {1096-8644},
support = {//German Research Foundation/ ; },
abstract = {OBJECTIVES: The calvaria from Cioclovina (Romania) has been argued to possess some traits commonly ascribed to individuals belonging to the Neanderthal lineage, including a suprainiac fossa. However, its supranuchal morphology has only been evaluated with a qualitative analysis of the ectocranial surface. We evaluate whether the morphology of the supranuchal area of this specimen is homologous to the Neanderthal condition.

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

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

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

@article {pmid31017917,
year = {2019},
author = {Leierer, L and Jambrina-Enríquez, M and Herrera-Herrera, AV and Connolly, R and Hernández, CM and Galván, B and Mallol, C},
title = {Insights into the timing, intensity and natural setting of Neanderthal occupation from the geoarchaeological study of combustion structures: A micromorphological and biomarker investigation of El Salt, unit Xb, Alcoy, Spain.},
journal = {PloS one},
volume = {14},
number = {4},
pages = {e0214955},
doi = {10.1371/journal.pone.0214955},
pmid = {31017917},
issn = {1932-6203},
abstract = {Middle Paleolithic lithic and faunal assemblages throughout Eurasia reflect short-term Neanderthal occupations, which suggest high group mobility. However, the timing of these short-term occupations, a key factor to assess group mobility and territorial range, remains unresolved. Anthropogenic combustion structures are prominent in the Middle Paleolithic record and conceal information on the timing and intensity and natural setting of their associated human occupations. This paper examines a concentration of eleven combustion structures from unit Xb of El Salt, a Middle Paleolithic site in Spain through a geoarchaeological approach, in search of temporal, human impact and paleoenvironmental indicators to assess the timing, intensity and natural setting of the associated human occupations. The study was conducted using micromorphology, lipid biomarker analysis and compound specific isotope analysis. Results show in situ hearths built on different diachronic topsoils rich in herbivore excrements and angiosperm plant residues with rare anthropogenic remains. These data are suggestive of low impact, short-term human occupations separated by relatively long periods of time, with possible indicators of seasonality. Results also show an absence of conifer biomarkers in the mentioned topsoils and presence of conifer charcoal among the fuel residues (ash), indicating that fire wood was brought to the site from elsewhere. A microscopic and molecular approach in the study of combustion structures allows us to narrow down the timescale of archaeological analysis and contributes valuable information towards an understanding of Neanderthal group mobility and settlement patterns.},
}

@article {pmid31014244,
year = {2019},
author = {Pfeifer, B and Kapan, DD},
title = {Estimates of introgression as a function of pairwise distances.},
journal = {BMC bioinformatics},
volume = {20},
number = {1},
pages = {207},
doi = {10.1186/s12859-019-2747-z},
pmid = {31014244},
issn = {1471-2105},
support = {1427772//Division of Biological Infrastructure/ ; },
mesh = {Databases, Genetic ; Gene Flow ; Genomics/*methods ; Hybridization, Genetic/*genetics ; *Models, Genetic ; Models, Statistical ; Polymorphism, Single Nucleotide ; Whole Genome Sequencing/*methods ; },
abstract = {BACKGROUND: Research over the last 10 years highlights the increasing importance of hybridization between species as a major force structuring the evolution of genomes and potentially providing raw material for adaptation by natural and/or sexual selection. Fueled by research in a few model systems where phenotypic hybrids are easily identified, research into hybridization and introgression (the flow of genes between species) has exploded with the advent of whole-genome sequencing and emerging methods to detect the signature of hybridization at the whole-genome or chromosome level. Amongst these are a general class of methods that utilize patterns of single-nucleotide polymorphisms (SNPs) across a tree as markers of hybridization. These methods have been applied to a variety of genomic systems ranging from butterflies to Neanderthals to detect introgression, however, when employed at a fine genomic scale these methods do not perform well to quantify introgression in small sample windows.

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

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

Databases, Genetic
Gene Flow
Genomics/*methods
Hybridization, Genetic/*genetics
*Models, Genetic
Models, Statistical
Polymorphism, Single Nucleotide
Whole Genome Sequencing/*methods

@article {pmid30981557,
year = {2019},
author = {Jacobs, GS and Hudjashov, G and Saag, L and Kusuma, P and Darusallam, CC and Lawson, DJ and Mondal, M and Pagani, L and Ricaut, FX and Stoneking, M and Metspalu, M and Sudoyo, H and Lansing, JS and Cox, MP},
title = {Multiple Deeply Divergent Denisovan Ancestries in Papuans.},
journal = {Cell},
volume = {177},
number = {4},
pages = {1010-1021.e32},
doi = {10.1016/j.cell.2019.02.035},
pmid = {30981557},
issn = {1097-4172},
abstract = {Genome sequences are known for two archaic hominins-Neanderthals and Denisovans-which interbred with anatomically modern humans as they dispersed out of Africa. We identified high-confidence archaic haplotypes in 161 new genomes spanning 14 island groups in Island Southeast Asia and New Guinea and found large stretches of DNA that are inconsistent with a single introgressing Denisovan origin. Instead, modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages that separated over 350 thousand years ago. Spatial and temporal structure among these lineages suggest that introgression from one of these Denisovan groups predominantly took place east of the Wallace line and continued until near the end of the Pleistocene. A third Denisovan lineage occurs in modern East Asians. This regional mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with multiple Denisovan groups that were geographically isolated from each other over deep evolutionary time.},
}

@article {pmid30975994,
year = {2019},
author = {Rotival, M and Quach, H and Quintana-Murci, L},
title = {Defining the genetic and evolutionary architecture of alternative splicing in response to infection.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {1671},
doi = {10.1038/s41467-019-09689-7},
pmid = {30975994},
issn = {2041-1723},
mesh = {African Continental Ancestry Group/genetics ; Alternative Splicing/*immunology ; Animals ; Biological Evolution ; European Continental Ancestry Group/genetics ; Genetic Variation/immunology ; Healthy Volunteers ; Humans ; Immunity/*genetics ; Infection/*immunology ; Male ; Neanderthals/genetics ; Polymorphism, Single Nucleotide ; Protein Isoforms/genetics/immunology ; Quantitative Trait Loci/immunology ; Selection, Genetic/*immunology ; Sequence Analysis, RNA ; Transcriptome/*immunology ; Whole Exome Sequencing ; },
abstract = {Host and environmental factors contribute to variation in human immune responses, yet the genetic and evolutionary drivers of alternative splicing in response to infection remain largely uncharacterised. Leveraging 970 RNA-sequencing profiles of resting and stimulated monocytes from 200 individuals of African- and European-descent, we show that immune activation elicits a marked remodelling of the isoform repertoire, while increasing the levels of erroneous splicing. We identify 1,464 loci associated with variation in isoform usage (sQTLs), 9% of them being stimulation-specific, which are enriched in disease-related loci. Furthermore, we detect a longstanding increased plasticity of immune gene splicing, and show that positive selection and Neanderthal introgression have both contributed to diversify the splicing landscape of human populations. Together, these findings suggest that differential isoform usage has been an important substrate of innovation in the long-term evolution of immune responses and a more recent vehicle of population local adaptation.},
}

African Continental Ancestry Group/genetics
Alternative Splicing/*immunology
Animals
Biological Evolution
European Continental Ancestry Group/genetics
Genetic Variation/immunology
Healthy Volunteers
Humans
Immunity/*genetics
Infection/*immunology
Male
Neanderthals/genetics
Polymorphism, Single Nucleotide
Protein Isoforms/genetics/immunology
Quantitative Trait Loci/immunology
Selection, Genetic/*immunology
Sequence Analysis, RNA
Transcriptome/*immunology
Whole Exome Sequencing

@article {pmid30943255,
year = {2019},
author = {Moncel, MH and Fernandes, P and Willmes, M and James, H and Grün, R},
title = {Rocks, teeth, and tools: New insights into early Neanderthal mobility strategies in South-Eastern France from lithic reconstructions and strontium isotope analysis.},
journal = {PloS one},
volume = {14},
number = {4},
pages = {e0214925},
doi = {10.1371/journal.pone.0214925},
pmid = {30943255},
issn = {1932-6203},
abstract = {Neanderthals had complex land use patterns, adapting to diversified landscapes and climates. Over the past decade, considerable progress has been made in reconstructing the chronology, land use and subsistence patterns, and occupation types of sites in the Rhône Valley, southeast France. In this study, Neanderthal mobility at the site of Payre is investigated by combining information from lithic procurement analysis ("chaîne evolutive" and "chaîne opératoire" concepts) and strontium isotope analysis of teeth (childhood foraging area), from two units (F and G). Both units date to the transition from Marine Isotope Stage (MIS) 8 to MIS 7, and show similar environmental conditions, but represent contrasting occupation durations. Level Gb (unit G) represents a long-term year-round use, in contrast to short-term seasonal use of the cave in level Fb (unit F). For both levels, lithic material and food were generally collected from a local to semi-local region. However, in level Gb, lithic materials were mainly collected from colluviums and food collected in the valley, whereas in level Fb, lithic procurement focused primarily on alluvial deposits and food was collected from higher elevation plateaus. These procurement or exchange patterns might be related to flint availability, knapping advantages of alluvial flint or occupation duration. The site of Payre is located in a flint rich circulation corridor and the movement of groups or exchanges between groups were organized along a north-south axis on the plateaus or towards the east following the river. The ridges were widely used as they are rich in flint, whereas the Rhône Valley is not an important source of lithic raw materials. Compared to other western European Middle Palaeolithic sites, these results indicate that procurement strategies have a moderate link with occupation types and duration, and with lithic technology. The Sr isotope ratios broadly match the proposed foraging areas, with the Rhône Valley being predominantly used in unit G and the ridges and limestone plateaus in unit F. While lithic reconstructions and childhood foraging are not directly related this suggests that the three analysed Neanderthals spend their childhood in the same general area and supports the idea of mobile Neanderthals in the Rhône Valley and neighbouring higher elevation plateaus. The combination of reconstructing lithic raw material sources, provisioning strategies, and strontium isotope analyses provides new details on how Neanderthals at Payre practised land use and mobility in the Early Middle Palaeolithic.},
}

@article {pmid30942856,
year = {2019},
author = {Harris, DN and Ruczinski, I and Yanek, LR and Becker, LC and Becker, DM and Guio, H and Cui, T and Chilton, FH and Mathias, RA and O'Connor, TD},
title = {Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World.},
journal = {Genome biology and evolution},
volume = {11},
number = {5},
pages = {1417-1430},
doi = {10.1093/gbe/evz071},
pmid = {30942856},
issn = {1759-6653},
abstract = {The metabolic conversion of dietary omega-3 and omega-6 18 carbon (18C) to long chain (>20 carbon) polyunsaturated fatty acids (LC-PUFAs) is vital for human life. The rate-limiting steps of this process are catalyzed by fatty acid desaturase (FADS) 1 and 2. Therefore, understanding the evolutionary history of the FADS genes is essential to our understanding of hominin evolution. The FADS genes have two haplogroups, ancestral and derived, with the derived haplogroup being associated with more efficient LC-PUFA biosynthesis than the ancestral haplogroup. In addition, there is a complex global distribution of these haplogroups that is suggestive of Neanderthal introgression. We confirm that Native American ancestry is nearly fixed for the ancestral haplogroup, and replicate a positive selection signal in Native Americans. This positive selection potentially continued after the founding of the Americas, although simulations suggest that the timing is dependent on the allele frequency of the ancestral Beringian population. We also find that the Neanderthal FADS haplotype is more closely related to the derived haplogroup and the Denisovan clusters closer to the ancestral haplogroup. Furthermore, the derived haplogroup has a time to the most recent common ancestor of 688,474 years before present. These results support an ancient polymorphism, as opposed to Neanderthal introgression, forming in the FADS region during the Pleistocene with possibly differential selection pressures on both haplogroups. The near fixation of the ancestral haplogroup in Native American ancestry calls for future studies to explore the potential health risk of associated low LC-PUFA levels in these populations.},
}

@article {pmid30904042,
year = {2019},
author = {Poza-Rey, EM and Gómez-Robles, A and Arsuaga, JL},
title = {Brain size and organization in the Middle Pleistocene hominins from Sima de los Huesos. Inferences from endocranial variation.},
journal = {Journal of human evolution},
volume = {129},
number = {},
pages = {67-90},
doi = {10.1016/j.jhevol.2019.01.006},
pmid = {30904042},
issn = {1095-8606},
abstract = {The Sima de los Huesos (SH) endocranial sample includes 16 complete or partial endocasts corresponding to European Middle Pleistocene hominins. Different anatomical and molecular studies have demonstrated that these hominins are phylogenetically related to Neanderthals, thus making them the earliest unquestionable representatives of the Neanderthal lineage. The description of endocranial variation in this population is fundamental to shedding light on the evolution of the Neanderthal brain. In this contribution, we analyze and describe endocranial variation in this sample, including aspects related to brain size (endocranial volume and encephalization) and brain organization (through qualitative descriptions and quantitative analyses). Our results indicate that the SH hominins show a transitional state between a primitive hominin endocranial configuration (which is found in Homo erectus and non-SH Middle Pleistocene Homo) and the derived configurations found in Neanderthals and modern humans, without a clear anticipation of classic Neanderthal endocranial traits. In comparison with other cranial and postcranial traits that show a fully Neanderthal or clear pre-Neanderthal condition in the SH collection, endocranial variation in these hominins is surprisingly primitive and shows no Neanderthal affinity. These results and the comparison with other cranial traits confirm that Neanderthals evolved in a mosaic fashion. Traits related to mastication (dental, facial and mandibular anatomy) led the Neanderthalization process, whereas neurocranial anatomy must have acquired a fully Neanderthal condition considerably later.},
}

@article {pmid30893326,
year = {2019},
author = {Di Maida, G and Mannino, MA and Krause-Kyora, B and Jensen, TZT and Talamo, S},
title = {Radiocarbon dating and isotope analysis on the purported Aurignacian skeletal remains from Fontana Nuova (Ragusa, Italy).},
journal = {PloS one},
volume = {14},
number = {3},
pages = {e0213173},
doi = {10.1371/journal.pone.0213173},
pmid = {30893326},
issn = {1932-6203},
abstract = {Proving voyaging at sea by Palaeolithic humans is a difficult archaeological task, even for short distances. In the Mediterranean, a commonly accepted sea crossing is that from the Italian Peninsula to Sicily by anatomically modern humans, purportedly of the Aurignacian culture. This claim, however, was only supported by the typological attribution to the Aurignacian of the lithic industries from the insular site of Fontana Nuova. AMS radiocarbon dating undertaken as part of our research shows that the faunal remains, previously considered Aurignacian, actually date to the Holocene. Absolute dating on dentinal collagen also attributes the human teeth from the site to the early Holocene, although we were unable to obtain ancient DNA to evaluate their ancestry. Ten radiocarbon dates on human and other taxa are comprised between 9910-9700 cal. BP and 8600-8480 cal. BP, indicating that Fontana Nuova was occupied by Mesolithic and not Aurignacian hunter-gatherers. Only a new study of the lithic assemblage could establish if the material from Fontana Nuova is a mixed collection that includes both late Upper Palaeolithic (Epigravettian) and Mesolithic artefacts, as can be suggested by taking into account both the results of our study and of the most recent reinterpretation of the lithics. Nevertheless, this research suggests that the notion that Aurignacian groups were present in Sicily should now be revised. Another outcome of our study is that we found that three specimens, attributed on grounds both of morphological and ZooMS identifications to Cervus elaphus, had δ13C values significantly higher than any available for such species in Europe.},
}

@article {pmid30889271,
year = {2019},
author = {Vyas, DN and Mulligan, CJ},
title = {Analyses of Neanderthal introgression suggest that Levantine and southern Arabian populations have a shared population history.},
journal = {American journal of physical anthropology},
volume = {169},
number = {2},
pages = {227-239},
doi = {10.1002/ajpa.23818},
pmid = {30889271},
issn = {1096-8644},
support = {BCS-1258965//National Science Foundation/ ; },
abstract = {OBJECTIVES: Modern humans are thought to have interbred with Neanderthals in the Near East soon after modern humans dispersed out of Africa. This introgression event likely took place in either the Levant or southern Arabia depending on the dispersal route out of Africa that was followed. In this study, we compare Neanderthal introgression in contemporary Levantine and southern Arabian populations to investigate Neanderthal introgression and to study Near Eastern population history.

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

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

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

@article {pmid30872714,
year = {2019},
author = {Wißing, C and Rougier, H and Baumann, C and Comeyne, A and Crevecoeur, I and Drucker, DG and Gaudzinski-Windheuser, S and Germonpré, M and Gómez-Olivencia, A and Krause, J and Matthies, T and Naito, YI and Posth, C and Semal, P and Street, M and Bocherens, H},
title = {Stable isotopes reveal patterns of diet and mobility in the last Neandertals and first modern humans in Europe.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {4433},
doi = {10.1038/s41598-019-41033-3},
pmid = {30872714},
issn = {2045-2322},
abstract = {Correlating cultural, technological and ecological aspects of both Upper Pleistocene modern humans (UPMHs) and Neandertals provides a useful approach for achieving robust predictions about what makes us human. Here we present ecological information for a period of special relevance in human evolution, the time of replacement of Neandertals by modern humans during the Late Pleistocene in Europe. Using the stable isotopic approach, we shed light on aspects of diet and mobility of the late Neandertals and UPMHs from the cave sites of the Troisième caverne of Goyet and Spy in Belgium. We demonstrate that their diet was essentially similar, relying on the same terrestrial herbivores, whereas mobility strategies indicate considerable differences between Neandertal groups, as well as in comparison to UPMHs. Our results indicate that UPMHs exploited their environment to a greater extent than Neandertals and support the hypothesis that UPMHs had a substantial impact not only on the population dynamics of large mammals but also on the whole structure of the ecosystem since their initial arrival in Europe.},
}

@article {pmid30861048,
year = {2019},
author = {Nowaczewska, W and Binkowski, M and Kubicka, AM and Piontek, J and Balzeau, A},
title = {Neandertal-like traits visible in the internal structure of non-supranuchal fossae of some recent Homo sapiens: The problem of their identification in hominins and phylogenetic implications.},
journal = {PloS one},
volume = {14},
number = {3},
pages = {e0213687},
doi = {10.1371/journal.pone.0213687},
pmid = {30861048},
issn = {1932-6203},
abstract = {Although recently the internal structure of the non-supranuchal fossa of Homo sapiens has been described and compared to that observed in the Neandertal suprainiac fossa, until now it has not been examined in any modern human children. In this study, the internal structure of this fossa in the occipital bones of three children (two aged 3‒4 years and one aged 5 years ± 16 months) and one adult individual representing recent Homo sapiens from Australia was analysed and compared to that of the Neandertal suprainiac fossa. In order to analyse the internal composition of the fossae of the examined specimens, initially, high-resolution micro-CT datasets were obtained for their occipital bones; next, 3D topographic maps of the variation in thickness of structural layers of the occipital bones were made and 2D virtual sections in the median region of these fossae were prepared. In the fossa of one immature individual, the thinning of the diploic layer characteristic of a Neandertal suprainiac fossa was firmly diagnosed. The other Neandertal-like trait, concerning the lack of substantial thinning of the external table of the bone in the region of the fossa, was established in two individuals (one child and one adult) due to the observation of an irregular pattern of the thickness of this table in the other specimens, suggesting the presence of an inflammatory process. Our study presents, for the first time, Neandertal-like traits (but not the whole set of features that justifies the autapomorphic status of the Neandertal supraniac fossa) in the internal structure of non-supranuchal fossae of some recent Homo sapiens. We discuss the phylogenetic implications of the results of our analysis and stress the reasons that use of the 3D topographic mapping method is important for the correct diagnosis of Neandertal traits of the internal structure of occipital fossae.},
}

@article {pmid30854435,
year = {2019},
author = {Morin, E and Meier, J and El Guennouni, K and Moigne, AM and Lebreton, L and Rusch, L and Valensi, P and Conolly, J and Cochard, D},
title = {New evidence of broader diets for archaic Homo populations in the northwestern Mediterranean.},
journal = {Science advances},
volume = {5},
number = {3},
pages = {eaav9106},
doi = {10.1126/sciadv.aav9106},
pmid = {30854435},
issn = {2375-2548},
abstract = {Investigating diet breadth is critical for understanding how archaic Homo populations, including Neanderthals, competed for seasonally scarce resources. The current consensus in Western Europe is that ungulates formed the bulk of the human diet during the Lower and Middle Paleolithic, while small fast prey taxa were virtually ignored. Here, we present a multisite taphonomic study of leporid assemblages from Southern France that supports frequent exploitation of small fast game during marine isotope stages 11 to 3. Along with recent evidence from Iberia, our results indicate that the consumption of small fast game was more common prior to the Upper Paleolithic than previously thought and that archaic hominins from the northwestern Mediterranean had broader diets than those from adjacent regions. Although likely of secondary importance relative to ungulates, the frequent exploitation of leporids documented here implies that human diet breadths were substantially more variable within Europe than assumed by current evolutionary models.},
}

@article {pmid30854422,
year = {2019},
author = {Rogers, J and Raveendran, M and Harris, RA and Mailund, T and Leppälä, K and Athanasiadis, G and Schierup, MH and Cheng, J and Munch, K and Walker, JA and Konkel, MK and Jordan, V and Steely, CJ and Beckstrom, TO and Bergey, C and Burrell, A and Schrempf, D and Noll, A and Kothe, M and Kopp, GH and Liu, Y and Murali, S and Billis, K and Martin, FJ and Muffato, M and Cox, L and Else, J and Disotell, T and Muzny, DM and Phillips-Conroy, J and Aken, B and Eichler, EE and Marques-Bonet, T and Kosiol, C and Batzer, MA and Hahn, MW and Tung, J and Zinner, D and Roos, C and Jolly, CJ and Gibbs, RA and Worley, KC and , },
title = {The comparative genomics and complex population history of Papio baboons.},
journal = {Science advances},
volume = {5},
number = {1},
pages = {eaau6947},
doi = {10.1126/sciadv.aau6947},
pmid = {30854422},
issn = {2375-2548},
support = {S10 RR026605/RR/NCRR NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; R01 GM059290/GM/NIGMS NIH HHS/United States ; P51 OD011133/OD/NIH HHS/United States ; //Wellcome Trust/United Kingdom ; R01 HG002385/HG/NHGRI NIH HHS/United States ; U01 MH106874/MH/NIMH NIH HHS/United States ; },
abstract = {Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus Papio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of Papio baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.},
}

@article {pmid30836076,
year = {2019},
author = {Gunz, P and Tilot, AK and Wittfeld, K and Teumer, A and Shapland, CY and van Erp, TGM and Dannemann, M and Vernot, B and Neubauer, S and Guadalupe, T and Fernández, G and Brunner, HG and Enard, W and Fallon, J and Hosten, N and Völker, U and Profico, A and Di Vincenzo, F and Manzi, G and Kelso, J and St Pourcain, B and Hublin, JJ and Franke, B and Pääbo, S and Macciardi, F and Grabe, HJ and Fisher, SE},
title = {Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity.},
journal = {Current biology : CB},
volume = {29},
number = {5},
pages = {895},
doi = {10.1016/j.cub.2019.02.008},
pmid = {30836076},
issn = {1879-0445},
support = {U24 RR021992/RR/NCRR NIH HHS/United States ; U24 RR025736/RR/NCRR NIH HHS/United States ; U54 EB020403/EB/NIBIB NIH HHS/United States ; },
}

@article {pmid30825980,
year = {2019},
author = {Pablos, A and Gómez-Olivencia, A and Maureille, B and Holliday, TW and Madelaine, S and Trinkaus, E and Couture-Veschambre, C},
title = {Neandertal foot remains from Regourdou 1 (Montignac-sur-Vézère, Dordogne, France).},
journal = {Journal of human evolution},
volume = {128},
number = {},
pages = {17-44},
doi = {10.1016/j.jhevol.2018.11.003},
pmid = {30825980},
issn = {1095-8606},
abstract = {Regourdou is a well-known Middle Paleolithic site which has yielded the fossil remains of a minimum of two Neandertal individuals. The first individual (Regourdou 1) is represented by a partial skeleton while the second one is represented by a calcaneus. The foot remains of Regourdou 1 have been used in a number of comparative studies, but to date a full description and comparison of all the foot remains from the Regourdou 1 Neandertal, coming from the old excavations and from the recent reanalysis of the faunal remains, does not exist. Here, we describe and comparatively assess the Regourdou 1 tarsals, metatarsals and phalanges. They display traits observed in other Neandertal feet, which are different from some traits of the Sima de los Huesos (Atapuerca) hominins and of Middle Paleolithic, Upper Paleolithic and recent modern humans. These Neandertal features are: a rectangular talar trochlea with a large lateral malleolar facet, a broad talar head, a broad calcaneus with a projecting sustentaculum tali, a wide and wedged navicular with a projecting medial tubercle, large and wide bases of the lateral metatarsals, and mediolaterally expanded and robust phalanges that also show hallux valgus in a strongly built hallux.},
}

@article {pmid30804177,
year = {2019},
author = {Haeusler, M and Trinkaus, E and Fornai, C and Müller, J and Bonneau, N and Boeni, T and Frater, N},
title = {Morphology, pathology, and the vertebral posture of the La Chapelle-aux-Saints Neandertal.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {11},
pages = {4923-4927},
doi = {10.1073/pnas.1820745116},
pmid = {30804177},
issn = {1091-6490},
mesh = {Aged ; Animals ; Humans ; Male ; Neanderthals/*anatomy & histology/*physiology ; Osteoarthritis/pathology/physiopathology ; Pelvis/anatomy & histology ; *Posture ; Spinal Curvatures/physiopathology ; Spine/*pathology/physiopathology ; },
abstract = {Although the early postural reconstructions of the Neandertals as incompletely erect were rejected half a century ago, recent studies of Neandertal vertebral remains have inferred a hypolordotic, flat lower back and spinal imbalance for them, including the La Chapelle-aux-Saints 1 skeleton. These studies form part of a persistent trend to view the Neandertals as less "human" than ourselves despite growing evidence for little if any differences in basic functional anatomy and behavioral capabilities. We have therefore reassessed the spinal posture of La Chapelle-aux-Saints 1 using a new pelvic reconstruction to infer lumbar lordosis, interarticulation of lower lumbar (L4-S1) and cervical (C4-T2) vertebrae, and consideration of his widespread age-related osteoarthritis. La Chapelle-aux-Saints 1 exhibits a pelvic incidence (and hence lumbar lordosis) similar to modern humans, articulation of lumbar and cervical vertebrae indicating pronounced lordosis, and Baastrup disease as a product of his advanced age, osteoarthritis, and lordosis. Our findings challenge the view of generally small spinal curvatures in Neandertals. Setting aside the developmentally abnormal Kebara 2 vertebral column, La Chapelle-aux-Saints 1 is joined by other Neandertals with sufficient vertebral remains in providing them with a fully upright (and human) axial posture.},
}

Aged
Animals
Humans
Male
Neanderthals/*anatomy & histology/*physiology
Osteoarthritis/pathology/physiopathology
Pelvis/anatomy & histology
*Posture
Spinal Curvatures/physiopathology
Spine/*pathology/physiopathology

@article {pmid30782806,
year = {2019},
author = {Jaouen, K and Richards, MP and Le Cabec, A and Welker, F and Rendu, W and Hublin, JJ and Soressi, M and Talamo, S},
title = {Exceptionally high δ15N values in collagen single amino acids confirm Neandertals as high-trophic level carnivores.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {11},
pages = {4928-4933},
doi = {10.1073/pnas.1814087116},
pmid = {30782806},
issn = {1091-6490},
mesh = {Amino Acids/*analysis ; Animals ; Carbon Isotopes/analysis ; Carnivora/*physiology ; Collagen/*chemistry ; *Food Chain ; Neanderthals/*physiology ; Nitrogen Isotopes/*analysis ; },
abstract = {Isotope and archeological analyses of Paleolithic food webs have suggested that Neandertal subsistence relied mainly on the consumption of large herbivores. This conclusion was primarily based on elevated nitrogen isotope ratios in Neandertal bone collagen and has been significantly debated. This discussion relies on the observation that similar high nitrogen isotopes values could also be the result of the consumption of mammoths, young animals, putrid meat, cooked food, freshwater fish, carnivores, or mushrooms. Recently, compound-specific C and N isotope analyses of bone collagen amino acids have been demonstrated to add significantly more information about trophic levels and aquatic food consumption. We undertook single amino acid C and N isotope analysis on two Neandertals, which were characterized by exceptionally high N isotope ratios in their bulk bone or tooth collagen. We report here both C and N isotope ratios on single amino acids of collagen samples for these two Neandertals and associated fauna. The samples come from two sites dating to the Middle to Upper Paleolithic transition period (Les Cottés and Grotte du Renne, France). Our results reinforce the interpretation of Neandertal dietary adaptations as successful top-level carnivores, even after the arrival of modern humans in Europe. They also demonstrate that high δ15N values of bone collagen can solely be explained by mammal meat consumption, as supported by archeological and zooarcheological evidence, without necessarily invoking explanations including the processing of food (cooking, fermenting), the consumption of mammoths or young mammals, or additional (freshwater fish, mushrooms) dietary protein sources.},
}

Amino Acids/*analysis
Animals
Carbon Isotopes/analysis
Carnivora/*physiology
Collagen/*chemistry
*Food Chain
Neanderthals/*physiology
Nitrogen Isotopes/*analysis

@article {pmid30777361,
year = {2019},
author = {Martinón-Torres, M and Bermúdez de Castro, JM and Martínez de Pinillos, M and Modesto-Mata, M and Xing, S and Martín-Francés, L and García-Campos, C and Wu, X and Liu, W},
title = {New permanent teeth from Gran Dolina-TD6 (Sierra de Atapuerca). The bearing of Homo antecessor on the evolutionary scenario of Early and Middle Pleistocene Europe.},
journal = {Journal of human evolution},
volume = {127},
number = {},
pages = {93-117},
doi = {10.1016/j.jhevol.2018.12.001},
pmid = {30777361},
issn = {1095-8606},
abstract = {Here we analyze the unpublished hominin dental remains recovered from the late Early Pleistocene Gran Dolina-TD6.2 level of the Sierra de Atapuerca (northern Spain), as well as provide a reassessment of the whole TD6.2 hominin dental sample. Comparative descriptions of the outer enamel surface (OES) and the enamel-dentine junction (EDJ) are provided. Overall, the data presented here support the taxonomic validity of Homo antecessor, since this species presents a unique mosaic of traits. Homo antecessor displays several primitive features for the genus Homo as well as some traits exclusively shared with Early and Middle Pleistocene Eurasian hominins. Some of these Eurasian traits were retained by the Middle Pleistocene hominins of Europe, and subsequently became the typical condition of the Neanderthal lineage. Although other skeletal parts present resemblances with Homo sapiens, TD6.2 teeth do not show any synapomorphy with modern humans. In addition, TD6.2 teeth can be well differentiated from those of Asian Homo erectus. The dental evidence is compatible with previous hypothesis about H. antecessor belonging to the basal population from which H. sapiens, Homo neanderthalensis, and Denisovans emerged. Future findings and additional research may help to elucidate the precise phylogenetic link among them.},
}

@article {pmid30777356,
year = {2019},
author = {Dinnis, R and Bessudnov, A and Reynolds, N and Devièse, T and Pate, A and Sablin, M and Sinitsyn, A and Higham, T},
title = {New data for the Early Upper Paleolithic of Kostenki (Russia).},
journal = {Journal of human evolution},
volume = {127},
number = {},
pages = {21-40},
doi = {10.1016/j.jhevol.2018.11.012},
pmid = {30777356},
issn = {1095-8606},
abstract = {Several questions remain regarding the timing and nature of the Neanderthal-anatomically modern human (AMH) transition in Europe. The situation in Eastern Europe is generally less clear due to the relatively few sites and a dearth of reliable radiocarbon dates. Claims have been made for both notably early AMH and notably late Neanderthal presence, as well as for early AMH (Aurignacian) dispersal into the region from Central/Western Europe. The Kostenki-Borshchevo complex (European Russia) of Early Upper Paleolithic (EUP) sites offers high-quality data to address these questions. Here we revise the chronology and cultural status of the key sites of Kostenki 17 and Kostenki 14. The Kostenki 17/II lithic assemblage shares important features with Proto-Aurignacian material, strengthening an association with AMHs. New radiocarbon dates for Kostenki 17/II of ∼41-40 ka cal BP agree with new dates for the recently excavated Kostenki 14/IVw, which shows some similarities to Kostenki 17/II. Dates of ≥41 ka cal BP from other Kostenki sites cannot be linked to diagnostic archaeological material, and therefore cannot be argued to date AMH occupation. Kostenki 14's Layer in Volcanic Ash assemblage, on the other hand, compares to Early Aurignacian material. New radiocarbon dates targeting diagnostic lithics date to 39-37 ka cal BP. Overall, Kostenki's early EUP is in good agreement with the archaeological record further west. Our results are therefore consistent with models predicting interregional penecontemporaneity of diagnostic EUP assemblages. Most importantly, our work highlights ongoing challenges for reliably radiocarbon dating the period. Dates for Kostenki 14 agreed with the samples' chronostratigraphic positions, but standard pre-treatment methods consistently produced incorrect ages for Kostenki 17/II. Extraction of hydroxyproline from bone collagen using preparative high-performance liquid chromatography, however, yielded results consistent with the samples' chronostratigraphic position and with the layer's archaeological contents. This suggests that for some sites compound-specific techniques are required to build reliable radiocarbon chronologies.},
}

@article {pmid30777355,
year = {2019},
author = {Ekshtain, R and Tryon, CA},
title = {Lithic raw material acquisition and use by early Homo sapiens at Skhul, Israel.},
journal = {Journal of human evolution},
volume = {127},
number = {},
pages = {149-170},
doi = {10.1016/j.jhevol.2018.10.005},
pmid = {30777355},
issn = {1095-8606},
abstract = {The site of Skhul in Israel has featured prominently in discussions about the early presence of Homo sapiens outside of Africa since its excavation in the 1930s. Until now, attention has been primarily focused on the site's fossil hominins and evidence for symbolic behavior in the form of burials and rare artifacts such as pierced shells and pigment objects. We present here the results of renewed analysis of the lithic artifacts from Skhul drawn from archival collections in the United States, United Kingdom, and Israel. Although lithic artifacts form the majority of the archaeological record from the site, they have rarely been the subject of comprehensive study. Our analyses of raw material selection, use and transport combined with technological analyses of artifact production methods (1) indicate selective transport to the site of large flakes, retouched pieces, and particularly Levallois points from non-local sources, and (2) demonstrate substantial variability in raw material procurement that fails to indicate clear differences in landscape use between H. sapiens and Neanderthals.},
}

@article {pmid30773169,
year = {2019},
author = {Buttura, RV and Ramalho, J and Lima, THA and Donadi, EA and Veiga-Castelli, LC and Mendes-Junior, CT and Castelli, EC},
title = {HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levels.},
journal = {Human immunology},
volume = {80},
number = {2},
pages = {112-119},
doi = {10.1016/j.humimm.2018.10.016},
pmid = {30773169},
issn = {1879-1166},
abstract = {HLA-F is one of the most conserved loci among the HLA gene family. The exact function of HLA-F is still under investigation. HLA-F might present tolerogenic features, participate in the stabilization of HLA molecules in open conformation, and also participate in the recycling of HLA molecules. Here we evaluate the variability and haplotype structure of the HLA-F distal promoter segment (from -1893 to -943) and how this segment is correlated with the coding region. Variability at the promoter segment was surveyed in 196 Brazilian samples using second-generation sequencing. The HLA-F promoter region presents two major haplotype lineages. Most of the variable sites are in perfect linkage and associated with a single promoter haplotype, here named F∗distal-C. This haplotype is associated with F∗01:01:02 alleles, while alleles from the F∗01:01:01 or F∗01:03 groups present closely related promoter sequences. F∗distal-C is quite frequent in Brazil and in worldwide populations, with frequencies ranging from 8.41% at the Iberian Population in Spain to 34.34% in Vietnam. F∗distal-C is also present in Neanderthal and Denisovan samples. In silico analyses demonstrated that F∗distal-C presents a different transcription factor binding profile compared with other HLA-F promoters. Moreover, individuals carrying this haplotype present higher HLA-F mRNA expression levels. Functional studies are required to define the exact mechanism underlying this higher HLA-F mRNA expression level associated with F∗distal-C and F∗01:01:02 alleles.},
}

@article {pmid30772945,
year = {2019},
author = {James, WPT and Johnson, RJ and Speakman, JR and Wallace, DC and Frühbeck, G and Iversen, PO and Stover, PJ},
title = {Nutrition and its role in human evolution.},
journal = {Journal of internal medicine},
volume = {285},
number = {5},
pages = {533-549},
doi = {10.1111/joim.12878},
pmid = {30772945},
issn = {1365-2796},
abstract = {Our understanding of human evolution has improved rapidly over recent decades, facilitated by large-scale cataloguing of genomic variability amongst both modern and archaic humans. It seems clear that the evolution of the ancestors of chimpanzees and hominins separated 7-9 million years ago with some migration out of Africa by the earlier hominins; Homo sapiens slowly emerged as climate change resulted in drier, less forested African conditions. The African populations expanded and evolved in many different conditions with slow mutation and selection rates in the human genome, but with much more rapid mutation occurring in mitochondrial DNA. We now have evidence stretching back 300 000 years of humans in their current form, but there are clearly four very different large African language groups that correlate with population DNA differences. Then, about 50 000-100 000 years ago a small subset of modern humans also migrated out of Africa resulting in a persistent signature of more limited genetic diversity amongst non-African populations. Hybridization with archaic hominins occurred around this time such that all non-African modern humans possess some Neanderthal ancestry and Melanesian populations additionally possess some Denisovan ancestry. Human populations both within and outside Africa also adapted to diverse aspects of their local environment including altitude, climate, UV exposure, diet and pathogens, in some cases leaving clear signatures of patterns of genetic variation. Notable examples include haemoglobin changes conferring resistance to malaria, other immune changes and the skin adaptations favouring the synthesis of vitamin D. As humans migrated across Eurasia, further major mitochondrial changes occurred with some interbreeding with ancient hominins and the development of alcohol intolerance. More recently, an ability to retain lactase persistence into adulthood has evolved rapidly under the environmental stimulus of pastoralism with the ability to husband lactating ruminants. Increased amylase copy numbers seem to relate to the availability of starchy foods, whereas the capacity to desaturase and elongate monounsaturated fatty acids in different societies seems to be influenced by whether there is a lack of supply of readily available dietary sources of long-chain polyunsaturated fatty acids. The process of human evolution includes genetic drift and adaptation to local environments, in part through changes in mitochondrial and nuclear DNA. These genetic changes may underlie susceptibilities to some modern human pathologies including folate-responsive neural tube defects, diabetes, other age-related pathologies and mental health disorders.},
}

@article {pmid30771245,
year = {2019},
author = {Becam, G and Verna, C and Gómez-Robles, A and Gómez-Olivencia, A and Albessard, L and Arnaud, J and Frelat, MA and Madelaine, S and Schwab, C and Souday, C and Turq, A and Balzeau, A},
title = {Isolated teeth from La Ferrassie: Reassessment of the old collections, new remains, and their implications.},
journal = {American journal of physical anthropology},
volume = {169},
number = {1},
pages = {132-142},
doi = {10.1002/ajpa.23798},
pmid = {30771245},
issn = {1096-8644},
support = {Research Group//Gobierno Vasco/Eusko Jaurlaritza/ ; IT1044-16//Gobierno Vasco/Eusko Jaurlaritza/ ; IT834-13//Gobierno Vasco/Eusko Jaurlaritza/ ; CGL2015-65387-C3-2-P-MINECO/FEDER-//Ministerio de Ciencia y Tecnología/ ; CGL2012-38434-C03-01//Ministerio de Ciencia y Tecnología/ ; //UMR 7194 CNRS-HNHP/UPVD/ ; },
abstract = {OBJECTIVES: We provide the description and comparative analysis of six new teeth from the site of La Ferrassie. Our goal is to discuss their taxonomic attribution, and to provide an updated inventory of Neandertal and modern human remains from La Ferrassie in their associated archeological context.

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

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

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

@article {pmid30737446,
year = {2019},
author = {Ríos, L and Kivell, TL and Lalueza-Fox, C and Estalrrich, A and García-Tabernero, A and Huguet, R and Quintino, Y and de la Rasilla, M and Rosas, A},
title = {Skeletal Anomalies in The Neandertal Family of El Sidrón (Spain) Support A Role of Inbreeding in Neandertal Extinction.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {1697},
doi = {10.1038/s41598-019-38571-1},
pmid = {30737446},
issn = {2045-2322},
support = {336301//European Research Council/International ; CGL2016-75109-P//Ministerio de Ciencia y Tecnolog&#x00ED;a (Ministry of Science and Technology)/ ; },
abstract = {Neandertals disappeared from the fossil record around 40,000 bp, after a demographic history of small and isolated groups with high but variable levels of inbreeding, and episodes of interbreeding with other Paleolithic hominins. It is reasonable to expect that high levels of endogamy could be expressed in the skeleton of at least some Neandertal groups. Genetic studies indicate that the 13 individuals from the site of El Sidrón, Spain, dated around 49,000 bp, constituted a closely related kin group, making these Neandertals an appropriate case study for the observation of skeletal signs of inbreeding. We present the complete study of the 1674 identified skeletal specimens from El Sidrón. Altogether, 17 congenital anomalies were observed (narrowing of the internal nasal fossa, retained deciduous canine, clefts of the first cervical vertebra, unilateral hypoplasia of the second cervical vertebra, clefting of the twelfth thoracic vertebra, diminutive thoracic or lumbar rib, os centrale carpi and bipartite scaphoid, tripartite patella, left foot anomaly and cuboid-navicular coalition), with at least four individuals presenting congenital conditions (clefts of the first cervical vertebra). At 49,000 years ago, the Neandertals from El Sidrón, with genetic and skeletal evidence of inbreeding, could be representative of the beginning of the demographic collapse of this hominin phenotype.},
}

@article {pmid30721683,
year = {2019},
author = {Sherwood, CC and Bradley, BJ},
title = {Brain Evolution: Mapping the Inner Neandertal.},
journal = {Current biology : CB},
volume = {29},
number = {3},
pages = {R95-R97},
doi = {10.1016/j.cub.2018.12.024},
pmid = {30721683},
issn = {1879-0445},
abstract = {Human populations that migrated out of Africa interbred with Neandertals. A new study assesses the effects of Neandertal gene variants on brain shape in modern humans, providing insights into the genomic basis of the uniquely globular human brain.},
}

@article {pmid30702428,
year = {2019},
author = {Miller, IF and Barton, RA and Nunn, CL},
title = {Quantitative uniqueness of human brain evolution revealed through phylogenetic comparative analysis.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
doi = {10.7554/eLife.41250},
pmid = {30702428},
issn = {2050-084X},
support = {BCS-1355902//National Science Foundation/ ; },
abstract = {While the human brain is clearly large relative to body size, less is known about the timing of brain and brain component expansion within primates and the relative magnitude of volumetric increases. Using Bayesian phylogenetic comparative methods and data for both extant and fossil species, we identified that a distinct shift in brain-body scaling occurred as hominins diverged from other primates, and again as humans and Neanderthals diverged from other hominins. Within hominins, we detected a pattern of directional and accelerating evolution towards larger brains, consistent with a positive feedback process in the evolution of the human brain. Contrary to widespread assumptions, we found that the human neocortex is not exceptionally large relative to other brain structures. Instead, our analyses revealed a single increase in relative neocortex volume at the origin of haplorrhines, and an increase in relative cerebellar volume in apes.},
}

@article {pmid30700871,
year = {2019},
author = {Douka, K and Slon, V and Jacobs, Z and Ramsey, CB and Shunkov, MV and Derevianko, AP and Mafessoni, F and Kozlikin, MB and Li, B and Grün, R and Comeskey, D and Devièse, T and Brown, S and Viola, B and Kinsley, L and Buckley, M and Meyer, M and Roberts, RG and Pääbo, S and Kelso, J and Higham, T},
title = {Age estimates for hominin fossils and the onset of the Upper Palaeolithic at Denisova Cave.},
journal = {Nature},
volume = {565},
number = {7741},
pages = {640-644},
doi = {10.1038/s41586-018-0870-z},
pmid = {30700871},
issn = {1476-4687},
abstract = {Denisova Cave in the Siberian Altai (Russia) is a key site for understanding the complex relationships between hominin groups that inhabited Eurasia in the Middle and Late Pleistocene epoch. DNA sequenced from human remains found at this site has revealed the presence of a hitherto unknown hominin group, the Denisovans1,2, and high-coverage genomes from both Neanderthal and Denisovan fossils provide evidence for admixture between these two populations3. Determining the age of these fossils is important if we are to understand the nature of hominin interaction, and aspects of their cultural and subsistence adaptations. Here we present 50 radiocarbon determinations from the late Middle and Upper Palaeolithic layers of the site. We also report three direct dates for hominin fragments and obtain a mitochondrial DNA sequence for one of them. We apply a Bayesian age modelling approach that combines chronometric (radiocarbon, uranium series and optical ages), stratigraphic and genetic data to calculate probabilistically the age of the human fossils at the site. Our modelled estimate for the age of the oldest Denisovan fossil suggests that this group was present at the site as early as 195,000 years ago (at 95.4% probability). All Neanderthal fossils-as well as Denisova 11, the daughter of a Neanderthal and a Denisovan4-date to between 80,000 and 140,000 years ago. The youngest Denisovan dates to 52,000-76,000 years ago. Direct radiocarbon dating of Upper Palaeolithic tooth pendants and bone points yielded the earliest evidence for the production of these artefacts in northern Eurasia, between 43,000 and 49,000 calibrated years before present (taken as AD 1950). On the basis of current archaeological evidence, it may be assumed that these artefacts are associated with the Denisovan population. It is not currently possible to determine whether anatomically modern humans were involved in their production, as modern-human fossil and genetic evidence of such antiquity has not yet been identified in the Altai region.},
}

@article {pmid30700870,
year = {2019},
author = {Jacobs, Z and Li, B and Shunkov, MV and Kozlikin, MB and Bolikhovskaya, NS and Agadjanian, AK and Uliyanov, VA and Vasiliev, SK and O'Gorman, K and Derevianko, AP and Roberts, RG},
title = {Timing of archaic hominin occupation of Denisova Cave in southern Siberia.},
journal = {Nature},
volume = {565},
number = {7741},
pages = {594-599},
doi = {10.1038/s41586-018-0843-2},
pmid = {30700870},
issn = {1476-4687},
abstract = {The Altai region of Siberia was inhabited for parts of the Pleistocene by at least two groups of archaic hominins-Denisovans and Neanderthals. Denisova Cave, uniquely, contains stratified deposits that preserve skeletal and genetic evidence of both hominins, artefacts made from stone and other materials, and a range of animal and plant remains. The previous site chronology is based largely on radiocarbon ages for fragments of bone and charcoal that are up to 50,000 years old; older ages of equivocal reliability have been estimated from thermoluminescence and palaeomagnetic analyses of sediments, and genetic analyses of hominin DNA. Here we describe the stratigraphic sequences in Denisova Cave, establish a chronology for the Pleistocene deposits and associated remains from optical dating of the cave sediments, and reconstruct the environmental context of hominin occupation of the site from around 300,000 to 20,000 years ago.},
}

@article {pmid30693948,
year = {2019},
author = {Pan, L and Zanolli, C},
title = {Comparative observations on the premolar root and pulp canal configurations of Middle Pleistocene Homo in China.},
journal = {American journal of physical anthropology},
volume = {168},
number = {3},
pages = {637-646},
doi = {10.1002/ajpa.23777},
pmid = {30693948},
issn = {1096-8644},
support = {XDB26000000//Strategic Priority Research Program of Chinese Academy of Sciences/ ; 41702026//National Natural Science Foundation of China/ ; 41872030//National Natural Science Foundation of China/ ; 173119//State Key Laboratory of Palaeobiology and Stratigraphy/ ; },
abstract = {OBJECTIVES: The aim of this study is to explore the root and root canal morphology of Homo fossil occupying China during the Middle Pleistocene period. Human occupation and evolutionary dynamics in East Asia during the Middle Pleistocene period is one of the most intriguing issues in paleoanthropology, with the coexistence of multiple lineages and regional morphs suggesting a complex population interaction scenario. Although premolar root and canal morphology has certain phylogenetic, taxonomic, and functional implications, its morphological diversity, possible evolutionary trend and characteristics regarding Middle Pleistocene hominins inhabiting East Asia are still insufficiently understood; where these populations fits within the Homo lineage (with respect to root and pulp canal structure) needs to be explored.

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

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

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

@article {pmid30683877,
year = {2019},
author = {Milks, A and Parker, D and Pope, M},
title = {External ballistics of Pleistocene hand-thrown spears: experimental performance data and implications for human evolution.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {820},
doi = {10.1038/s41598-018-37904-w},
pmid = {30683877},
issn = {2045-2322},
support = {817687//RCUK | Arts and Humanities Research Council (AHRC)/ ; },
abstract = {The appearance of weaponry - technology designed to kill - is a critical but poorly established threshold in human evolution. It is an important behavioural marker representing evolutionary changes in ecology, cognition, language and social behaviours. While the earliest weapons are often considered to be hand-held and consequently short-ranged, the subsequent appearance of distance weapons is a crucial development. Projectiles are seen as an improvement over contact weapons, and are considered by some to have originated only with our own species in the Middle Stone Age and Upper Palaeolithic. Despite the importance of distance weapons in the emergence of full behavioral modernity, systematic experimentation using trained throwers to evaluate the ballistics of thrown spears during flight and at impact is lacking. This paper addresses this by presenting results from a trial of trained javelin athletes, providing new estimates for key performance parameters. Overlaps in distances and impact energies between hand-thrown spears and spearthrowers are evidenced, and skill emerges as a significant factor in successful use. The results show that distance hunting was likely within the repertoire of hunting strategies of Neanderthals, and the resulting behavioural flexibility closely mirrors that of our own species.},
}

@article {pmid30672457,
year = {2019},
author = {Henry, JP},
title = {[Genetics and origin of Homo sapiens].},
journal = {Medecine sciences : M/S},
volume = {35},
number = {1},
pages = {39-45},
doi = {10.1051/medsci/2018311},
pmid = {30672457},
issn = {1958-5381},
mesh = {Africa ; Animals ; Asia ; Biological Evolution ; DNA/analysis/chemistry ; Europe ; *Evolution, Molecular ; *Genome, Human ; Hominidae/*genetics ; Human Genome Project ; Humans ; Neanderthals/genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Selection, Genetic ; Sequence Homology ; },
abstract = {Usually, paleoanthropology studies remains and artefacts. However, more recently, genetics offer new avenues. Information on humanisation mechanisms has been obtained from comparison with primate or archaic Homo DNA sequences. Likewise, the 1 000 Genomes Project has characterized the geographic spectrum of human genetic variation offering a basis for a genomic study of Homo sapiens phylogeny. From these studies, a model, Out of Africa, was derived. His origin is Africa, where he lived 200 000 years ago. A small fraction of the population left Africa between 50 and 100 000 years ago that have populated the rest of the world, to Europe, coastal Asia to Australia and mainland Asia to Behring Land Bridge and America. The model is supported by the decrease of genetic diversity with the distance to Eastern Africa (serial founder effect). In Europe and Asia, Homo sapiens met archaic Homo neanderthalis and H denisova. The presence of 1-3% neanderthalis sequences in modern Homo ADN indicates admixtures between these groups. Some archaic sequences are on positive selection pressure, thus suggesting that the extinct hominins might have facilitated the adaptation of H sapiens to new environments.},
}

Africa
Animals
Asia
Biological Evolution
DNA/analysis/chemistry
Europe
*Evolution, Molecular
*Genome, Human
Hominidae/*genetics
Human Genome Project
Humans
Neanderthals/genetics
Phylogeny
Polymorphism, Single Nucleotide
Selection, Genetic
Sequence Homology

@article {pmid30664696,
year = {2019},
author = {Cortés-Sánchez, M and Jiménez-Espejo, FJ and Simón-Vallejo, MD and Stringer, C and Lozano Francisco, MC and García-Alix, A and Vera Peláez, JL and Odriozola, CP and Riquelme-Cantal, JA and Parrilla Giráldez, R and Maestro González, A and Ohkouchi, N and Morales-Muñiz, A},
title = {An early Aurignacian arrival in southwestern Europe.},
journal = {Nature ecology & evolution},
volume = {3},
number = {2},
pages = {207-212},
doi = {10.1038/s41559-018-0753-6},
pmid = {30664696},
issn = {2397-334X},
mesh = {*Archaeology ; Bayes Theorem ; Fossils ; *Human Migration ; Humans ; Radiometric Dating ; Spain ; },
abstract = {Westernmost Europe constitutes a key location in determining the timing of the replacement of Neanderthals by anatomically modern humans (AMHs). In this study, the replacement of late Mousterian industries by Aurignacian ones at the site of Bajondillo Cave (Málaga, southern Spain) is reported. On the basis of Bayesian analyses, a total of 26 radiocarbon dates, including 17 new ones, show that replacement at Bajondillo took place in the millennia centring on ~45-43 calibrated thousand years before the present (cal ka BP)-well before the onset of Heinrich event 4 (~40.2-38.3 cal ka BP). These dates indicate that the arrival of AMHs at the southernmost tip of Iberia was essentially synchronous with that recorded in other regions of Europe, and significantly increases the areal expansion reached by early AMHs at that time. In agreement with human dispersal scenarios on other continents, such rapid expansion points to coastal corridors as favoured routes for early AMH. The new radiocarbon dates align Iberian chronologies with AMH dispersal patterns in Eurasia.},
}

*Archaeology
Bayes Theorem
Fossils
*Human Migration
Humans
Radiometric Dating
Spain

@article {pmid30651539,
year = {2019},
author = {Mondal, M and Bertranpetit, J and Lao, O},
title = {Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {246},
doi = {10.1038/s41467-018-08089-7},
pmid = {30651539},
issn = {2041-1723},
abstract = {Since anatomically modern humans dispersed Out of Africa, the evolutionary history of Eurasian populations has been marked by introgressions from presently extinct hominins. Some of these introgressions have been identified using sequenced ancient genomes (Neanderthal and Denisova). Other introgressions have been proposed for still unidentified groups using the genetic diversity present in current human populations. We built a demographic model based on deep learning in an Approximate Bayesian Computation framework to infer the evolutionary history of Eurasian populations including past introgression events in Out of Africa populations fitting the current genetic evidence. In addition to the reported Neanderthal and Denisovan introgressions, our results support a third introgression in all Asian and Oceanian populations from an archaic population. This population is either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage. We propose the use of deep learning methods for clarifying situations with high complexity in evolutionary genomics.},
}

@article {pmid30647110,
year = {2019},
author = {Petr, M and Pääbo, S and Kelso, J and Vernot, B},
title = {Limits of long-term selection against Neandertal introgression.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {5},
pages = {1639-1644},
doi = {10.1073/pnas.1814338116},
pmid = {30647110},
issn = {1091-6490},
mesh = {Alleles ; Animals ; Conserved Sequence/genetics ; DNA/genetics ; Europe ; European Continental Ancestry Group/genetics ; Evolution, Molecular ; Gene Flow/genetics ; Humans ; Neanderthals/*genetics ; RNA, Untranslated/genetics ; Selection, Genetic/*genetics ; },
abstract = {Several studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45,000 years. Here, we show that this decline is an artifact likely caused by gene flow between modern human populations, which is not taken into account by statistics previously used to estimate Neandertal ancestry. When we apply a statistic that avoids assumptions about modern human demography by taking advantage of two high-coverage Neandertal genomes, we find no evidence for a change in Neandertal ancestry in Europe over the past 45,000 years. We use whole-genome simulations of selection and introgression to investigate a wide range of model parameters and find that negative selection is not expected to cause a significant long-term decline in genome-wide Neandertal ancestry. Nevertheless, these models recapitulate previously observed signals of selection against Neandertal alleles, in particular the depletion of Neandertal ancestry in conserved genomic regions. Surprisingly, we find that this depletion is strongest in regulatory and conserved noncoding regions and in the most conserved portion of protein-coding sequences.},
}

Alleles
Animals
Conserved Sequence/genetics
DNA/genetics
Europe
European Continental Ancestry Group/genetics
Evolution, Molecular
Gene Flow/genetics
Humans
Neanderthals/*genetics
RNA, Untranslated/genetics
Selection, Genetic/*genetics

@article {pmid30590594,
year = {2019},
author = {Taylor, ME and Snelling, T and Smith, DF and Drickamer, K},
title = {Absence of a human ortholog of rodent Kupffer cell galactose-binding receptor encoded by the CLEC4f gene.},
journal = {Glycobiology},
volume = {29},
number = {4},
pages = {332-345},
doi = {10.1093/glycob/cwy113},
pmid = {30590594},
issn = {1460-2423},
support = {093599//Wellcome Trust/United Kingdom ; BB/P005659/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M011178/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {The murine CLEC4f gene encodes the Kupffer cell receptor, a galactose-binding receptor containing a C-type carbohydrate-recognition domain. Orthologs have been identified in nearly 100 species. The receptors from rat and mouse have previously been characterized and data presented here show that functional CLEC4f protein is expressed in domestic cattle (Bos taurus). However, the human CLEC4f gene does not encode a functional receptor because a mutation in the splice acceptor site of the final exon prevents appropriate splicing and a missense mutation disrupts the sugar-binding site. Transcriptomic and PCR analysis of transcripts confirms the absence of a spliced transcript containing the final exon and only background levels of transcripts are detected in human tissues. These mutations are also present in the CLEC4f gene in Neanderthals. In contrast to humans, closely related species, including chimpanzees, do have CLEC4f genes that encode full-length receptors. Affinity chromatography and glycan array results demonstrate that the chimpanzee, bovine and murine proteins all bind to galactose, but they show preferences for different subsets of galactose-containing glycans. In non-human primates, the receptor is expressed in spleen rather than in liver. The results indicate that the CLEC4f protein probably has distinct functions in different species. Absence of the receptor precludes using it for targeting of glycoconjugates to cells in human liver. The fact that CLEC4f protein is expressed in spleen in non-human primates and the close evolutionary relationship of the CLEC4f protein to langerin (CD207) suggest that it may function in the immune system, possibly as a pathogen receptor.},
}

@article {pmid30589914,
year = {2018},
author = {Velliky, EC and Porr, M and Conard, NJ},
title = {Ochre and pigment use at Hohle Fels cave: Results of the first systematic review of ochre and ochre-related artefacts from the Upper Palaeolithic in Germany.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0209874},
doi = {10.1371/journal.pone.0209874},
pmid = {30589914},
issn = {1932-6203},
mesh = {*Caves ; *Coloring Agents/chemistry/history ; *Culture ; Germany ; History, Ancient ; Humans ; Paintings/*history ; },
abstract = {Though many European Upper Palaeolithic sites document early examples of symbolic material expressions (e.g., cave art, personal ornaments, figurines), there exist few reports on the use of earth pigments outside of cave art-and occasionally Neanderthal-contexts. Here, we present the first in-depth study of the diachronic changes in ochre use throughout an entire Upper Palaeolithic sequence at Hohle Fels cave, Germany, spanning from ca. 44,000-14,500 cal. yr. BP. A reassessment of the assemblage has yielded 869 individual ochre artefacts, of which 27 show traces of anthropogenic modification. The ochre artefacts are from all Upper Palaeolithic layers, stemming from the earliest Aurignacian horizons to the Holocene. This wide temporal spread demonstrates the long-term presence and continuity of ochre use in a part of Europe where it has not been systematically reported before. The anthropogenic modifications present on the ochre artefacts from the Gravettian and Magdalenian are consistent with pigment powder production, whereas the only modified piece from the Aurignacian displays a possible engraved motif. The non-modified artefacts show that more hematite-rich specular ochres as well as fine-grained deep red iron oxide clays were preferred during the Gravettian and Magdalenian, while the Aurignacian layers contain a broader array of colours and textures. Furthermore, numerous other artefacts such as faunal elements, personal ornaments, shells, and an ochre grindstone further strengthen the conclusion that ochre behaviours were well established during the onset of the Aurignacian and subsequently flourished throughout the Upper Palaeolithic at Hohle Fels cave.},
}

*Caves
*Coloring Agents/chemistry/history
*Culture
Germany
History, Ancient
Humans
Paintings/*history

@article {pmid30583844,
year = {2019},
author = {Lague, MR and Chirchir, H and Green, DJ and Mbua, E and Harris, JWK and Braun, DR and Griffin, NL and Richmond, BG},
title = {Cross-sectional properties of the humeral diaphysis of Paranthropus boisei: Implications for upper limb function.},
journal = {Journal of human evolution},
volume = {126},
number = {},
pages = {51-70},
doi = {10.1016/j.jhevol.2018.05.002},
pmid = {30583844},
issn = {1095-8606},
abstract = {A ∼1.52 Ma adult upper limb skeleton of Paranthropus boisei (KNM-ER 47000) recovered from the Koobi Fora Formation, Kenya (FwJj14E, Area 1A) includes most of the distal half of a right humerus (designated KNM-ER 47000B). Natural transverse fractures through the diaphysis of KNM-ER 470000B provide unobstructed views of cortical bone at two sections typically used for analyzing cross-sectional properties of hominids (i.e., 35% and 50% of humerus length from the distal end). Here we assess cross-sectional properties of KNM-ER 47000B and two other P. boisei humeri (OH 80-10, KNM-ER 739). Cross-sectional properties for P. boisei associated with bending/torsional strength (section moduli) and relative cortical thickness (%CA; percent cortical area) are compared to those reported for nonhuman hominids, AL 288-1 (Australopithecus afarensis), and multiple species of fossil and modern Homo. Polar section moduli (Zp) are assessed relative to a mechanically relevant measure of body size (i.e., the product of mass [M] and humerus length [HL]). At both diaphyseal sections, P. boisei exhibits %CA that is high among extant hominids (both human and nonhuman) and similar to that observed among specimens of Pleistocene Homo. High values for Zp relative to size (M × HL) indicate that P. boisei had humeral bending strength greater than that of modern humans and Neanderthals and similar to that of great apes, A. afarensis, and Homo habilis. Such high humeral strength is consistent with other skeletal features of P. boisei (reviewed here) that suggest routine use of powerful upper limbs for arboreal climbing.},
}

@article {pmid30573755,
year = {2018},
author = {Van Laer, B and Kapp, U and Soler-Lopez, M and Moczulska, K and Pääbo, S and Leonard, G and Mueller-Dieckmann, C},
title = {Molecular comparison of Neanderthal and Modern Human adenylosuccinate lyase.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {18008},
doi = {10.1038/s41598-018-36195-5},
pmid = {30573755},
issn = {2045-2322},
abstract = {The availability of genomic data from extinct homini such as Neanderthals has caused a revolution in palaeontology allowing the identification of modern human-specific protein substitutions. Currently, little is known as to how these substitutions alter the proteins on a molecular level. Here, we investigate adenylosuccinate lyase, a conserved enzyme involved in purine metabolism for which several substitutions in the modern human protein (hADSL) have been described to affect intelligence and behaviour. During evolution, modern humans acquired a specific substitution (Ala429Val) in ADSL distinguishing it from the ancestral variant present in Neanderthals (nADSL). We show here that despite this conservative substitution being solvent exposed and located distant from the active site, there is a difference in thermal stability, but not enzymology or ligand binding between nADSL and hADSL. Substitutions near residue 429 which do not profoundly affect enzymology were previously reported to cause neurological symptoms in humans. This study also reveals that ADSL undergoes conformational changes during catalysis which, together with the crystal structure of a hitherto undetermined product bound conformation, explains the molecular origin of disease for several modern human ADSL mutants.},
}

@article {pmid30566634,
year = {2019},
author = {Reher, D and Key, FM and Andrés, AM and Kelso, J},
title = {Immune Gene Diversity in Archaic and Present-day Humans.},
journal = {Genome biology and evolution},
volume = {11},
number = {1},
pages = {232-241},
doi = {10.1093/gbe/evy271},
pmid = {30566634},
issn = {1759-6653},
mesh = {Animals ; Genetic Variation ; Humans ; Immunity, Innate/*genetics ; *Major Histocompatibility Complex ; Neanderthals/*genetics/immunology ; },
abstract = {Genome-wide analyses of two Neandertals and a Denisovan have shown that these archaic humans had lower genetic heterozygosity than present-day people. A similar reduction in genetic diversity of protein-coding genes (gene diversity) was found in exome sequences of three Neandertals. Reduced gene diversity, particularly in genes involved in immunity, may have important functional consequences. In fact, it has been suggested that reduced diversity in immune genes may have contributed to Neandertal extinction. We therefore explored gene diversity in different human groups, and at different time points on the Neandertal lineage, with a particular focus on the diversity of genes involved in innate immunity and genes of the Major Histocompatibility Complex (MHC).We find that the two Neandertals and a Denisovan have similar gene diversity, all significantly lower than any present-day human. This is true across gene categories, with no gene set showing an excess decrease in diversity compared with the genome-wide average. Innate immune-related genes show a similar reduction in diversity to other genes, both in present-day and archaic humans. There is also no observable decrease in gene diversity over time in Neandertals, suggesting that there may have been no ongoing reduction in gene diversity in later Neandertals, although this needs confirmation with a larger sample size. In both archaic and present-day humans, genes with the highest levels of diversity are enriched for MHC-related functions. In fact, in archaic humans the MHC genes show evidence of having retained more diversity than genes involved only in the innate immune system.},
}

Animals
Genetic Variation
Humans
Immunity, Innate/*genetics
*Major Histocompatibility Complex
Neanderthals/*genetics/immunology

@article {pmid30566479,
year = {2018},
author = {Mohammed Ismail, W and Pagel, KA and Pejaver, V and Zhang, SV and Casasa, S and Mort, M and Cooper, DN and Hahn, MW and Radivojac, P},
title = {The sequencing and interpretation of the genome obtained from a Serbian individual.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0208901},
doi = {10.1371/journal.pone.0208901},
pmid = {30566479},
issn = {1932-6203},
mesh = {Animals ; Ethnic Groups/*genetics ; Female ; *Genetic Predisposition to Disease ; *Genetic Variation ; *Genome, Human ; Genome-Wide Association Study ; Humans ; Male ; Neanderthals/genetics ; Serbia/ethnology ; },
abstract = {Recent genetic studies and whole-genome sequencing projects have greatly improved our understanding of human variation and clinically actionable genetic information. Smaller ethnic populations, however, remain underrepresented in both individual and large-scale sequencing efforts and hence present an opportunity to discover new variants of biomedical and demographic significance. This report describes the sequencing and analysis of a genome obtained from an individual of Serbian origin, introducing tens of thousands of previously unknown variants to the currently available pool. Ancestry analysis places this individual in close proximity to Central and Eastern European populations; i.e., closest to Croatian, Bulgarian and Hungarian individuals and, in terms of other Europeans, furthest from Ashkenazi Jewish, Spanish, Sicilian and Baltic individuals. Our analysis confirmed gene flow between Neanderthal and ancestral pan-European populations, with similar contributions to the Serbian genome as those observed in other European groups. Finally, to assess the burden of potentially disease-causing/clinically relevant variation in the sequenced genome, we utilized manually curated genotype-phenotype association databases and variant-effect predictors. We identified several variants that have previously been associated with severe early-onset disease that is not evident in the proband, as well as putatively impactful variants that could yet prove to be clinically relevant to the proband over the next decades. The presence of numerous private and low-frequency variants, along with the observed and predicted disease-causing mutations in this genome, exemplify some of the global challenges of genome interpretation, especially in the context of under-studied ethnic groups.},
}

Animals
Ethnic Groups/*genetics
Female
*Genetic Predisposition to Disease
*Genetic Variation
*Genome, Human
Genome-Wide Association Study
Humans
Male
Neanderthals/genetics
Serbia/ethnology

@article {pmid30566085,
year = {2018},
author = {Murphy, E and Benítez-Burraco, A},
title = {Paleo-oscillomics: inferring aspects of Neanderthal language abilities from gene regulation of neural oscillations.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {96},
number = {},
pages = {111-124},
doi = {10.4436/JASS.96010},
pmid = {30566085},
issn = {2037-0644},
mesh = {Animals ; Anthropology, Physical ; Computational Biology ; *Cultural Evolution ; DNA Methylation/genetics ; Genetic Techniques ; *Language ; *Neanderthals/genetics/physiology ; Nervous System Physiological Phenomena/genetics ; Speech/*physiology ; },
abstract = {Language seemingly evolved from changes in brain anatomy and wiring. We argue that language evolution can be better understood if particular changes in phasal and cross-frequency coupling properties of neural oscillations, resulting in core features of language, are considered. Because we cannot track the oscillatory activity of the brain from extinct hominins, we used our current understanding of the language oscillogenome (that is, the set of genes responsible for basic aspects of the oscillatory activity relevant for language) to infer some properties of the Neanderthal oscillome. We have found that several candidates for the language oscillogenome show differences in their methylation patterns between Neanderthals and humans. We argue that differences in their expression levels could be informative of differences in cognitive functions important for language.},
}

Animals
Anthropology, Physical
Computational Biology
*Cultural Evolution
DNA Methylation/genetics
Genetic Techniques
*Language
*Neanderthals/genetics/physiology
Nervous System Physiological Phenomena/genetics
Speech/*physiology

@article {pmid30564397,
year = {2018},
author = {Savriama, Y and Valtonen, M and Kammonen, JI and Rastas, P and Smolander, OP and Lyyski, A and Häkkinen, TJ and Corfe, IJ and Gerber, S and Salazar-Ciudad, I and Paulin, L and Holm, L and Löytynoja, A and Auvinen, P and Jernvall, J},
title = {Bracketing phenogenotypic limits of mammalian hybridization.},
journal = {Royal Society open science},
volume = {5},
number = {11},
pages = {180903},
doi = {10.1098/rsos.180903},
pmid = {30564397},
issn = {2054-5703},
abstract = {An increasing number of mammalian species have been shown to have a history of hybridization and introgression based on genetic analyses. Only relatively few fossils, however, preserve genetic material, and morphology must be used to identify the species and determine whether morphologically intermediate fossils could represent hybrids. Because dental and cranial fossils are typically the key body parts studied in mammalian palaeontology, here we bracket the potential for phenotypically extreme hybridizations by examining uniquely preserved cranio-dental material of a captive hybrid between grey and ringed seals. We analysed how distinct these species are genetically and morphologically, how easy it is to identify the hybrids using morphology and whether comparable hybridizations happen in the wild. We show that the genetic distance between these species is more than twice the modern human-Neanderthal distance, but still within that of morphologically similar species pairs known to hybridize. By contrast, morphological and developmental analyses show grey and ringed seals to be highly disparate, and that the hybrid is a predictable intermediate. Genetic analyses of the parent populations reveal introgression in the wild, suggesting that grey-ringed seal hybridization is not limited to captivity. Taken together, we postulate that there is considerable potential for mammalian hybridization between phenotypically disparate taxa.},
}

@article {pmid30564067,
year = {2018},
author = {Benítez-Burraco, A},
title = {Differences in the Neanderthal BRCA2 gene might be related to their distinctive cognitive profile.},
journal = {Hereditas},
volume = {155},
number = {},
pages = {38},
doi = {10.1186/s41065-018-0076-2},
pmid = {30564067},
issn = {1601-5223},
mesh = {Animals ; Brain/growth & development ; *Cognition ; *Genes, BRCA2 ; Neanderthals/*genetics ; },
abstract = {The unique divergence of the BRCA2 gene in Neanderthals compared to modern humans has been hypothesized to account for a differential susceptibility to cancer. However, the role of the gene in brain development and its connection with autism suggest that these differences might be (also) related to the more encapsulated nature of the Neanderthal cognition and their (inferred) autistic-like features.},
}

Animals
Brain/growth & development
*Cognition
*Genes, BRCA2
Neanderthals/*genetics

@article {pmid30563976,
year = {2018},
author = {Gibney, E and Callaway, E and Cyranoski, D and Gaind, N and Tollefson, J and Courtland, R and Law, YH and Maher, B and Else, H and Castelvecchi, D},
title = {Nature's 10: Ten people who mattered in science in 2018.},
journal = {Nature},
volume = {564},
number = {7736},
pages = {325-335},
doi = {10.1038/d41586-018-07683-5},
pmid = {30563976},
issn = {1476-4687},
mesh = {Animals ; Astronomy/*trends ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Electric Conductivity ; Environmental Pollution/*prevention & control ; Female ; *Forensic Genetics ; *Gene Editing ; Global Warming/*statistics & numerical data ; Graphite/*chemistry ; Humans ; Hybridization, Genetic ; Male ; *Minor Planets ; *Minority Groups ; Neanderthals/*genetics ; *Open Access Publishing ; Paleontology ; Pedigree ; Plastics ; Twins/*genetics ; },
}

Animals
Astronomy/*trends
Clustered Regularly Interspaced Short Palindromic Repeats/genetics
Electric Conductivity
Environmental Pollution/*prevention & control
Female
*Forensic Genetics
*Gene Editing
Global Warming/*statistics & numerical data
Graphite/*chemistry
Humans
Hybridization, Genetic
Male
*Minor Planets
*Minority Groups
Neanderthals/*genetics
*Open Access Publishing
Paleontology
Pedigree
Plastics
Twins/*genetics

@article {pmid30554901,
year = {2019},
author = {Gunz, P and Tilot, AK and Wittfeld, K and Teumer, A and Shapland, CY and van Erp, TGM and Dannemann, M and Vernot, B and Neubauer, S and Guadalupe, T and Fernández, G and Brunner, HG and Enard, W and Fallon, J and Hosten, N and Völker, U and Profico, A and Di Vincenzo, F and Manzi, G and Kelso, J and St Pourcain, B and Hublin, JJ and Franke, B and Pääbo, S and Macciardi, F and Grabe, HJ and Fisher, SE},
title = {Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity.},
journal = {Current biology : CB},
volume = {29},
number = {1},
pages = {120-127.e5},
doi = {10.1016/j.cub.2018.10.065},
pmid = {30554901},
issn = {1879-0445},
support = {U24 RR021992/RR/NCRR NIH HHS/United States ; U24 RR025736/RR/NCRR NIH HHS/United States ; U54 EB020403/EB/NIBIB NIH HHS/United States ; },
abstract = {One of the features that distinguishes modern humans from our extinct relatives and ancestors is a globular shape of the braincase [1-4]. As the endocranium closely mirrors the outer shape of the brain, these differences might reflect altered neural architecture [4, 5]. However, in the absence of fossil brain tissue, the underlying neuroanatomical changes as well as their genetic bases remain elusive. To better understand the biological foundations of modern human endocranial shape, we turn to our closest extinct relatives: the Neandertals. Interbreeding between modern humans and Neandertals has resulted in introgressed fragments of Neandertal DNA in the genomes of present-day non-Africans [6, 7]. Based on shape analyses of fossil skull endocasts, we derive a measure of endocranial globularity from structural MRI scans of thousands of modern humans and study the effects of introgressed fragments of Neandertal DNA on this phenotype. We find that Neandertal alleles on chromosomes 1 and 18 are associated with reduced endocranial globularity. These alleles influence expression of two nearby genes, UBR4 and PHLPP1, which are involved in neurogenesis and myelination, respectively. Our findings show how integration of fossil skull data with archaic genomics and neuroimaging can suggest developmental mechanisms that may contribute to the unique modern human endocranial shape.},
}

@article {pmid30545868,
year = {2018},
author = {Gibbons, A},
title = {Why modern humans have round heads.},
journal = {Science (New York, N.Y.)},
volume = {362},
number = {6420},
pages = {1229},
doi = {10.1126/science.362.6420.1229-a},
pmid = {30545868},
issn = {1095-9203},
mesh = {Animals ; *Biological Evolution ; Brain/*anatomy & histology ; *DNA, Ancient ; Head/*anatomy & histology ; Humans ; Neanderthals/*genetics ; },
}

Animals
*Biological Evolution
Brain/*anatomy & histology
*DNA, Ancient
Head/*anatomy & histology
Humans
Neanderthals/*genetics

@article {pmid30545758,
year = {2019},
author = {Banerjee, N and Polushina, T and Bettella, F and Steen, VM and Andreassen, OA and Le Hellard, S},
title = {Analysis of differentially methylated regions in great apes and extinct hominids provides support for the evolutionary hypothesis of schizophrenia.},
journal = {Schizophrenia research},
volume = {206},
number = {},
pages = {209-216},
doi = {10.1016/j.schres.2018.11.025},
pmid = {30545758},
issn = {1573-2509},
abstract = {INTRODUCTION: The persistence of schizophrenia in human populations separated by geography and time led to the evolutionary hypothesis that proposes schizophrenia as a by-product of the higher cognitive abilities of modern humans. To explore this hypothesis, we used here an evolutionary epigenetics approach building on differentially methylated regions (DMRs) of the genome.

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

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

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

@article {pmid30540784,
year = {2018},
author = {Caricola, I and Zupancich, A and Moscone, D and Mutri, G and Falcucci, A and Duches, R and Peresani, M and Cristiani, E},
title = {An integrated method for understanding the function of macro-lithic tools. Use wear, 3D and spatial analyses of an Early Upper Palaeolithic assemblage from North Eastern Italy.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0207773},
doi = {10.1371/journal.pone.0207773},
pmid = {30540784},
issn = {1932-6203},
mesh = {Animals ; Archaeology/*methods ; Caves ; Fossils/*diagnostic imaging ; Humans ; Italy ; Neanderthals ; Spatial Analysis ; Technology ; },
abstract = {The article presents an original analysis which combines use-wear, 3D modelling and spatial analyses to experimental archaeology in order to investigate Early Upper Palaeolithic flint-knapping gestures and techniques involving the use of macro-lithic tools. In particular, the methodological framework proposed in this paper was applied to the study of Protoaurignacian and Aurignacian macro-tools from Fumane Cave (Verona, Italy). Combining spatial analysis and use wear investigation, both at low and high magnifications, permitted the identification and detailed description of the use-related traces affecting both the hammerstones and retouchers which, at Fumane Cave, were used at different stages during flint tool production. Several experimental activities were performed including core reduction, maintenance, and blank production together with different types of edge retouching. From a methodological perspective, the protocol of analysis permitted to codify specific traces and to produce quantitative data related to their geometry and distribution over the tool's surface, according to the activities and gestures performed. The results obtained allowed a careful investigation of the function and the gestures associated to the use of the macro-lithic tools coming from the Protoaurignacian and Aurignacian levels of Fumane Cave while providing a methodological tool for interpreting different archaeological samples.},
}

Animals
Archaeology/*methods
Caves
Fossils/*diagnostic imaging
Humans
Italy
Neanderthals
Spatial Analysis
Technology

@article {pmid30520032,
year = {2019},
author = {Bruner, E},
title = {Human paleoneurology: Shaping cortical evolution in fossil hominids.},
journal = {The Journal of comparative neurology},
volume = {527},
number = {10},
pages = {1753-1765},
doi = {10.1002/cne.24591},
pmid = {30520032},
issn = {1096-9861},
support = {CGL2015-65387-C3-3-P//Ministerio de Economía y Competitividad/ ; },
abstract = {Evolutionary neuroanatomy must integrate two different sources of information, namely from fossil and from living species. Fossils supply information concerning the process of evolution, whereas living species supply information on the product of evolution. Unfortunately, the fossil record is partial and fragmented, and often cannot support validations for specific evolutionary hypotheses. Living species can provide more comprehensive indications, but they do not represent ancestral groups or primitive forms. Macaques or chimpanzees are frequently used as proxy for human ancestral conditions, despite the fact they are divergent and specialized lineages, with their own biological features. Similarly, in paleoanthropology independent lineages (such as Neanderthals) should not be confused with ancestral modern human stages. In this comparative framework, paleoneurology deals with the analysis of the endocranial cavity in extinct species, in order to make inferences on brain evolution. A main target of this field is to distinguish the endocranial variations due to brain changes, from those due to cranial constraints. Digital anatomy and computed morphometrics have provided major advances in this field. However, brains and endocasts can be hard to analyze with geometrical models, because of uncertainties due to the localization of cortical landmarks and boundaries. The study of the evolution of the parietal cortex supplies an interesting case-study in which paleontological and neontological data can integrate and test evolutionary hypotheses based on multiple sources of evidence. The relationships with visuospatial functions and brain-body-tool integration stress further that the analysis of the cognitive system should go beyond the neural boundaries of the brain.},
}

@article {pmid30478367,
year = {2018},
author = {Mirazón Lahr, M},
title = {The not-so-dangerous lives of Neanderthals.},
journal = {Nature},
volume = {563},
number = {7733},
pages = {634-636},
doi = {10.1038/d41586-018-07343-8},
pmid = {30478367},
issn = {1476-4687},
mesh = {Animals ; Anthropology ; *Hominidae ; Humans ; *Neanderthals ; Prevalence ; },
}

Animals
Anthropology
*Hominidae
Humans
*Neanderthals
Prevalence

@article {pmid30478305,
year = {2019},
author = {Villanea, FA and Schraiber, JG},
title = {Multiple episodes of interbreeding between Neanderthal and modern humans.},
journal = {Nature ecology & evolution},
volume = {3},
number = {1},
pages = {39-44},
doi = {10.1038/s41559-018-0735-8},
pmid = {30478305},
issn = {2397-334X},
support = {R35 GM124745/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Gene Flow ; Genome, Human ; Humans ; *Hybridization, Genetic ; Models, Theoretical ; Neanderthals/*genetics ; },
abstract = {Neanderthals and anatomically modern humans overlapped geographically for a period of over 30,000 years following human migration out of Africa. During this period, Neanderthals and humans interbred, as evidenced by Neanderthal portions of the genome carried by non-African individuals today. A key observation is that the proportion of Neanderthal ancestry is ~12-20% higher in East Asian individuals relative to European individuals. Here, we explore various demographic models that could explain this observation. These include distinguishing between a single admixture event and multiple Neanderthal contributions to either population, and the hypothesis that reduced Neanderthal ancestry in modern Europeans resulted from more recent admixture with a ghost population that lacked a Neanderthal ancestry component (the 'dilution' hypothesis). To summarize the asymmetric pattern of Neanderthal allele frequencies, we compiled the joint fragment frequency spectrum of European and East Asian Neanderthal fragments and compared it with both analytical theory and data simulated under various models of admixture. Using maximum-likelihood and machine learning, we found that a simple model of a single admixture did not fit the empirical data, and instead favour a model of multiple episodes of gene flow into both European and East Asian populations. These findings indicate a longer-term, more complex interaction between humans and Neanderthals than was previously appreciated.},
}

Animals
Gene Flow
Genome, Human
Humans
*Hybridization, Genetic
Models, Theoretical
Neanderthals/*genetics

@article {pmid30478304,
year = {2019},
author = {Mafessoni, F},
title = {Encounters with archaic hominins.},
journal = {Nature ecology & evolution},
volume = {3},
number = {1},
pages = {14-15},
doi = {10.1038/s41559-018-0729-6},
pmid = {30478304},
issn = {2397-334X},
mesh = {Animals ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; },
}

Animals
Fossils
*Hominidae
Humans
*Neanderthals

@article {pmid30462354,
year = {2019},
author = {Becam, G and Chevalier, T},
title = {Neandertal features of the deciduous and permanent teeth from Portel-Ouest Cave (Ariège, France).},
journal = {American journal of physical anthropology},
volume = {168},
number = {1},
pages = {45-69},
doi = {10.1002/ajpa.23719},
pmid = {30462354},
issn = {1096-8644},
support = {//Association des Membres des Palmes Académiques des Pyrénées-Orientales/ ; //Muséum national d'Histoire naturelle de Paris/ ; //UMR 7194, laboratoire Histoire Naturelle de l'Homme Préhistorique/ ; },
abstract = {OBJECTIVES: We describe 14 unpublished and nine published teeth from the Mousterian level of Portel-Ouest (Ariège, France), dated to 44 ka. In a comparative context, we explore the taxonomical affinities of those teeth with Neandertals and modern humans which are both known to exist at that time. We further make some paleobiological inferences about this human group.

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

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

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

@article {pmid30429606,
year = {2018},
author = {Beier, J and Anthes, N and Wahl, J and Harvati, K},
title = {Similar cranial trauma prevalence among Neanderthals and Upper Palaeolithic modern humans.},
journal = {Nature},
volume = {563},
number = {7733},
pages = {686-690},
doi = {10.1038/s41586-018-0696-8},
pmid = {30429606},
issn = {1476-4687},
mesh = {Adult ; Age Determination by Skeleton ; Animals ; Brain Injuries, Traumatic/epidemiology/*history/pathology ; Child ; Female ; *Fossils ; History, Ancient ; Humans ; Incidence ; Life Style/history ; Male ; *Neanderthals ; Prevalence ; Sex Determination by Skeleton ; Skull/*pathology ; Uncertainty ; Violence/history ; Young Adult ; },
abstract = {Neanderthals are commonly depicted as leading dangerous lives and permanently struggling for survival. This view largely relies on the high incidences of trauma that have been reported1,2 and have variously been attributed to violent social behaviour3,4, highly mobile hunter-gatherer lifestyles2 or attacks by carnivores5. The described Neanderthal pattern of predominantly cranial injuries is further thought to reflect violent encounters with large prey mammals, resulting from the use of close-range hunting weapons1. These interpretations directly shape our understanding of Neanderthal lifestyles, health and hunting abilities, yet mainly rest on descriptive, case-based evidence. Quantitative, population-level studies of traumatic injuries are rare. Here we reassess the hypothesis of higher cranial trauma prevalence among Neanderthals using a population-level approach-accounting for preservation bias and other contextual data-and an exhaustive fossil database. We show that Neanderthals and early Upper Palaeolithic anatomically modern humans exhibit similar overall incidences of cranial trauma, which are higher for males in both taxa, consistent with patterns shown by later populations of modern humans. Beyond these similarities, we observed species-specific, age-related variation in trauma prevalence, suggesting that there were differences in the timing of injuries during life or that there was a differential mortality risk of trauma survivors in the two groups. Finally, our results highlight the importance of preservation bias in studies of trauma prevalence.},
}

Adult
Age Determination by Skeleton
Animals
Brain Injuries, Traumatic/epidemiology/*history/pathology
Child
Female
*Fossils
History, Ancient
Humans
Incidence
Life Style/history
Male
*Neanderthals
Prevalence
Sex Determination by Skeleton
Skull/*pathology
Uncertainty
Violence/history
Young Adult