@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 = {},
number = {},
pages = {},
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},
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 {pmid28567860,
year = {2017},
author = {Hardy, K and Buckley, S},
title = {Earliest evidence of bitumen from Homo sp. teeth is from El Sidrón.},
journal = {American journal of physical anthropology},
volume = {164},
number = {1},
pages = {212-213},
doi = {10.1002/ajpa.23255},
pmid = {28567860},
issn = {1096-8644},
mesh = {Animals ; Dentistry ; *Hominidae ; Hydrocarbons ; *Neanderthals ; Tooth ; },
}

Animals
Dentistry
*Hominidae
Hydrocarbons
*Neanderthals
Tooth

@article {pmid30215675,
year = {2018},
author = {Kawash, JK and Smith, SD and Karaiskos, S and Grigoriev, A},
title = {ARIADNA: machine learning method for ancient DNA variant discovery.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {25},
number = {6},
pages = {619-627},
pmid = {30215675},
issn = {1756-1663},
mesh = {Animals ; DNA, Ancient/*chemistry ; *Genetic Variation ; Genome ; *Machine Learning ; Mammoths/genetics ; Mutation ; Neanderthals/genetics ; },
abstract = {Ancient DNA (aDNA) studies often rely on standard methods of mutation calling, optimized for high-quality contemporary DNA but not for excessive contamination, time- or environment-related damage of aDNA. In the absence of validated datasets and despite showing extreme sensitivity to aDNA quality, these methods have been used in many published studies, sometimes with additions of arbitrary filters or modifications, designed to overcome aDNA degradation and contamination problems. The general lack of best practices for aDNA mutation calling may lead to inaccurate results. To address these problems, we present ARIADNA (ARtificial Intelligence for Ancient DNA), a novel approach based on machine learning techniques, using specific aDNA characteristics as features to yield improved mutation calls. In our comparisons of variant callers across several ancient genomes, ARIADNA consistently detected higher-quality genome variants with fast runtimes, while reducing the false positive rate compared with other approaches.},
}

Animals
DNA, Ancient/*chemistry
*Genetic Variation
Genome
*Machine Learning
Mammoths/genetics
Mutation
Neanderthals/genetics

@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},
}

@article {pmid28754955,
year = {2017},
author = {Drucker, DG and Naito, YI and Péan, S and Prat, S and Crépin, L and Chikaraishi, Y and Ohkouchi, N and Puaud, S and Lázničková-Galetová, M and Patou-Mathis, M and Yanevich, A and Bocherens, H},
title = {Isotopic analyses suggest mammoth and plant in the diet of the oldest anatomically modern humans from far southeast Europe.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {6833},
pmid = {28754955},
issn = {2045-2322},
mesh = {Animals ; *Carnivory ; Collagen/chemistry ; *Diet ; Europe ; *Fossils ; *Herbivory ; Humans ; Neanderthals/physiology ; Nitrogen Isotopes/analysis ; },
abstract = {Relatively high 15N abundances in bone collagen of early anatomically modern humans in Europe have often been interpreted as a specific consumption of freshwater resources, even if mammoth is an alternative high 15N prey. At Buran-Kaya III, access to associated fauna in a secured archaeological context and application of recently developed isotopic analyses of individuals amino acids offer the opportunity to further examine this hypothesis. The site of Buran-Kaya III is located in south Crimea and has provided a rich archaeological sequence including two Upper Palaeolithic layers, from which human fossils were retrieved and directly dated as from 37.8 to 33.1 ka cal BP. Results from bulk collagen of three human remains suggests the consumption of a high 15N prey besides the contribution of saiga, red deer, horse and hare, whose butchered remains were present at the site. In contrast to bulk collagen, phenylalanine and glutamic acid 15N abundances reflect not only animal but also plant protein contributions to omnivorous diet, and allow disentangling aquatic from terrestrial resource consumption. The inferred human trophic position values point to terrestrial-based diet, meaning a significant contribution of mammoth meat, in addition to a clear intake of plant protein.},
}

Animals
*Carnivory
Collagen/chemistry
*Diet
Europe
*Fossils
*Herbivory
Humans
Neanderthals/physiology
Nitrogen Isotopes/analysis

@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 = {},
number = {},
pages = {},
doi = {10.1073/pnas.1820745116},
pmid = {30804177},
issn = {1091-6490},
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.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1073/pnas.1814087116},
pmid = {30782806},
issn = {1091-6490},
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.},
}

@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 Iverson, PO and Stover, PJ},
title = {Nutrition and its role in human evolution.},
journal = {Journal of internal medicine},
volume = {},
number = {},
pages = {},
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 = {},
number = {},
pages = {},
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 = {CGL2016-75109-P//Ministerio de Ciencia y Tecnología (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 = {},
number = {},
pages = {},
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 {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},
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.},
}

@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},
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.},
}

@article {pmid30590594,
year = {2018},
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 = {},
number = {},
pages = {},
doi = {10.1093/glycob/cwy113},
pmid = {30590594},
issn = {1460-2423},
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},
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.},
}

@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},
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.},
}

@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},
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.},
}

@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 = {},
doi = {10.4436/JASS.96010},
pmid = {30566085},
issn = {2037-0644},
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.},
}

@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 {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 = {2018},
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 = {},
number = {},
pages = {},
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 {pmid30520032,
year = {2018},
author = {Bruner, E},
title = {Human paleoneurology: Shaping cortical evolution in fossil hominids.},
journal = {The Journal of comparative neurology},
volume = {},
number = {},
pages = {},
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 ; },
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.},
}

@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},
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.},
}

@article {pmid30410429,
year = {2018},
author = {Michalak, P and Kang, L},
title = {Unique divergence of the breast cancer 2 (BRCA2) gene in Neanderthals.},
journal = {Hereditas},
volume = {155},
number = {},
pages = {34},
pmid = {30410429},
issn = {1601-5223},
mesh = {Alleles ; Animals ; BRCA2 Protein/*genetics ; *Evolution, Molecular ; Humans ; Neanderthals/*genetics ; Polymorphism, Single Nucleotide ; },
abstract = {Unique divergence of the BRCA2, a tumor suppressor gene, in Neanderthals relative to other primates, including modern humans, is highlighted. This divergence with potentially pathogenic consequences raises a question about cancer susceptibility in the archaic species that was replaced by modern humans about 40,000 years ago.},
}

Alleles
Animals
BRCA2 Protein/*genetics
*Evolution, Molecular
Humans
Neanderthals/*genetics
Polymorphism, Single Nucleotide

@article {pmid30402544,
year = {2018},
author = {Smith, TM and Austin, C and Green, DR and Joannes-Boyau, R and Bailey, S and Dumitriu, D and Fallon, S and Grün, R and James, HF and Moncel, MH and Williams, IS and Wood, R and Arora, M},
title = {Wintertime stress, nursing, and lead exposure in Neanderthal children.},
journal = {Science advances},
volume = {4},
number = {10},
pages = {eaau9483},
pmid = {30402544},
issn = {2375-2548},
abstract = {Scholars endeavor to understand the relationship between human evolution and climate change. This is particularly germane for Neanderthals, who survived extreme Eurasian environmental variation and glaciations, mysteriously going extinct during a cool interglacial stage. Here, we integrate weekly records of climate, tooth growth, and metal exposure in two Neanderthals and one modern human from southeastern France. The Neanderthals inhabited cooler and more seasonal periods than the modern human, evincing childhood developmental stress during wintertime. In one instance, this stress may have included skeletal mobilization of elemental stores and weight loss; this individual was born in the spring and appears to have weaned 2.5 years later. Both Neanderthals were exposed to lead at least twice during the deep winter and/or early spring. This multidisciplinary approach elucidates direct relationships between ancient environments and hominin paleobiology.},
}

@article {pmid30387382,
year = {2018},
author = {Kamnikar, KR and Herrmann, NP and Plemons, AM},
title = {New Approaches to Juvenile Age Estimation in Forensics: Application of Transition Analysis via the Shackelford et al. Method to a Diverse Modern Subadult Sample.},
journal = {Human biology},
volume = {90},
number = {1},
pages = {11-30},
pmid = {30387382},
issn = {1534-6617},
abstract = {Dental development is one of the most widely utilized and accurate methods available for estimating age in subadult skeletal remains. The timing of tooth growth and development is regulated by genetics and less affected by external factors, allowing reliable estimates of chronological age. Traditional methodology focuses on comparing tooth developmental scores to corresponding age charts. Using the Moorrees, Fanning, and Hunt (MFH) developmental scores, Shackelford and colleagues embed the dental development method in a statistical framework based on transition analysis. They generated numerical parameters underlining each "stage" and age-at-death distribution and applied them to fossil hominins and Neanderthals with limited application to modern humans. We use this same method on a subadult test sample (n = 201), representing modern individuals that may become part of the forensic record. We assess the probability coverage of the Shackelford et al. method derived from MFH standards as it applies to all available dentition. Results indicate promise: the age range at 90% and 95% confidence levels includes the chronological age of almost every individual tested. The maximum likelihood age estimates underestimate age by 0.5-2.5 years for individuals 0-15 years of age and by >2.5 years for individuals 16-18 years of age, as previously shown. In an attempt to refine the method, we adjusted the numerical parameters underlying the stages for developing teeth based on a combined modern reference sample (n = 1,964) and tested these revised parameters using the same test sample. The estimated ages from the modified method differ from the original Shackelford et al. methodology by underestimating age to a lesser degree. The modified method does include mean age-at-attainment values for earlier stages of several teeth, allowing for the calculation of narrower confidence intervals. While this study highlights areas of future research in refining dental developmental aging by transition analysis, it also demonstrates that the Shackelford et al. method is applicable and accurate when aging modern subadults in forensic work.},
}

@article {pmid30386687,
year = {2018},
author = {Akhtari, FS and Havener, TM and Fukudo, M and Jack, JR and McLeod, HL and Wiltshire, T and Motsinger-Reif, AA},
title = {The influence of Neanderthal alleles on cytotoxic response.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5691},
pmid = {30386687},
issn = {2167-8359},
abstract = {Various studies have shown that people of Eurasian origin contain traces of DNA inherited from interbreeding with Neanderthals. Recent studies have demonstrated that these Neanderthal variants influence a range of clinically important traits and diseases. Thus, understanding the genetic factors responsible for the variability in individual response to drug or chemical exposure is a key goal of pharmacogenomics and toxicogenomics, as dose responses are clinically and epidemiologically important traits. It is well established that ethnic and racial differences are important in dose response traits, but to our knowledge the influence of Neanderthal ancestry on response to xenobiotics is unknown. Towards this aim, we examined if Neanderthal ancestry plays a role in cytotoxic response to anti-cancer drugs and toxic environmental chemicals. We identified common Neanderthal variants in lymphoblastoid cell lines (LCLs) derived from the globally diverse 1000 Genomes Project and Caucasian cell lines from the Children's Hospital of Oakland Research Institute. We analyzed the effects of these Neanderthal alleles on cytotoxic response to 29 anti-cancer drugs and 179 environmental chemicals at varying concentrations using genome-wide data. We identified and replicated single nucleotide polymorphisms (SNPs) from these association results, including a SNP in the SNORD-113 cluster. Our results also show that the Neanderthal alleles cumulatively lead to increased sensitivity to both the anti-cancer drugs and the environmental chemicals. Our results demonstrate the influence of Neanderthal ancestry-informative markers on cytotoxic response. These results could be important in identifying biomarkers for personalized medicine or in dissecting the underlying etiology of dose response traits.},
}

@article {pmid30383862,
year = {2018},
author = {Chen, Z and DeSalle, R and Schiffman, M and Herrero, R and Wood, CE and Ruiz, JC and Clifford, GM and Chan, PKS and Burk, RD},
title = {Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans.},
journal = {PLoS pathogens},
volume = {14},
number = {11},
pages = {e1007352},
pmid = {30383862},
issn = {1553-7374},
support = {P30 AI124414/AI/NIAID NIH HHS/United States ; P30 CA013330/CA/NCI NIH HHS/United States ; },
abstract = {Recent discoveries on the origins of modern humans from multiple archaic hominin populations and the diversity of human papillomaviruses (HPVs) suggest a complex scenario of virus-host evolution. To evaluate the origin of HPV pathogenesis, we estimated the phylogeny, timing, and dispersal of HPV16 variants using a Bayesian Markov Chain Monte Carlo framework. To increase precision, we identified and characterized non-human primate papillomaviruses from New and Old World monkeys to set molecular clock models. We demonstrate specific host niche adaptation of primate papillomaviruses with subsequent coevolution with their primate hosts for at least 40 million years. Analyses of 212 HPV16 complete genomes and 3582 partial sequences estimated ancient divergence of HPV16 variants (between A and BCD lineages) from their most recent common ancestors around half a million years ago, roughly coinciding with the timing of the split between archaic Neanderthals and modern Homo sapiens, and nearly three times longer than divergence times of modern Homo sapiens. HPV16 A lineage variants were significantly underrepresented in present African populations, whereas the A sublineages were highly prevalent in European (A1-3) and Asian (A4) populations, indicative of viral sexual transmission from Neanderthals to modern non-African humans through multiple interbreeding events in the past 80 thousand years. Remarkably, the human leukocyte antigen B*07:02 and C*07:02 alleles associated with increased risk in cervix cancer represent introgressed regions from Neanderthals in present-day Eurasians. The archaic hominin-host-switch model was also supported by other HPV variants. Niche adaptation and virus-host codivergence appear to influence the pathogenesis of papillomaviruses.},
}

@article {pmid30377294,
year = {2018},
author = {Gómez-Olivencia, A and Barash, A and García-Martínez, D and Arlegi, M and Kramer, P and Bastir, M and Been, E},
title = {3D virtual reconstruction of the Kebara 2 Neandertal thorax.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {4387},
pmid = {30377294},
issn = {2041-1723},
mesh = {Animals ; *Fossils ; Humans ; *Imaging, Three-Dimensional ; Male ; Middle Aged ; Neanderthals/*anatomy & histology ; Organ Size ; Principal Component Analysis ; Thorax/*anatomy & histology ; },
abstract = {The size and shape of the Neandertal thorax has been debated since the first discovery of Neandertal ribs more than 150 years ago, with workers proposing different interpretations ranging from a Neandertal thoracic morphology that is indistinguishable from modern humans, to one that was significantly different from them. Here, we provide a virtual 3D reconstruction of the thorax of the adult male Kebara 2 Neandertal. Our analyses reveal that the Kebara 2 thorax is significantly different but not larger from that of modern humans, wider in its lower segment, which parallels his wide bi-iliac breadth, and with a more invaginated vertebral column. Kinematic analyses show that rib cages that are wider in their lower segment produce greater overall size increments (respiratory capacity) during inspiration. We hypothesize that Neandertals may have had a subtle, but somewhat different breathing mechanism compared to modern humans.},
}

Animals
*Fossils
Humans
*Imaging, Three-Dimensional
Male
Middle Aged
Neanderthals/*anatomy & histology
Organ Size
Principal Component Analysis
Thorax/*anatomy & histology

@article {pmid30359256,
year = {2018},
author = {de Filippo, C and Meyer, M and Prüfer, K},
title = {Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences.},
journal = {BMC biology},
volume = {16},
number = {1},
pages = {121},
pmid = {30359256},
issn = {1741-7007},
abstract = {BACKGROUND: The study of ancient DNA is hampered by degradation, resulting in short DNA fragments. Advances in laboratory methods have made it possible to retrieve short DNA fragments, thereby improving access to DNA preserved in highly degraded, ancient material. However, such material contains large amounts of microbial contamination in addition to DNA fragments from the ancient organism. The resulting mixture of sequences constitutes a challenge for computational analysis, since microbial sequences are hard to distinguish from the ancient sequences of interest, especially when they are short.

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

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

@article {pmid30351468,
year = {2019},
author = {Pablos, A and Gómez-Olivencia, A and Arsuaga, JL},
title = {A Neandertal foot phalanx from the Galería de las Estatuas site (Sierra de Atapuerca, Spain).},
journal = {American journal of physical anthropology},
volume = {168},
number = {1},
pages = {222-228},
doi = {10.1002/ajpa.23729},
pmid = {30351468},
issn = {1096-8644},
support = {//Fundación Atapuerca/ ; //Junta de Castilla y León/ ; CGL2015-65387-C3-2-P MINECO/FEDER//Ministerio de Economía y Competitividad/ ; },
abstract = {OBJECTIVES: The Galería de las Estatuas site (GE), a new Mousterian site at the Sierra de Atapuerca site complex (Spain), has revealed a Late Pleistocene detrital sequence with at least five lithostratigraphic units. These units have yielded evidence of Mousterian occupations with sporadic carnivore activity, and have provided datings of 80-112 ka BP using single-grain optically stimulated luminescence. This places the sequence at the end of MIS5 and beginning of the MIS4. We described here a complete adult human distal foot phalanx (GE-1573) recovered during the 2017 field season in the interface between lithostratigraphic units 3 and 4 (107-112 ka BP) in the GE-I test pit.

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

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

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

@article {pmid30351445,
year = {2019},
author = {Stelzer, S and Neubauer, S and Hublin, JJ and Spoor, F and Gunz, P},
title = {Morphological trends in arcade shape and size in Middle Pleistocene Homo.},
journal = {American journal of physical anthropology},
volume = {168},
number = {1},
pages = {70-91},
doi = {10.1002/ajpa.23721},
pmid = {30351445},
issn = {1096-8644},
support = {//Max Planck Society/ ; },
abstract = {OBJECTIVES: Middle Pleistocene fossil hominins, often summarized as Homo heidelbergensis sensu lato, are difficult to interpret due to a fragmentary fossil record and ambiguous combinations of primitive and derived characters. Here, we focus on one aspect of facial shape and analyze shape variation of the dental arcades of these fossils together with other Homo individuals.

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

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

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

@article {pmid30332432,
year = {2018},
author = {Cortés-Sánchez, M and Riquelme-Cantal, JA and Simón-Vallejo, MD and Parrilla Giráldez, R and Odriozola, CP and Calle Román, L and Carrión, JS and Monge Gómez, G and Rodríguez Vidal, J and Moyano Campos, JJ and Rico Delgado, F and Nieto Julián, JE and Antón García, D and Martínez-Aguirre, MA and Jiménez Barredo, F and Cantero-Chinchilla, FN},
title = {Pre-Solutrean rock art in southernmost Europe: Evidence from Las Ventanas Cave (Andalusia, Spain).},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0204651},
pmid = {30332432},
issn = {1932-6203},
abstract = {The south of Iberia conserves an important group of Palaeolithic rock art sites. The graphisms have been mostly attributed to the Solutrean and Magdalenian periods, while the possibility that older remains exist has provoked extensive debate. This circumstance has been linked to both the cited periods, until recently, due to the transition from the Middle to Upper Palaeolithic in the extreme southwest of Europe as well as the non-existence of some of the early periods of Palaeolithic art documented in northern Iberia. This study presents the results of interdisciplinary research conducted in Las Ventanas Cave. These results enabled us to identify a new Palaeolithic rock art site. The technical, stylistic and temporal traits point to certain similarities with the range of exterior deep engravings in Cantabrian Palaeolithic rock art. Ventanas appears to corroborate the age attributed to those kinds of graphic expression and points to the early arrival of the Upper Palaeolithic in the south of Iberia. Importantly, the results provide information on the pre-Solutrean date attributed to trilinear hind figures. These findings challenge the supposed Neanderthal survival idea at one of the main late Middle Palaeolithic southern Iberian sites (Carigüela) and, due to the parallels between them and an engraving attributed to this period in Gibraltar, it raises the possibility of interaction between modern humans and Neanderthals in the extreme southwest of Europe.},
}

@article {pmid30327578,
year = {2018},
author = {Williams, AC and Hill, LJ},
title = {Nicotinamide's Ups and Downs: Consequences for Fertility, Development, Longevity and Diseases of Poverty and Affluence.},
journal = {International journal of tryptophan research : IJTR},
volume = {11},
number = {},
pages = {1178646918802289},
pmid = {30327578},
issn = {1178-6469},
abstract = {To further explore the role of dietary nicotinamide in both brain development and diseases, particularly those of ageing. Articles cover neurodegenerative disease and cancer. Also discussed are the effects of nicotinamide, contained in meat and supplements and derived from symbionts, on the major transitions of disease and fertility from ancient times up to the present day. A key role for the tryptophan - NAD 'de novo' and immune tolerance pathway are discussed at length in the context of fertility and longevity and the transitions from immune paresis to Treg-mediated immune tolerance and then finally to intolerance and their associated diseases. Abstract: Nicotinamide in human evolution increased cognitive power in a positive feedback loop originally involving hunting. As the precursor to metabolic master molecule NAD it is, as vitamin B3, vital for health. Paradoxically, a lower dose on a diverse plant then cereal-based diet fuelled population booms from the Mesolithic onwards, by upping immune tolerance of the foetus. Increased tolerance of risky symbionts, whether in the gut or TB, that excrete nicotinamide co-evolved as buffers for when diet was inadequate. High biological fertility, despite disease trade-offs, avoided the extinction of Homo sapiens and heralded the dawn of a conscious, creative, and pro-fertility culture. Nicotinamide equity now would stabilise populations and prevent NAD-based diseases of poverty and affluence.},
}

@article {pmid30326183,
year = {2018},
author = {Hardy, K and Buckley, S and Copeland, L},
title = {Pleistocene dental calculus: Recovering information on Paleolithic food items, medicines, paleoenvironment and microbes.},
journal = {Evolutionary anthropology},
volume = {27},
number = {5},
pages = {234-246},
doi = {10.1002/evan.21718},
pmid = {30326183},
issn = {1520-6505},
mesh = {Animals ; Cooking ; Dental Calculus/*chemistry/history/*microbiology ; Diet/*history ; Environment ; Fossils ; History, Ancient ; Hominidae ; Neanderthals ; Starch/chemistry ; Vegetables/chemistry ; },
abstract = {Dental calculus is now widely used to recover information on items ingested in the past. It is particularly valuable in the earlier Paleolithic, where recovered data may represent the only evidence for plant use. Several recovery methods are used and each one produces different results. Biomolecular markers and genetic material recovered from dental calculus is providing new data on identifiable dietary and medicinal items and human microbial communities. The recovery of microfossils, in particular, starch granules, has triggered a new awareness of the role of plants in the diet throughout the Paleolithic. However, the minute amount of material recovered has little relationship with food eaten during a person's life, while salivary amylase breaks down cooked starch. Therefore, broader dietary interpretations and detection of cooked food are problematic. The study of ancient dental calculus holds great potential to recover information about past lives, within realistic parameters.},
}

Animals
Cooking
Dental Calculus/*chemistry/history/*microbiology
Diet/*history
Environment
Fossils
History, Ancient
Hominidae
Neanderthals
Starch/chemistry
Vegetables/chemistry

@article {pmid30310091,
year = {2018},
author = {Gravina, B and Bachellerie, F and Caux, S and Discamps, E and Faivre, JP and Galland, A and Michel, A and Teyssandier, N and Bordes, JG},
title = {No Reliable Evidence for a Neanderthal-Châtelperronian Association at La Roche-à-Pierrot, Saint-Césaire.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {15134},
pmid = {30310091},
issn = {2045-2322},
abstract = {The demise of Neanderthals and their interaction with dispersing anatomically modern human populations remain some of the most contentious issues in palaeoanthropology. The Châtelperronian, now generally recognized as the first genuine Upper Palaeolithic industry in Western Europe and commonly attributed to the Neanderthals, plays a pivotal role in these debates. The Neanderthal authorship of this techno-complex is based on reported associations of Neanderthal skeletal material with Châtelperronian assemblages at only two sites, La Roche-à-Pierrot (Saint-Césaire) and the Grotte du Renne (Arcy-sur-Cure). The reliability of such an association has, however, been the subject of heated controversy. Here we present a detailed taphonomic, spatial and typo-technological reassessment of the level (EJOP sup) containing the Neanderthal skeletal material at Saint-Césaire. Our assessment of a new larger sample of lithic artifacts, combined with a systematic refitting program and spatial projections of diagnostic artifacts, produced no reliable evidence for a Neanderthal-Châtelperronian association at the site. These results significantly impact current models concerning the Middle-to-Upper Palaeolithic transition in Western Europe and force a critical reappraisal of who exactly were the makers of the Châtelperronian.},
}

@article {pmid30309914,
year = {2018},
author = {Hoffmann, DL and Standish, CD and García-Diez, M and Pettitt, PB and Milton, JA and Zilhão, J and Alcolea-González, JJ and Cantalejo-Duarte, P and Collado, H and de Balbín, R and Lorblanchet, M and Ramos-Muñoz, J and Weniger, GC and Pike, AWG},
title = {Response to Comment on "U-Th dating of carbonate crusts reveals Neandertal origin of Iberian cave art".},
journal = {Science (New York, N.Y.)},
volume = {362},
number = {6411},
pages = {},
doi = {10.1126/science.aau1736},
pmid = {30309914},
issn = {1095-9203},
mesh = {Carbonates ; *Caves ; *Neanderthals ; Reproducibility of Results ; Spain ; },
abstract = {Slimak et al challenge the reliability of our oldest (>65,000 years) U-Th dates on carbonates associated with cave paintings in Spain. They cite a supposed lack of parietal art for the 25,000 years following this date, along with potential methodological issues relating to open-system behavior and corrections to detrital or source water 230Th. We show that their criticisms are unfounded.},
}

Carbonates
*Caves
*Neanderthals
Reproducibility of Results
Spain

@article {pmid30308076,
year = {2018},
author = {Bamford, CGG and Aranday-Cortes, E and Filipe, IC and Sukumar, S and Mair, D and Filipe, ADS and Mendoza, JL and Garcia, KC and Fan, S and Tishkoff, SA and McLauchlan, J},
title = {A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages.},
journal = {PLoS pathogens},
volume = {14},
number = {10},
pages = {e1007307},
pmid = {30308076},
issn = {1553-7374},
support = {MC_UU_12014/1//Medical Research Council/United Kingdom ; },
mesh = {Animals ; Antiviral Agents/*therapeutic use ; Biological Evolution ; Cardiovirus Infections/*drug therapy/genetics/virology ; Cells, Cultured ; Encephalomyocarditis virus/drug effects/isolation & purification ; Gene Expression Regulation ; Hepacivirus/drug effects/isolation & purification ; Hepatitis C/*drug therapy/genetics/virology ; Humans ; Interleukins/*genetics ; Pan troglodytes ; *Polymorphism, Single Nucleotide ; Species Specificity ; Zika Virus/drug effects/isolation & purification ; Zika Virus Infection/*drug therapy/genetics/virology ; },
abstract = {As antimicrobial signalling molecules, type III or lambda interferons (IFNλs) are critical for defence against infection by diverse pathogens, including bacteria, fungi and viruses. Counter-intuitively, expression of one member of the family, IFNλ4, is associated with decreased clearance of hepatitis C virus (HCV) in the human population; by contrast, a natural frameshift mutation that abrogates IFNλ4 production improves HCV clearance. To further understand how genetic variation between and within species affects IFNλ4 function, we screened a panel of all known extant coding variants of human IFNλ4 for their antiviral potential and identify three that substantially affect activity: P70S, L79F and K154E. The most notable variant was K154E, which was found in African Congo rainforest 'Pygmy' hunter-gatherers. K154E greatly enhanced in vitro activity in a range of antiviral (HCV, Zika virus, influenza virus and encephalomyocarditis virus) and gene expression assays. Remarkably, E154 is the ancestral residue in mammalian IFNλ4s and is extremely well conserved, yet K154 has been fixed throughout evolution of the hominid genus Homo, including Neanderthals. Compared to chimpanzee IFNλ4, the human orthologue had reduced activity due to amino acid K154. Comparison of published gene expression data from humans and chimpanzees showed that this difference in activity between K154 and E154 in IFNλ4 correlates with differences in antiviral gene expression in vivo during HCV infection. Mechanistically, our data show that the human-specific K154 negatively affects IFNλ4 activity through a novel means by reducing its secretion and potency. We thus demonstrate that attenuated activity of IFNλ4 is conserved among humans and postulate that differences in IFNλ4 activity between species contribute to distinct host-specific responses to-and outcomes of-infection, such as HCV infection. The driver of reduced IFNλ4 antiviral activity in humans remains unknown but likely arose between 6 million and 360,000 years ago in Africa.},
}

Animals
Antiviral Agents/*therapeutic use
Biological Evolution
Cardiovirus Infections/*drug therapy/genetics/virology
Cells, Cultured
Encephalomyocarditis virus/drug effects/isolation & purification
Gene Expression Regulation
Hepacivirus/drug effects/isolation & purification
Hepatitis C/*drug therapy/genetics/virology
Humans
Interleukins/*genetics
Pan troglodytes
*Polymorphism, Single Nucleotide
Species Specificity
Zika Virus/drug effects/isolation & purification
Zika Virus Infection/*drug therapy/genetics/virology

@article {pmid30301990,
year = {2018},
author = {},
title = {Neanderthal liaisons bestowed virus-fighting genes on humans.},
journal = {Nature},
volume = {562},
number = {7726},
pages = {166},
doi = {10.1038/d41586-018-06940-x},
pmid = {30301990},
issn = {1476-4687},
}

@article {pmid30293985,
year = {2018},
author = {Rodríguez, W and Mazet, O and Grusea, S and Arredondo, A and Corujo, JM and Boitard, S and Chikhi, L},
title = {The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure.},
journal = {Heredity},
volume = {121},
number = {6},
pages = {663-678},
pmid = {30293985},
issn = {1365-2540},
abstract = {In the last years, a wide range of methods allowing to reconstruct past population size changes from genome-wide data have been developed. At the same time, there has been an increasing recognition that population structure can generate genetic data similar to those produced under models of population size change. Recently, Mazet et al. (Heredity 116:362-371, 2016) showed that, for any model of population structure, it is always possible to find a panmictic model with a particular function of population size changes, having exactly the same distribution of T2 (the coalescence time for a sample of size two) as that of the structured model. They called this function IICR (Inverse Instantaneous Coalescence Rate) and showed that it does not necessarily correspond to population size changes under non-panmictic models. Besides, most of the methods used to analyse data under models of population structure tend to arbitrarily fix that structure and to minimise or neglect population size changes. Here, we extend the seminal work of Herbots (PhD thesis, University of London, 1994) on the structured coalescent and propose a new framework, the Non-Stationary Structured Coalescent (NSSC) that incorporates demographic events (changes in gene flow and/or deme sizes) to models of nearly any complexity. We show how to compute the IICR under a wide family of stationary and non-stationary models. As an example we address the question of human and Neanderthal evolution and discuss how the NSSC framework allows to interpret genomic data under this new perspective.},
}

@article {pmid30290142,
year = {2018},
author = {Enard, D and Petrov, DA},
title = {Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans.},
journal = {Cell},
volume = {175},
number = {2},
pages = {360-371.e13},
pmid = {30290142},
issn = {1097-4172},
support = {R01 GM100366/GM/NIGMS NIH HHS/United States ; R35 GM118165/GM/NIGMS NIH HHS/United States ; },
abstract = {Neanderthals and modern humans interbred at least twice in the past 100,000 years. While there is evidence that most introgressed DNA segments from Neanderthals to modern humans were removed by purifying selection, less is known about the adaptive nature of introgressed sequences that were retained. We hypothesized that interbreeding between Neanderthals and modern humans led to (1) the exposure of each species to novel viruses and (2) the exchange of adaptive alleles that provided resistance against these viruses. Here, we find that long, frequent-and more likely adaptive-segments of Neanderthal ancestry in modern humans are enriched for proteins that interact with viruses (VIPs). We found that VIPs that interact specifically with RNA viruses were more likely to belong to introgressed segments in modern Europeans. Our results show that retained segments of Neanderthal ancestry can be used to detect ancient epidemics.},
}

@article {pmid30290135,
year = {2018},
author = {Huerta-Sánchez, E and Casey, FP},
title = {Simultaneous Viral Exposure and Protection from Neanderthal Introgression.},
journal = {Cell},
volume = {175},
number = {2},
pages = {306-307},
doi = {10.1016/j.cell.2018.09.019},
pmid = {30290135},
issn = {1097-4172},
abstract = {In this issue, Enard and Petrov present intriguing results on the possibility of genetic traces left behind in our genomes from adaptation to past viral epidemics that may have been initiated by interaction with Neanderthal archaic hominins. The work highlights how powerful infectious agents can act as a selective force to shape our genetic makeup.},
}

@article {pmid30287834,
year = {2018},
author = {Jones, JR and Richards, MP and Straus, LG and Reade, H and Altuna, J and Mariezkurrena, K and Marín-Arroyo, AB},
title = {Changing environments during the Middle-Upper Palaeolithic transition in the eastern Cantabrian Region (Spain): direct evidence from stable isotope studies on ungulate bones.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {14842},
pmid = {30287834},
issn = {2045-2322},
support = {H2020-MSCA-IF-2014-656122)//European Commission (EC)/ ; },
abstract = {Environmental change has been proposed as a factor that contributed to the extinction of the Neanderthals in Europe during MIS3. Currently, the different local environmental conditions experienced at the time when Anatomically Modern Humans (AMH) met Neanderthals are not well known. In the Western Pyrenees, particularly, in the eastern end of the Cantabrian coast of the Iberian Peninsula, extensive evidence of Neanderthal and subsequent AMH activity exists, making it an ideal area in which to explore the palaeoenvironments experienced and resources exploited by both human species during the Middle to Upper Palaeolithic transition. Red deer and horse were analysed using bone collagen stable isotope analysis to reconstruct environmental conditions across the transition. A shift in the ecological niche of horses after the Mousterian demonstrates a change in environment, towards more open vegetation, linked to wider climatic change. In the Mousterian, Aurignacian and Gravettian, high inter-individual nitrogen ranges were observed in both herbivores. This could indicate that these individuals were procured from areas isotopically different in nitrogen. Differences in sulphur values between sites suggest some variability in the hunting locations exploited, reflecting the human use of different parts of the landscape. An alternative and complementary explanation proposed is that there were climatic fluctuations within the time of formation of these archaeological levels, as observed in pollen, marine and ice cores.},
}

@article {pmid30281595,
year = {2018},
author = {Zanolli, C and Martinón-Torres, M and Bernardini, F and Boschian, G and Coppa, A and Dreossi, D and Mancini, L and Martínez de Pinillos, M and Martín-Francés, L and Bermúdez de Castro, JM and Tozzi, C and Tuniz, C and Macchiarelli, R},
title = {The Middle Pleistocene (MIS 12) human dental remains from Fontana Ranuccio (Latium) and Visogliano (Friuli-Venezia Giulia), Italy. A comparative high resolution endostructural assessment.},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0189773},
pmid = {30281595},
issn = {1932-6203},
abstract = {The penecontemporaneous Middle Pleistocene sites of Fontana Ranuccio (Latium) and Visogliano (Friuli-Venezia Giulia), set c. 450 km apart in central and northeastern Italy, respectively, have yielded some among the oldest human fossil remains testifying to a peopling phase of the Italian Peninsula broadly during the glacial MIS 12, a stage associated with one among the harshest climatic conditions in the Northern hemisphere during the entire Quaternary period. Together with the large samples from Atapuerca Sima de los Huesos, Spain, and Caune de l'Arago at Tautavel, France, the remains from Fontana Ranuccio and Visogliano are among the few mid-Middle Pleistocene dental assemblages from Western Europe available for investigating the presence of an early Neanderthal signature in their inner structure. We applied two- three-dimensional techniques of virtual imaging and geometric morphometrics to the high-resolution X-ray microtomography record of the dental remains from these two Italian sites and compared the results to the evidence from a selected number of Pleistocene and extant human specimens/samples from Europe and North Africa. Depending on their preservation quality and on the degree of occlusal wear, we comparatively assessed: (i) the crown enamel and radicular dentine thickness topographic variation of a uniquely represented lower incisor; (ii) the lateral crown tissue proportions of premolars and molars; (iii) the enamel-dentine junction, and (iv) the pulp cavity morphology of all available specimens. Our analyses reveal in both samples a Neanderthal-like inner structural signal, for some aspects also resembling the condition shown by the contemporary assemblage from Atapuerca SH, and clearly distinct from the recent human figures. This study provides additional evidence indicating that an overall Neanderthal morphological dental template was preconfigured in Western Europe at least 430 to 450 ka ago.},
}

@article {pmid30281589,
year = {2018},
author = {Martín-Francés, L and Martinón-Torres, M and Martínez de Pinillos, M and García-Campos, C and Modesto-Mata, M and Zanolli, C and Rodríguez, L and Bermúdez de Castro, JM},
title = {Tooth crown tissue proportions and enamel thickness in Early Pleistocene Homo antecessor molars (Atapuerca, Spain).},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0203334},
pmid = {30281589},
issn = {1932-6203},
abstract = {Tooth crown tissue proportions and enamel thickness distribution are considered reliable characters for inferring taxonomic identity, phylogenetic relationships, dietary and behavioural adaptations in fossil and extant hominids. While most Pleistocene hominins display variations from thick to hyper-thick enamel, Neanderthals exhibit relatively thinner. However, the chronological and geographical origin for the appearance of this typical Neanderthal condition is still unknown. The European late Early Pleistocene species Homo antecessor (Gran Dolina-TD6 site, Sierra de Atapuerca) represents an opportunity to investigate the appearance of the thin condition in the fossil record. In this study, we aim to test the hypothesis if H. antecessor molars approximates the Neanderthal condition for tissue proportions and enamel thickness. To do so, for the first time we characterised the molar inner structural organization in this Early Pleistocene hominin taxon (n = 17) and compared it to extinct and extant populations of the genus Homo from African, Asian and European origin (n = 355). The comparative sample includes maxillary and mandibular molars belonging to H. erectus, East and North African Homo, European Middle Pleistocene Homo, Neanderthals, and fossil and extant H. sapiens. We used high-resolution images to investigate the endostructural configuration of TD6 molars (tissue proportions, enamel thickness and distribution). TD6 permanent molars tend to exhibit on average thick absolute and relative enamel in 2D and 3D estimates, both in the complete crown and the lateral enamel. This condition is shared with the majority of extinct and extant hominin sample, except for Neanderthals and some isolated specimens. However, while the total crown percentage of dentine in TD6 globally resembles the low modern values, the lateral crown percentage of dentine tends to be much higher, closer to the Neanderthal signal. Similarly, the H. antecessor molar enamel distribution maps reveal a relative distribution pattern that is more similar to the Neanderthal condition (with the thickest enamel more spread at the periphery of the occlusal basin) rather than that of other fossil specimens and modern humans (with thicker cuspal enamel). Future studies on European Middle Pleistocene populations will provide more insights into the evolutionary trajectory of the typical Neanderthal dental structural organization.},
}

@article {pmid30278065,
year = {2018},
author = {Hoover, KC},
title = {Intragenus (Homo) variation in a chemokine receptor gene (CCR5).},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0204989},
pmid = {30278065},
issn = {1932-6203},
abstract = {Humans have a comparatively higher rate of more polymorphisms in regulatory regions of the primate CCR5 gene, an immune system gene with both general and specific functions. This has been interpreted as allowing flexibility and diversity of gene expression in response to varying disease loads. A broad expression repertoire is useful to humans-the only globally distributed primate-due to our unique adaptive pattern that increased pathogen exposure and disease loads (e.g., sedentism, subsistence practices). The main objective of the study was to determine if the previously observed human pattern of increased variation extended to other members of our genus, Homo. The data for this study are mined from the published genomes of extinct hominins (four Neandertals and two Denisovans), an ancient human (Ust'-Ishim), and modern humans (1000 Genomes). An average of 15 polymorphisms per individual were found in human populations (with a total of 262 polymorphisms). There were 94 polymorphisms identified across extinct Homo (an average of 13 per individual) with 41 previously observed in modern humans and 53 novel polymorphisms (32 in Denisova and 21 in Neandertal). Neither the frequency nor distribution of polymorphisms across gene regions exhibit significant differences within the genus Homo. Thus, humans are not unique with regards to the increased frequency of regulatory polymorphisms and the evolution of variation patterns across CCR5 gene appears to have originated within the genus. A broader evolutionary perspective on regulatory flexibility may be that it provided an advantage during the transition to confrontational foraging (and later hunting) that altered human-environment interaction as well as during migration to Eurasia and encounters with novel pathogens.},
}

@article {pmid30271997,
year = {2018},
author = {García-Martínez, D and Torres-Tamayo, N and Torres-Sánchez, I and García-Río, F and Rosas, A and Bastir, M},
title = {Ribcage measurements indicate greater lung capacity in Neanderthals and Lower Pleistocene hominins compared to modern humans.},
journal = {Communications biology},
volume = {1},
number = {},
pages = {117},
pmid = {30271997},
issn = {2399-3642},
abstract = {Our most recent fossil relatives, the Neanderthals, had a large brain and a very heavy body compared to modern humans. This type of body requires high levels of energetic intake. While food (meat and fat consumption) is a source of energy, oxygen via respiration is also necessary for metabolism. We would therefore expect Neanderthals to have large respiratory capacities. Here we estimate the pulmonary capacities of Neanderthals, based on costal measurements and physiological data from a modern human comparative sample. The Kebara 2 male had a lung volume of about 9.04 l; Tabun C1, a female individual, a lung volume of 5.85 l; and a Neanderthal from the El Sidrón site, a lung volume of 9.03 l. These volumes are approximately 20% greater than the corresponding volumes of modern humans of the same body size and sex. These results show that the Neanderthal body was highly sensitive to energy supply.},
}

@article {pmid30263956,
year = {2018},
author = {Karakostis, FA and Hotz, G and Tourloukis, V and Harvati, K},
title = {Evidence for precision grasping in Neandertal daily activities.},
journal = {Science advances},
volume = {4},
number = {9},
pages = {eaat2369},
pmid = {30263956},
issn = {2375-2548},
abstract = {Neandertal manual activities, as previously reconstructed from their robust hand skeletons, are thought to involve systematic power grasping rather than precise hand movements. However, this interpretation is at odds with increasing archeological evidence for sophisticated cultural behavior. We reevaluate the manipulative behaviors of Neandertals and early modern humans using a historical reference sample with extensive genealogical and lifelong occupational documentation, in combination with a new and precise three-dimensional multivariate analysis of hand muscle attachments. Results show that Neandertal muscle marking patterns overlap exclusively with documented lifelong precision workers, reflecting systematic precision grasping consistent with the use of their associated cultural remains. Our findings challenge the established interpretation of Neandertal behavior and establish a solid link between biological and cultural remains in the fossil record.},
}

@article {pmid30237321,
year = {2018},
author = {Slimak, L and Fietzke, J and Geneste, JM and Ontañón, R},
title = {Comment on "U-Th dating of carbonate crusts reveals Neandertal origin of Iberian cave art".},
journal = {Science (New York, N.Y.)},
volume = {361},
number = {6408},
pages = {},
doi = {10.1126/science.aau1371},
pmid = {30237321},
issn = {1095-9203},
mesh = {Archaeology ; Carbonates ; *Caves ; Fossils ; *Neanderthals ; },
abstract = {Hoffmann et al (Reports, 23 February 2018, p. 912) report the discovery of parietal art older than 64,800 years and attributed to Neanderthals, at least 25 millennia before the oldest parietal art ever found. Instead, critical evaluation of their geochronological data seems to provide stronger support for an age of 47,000 years, which is much more consistent with the archaeological background in hand.},
}

Archaeology
Carbonates
*Caves
Fossils
*Neanderthals

@article {pmid30230470,
year = {2018},
author = {Charlier, P and Coppens, Y and Héry-Arnaud, G and Hassin, J},
title = {[A biological anthropology of the disappearance of the Neandertal Man: recent data].},
journal = {Medecine sciences : M/S},
volume = {34},
number = {8-9},
pages = {745-748},
doi = {10.1051/medsci/20183408024},
pmid = {30230470},
issn = {1958-5381},
mesh = {Animals ; Anthropology/*methods ; Anthropology, Physical ; Biological Evolution ; *Extinction, Biological ; Female ; Fossils ; Humans ; Male ; *Neanderthals ; },
abstract = {What could have been the causes of the disappearance of Neanderthals? We will try here to make a synthesis between one of the fundamental questions of biological anthropology relating to human evolution (hypotheses on the causes of the extinction of Neanderthals) and evolutionary bio-medical concepts, some of which have recently been reformulated thanks to the progress of paleogenomics (ancestral inheritance of the current human immune system, paleo-microbiology, host-pathogen relationship…).},
}

Animals
Anthropology/*methods
Anthropology, Physical
Biological Evolution
*Extinction, Biological
Female
Fossils
Humans
Male
*Neanderthals

@article {pmid30226838,
year = {2018},
author = {Skov, L and Hui, R and Shchur, V and Hobolth, A and Scally, A and Schierup, MH and Durbin, R},
title = {Detecting archaic introgression using an unadmixed outgroup.},
journal = {PLoS genetics},
volume = {14},
number = {9},
pages = {e1007641},
pmid = {30226838},
issn = {1553-7404},
support = {WT206194//Wellcome Trust/United Kingdom ; WT207492//Wellcome Trust/United Kingdom ; },
mesh = {African Continental Ancestry Group/genetics ; Animals ; Asian Continental Ancestry Group/genetics ; European Continental Ancestry Group/genetics ; Fossils ; Genome, Human/*genetics ; Hominidae/*genetics ; Humans ; Hybridization, Genetic/*genetics ; Neanderthals/*genetics ; Oceanic Ancestry Group/genetics ; Phylogeny ; },
abstract = {Human populations outside of Africa have experienced at least two bouts of introgression from archaic humans, from Neanderthals and Denisovans. In Papuans there is prior evidence of both these introgressions. Here we present a new approach to detect segments of individual genomes of archaic origin without using an archaic reference genome. The approach is based on a hidden Markov model that identifies genomic regions with a high density of single nucleotide variants (SNVs) not seen in unadmixed populations. We show using simulations that this provides a powerful approach to identifying segments of archaic introgression with a low rate of false detection, given data from a suitable outgroup population is available, without the archaic introgression but containing a majority of the variation that arose since initial separation from the archaic lineage. Furthermore our approach is able to infer admixture proportions and the times both of admixture and of initial divergence between the human and archaic populations. We apply the model to detect archaic introgression in 89 Papuans and show how the identified segments can be assigned to likely Neanderthal or Denisovan origin. We report more Denisovan admixture than previous studies and find a shift in size distribution of fragments of Neanderthal and Denisovan origin that is compatible with a difference in admixture time. Furthermore, we identify small amounts of Denisova ancestry in South East Asians and South Asians.},
}

African Continental Ancestry Group/genetics
Animals
Asian Continental Ancestry Group/genetics
European Continental Ancestry Group/genetics
Fossils
Genome, Human/*genetics
Hominidae/*genetics
Humans
Hybridization, Genetic/*genetics
Neanderthals/*genetics
Oceanic Ancestry Group/genetics
Phylogeny

@article {pmid30209385,
year = {2018},
author = {},
title = {The earliest known drawing in history sends a message through 73,000 years.},
journal = {Nature},
volume = {561},
number = {7722},
pages = {149},
doi = {10.1038/d41586-018-06657-x},
pmid = {30209385},
issn = {1476-4687},
mesh = {*Archaeology ; Carbonates ; Caves ; *Neanderthals ; },
}

*Archaeology
Carbonates
Caves
*Neanderthals

@article {pmid30209350,
year = {2018},
author = {Clyde, D},
title = {The girl with Neanderthal and Denisovan parents.},
journal = {Nature reviews. Genetics},
volume = {19},
number = {11},
pages = {668-669},
doi = {10.1038/s41576-018-0054-6},
pmid = {30209350},
issn = {1471-0064},
}

@article {pmid30201119,
year = {2018},
author = {Conde-Valverde, M and Quam, R and Martínez, I and Arsuaga, JL and Daura, J and Sanz, M and Zilhão, J},
title = {The bony labyrinth in the Aroeira 3 Middle Pleistocene cranium.},
journal = {Journal of human evolution},
volume = {124},
number = {},
pages = {105-116},
doi = {10.1016/j.jhevol.2018.08.003},
pmid = {30201119},
issn = {1095-8606},
abstract = {The discovery of a partial cranium at the site of Aroeira (Portugal) dating to 389-436 ka augments the current sample of Middle Pleistocene European crania and makes this specimen penecontemporaneous with the fossils from the geographically close Atapuerca Sima de los Huesos (SH) and Arago sites. A recent study of the cranium documented a unique combination of primitive and derived features. The Aroeira 3 cranium preserves the right temporal bone, including the petrosal portion. Virtual reconstruction of the bony labyrinth from μCT scans provides an opportunity to examine its morphology. A series of standard linear and angular measures of the semicircular canals and cochlea in Aroeira 3 were compared with other fossil hominins and recent humans. Our analysis has revealed the absence of derived Neandertal features in Aroeira 3. In particular, the specimen lacks both the derived canal proportions and the low position of the posterior canal, two of the most diagnostic features of the Neandertal bony labyrinth, and Aroeira 3 is more primitive in these features than the Atapuerca (SH) sample. One potentially derived feature (low shape index of the cochlear basal turn) is shared between Aroeira 3 and the Atapuerca (SH) hominins, but is absent in Neandertals. The results of our study provide new insights into Middle Pleistocene population dynamics close to the origin of the Neandertal clade. In particular, the contrasting inner ear morphology between Aroeira 3 and the Atapuerca (SH) hominins suggests a degree of demographic isolation, despite the close geographic proximity and similar age of these two sites.},
}

@article {pmid30177445,
year = {2018},
author = {Goldfield, AE and Booton, R and Marston, JM},
title = {Modeling the role of fire and cooking in the competitive exclusion of Neanderthals.},
journal = {Journal of human evolution},
volume = {124},
number = {},
pages = {91-104},
doi = {10.1016/j.jhevol.2018.07.006},
pmid = {30177445},
issn = {1095-8606},
abstract = {The Neanderthal body was more robust and energetically costly than the bodies of anatomically modern humans (AMH). Different metabolic budgets between competing populations of Neanderthals and AMH may have been a factor in the varied ranges of behavior and timelines for Neanderthal extinction that we see in the Paleolithic archaeological record. This paper uses an adaptation of the Lotka-Volterra model to determine whether metabolic differences alone could have accounted for Neanderthal extinction. In addition, we use a modeling approach to investigate Neanderthal fire use, evidence for which is much debated and is variable throughout different climatic phases of the Middle Paleolithic. The increased caloric yield from a cooked versus a raw diet may have played an important role in population competition between Neanderthals and AMH. We arrive at two key conclusions. First, given differences in metabolic budget between Neanderthals and AMH and their dependence on similar or overlapping food resources, Neanderthal extinction is likely inevitable over the long term. Second, the rate of Neanderthal extinction increases as the frequency of AMH fire use increases. Results highlight the importance of understanding the variable behaviors at play on a regional scale in order to understand global Neanderthal extinction. We also emphasize the importance of understanding the role of fire use in the Middle to Upper Paleolithic transition.},
}

@article {pmid30173883,
year = {2018},
author = {Aubert, M and Brumm, A and Huntley, J},
title = {Early dates for 'Neanderthal cave art' may be wrong.},
journal = {Journal of human evolution},
volume = {125},
number = {},
pages = {215-217},
doi = {10.1016/j.jhevol.2018.08.004},
pmid = {30173883},
issn = {1095-8606},
}

@article {pmid30153108,
year = {2018},
author = {Delpiano, D and Heasley, K and Peresani, M},
title = {Assessing Neanderthal land use and lithic raw material management in Discoid technology.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {96},
number = {},
pages = {},
doi = {10.4436/JASS.96006},
pmid = {30153108},
issn = {2037-0644},
abstract = {Neanderthal groups developed different models of mobility and exploitation of resources across their territory: these differences can be linked to various knapping methods and are probably related to adaptative strategies and responses at many ecological and cultural levels. Neanderthals associated with Discoid knapping are known to depend on an opportunistic exploitation of lithic raw materials for daily food procurement and be more mobile than others using different technologies. However, we have no defined data for most of the geographical contexts where this technocomplex was found. This study analyzes the southern Alpine site of Grotta di Fumane, where the final Mousterian is characterized by the succession of well defined cultural entities. Unit A9 presents with entirely Discoid technology and is embedded between fully Levallois levels. The level was recently extensively investigated for almost 68m² on 9,000 lithic pieces. To study the lithic assemblage of Unit A9 we applied a techno-economical analysis designed to infer the spatial fragmentation of the reduction sequences, and results were corroborated through the characterization of cortex and raw materials based on geological surveys and experimental comparisons. Results show that raw materials collected within a radius of 5km, by far the most frequently used, exhibit complete and ordinary reduction sequences, which were further attested by multiple refittings. Beyond this area, semi-local raw materials (5-10 km) are introduced to perform specific tasks, and are reduced according to their different physical qualities. These data, combined with the presence of lithotypes and fossils collected from longer distances (ten to hundreds of kilometers), and to the recycling of old patinated artifacts, indicate a complex and diversified behavior encompassing both: a) opportunistic and daily residential exploitation within a local territory; b) logistical planning of the economical organization in the semi-local to exotic territory according to quality and distance of available raw materials sources.},
}

@article {pmid30150388,
year = {2018},
author = {Staubwasser, M and Drăgușin, V and Onac, BP and Assonov, S and Ersek, V and Hoffmann, DL and Veres, D},
title = {Impact of climate change on the transition of Neanderthals to modern humans in Europe.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {37},
pages = {9116-9121},
pmid = {30150388},
issn = {1091-6490},
mesh = {Animals ; *Archaeology ; *Climate Change ; Europe ; *Extinction, Biological ; History, Ancient ; Humans ; *Neanderthals ; },
abstract = {Two speleothem stable isotope records from East-Central Europe demonstrate that Greenland Stadial 12 (GS12) and GS10-at 44.3-43.3 and 40.8-40.2 ka-were prominent intervals of cold and arid conditions. GS12, GS11, and GS10 are coeval with a regional pattern of culturally (near-)sterile layers within Europe's diachronous archeologic transition from Neanderthals to modern human Aurignacian. Sterile layers coeval with GS12 precede the Aurignacian throughout the middle and upper Danube region. In some records from the northern Iberian Peninsula, such layers are coeval with GS11 and separate the Châtelperronian from the Aurignacian. Sterile layers preceding the Aurignacian in the remaining Châtelperronian domain are coeval with GS10 and the previously reported 40.0- to 40.8-ka cal BP [calendar years before present (1950)] time range of Neanderthals' disappearance from most of Europe. This suggests that ecologic stress during stadial expansion of steppe landscape caused a diachronous pattern of depopulation of Neanderthals, which facilitated repopulation by modern humans who appear to have been better adapted to this environment. Consecutive depopulation-repopulation cycles during severe stadials of the middle pleniglacial may principally explain the repeated replacement of Europe's population and its genetic composition.},
}

Animals
*Archaeology
*Climate Change
Europe
*Extinction, Biological
History, Ancient
Humans
*Neanderthals

@article {pmid30147753,
year = {2018},
author = {Guichard, E and Peona, V and Malagoli Tagliazucchi, G and Abitante, L and Jagoda, E and Musella, M and Ricci, M and Rubio-Roldán, A and Sarno, S and Luiselli, D and Pettener, D and Taccioli, C and Pagani, L and Garcia-Perez, JL and Boattini, A},
title = {Impact of non-LTR retrotransposons in the differentiation and evolution of anatomically modern humans.},
journal = {Mobile DNA},
volume = {9},
number = {},
pages = {28},
pmid = {30147753},
issn = {1759-8753},
support = {//Wellcome Trust/United Kingdom ; 295733//European Research Council/International ; },
abstract = {Background: Transposable elements are biologically important components of eukaryote genomes. In particular, non-LTR retrotransposons (N-LTRrs) played a key role in shaping the human genome throughout evolution. In this study, we compared retrotransposon insertions differentially present in the genomes of Anatomically Modern Humans, Neanderthals, Denisovans and Chimpanzees, in order to assess the possible impact of retrotransposition in the differentiation of the human lineage.

Results: We first identified species-specific N-LTRrs and established their distribution in present day human populations. These analyses shortlisted a group of N-LTRr insertions that were found exclusively in Anatomically Modern Humans. These insertions are associated with an increase in the number of transcriptional/splicing variants of those genes they inserted in. The analysis of the functionality of genes containing human-specific N-LTRr insertions reflects changes that occurred during human evolution. In particular, the expression of genes containing the most recent N-LTRr insertions is enriched in the brain, especially in undifferentiated neurons, and these genes associate in networks related to neuron maturation and migration. Additionally, we identified candidate N-LTRr insertions that have likely produced new functional variants exclusive to modern humans, whose genomic loci show traces of positive selection.

Conclusions: Our results strongly suggest that N-LTRr impacted our differentiation as a species, most likely inducing an increase in neural complexity, and have been a constant source of genomic variability all throughout the evolution of the human lineage.},
}

@article {pmid30139851,
year = {2018},
author = {Vogel, G},
title = {Ancient DNA reveals tryst between extinct human species.},
journal = {Science (New York, N.Y.)},
volume = {361},
number = {6404},
pages = {737},
doi = {10.1126/science.361.6404.737},
pmid = {30139851},
issn = {1095-9203},
mesh = {Animals ; *Biological Evolution ; Bone and Bones ; *DNA, Ancient ; *Extinction, Biological ; Fathers/history ; Female ; History, Ancient ; Humans ; Mothers/history ; Neanderthals/*genetics ; Women/*history ; },
}

Animals
*Biological Evolution
Bone and Bones
*DNA, Ancient
*Extinction, Biological
Fathers/history
Female
History, Ancient
Humans
Mothers/history
Neanderthals/*genetics
Women/*history

@article {pmid30135579,
year = {2018},
author = {Slon, V and Mafessoni, F and Vernot, B and de Filippo, C and Grote, S and Viola, B and Hajdinjak, M and Peyrégne, S and Nagel, S and Brown, S and Douka, K and Higham, T and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Kelso, J and Meyer, M and Prüfer, K and Pääbo, S},
title = {The genome of the offspring of a Neanderthal mother and a Denisovan father.},
journal = {Nature},
volume = {561},
number = {7721},
pages = {113-116},
pmid = {30135579},
issn = {1476-4687},
abstract = {Neanderthals and Denisovans are extinct groups of hominins that separated from each other more than 390,000 years ago1,2. Here we present the genome of 'Denisova 11', a bone fragment from Denisova Cave (Russia)3 and show that it comes from an individual who had a Neanderthal mother and a Denisovan father. The father, whose genome bears traces of Neanderthal ancestry, came from a population related to a later Denisovan found in the cave4-6. The mother came from a population more closely related to Neanderthals who lived later in Europe2,7 than to an earlier Neanderthal found in Denisova Cave8, suggesting that migrations of Neanderthals between eastern and western Eurasia occurred sometime after 120,000 years ago. The finding of a first-generation Neanderthal-Denisovan offspring among the small number of archaic specimens sequenced to date suggests that mixing between Late Pleistocene hominin groups was common when they met.},
}

@article {pmid30135563,
year = {2018},
author = {Srinivasan, S and Bettella, F and Frei, O and Hill, WD and Wang, Y and Witoelar, A and Schork, AJ and Thompson, WK and Davies, G and Desikan, RS and Deary, IJ and Melle, I and Ueland, T and Dale, AM and Djurovic, S and Smeland, OB and Andreassen, OA},
title = {Enrichment of genetic markers of recent human evolution in educational and cognitive traits.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {12585},
pmid = {30135563},
issn = {2045-2322},
support = {Disconnected mind grant//Age UK/ ; MR/K026992/1//Biotechnology and Biological Sciences Research Council (BBSRC)/ ; MR/K026992/1//Medical Research Council/United Kingdom ; 225989//Norges Forskningsråd (Research Council of Norway)/ ; 248778//Norges Forskningsråd (Research Council of Norway)/ ; 223273//Norges Forskningsråd (Research Council of Norway)/ ; 2016-064//Ministry of Health and Care Services | Helse Sør-Øst RHF (Southern and Eastern Norway Regional Health Authority)/ ; },
abstract = {Higher cognitive functions are regarded as one of the main distinctive traits of humans. Evidence for the cognitive evolution of human beings is mainly based on fossil records of an expanding cranium and an increasing complexity of material culture artefacts. However, the molecular genetic factors involved in the evolution are still relatively unexplored. Here, we investigated whether genomic regions that underwent positive selection in humans after divergence from Neanderthals are enriched for genetic association with phenotypes related to cognitive functions. We used genome wide association data from a study of college completion (N = 111,114), one of educational attainment (N = 293,623) and two different studies of general cognitive ability (N = 269,867 and 53,949). We found nominally significant polygenic enrichment of associations with college completion (p = 0.025), educational attainment (p = 0.043) and general cognitive ability (p = 0.015 and 0.025, respectively), suggesting that variants influencing these phenotypes are more prevalent in evolutionarily salient regions. The enrichment remained significant after controlling for other known genetic enrichment factors, and for affiliation to genes highly expressed in the brain. These findings support the notion that phenotypes related to higher order cognitive skills typical of humans have a recent genetic component that originated after the separation of the human and Neanderthal lineages.},
}

@article {pmid30135540,
year = {2018},
author = {Warren, M},
title = {Mum's a Neanderthal, Dad's a Denisovan: First discovery of an ancient-human hybrid.},
journal = {Nature},
volume = {560},
number = {7719},
pages = {417-418},
doi = {10.1038/d41586-018-06004-0},
pmid = {30135540},
issn = {1476-4687},
}

@article {pmid30097198,
year = {2018},
author = {Bruner, E and Fedato, A and Silva-Gago, M and Alonso-Alcalde, R and Terradillos-Bernal, M and Fernández-Durantes, MÁ and Martín-Guerra, E},
title = {Cognitive archeology, body cognition, and hand-tool interaction.},
journal = {Progress in brain research},
volume = {238},
number = {},
pages = {325-345},
doi = {10.1016/bs.pbr.2018.06.013},
pmid = {30097198},
issn = {1875-7855},
mesh = {Animals ; Archaeology ; *Biological Evolution ; Brain/*physiology ; Cognition/*physiology ; Functional Laterality/*physiology ; Humans ; Neanderthals ; Paleontology ; Tool Use Behavior/*physiology ; },
abstract = {Body cognition and lateralization can be investigated in fossils by integrating anatomical and functional aspects. Paleoneurology cannot provide strong evidence in this sense, because hemispheric asymmetries are shared in all extinct human species, and motor cortical areas are difficult to delineate in endocranial casts. However, paleoneurological analyses also suggest that modern humans and Neanderthals underwent an expansion of parietal regions crucial for visuospatial integration and eye-hand-tool management. Because of our technological specialization, haptic cognition can be particularly targeted by evolutionary processes. Hand-tool relationships can be investigated through physical and physiological correlates. In terms of metrics, size is the main factor of hand morphological variation among adult humans, followed by the ratio between thumb length and palmar size. In modern humans, emotional changes during hand-tool contact can be measured by electrodermal activity. During tool manipulation, electrodermal response, which is a physiological correlate of emotional engagement, shows differences between males and females, and it is different for distinct Paleolithic technologies. Emotional engagement, hand management, and haptic cognition are part of a specialized prosthetic technological capacity of modern humans and can provide indirect evidence of cognitive discontinuities in the archeological record.},
}

Animals
Archaeology
*Biological Evolution
Brain/*physiology
Cognition/*physiology
Functional Laterality/*physiology
Humans
Neanderthals
Paleontology
Tool Use Behavior/*physiology

@article {pmid30072539,
year = {2018},
author = {Tucci, S and Vohr, SH and McCoy, RC and Vernot, B and Robinson, MR and Barbieri, C and Nelson, BJ and Fu, W and Purnomo, GA and Sudoyo, H and Eichler, EE and Barbujani, G and Visscher, PM and Akey, JM and Green, RE},
title = {Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia.},
journal = {Science (New York, N.Y.)},
volume = {361},
number = {6401},
pages = {511-516},
doi = {10.1126/science.aar8486},
pmid = {30072539},
issn = {1095-9203},
support = {R01 GM110068/GM/NIGMS NIH HHS/United States ; //European Research Council/International ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Adaptation, Biological/*genetics ; Animals ; *Biological Evolution ; Body Height/*genetics ; Dwarfism/*genetics ; Gene Flow ; Genome, Human ; Humans ; Indonesia ; *Islands ; Neanderthals/genetics ; Population/*genetics ; *Selection, Genetic ; },
abstract = {Flores Island, Indonesia, was inhabited by the small-bodied hominin species Homo floresiensis, which has an unknown evolutionary relationship to modern humans. This island is also home to an extant human pygmy population. Here we describe genome-scale single-nucleotide polymorphism data and whole-genome sequences from a contemporary human pygmy population living on Flores near the cave where H. floresiensis was found. The genomes of Flores pygmies reveal a complex history of admixture with Denisovans and Neanderthals but no evidence for gene flow with other archaic hominins. Modern individuals bear the signatures of recent positive selection encompassing the FADS (fatty acid desaturase) gene cluster, likely related to diet, and polygenic selection acting on standing variation that contributed to their short-stature phenotype. Thus, multiple independent instances of hominin insular dwarfism occurred on Flores.},
}

Adaptation, Biological/*genetics
Animals
*Biological Evolution
Body Height/*genetics
Dwarfism/*genetics
Gene Flow
Genome, Human
Humans
Indonesia
*Islands
Neanderthals/genetics
Population/*genetics
*Selection, Genetic

@article {pmid30029803,
year = {2019},
author = {Charlier, P and Gaultier, F and Héry-Arnaud, G},
title = {Interbreeding between Neanderthals and modern humans: Remarks and methodological dangers of a dental calculus microbiome analysis.},
journal = {Journal of human evolution},
volume = {126},
number = {},
pages = {124-126},
doi = {10.1016/j.jhevol.2018.06.007},
pmid = {30029803},
issn = {1095-8606},
}

@article {pmid30026576,
year = {2018},
author = {Sorensen, AC and Claud, E and Soressi, M},
title = {Neandertal fire-making technology inferred from microwear analysis.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {10065},
pmid = {30026576},
issn = {2045-2322},
support = {PGW-13-42//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; },
abstract = {Fire use appears to have been relatively common among Neandertals in the Middle Palaeolithic. However, the means by which Neandertals procured their fire-either through the collection of natural fire, or by producing it themselves using tools-is still a matter of debate. We present here the first direct artefactual evidence for regular, systematic fire production by Neandertals. From archaeological layers attributed to late Mousterian industries at multiple sites throughout France, primarily to the Mousterian of Acheulean Tradition (MTA) technoculture (ca. 50,000 years BP), we identify using microwear analysis dozens of late Middle Palaeolithic bifacial tools that exhibit macroscopic and microscopic traces suggesting repeated percussion and/or forceful abrasion with a hard mineral material. Both the locations and nature of the polish and associated striations are comparable to those obtained experimentally by obliquely percussing fragments of pyrite (FeS2) against the flat/convex sides of a biface to make fire. The striations within these discrete use zones are always oriented roughly parallel to the longitudinal axis of the tool, allowing us to rule out taphonomic origins for these traces. We therefore suggest that the occasional use of bifaces as 'strike-a-lights' was a technocultural feature shared among the late Neandertals in France.},
}

@article {pmid30022013,
year = {2018},
author = {Dolgova, O and Lao, O},
title = {Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes.},
journal = {Genes},
volume = {9},
number = {7},
pages = {},
pmid = {30022013},
issn = {2073-4425},
abstract = {The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered. It is currently known that AMH interbred with archaic hominins once they left the African continent. Current non-African human genomes carry fragments of archaic origin. This review focuses on the fitness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on fitness and testing hypotheses about the role of selection within the context of health and disease.},
}

@article {pmid30002396,
year = {2018},
author = {Gómez-Olivencia, A and Sala, N and Núñez-Lahuerta, C and Sanchis, A and Arlegi, M and Rios-Garaizar, J},
title = {First data of Neandertal bird and carnivore exploitation in the Cantabrian Region (Axlor; Barandiaran excavations; Dima, Biscay, Northern Iberian Peninsula).},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {10551},
pmid = {30002396},
issn = {2045-2322},
abstract = {Neandertals were top predators who basically relied on middle- to large-sized ungulates for dietary purposes, but there is growing evidence that supports their consumption of plants, leporids, tortoises, marine resources, carnivores and birds. The Iberian Peninsula has provided the most abundant record of bird exploitation for meat in Europe, starting in the Middle Pleistocene. However, the bird and carnivore exploitation record was hitherto limited to the Mediterranean area of the Iberian Peninsula. Here we present the first evidence of bird and carnivore exploitation by Neandertals in the Cantabrian region. We have found cut-marks in two golden eagles, one raven, one wolf and one lynx remain from the Mousterian levels of Axlor. The obtaining of meat was likely the primary purpose of the cut-marks on the golden eagle and lynx remains. Corvids, raptors, felids and canids in Axlor could have likely acted as commensals of the Neandertals, scavenging upon the carcasses left behind by these hunter-gatherers. This could have brought them closer to Neandertal groups who could have preyed upon them. These new results provide additional information on their dietary scope and indicate a more complex interaction between Neandertals and their environment.},
}

@article {pmid29983156,
year = {2018},
author = {García-Martínez, D and Radovčić, D and Radovčić, J and Cofran, Z and Rosas, A and Bastir, M},
title = {Over 100 years of Krapina: New insights into the Neanderthal thorax from the study of rib cross-sectional morphology.},
journal = {Journal of human evolution},
volume = {122},
number = {},
pages = {124-132},
doi = {10.1016/j.jhevol.2018.05.009},
pmid = {29983156},
issn = {1095-8606},
abstract = {The Krapina costal sample was studied by Gorjanović-Kramberger in the early twentieth century. He pointed out unique features in the sample such as the rounder rib cross-section, which was recently confirmed in other Neanderthal specimens. Round rib cross-sections are characteristic of Homo ergaster, suggesting this may be plesiomorphic for Pleistocene Homo, but it is unknown whether Homo antecessor also had this rib shape. Furthermore, the influence of allometry on the cross-sectional shape of ribs is still unknown. The large costal sample from Krapina allows us to address these issues. We quantified cross-section morphology at the midshaft throughout a closed curve of one landmark and nine sliding semilandmarks in the Krapina costal remains (n = 7), as well as in other Neanderthals (n = 50), H. antecessor (n = 3) and modern humans, both fossil (n = 12) and recent (n = 160). We used principal components analysis and mean comparisons to explore interspecific differences, regression analysis to investigate allometry, and partial least squares analysis to examine covariation of cross-section shape and overall rib morphology. Neanderthal cross-sections tended to be larger than those of recent humans except for the Krapina and Tabun remains. Regarding shape, inter-group differences were found only in the diaphragmatic thorax, where Neanderthal and H. antecessor ribs were statistically significantly rounder than those of modern humans. Allometry accounted for covariation of size on shape, but the Neandertal and modern human trajectories had different slopes. While our results based on the Krapina costal sample are similar to previous findings, we also make several new insights: 1) the cross-section morphology observed in Neanderthals was probably present in H. antecessor, albeit less marked; 2) the distinct roundness of Neanderthal cross-sections is not related to size; 3) rounder cross-sections are correlated with ribs presenting less curvature in cranial view and a low degree of torsion in recent humans. These results are important for the interpretation of fragmentary Neanderthal costal remains, and the fact that the differences are marked only in the diaphragmatic thorax could have implications for breathing kinematics.},
}

@article {pmid29942018,
year = {2018},
author = {Hoffmann, DL and Standish, CD and Pike, AWG and García-Diez, M and Pettitt, PB and Angelucci, DE and Villaverde, V and Zapata, J and Milton, JA and Alcolea-González, J and Cantalejo-Duarte, P and Collado, H and de Balbín, R and Lorblanchet, M and Ramos-Muñoz, J and Weniger, GC and Zilhão, J},
title = {Dates for Neanderthal art and symbolic behaviour are reliable.},
journal = {Nature ecology & evolution},
volume = {2},
number = {7},
pages = {1044-1045},
doi = {10.1038/s41559-018-0598-z},
pmid = {29942018},
issn = {2397-334X},
}

@article {pmid29942012,
year = {2018},
author = {Gaudzinski-Windheuser, S and Noack, ES and Pop, E and Herbst, C and Pfleging, J and Buchli, J and Jacob, A and Enzmann, F and Kindler, L and Iovita, R and Street, M and Roebroeks, W},
title = {Evidence for close-range hunting by last interglacial Neanderthals.},
journal = {Nature ecology & evolution},
volume = {2},
number = {7},
pages = {1087-1092},
doi = {10.1038/s41559-018-0596-1},
pmid = {29942012},
issn = {2397-334X},
abstract = {Animal resources have been part of hominin diets since around 2.5 million years ago, with sharp-edged stone tools facilitating access to carcasses. How exactly hominins acquired animal prey and how hunting strategies varied through time and space is far from clear. The oldest possible hunting weapons known from the archaeological record are 300,000 to 400,000-year-old sharpened wooden staves. These may have been used as throwing and/or close-range thrusting spears, but actual data on how such objects were used are lacking, as unambiguous lesions caused by such weapon-like objects are unknown for most of human prehistory. Here, we report perforations observed on two fallow deer skeletons from Neumark-Nord, Germany, retrieved during excavations of 120,000-year-old lake shore deposits with abundant traces of Neanderthal presence. Detailed studies of the perforations, including micro-computed tomography imaging and ballistic experiments, demonstrate that they resulted from the close-range use of thrusting spears. Such confrontational ways of hunting require close cooperation between participants, and over time may have shaped important aspects of hominin biology and behaviour.},
}

@article {pmid29937092,
year = {2018},
author = {Li, J and Hong, X and Mesiano, S and Muglia, LJ and Wang, X and Snyder, M and Stevenson, DK and Shaw, GM},
title = {Natural Selection Has Differentiated the Progesterone Receptor among Human Populations.},
journal = {American journal of human genetics},
volume = {103},
number = {1},
pages = {45-57},
pmid = {29937092},
issn = {1537-6605},
support = {RC2 HL101748/HL/NHLBI NIH HHS/United States ; },
abstract = {The progesterone receptor (PGR) plays a central role in maintaining pregnancy and is significantly associated with medical conditions such as preterm birth that affects 12.6% of all the births in U.S. PGR has been evolving rapidly since the common ancestor of human and chimpanzee, and we herein investigated evolutionary dynamics of PGR during recent human migration and population differentiation. Our study revealed substantial population differentiation at the PGR locus driven by natural selection, where very recent positive selection in East Asians has substantially decreased its genetic diversity by nearly fixing evolutionarily novel alleles. On the contrary, in European populations, the PGR locus has been promoted to a highly polymorphic state likely due to balancing selection. Integrating transcriptome data across multiple tissue types together with large-scale genome-wide association data for preterm birth, our study demonstrated the consequence of the selection event in East Asians on remodeling PGR expression specifically in the ovary and determined a significant association of early spontaneous preterm birth with the evolutionarily selected variants. To reconstruct its evolutionary trajectory on the human lineage, we observed substantial differentiation between modern and archaic humans at the PGR locus, including fixation of a deleterious missense allele in the Neanderthal genome that was later introgressed in modern human populations. Taken together, our study revealed substantial evolutionary innovation in PGR even during very recent human evolution, and its different forms among human populations likely result in differential susceptibility to progesterone-associated disease conditions including preterm birth.},
}

@article {pmid29931305,
year = {2018},
author = {Prüfer, K},
title = {snpAD: an ancient DNA genotype caller.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {24},
pages = {4165-4171},
pmid = {29931305},
issn = {1367-4811},
abstract = {Motivation: The study of ancient genomes can elucidate the evolutionary past. However, analyses are complicated by base-modifications in ancient DNA molecules that result in errors in DNA sequences. These errors are particularly common near the ends of sequences and pose a challenge for genotype calling.

Results: I describe an iterative method that estimates genotype frequencies and errors along sequences to allow for accurate genotype calling from ancient sequences. The implementation of this method, called snpAD, performs well on high-coverage ancient data, as shown by simulations and by subsampling the data of a high-coverage Neandertal genome. Although estimates for low-coverage genomes are less accurate, I am able to derive approximate estimates of heterozygosity from several low-coverage Neandertals. These estimates show that low heterozygosity, compared to modern humans, was common among Neandertals.

The C++ code of snpAD is freely available at http://bioinf.eva.mpg.de/snpAD/.

Supplementary information: Supplementary data are available at Bioinformatics online.},
}

@article {pmid29930123,
year = {2018},
author = {Galway-Witham, J and Stringer, C},
title = {How did Homo sapiens evolve?.},
journal = {Science (New York, N.Y.)},
volume = {360},
number = {6395},
pages = {1296-1298},
doi = {10.1126/science.aat6659},
pmid = {29930123},
issn = {1095-9203},
mesh = {Animals ; *Biological Evolution ; Body Size/genetics ; Fossils ; Genetic Research ; Humans ; *Models, Biological ; Neanderthals/genetics ; Phylogeny ; },
}

Animals
*Biological Evolution
Body Size/genetics
Fossils
Genetic Research
Humans
*Models, Biological
Neanderthals/genetics
Phylogeny

@article {pmid29930117,
year = {2018},
author = {Cohen, J},
title = {Neanderthal brain organoids come to life.},
journal = {Science (New York, N.Y.)},
volume = {360},
number = {6395},
pages = {1284},
doi = {10.1126/science.360.6395.1284},
pmid = {29930117},
issn = {1095-9203},
}