@article {pmid31940356,
year = {2020},
author = {Villa, P and Soriano, S and Pollarolo, L and Smriglio, C and Gaeta, M and D'Orazio, M and Conforti, J and Tozzi, C},
title = {Neandertals on the beach: Use of marine resources at Grotta dei Moscerini (Latium, Italy).},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0226690},
doi = {10.1371/journal.pone.0226690},
pmid = {31940356},
issn = {1932-6203},
abstract = {Excavated in 1949, Grotta dei Moscerini, dated MIS 5 to early MIS 4, is one of two Italian Neandertal sites with a large assemblage of retouched shells (n = 171) from 21 layers. The other occurrence is from the broadly contemporaneous layer L of Grotta del Cavallo in southern Italy (n = 126). Eight other Mousterian sites in Italy and one in Greece also have shell tools but in a very small number. The shell tools are made on valves of the smooth clam Callista chione. The general idea that the valves of Callista chione were collected by Neandertals on the beach after the death of the mollusk is incomplete. At Moscerini 23.9% of the specimens were gathered directly from the sea floor as live animals by skin diving Neandertals. Archaeological data from sites in Italy, France and Spain confirm that shell fishing and fresh water fishing was a common activity of Neandertals, as indicated by anatomical studies recently published by E. Trinkaus. Lithic analysis provides data to show the relation between stone tools and shell tools. Several layers contain pumices derived from volcanic eruptions in the Ischia Island or the Campi Flegrei (prior to the Campanian Ignimbrite mega-eruption). Their rounded edges indicate that they were transported by sea currents to the beach at the base of the Moscerini sequence. Their presence in the occupation layers above the beach is discussed. The most plausible hypothesis is that they were collected by Neandertals. Incontrovertible evidence that Neandertals collected pumices is provided by a cave in Liguria. Use of pumices as abraders is well documented in the Upper Paleolithic. We prove that the exploitation of submerged aquatic resources and the collection of pumices common in the Upper Paleolithic were part of Neandertal behavior well before the arrival of modern humans in Western Europe.},
}

@article {pmid31889305,
year = {2019},
author = {Gómez-Olivencia, A and López-Onaindia, D and Sala, N and Balzeau, A and Pantoja-Pérez, A and Arganda-Carreras, I and Arlegi, M and Rios-Garaizar, J and Gómez-Robles, A},
title = {The human remains from Axlor (Dima, Biscay, northern Iberian Peninsula).},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.23989},
pmid = {31889305},
issn = {1096-8644},
support = {IT1418-19//Eusko Jaurlaritza-Gobierno Vasco/ ; IJCI-2017-32804//Juan de la Cierva Incorporación Program/ ; PGC2018-093925-B-C33//Ministerio de Ciencia, Innovación y Universidades/ ; RYC-2017-22558//Ramón y Cajal fellowship/ ; },
abstract = {OBJECTIVES: We provide the description and comparative analysis of all the human fossil remains found at Axlor during the excavations carried out by J. M. de Barandiarán from 1967 to 1974: a cranial vault fragment and eight teeth, five of which likely belonged to the same individual, although two are currently lost. Our goal is to describe in detail all these human remains and discuss both their taxonomic attribution and their stratigraphic context.

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

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

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

@article {pmid31551547,
year = {2019},
author = {Callaway, E},
title = {First portrait of mysterious Denisovans drawn from DNA.},
journal = {Nature},
volume = {573},
number = {7775},
pages = {475-476},
doi = {10.1038/d41586-019-02820-0},
pmid = {31551547},
issn = {1476-4687},
mesh = {Animals ; DNA ; DNA Methylation ; Fossils ; Hominidae/*genetics ; Neanderthals/*genetics ; },
}

Animals
DNA
DNA Methylation
Fossils
Hominidae/*genetics
Neanderthals/*genetics

@article {pmid31878873,
year = {2019},
author = {Bücking, R and Cox, MP and Hudjashov, G and Saag, L and Sudoyo, H and Stoneking, M},
title = {Archaic mitochondrial DNA inserts in modern day nuclear genomes.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {1017},
doi = {10.1186/s12864-019-6392-8},
pmid = {31878873},
issn = {1471-2164},
abstract = {BACKGROUND: Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs).

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

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

@article {pmid31873124,
year = {2019},
author = {Ottoni, C and Guellil, M and Ozga, AT and Stone, AC and Kersten, O and Bramanti, B and Porcier, S and Van Neer, W},
title = {Metagenomic analysis of dental calculus in ancient Egyptian baboons.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {19637},
doi = {10.1038/s41598-019-56074-x},
pmid = {31873124},
issn = {2045-2322},
abstract = {Dental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, ancient metagenomics made it possible to unlock the wealth of microbial and dietary information of dental calculus to reconstruct oral microbiomes and lifestyle of humans from the past. Although most studies have so far focused on ancient humans, dental calculus is known to form in a wide range of animals, potentially informing on how human-animal interactions changed the animals' oral ecology. Here, we characterise the oral microbiome of six ancient Egyptian baboons held in captivity during the late Pharaonic era (9th-6th centuries BC) and of two historical baboons from a zoo via shotgun metagenomics. We demonstrate that these captive baboons possessed a distinctive oral microbiome when compared to ancient and modern humans, Neanderthals and a wild chimpanzee. These results may reflect the omnivorous dietary behaviour of baboons, even though health, food provisioning and other factors associated with human management, may have changed the baboons' oral microbiome. We anticipate our study to be a starting point for more extensive studies on ancient animal oral microbiomes to examine the extent to which domestication and human management in the past affected the diet, health and lifestyle of target animals.},
}

@article {pmid31558829,
year = {2019},
author = {Sano, K and Arrighi, S and Stani, C and Aureli, D and Boschin, F and Fiore, I and Spagnolo, V and Ricci, S and Crezzini, J and Boscato, P and Gala, M and Tagliacozzo, A and Birarda, G and Vaccari, L and Ronchitelli, A and Moroni, A and Benazzi, S},
title = {The earliest evidence for mechanically delivered projectile weapons in Europe.},
journal = {Nature ecology & evolution},
volume = {3},
number = {10},
pages = {1409-1414},
pmid = {31558829},
issn = {2397-334X},
support = {724046/ERC_/European Research Council/International ; },
mesh = {Europe ; Fossils ; Humans ; Italy ; *Neanderthals ; Weapons ; },
abstract = {Microscopic analysis of backed lithic pieces from the Uluzzian technocomplex (45-40 thousand yr ago) at Grotta del Cavallo (southern Italy) reveals their use as mechanically delivered projectile weapons, attributed to anatomically modern humans. Use-wear and residue analyses indicate that the lithics were hunting armatures hafted with complex adhesives, while experimental and ethnographic comparisons support their use as projectiles. The use of projectiles conferred a hunting strategy with a higher impact energy and a potential subsistence advantage over other populations and species.},
}

Europe
Fossils
Humans
Italy
*Neanderthals
Weapons

@article {pmid31809748,
year = {2019},
author = {Wall, JD and Ratan, A and Stawiski, E and , },
title = {Identification of African-Specific Admixture between Modern and Archaic Humans.},
journal = {American journal of human genetics},
volume = {105},
number = {6},
pages = {1254-1261},
doi = {10.1016/j.ajhg.2019.11.005},
pmid = {31809748},
issn = {1537-6605},
abstract = {Recent work has demonstrated that two archaic human groups (Neanderthals and Denisovans) interbred with modern humans and contributed to the contemporary human gene pool. These findings relied on the availability of high-coverage genomes from both Neanderthals and Denisovans. Here we search for evidence of archaic admixture from a worldwide panel of 1,667 individuals using an approach that does not require the presence of an archaic human reference genome. We find no evidence for archaic admixture in the Andaman Islands, as previously claimed, or on the island of Flores, where Homo floresiensis fossils have been found. However, we do find evidence for at least one archaic admixture event in sub-Saharan Africa, with the strongest signal in Khoesan and Pygmy individuals from Southern and Central Africa. The locations of these putative archaic admixture tracts are weighted against functional regions of the genome, consistent with the long-term effects of purifying selection against introgressed genetic material.},
}

@article {pmid31802585,
year = {2019},
author = {Langley, MC and Benítez-Burraco, A and Kempe, V},
title = {Playing with language, creating complexity: Has play contributed to the evolution of complex language?.},
journal = {Evolutionary anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/evan.21810},
pmid = {31802585},
issn = {1520-6505},
support = {FFI2016-78034-C2-2-P//Spanish Ministry of Economy and Competitiveness/ ; },
abstract = {We argue that enhanced play may have contributed to the emergence of complex language systems in modern humans (Homo sapiens). To support this idea, we first discuss evidence for an expansion of playing behavior connected to the extended childhood of modern human children, and the potential of this period for the transmission of complex cultural traits, including language. We then link two of the most important functions of play-exploration and innovation-to the potential for cumulative cultural evolution in general and for the emergence of complex language in particular. If correct, the shorter childhood of Neanderthals-involving restrictions on time to experiment and innovate-may have restricted their language (and other symbolic) system/s. Consequently, fully investigating the role that play may have had in the transmission of language and the development of symbolic cultures in both modern humans and Neanderthals provides a new avenue of research for Paleolithic archaeology and related disciplines.},
}

@article {pmid31800577,
year = {2019},
author = {Weniger, GC and de Andrés-Herrero, M and Bolin, V and Kehl, M and Otto, T and Potì, A and Tafelmaier, Y},
title = {Late Glacial rapid climate change and human response in the Westernmost Mediterranean (Iberia and Morocco).},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0225049},
doi = {10.1371/journal.pone.0225049},
pmid = {31800577},
issn = {1932-6203},
abstract = {This paper investigates the correlation between climate, environment and human land use in the Westernmost Mediterranean on both sides of the Strait of Gibraltar during the Late Glacial. Using a multi-proxy approach on a sample of 300 sites from the Solutrean and Magdalenian of the Iberian Peninsula and from the Iberomaurusian in Morocco, we find evidence for significant changes in settlement patterns and site density after the Last Glacial Maximum. In Southern Iberia, during Heinrich Stadial 1, hyperarid zones expanded drastically from the south-eastern coast to the West through the Interior. This aridification process heavily affected Magdalenian settlement in the South and caused a strong decline of hunter-gatherer population. Southern Iberia during Heinrich Stadial 1 turned out to be a high-risk environment when compared to Northern Iberia. At the same time, the Late Iberomaurusian of Morocco, although considered to be situated in a high-risk environment as well, experiences an increase of sites and expansion of settlement area.},
}

@article {pmid31797875,
year = {2019},
author = {Mallol, C and Hernández, C and Mercier, N and Falguères, C and Carrancho, Á and Cabanes, D and Vidal-Matutano, P and Connolly, R and Pérez, L and Mayor, A and Ben Arous, E and Galván, B},
title = {Fire and brief human occupations in Iberia during MIS 4: Evidence from Abric del Pastor (Alcoy, Spain).},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {18281},
doi = {10.1038/s41598-019-54305-9},
pmid = {31797875},
issn = {2045-2322},
support = {ERC-CoG-2014-PALEOCHAR//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; ERC-CoG-2014-PALEOCHAR//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {There is a relatively low amount of Middle Paleolithic sites in Europe dating to MIS 4. Of the few that exist, several of them lack evidence for anthropogenic fire, raising the question of how this period of global cooling may have affected the Neanderthal population. The Iberian Peninsula is a key area to explore this issue, as it has been considered as a glacial refugium during critical periods of the Neanderthal timeline and might therefore yield archaeological contexts in which we can explore possible changes in the behaviour and settlement patterns of Neanderthal groups during MIS 4. Here we report recent data from Abric del Pastor, a small rock shelter in Alcoy (Alicante, Spain) with a stratified deposit containing Middle Palaeolithic remains. We present absolute dates that frame the sequence within MIS 4 and multi-proxy geoarchaeological evidence of in situ anthropogenic fire, including microscopic evidence of in situ combustion residues and thermally altered sediment. We also present archaeostratigraphic evidence of recurrent, functionally diverse, brief human occupation of the rock shelter. Our results suggest that Neanderthals occupied the Central Mediterranean coast of the Iberian Peninsula during MIS 4, that these Neanderthals were not undergoing climatic stress and they were habitual fire users.},
}

@article {pmid31797354,
year = {2019},
author = {Karban, ME},
title = {Occipital hemi-bun development and shape covariation in a longitudinal extant human growth sample.},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.23981},
pmid = {31797354},
issn = {1096-8644},
abstract = {OBJECTIVES: Although the homology of the Neanderthal occipital bun and anatomically modern human "hemi-bun" has long been debated, little is known about the developmental timing and patterning of these two patterns of prominent occipital squama convexity. In this study, occipital hemi-bun ontogeny and cranial shape covariation are assessed in a comparative extant human sample.

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

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

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

@article {pmid31774843,
year = {2019},
author = {Vaesen, K and Scherjon, F and Hemerik, L and Verpoorte, A},
title = {Inbreeding, Allee effects and stochasticity might be sufficient to account for Neanderthal extinction.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0225117},
doi = {10.1371/journal.pone.0225117},
pmid = {31774843},
issn = {1932-6203},
abstract = {The replacement of Neanderthals by Anatomically Modern Humans has typically been attributed to environmental pressure or a superiority of modern humans with respect to competition for resources. Here we present two independent models that suggest that no such heatedly debated factors might be needed to account for the demise of Neanderthals. Starting from the observation that Neanderthal populations already were small before the arrival of modern humans, the models implement three factors that conservation biology identifies as critical for a small population's persistence, namely inbreeding, Allee effects and stochasticity. Our results indicate that the disappearance of Neanderthals might have resided in the smallness of their population(s) alone: even if they had been identical to modern humans in their cognitive, social and cultural traits, and even in the absence of inter-specific competition, Neanderthals faced a considerable risk of extinction. Furthermore, we suggest that if modern humans contributed to the demise of Neanderthals, that contribution might have had nothing to do with resource competition, but rather with how the incoming populations geographically restructured the resident populations, in a way that reinforced Allee effects, and the effects of inbreeding and stochasticity.},
}

@article {pmid31774826,
year = {2019},
author = {Krueger, KL and Willman, JC and Matthews, GJ and Hublin, JJ and Pérez-Pérez, A},
title = {Anterior tooth-use behaviors among early modern humans and Neandertals.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0224573},
doi = {10.1371/journal.pone.0224573},
pmid = {31774826},
issn = {1932-6203},
abstract = {Early modern humans (EMH) are often touted as behaviorally advanced to Neandertals, with more sophisticated technologies, expanded resource exploitation, and more complex clothing production. However, recent analyses have indicated that Neandertals were more nuanced in their behavioral adaptations, with the production of the Châtelperronian technocomplex, the processing and cooking of plant foods, and differences in behavioral adaptations according to habitat. This study adds to this debate by addressing the behavioral strategies of EMH (n = 30) within the context of non-dietary anterior tooth-use behaviors to glean possible differences between them and their Neandertal (n = 45) counterparts. High-resolution casts of permanent anterior teeth were used to collect microwear textures of fossil and comparative bioarchaeological samples using a Sensofar white-light confocal profiler with a 100x objective lens. Labial surfaces were scanned, totaling a work envelope of 204 x 276 μm for each individual. The microwear textures were examined for post-mortem damage and uploaded to SSFA software packages for surface characterization. Statistical analyses were performed to examine differences in central tendencies and distributions of anisotropy and textural fill volume variables among the EMH sample itself by habitat, location, and time interval, and between the EMH and Neandertal samples by habitat and location. Descriptive statistics for the EMH sample were compared to seven bioarchaeological samples (n = 156) that utilized different tooth-use behaviors to better elucidate specific activities that may have been performed by EMH. Results show no significant differences between the means within the EMH sample by habitat, location, or time interval. Furthermore, there are no significant differences found here between EMH and Neandertals. Comparisons to the bioarchaeological samples suggest both fossil groups participated in clamping and grasping activities. These results indicate that EMH and Neandertals were similar in their non-dietary anterior tooth-use behaviors and provide additional evidence for overlapping behavioral strategies employed by these two hominins.},
}

@article {pmid31765984,
year = {2019},
author = {Garralda, MD and Maureille, B and Le Cabec, A and Oxilia, G and Benazzi, S and Skinner, MM and Hublin, JJ and Vandermeersch, B},
title = {The Neanderthal teeth from Marillac (Charente, Southwestern France): Morphology, comparisons and paleobiology.},
journal = {Journal of human evolution},
volume = {138},
number = {},
pages = {102683},
doi = {10.1016/j.jhevol.2019.102683},
pmid = {31765984},
issn = {1095-8606},
abstract = {Few European sites have yielded human dental remains safely dated to the end of MIS 4/beginning of MIS 3. One of those sites is Marillac (Southwestern France), a collapsed karstic cave where archeological excavations (1967-1980) conducted by B. Vandermeersch unearthed numerous faunal and human remains, as well as a few Mousterian Quina tools. The Marillac sinkhole was occasionally used by humans to process the carcasses of different prey, but there is no evidence for a residential use of the site, nor have any hearths been found. Rare carnivore bones were also discovered, demonstrating that the sinkhole was seasonally used, not only by Neanderthals, but also by predators across several millennia. The lithostratigraphic units containing the human remains were dated to ∼60 kyr. The fossils consisted of numerous fragments of skulls and jaws, isolated teeth and several post-cranial bones, many of them with traces of perimortem manipulations. For those already published, their morphological characteristics and chronostratigraphic context allowed their attribution to Neanderthals. This paper analyzes sixteen unpublished human teeth (fourteen permanent and two deciduous) by investigating the external morphology and metrical variation with respect to other Neanderthal remains and a sample from modern populations. We also investigate their enamel thickness distribution in 2D and 3D, the enamel-dentine junction morphology (using geometric morphometrics) of one molar and two premolars, the roots and the possible expression of taurodontism, as well as pathologies and developmental defects. The anterior tooth use and paramasticatory activities are also discussed. Morphological and structural alterations were found on several teeth, and interpreted in light of human behavior (tooth-pick) and carnivores' actions (partial digestion). The data are interpreted in the context of the available information for the Eurasian Neanderthals.},
}

@article {pmid31733113,
year = {2019},
author = {Andrews, P and Johnson, RJ},
title = {Evolutionary basis for the human diet: consequences for human health.},
journal = {Journal of internal medicine},
volume = {},
number = {},
pages = {},
doi = {10.1111/joim.13011},
pmid = {31733113},
issn = {1365-2796},
abstract = {The relationship of evolution with diet and environment can provide insights into modern disease. Fossil evidence shows apes and early human ancestors were fruit-eaters living in environments with strongly seasonal climates. Rapid cooling at the end of the middle Miocene (15-12Ma: millions of years ago) increased seasonality in Africa and Europe, and ape survival may be linked with a mutation in uric acid metabolism. Climate stabilized in the later Miocene and Pliocene (12-5Ma), and fossil apes and early hominins were both adapted for life on ground and in trees. Around 2.5Ma, early species of Homo introduced more animal products into their diet, and this coincided with developing bipedalism, stone tool technology and increase in brain size. Early species of Homo such as Homo habilis still lived in woodland habitats, and the major habitat shift in human evolution occurred at 1.8Ma with the origin of Homo erectus. Homo erectus had increased body size, greater hunting skills and a diet rich in meat, control of fire and understanding about cooking food, and moved from woodland to savanna. Group size may also have increased at the same time, facilitating the transmission of knowledge from one generation to the next. The earliest fossils of Homo sapiens appeared about 300kyr, but they had separated from Neanderthals by 480kyr or earlier. Their diet shifted towards grain-based foods about 100kyr ago, and settled agriculture developed about 10kyr ago. This pattern remains for many populations to this day and provides important insights into current burden of lifestyle diseases.},
}

@article {pmid31725722,
year = {2019},
author = {V Barroso, G and Puzović, N and Dutheil, JY},
title = {Inference of recombination maps from a single pair of genomes and its application to ancient samples.},
journal = {PLoS genetics},
volume = {15},
number = {11},
pages = {e1008449},
doi = {10.1371/journal.pgen.1008449},
pmid = {31725722},
issn = {1553-7404},
abstract = {Understanding the causes and consequences of recombination landscape evolution is a fundamental goal in genetics that requires recombination maps from across the tree of life. Such maps can be obtained from population genomic datasets, but require large sample sizes. Alternative methods are therefore necessary to research organisms where such datasets cannot be generated easily, such as non-model or ancient species. Here we extend the sequentially Markovian coalescent model to jointly infer demography and the spatial variation in recombination rate. Using extensive simulations and sequence data from humans, fruit-flies and a fungal pathogen, we demonstrate that iSMC accurately infers recombination maps under a wide range of scenarios-remarkably, even from a single pair of unphased genomes. We exploit this possibility and reconstruct the recombination maps of ancient hominins. We report that the ancient and modern maps are correlated in a manner that reflects the established phylogeny of Neanderthals, Denisovans, and modern human populations.},
}

@article {pmid31710710,
year = {2019},
author = {Rmoutilová, R and Gómez-Olivencia, A and Brůžek, J and Holliday, T and Ledevin, R and Couture-Veschambre, C and Madelaine, S and Džupa, V and Velemínská, J and Maureille, B},
title = {A case of marked bilateral asymmetry in the sacral alae of the Neandertal specimen Regourdou 1 (Périgord, France).},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.23968},
pmid = {31710710},
issn = {1096-8644},
support = {ANR-10-LABX-52//French National Research Agency/ ; 1088217//Agency of Charles University/ ; //Irene Levi Sala CARE Archaeological Foundation/ ; //Leakey Foundation/ ; LEQSF(2015-18)-RD-A-22//Louisiana Board of Regents/ ; PGC2018-093925-B-C33//Ministerio de Ciencia, Innovación y Universidades/ ; CGL2015-65387-C3-2-P//Ministerio de Economía y Competitividad/ ; 2016-1R40240-00007349-00007350//Région Nouvelle Aquitaine/ ; 1044-16//Universidad del País Vasco/Euskal Herriko Unibertsitatea/ ; IT1418-19//Eusko Jaurlaritza-Gobierno Vasco/ ; },
abstract = {OBJECTIVES: A marked asymmetry was previously reported in the sacral alae and S1-L5 facets orientation of the Neandertal individual Regourdou 1. Here, we provide a detailed description and quantification of the morphology and degree of asymmetry of this sacrum.

MATERIAL AND METHODS: Regourdou 1 was compared to a modern human sample composed of 24 females and 17 males, and to other Neandertal individuals. Both traditional and geometric morphometric analyses were used in order to quantify the degree of sacral asymmetry of Regourdou 1.

RESULTS: The asymmetry of both sacral alae and facets orientation substantially exceeds directional and absolute asymmetry of the healthy modern sample. Regourdou 1 shows a considerably shorter right ala, which is absolutely and relatively outside of the modern and Neandertal variations.

CONCLUSION: Regourdou 1 shows marked sacral asymmetry that probably originated in early ontogenetic development. An asymmetric sacrum reflects asymmetric load dissipation and could relate to other morphological abnormalities observed in the skeleton, especially the mild scoliosis of the spine and the asymmetry of the femoral diaphyses. Further investigation is necessary to elucidate the relationship between those morphologies as well as a potential impact on the life of the individual.},
}

@article {pmid31702050,
year = {2019},
author = {Gokcumen, O},
title = {Archaic hominin introgression into modern human genomes.},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.23951},
pmid = {31702050},
issn = {1096-8644},
support = {1714867//United States National Science Foundation/ ; },
abstract = {Ancient genomes from multiple Neanderthal and the Denisovan individuals, along with DNA sequence data from diverse contemporary human populations strongly support the prevalence of gene flow among different hominins. Recent studies now provide evidence for multiple gene flow events that leave genetic signatures in extant and ancient human populations. These events include older gene flow from an unknown hominin in Africa predating out-of-Africa migrations, and in the last 50,000-100,000 years, multiple gene flow events from Neanderthals into ancestral Eurasian human populations, and at least three distinct introgression events from a lineage close to Denisovans into ancestors of extant Southeast Asian and Oceanic populations. Some of these introgression events may have happened as late as 20,000 years before present and reshaped the way in which we think about human evolution. In this review, I aim to answer anthropologically relevant questions with regard to recent research on ancient hominin introgression in the human lineage. How have genomic data from archaic hominins changed our view of human evolution? Is there any doubt about whether introgression from ancient hominins to the ancestors of present-day humans occurred? What is the current view of human evolutionary history from the genomics perspective? What is the impact of introgression on human phenotypes?},
}

@article {pmid31701003,
year = {2019},
author = {Rodríguez-Hidalgo, A and Morales, JI and Cebrià, A and Courtenay, LA and Fernández-Marchena, JL and García-Argudo, G and Marín, J and Saladié, P and Soto, M and Tejero, JM and Fullola, JM},
title = {The Châtelperronian Neanderthals of Cova Foradada (Calafell, Spain) used imperial eagle phalanges for symbolic purposes.},
journal = {Science advances},
volume = {5},
number = {11},
pages = {eaax1984},
pmid = {31701003},
issn = {2375-2548},
abstract = {Evidence for the symbolic behavior of Neanderthals in the use of personal ornaments is relatively scarce. Among the few ornaments documented, eagle talons, which were presumably used as pendants, are the most frequently recorded. This phenomenon appears concentrated in a specific area of southern Europe during a span of 80 thousand years. Here, we present the analysis of one eagle pedal phalange recovered from the Châtelperronian layer of Foradada Cave (Spain). Our research broadens the known geographical and temporal range of this symbolic behavior, providing the first documentation of its use among the Iberian populations, as well as of its oldest use in the peninsula. The recurrent appearance of large raptor talons throughout the Middle Paleolithic time frame, including their presence among the last Neanderthal populations, raises the question of the survival of some cultural elements of the Middle Paleolithic into the transitional Middle to Upper Paleolithic assemblages and beyond.},
}

@article {pmid31676766,
year = {2019},
author = {Greenbaum, G and Getz, WM and Rosenberg, NA and Feldman, MW and Hovers, E and Kolodny, O},
title = {Disease transmission and introgression can explain the long-lasting contact zone of modern humans and Neanderthals.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {5003},
pmid = {31676766},
issn = {2041-1723},
support = {BCS-1515127//NSF | Directorate for Social, Behavioral & Economic Sciences | Division of Behavioral and Cognitive Sciences (Behavioral & Cognitive Sciences)/ ; },
abstract = {Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to the spread of modern humans into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. Here, we propose that infectious-disease dynamics can explain the localization and persistence of the inter-species boundary. We further propose, and support with dynamical-systems models, that introgression-based transmission of alleles related to the immune system would have gradually diminished this barrier to pervasive inter-species interaction, leading to the eventual release of the inter-species boundary from its geographic localization. Asymmetries between the species in the characteristics of their associated 'pathogen packages' could have generated feedback that allowed modern humans to overcome disease burden earlier than Neanderthals, giving them an advantage in their subsequent spread into Eurasia.},
}

@article {pmid31675491,
year = {2019},
author = {Kozowyk, PRB and Poulis, JA},
title = {A new experimental methodology for assessing adhesive properties shows that Neandertals used the most suitable material available.},
journal = {Journal of human evolution},
volume = {137},
number = {},
pages = {102664},
doi = {10.1016/j.jhevol.2019.102664},
pmid = {31675491},
issn = {1095-8606},
abstract = {The use of adhesives for hafting stone tools at least 191 ka was a major technological development. Stone tools could be more securely attached to handles, thus improving their efficiency and practicality. To produce functional adhesives required forethought and planning, as well as expertise and knowledge of the resources available in the landscape. This makes adhesives important in discussions about Neandertal and early modern human technological and mental capabilities. However, we currently know very little about how these early adhesive materials behaved under different circumstances, or why certain materials were used and others were not. Here we present the results of controlled laboratory bulk property tests (hardness, rheology and thermogravimetric analysis) on replica Paleolithic adhesives. We conclude that birch tar is more versatile, has better working properties, and is more reusable than pine resin, the most likely alternative material. Neandertals may therefore have invested more time and resources to produce birch tar because it was the best material available, both functionally and economically, throughout the majority of Europe during the Middle to Late Pleistocene. Our results further demonstrate that Neandertals had high levels of technological expertise and knowledge of the natural resources available to them in their environment.},
}

@article {pmid31663021,
year = {2019},
author = {Carter, T and Contreras, DA and Holcomb, J and Mihailović, DD and Karkanas, P and Guérin, G and Taffin, N and Athanasoulis, D and Lahaye, C},
title = {Earliest occupation of the Central Aegean (Naxos), Greece: Implications for hominin and Homo sapiens' behavior and dispersals.},
journal = {Science advances},
volume = {5},
number = {10},
pages = {eaax0997},
pmid = {31663021},
issn = {2375-2548},
abstract = {We present evidence of Middle Pleistocene activity in the central Aegean Basin at the chert extraction and reduction complex of Stelida (Naxos, Greece). Luminescence dating places ~9000 artifacts in a stratigraphic sequence from ~13 to 200 thousand years ago (ka ago). These artifacts include Mousterian products, which arguably provide first evidence for Neanderthals in the region. This dated material attests to a much earlier history of regional exploration than previously believed, opening the possibility of alternative routes into Southeast Europe from Anatolia (and Africa) for (i) hominins, potentially during sea level lowstands (e.g., Marine Isotope Stage 8) permitting terrestrial crossings across the Aegean, and (ii) Homo sapiens of the Early Upper Paleolithic (Aurignacian), conceivably by sea.},
}

@article {pmid31651929,
year = {2019},
author = {Abdelhady, AA and Elewa, AMT and El-Dawy, MH},
title = {The position of Neandertal and Homo erectus within the hominid clade based on craniodental morphology and whole mtDNA genomes.},
journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen},
volume = {},
number = {},
pages = {},
doi = {10.1127/homo/2019/1119},
pmid = {31651929},
issn = {1618-1301},
abstract = {To evaluate the taxonomic position of the Neandertal and Homo erectus within the hominid clade, the variation among and within the hominid taxa was assessed based on the craniodental morphology and integrated with molecular analyses of the whole mtDNA genomes. Ordination and clustering of the Procrustes craniodental landmarks have showed a notable shape transformation from the earliest hominid species to the modern humans. Although levels of distinction between the analyzed taxa (Homo, Pan, Gorilla, and Pongo) are generally corresponding to probable expectations based on their taxonomic rank, few exceptions were found. Notably, the craniodental morphology of Homo erectus showed a greater dissimilarity to other Homo species, where it consistently overlapped or grouped with Pan species on all ordination plots and clustering. In addition, the direct link between European humans and Neandertals, which is well-characterized on all of the phylogenetic trees based on maximum parsimony and maximum likelihood methods, was not outlined in the morphologic-based clustering. Both morphological and molecular distances between Neandertal and modern humans were consistently greater than the distances among modern humans, however, the distances are still smaller than those between any two distinct species (so they are subspecies). The topology of the phylogenetic trees based on the whole mtDNA has shown a minor discrepancy with the results obtained from the craniodental morphologies.},
}

@article {pmid31637998,
year = {2019},
author = {Delgobo, M and Mendes, DA and Kozlova, E and Rocha, EL and Rodrigues-Luiz, GF and Mascarin, L and Dias, G and Patrício, DO and Dierckx, T and Bicca, MA and Bretton, G and Tenório de Menezes, YK and Starick, MR and Rovaris, D and Del Moral, J and Mansur, DS and Van Weyenbergh, J and Báfica, A},
title = {An evolutionary recent IFN/IL-6/CEBP axis is linked to monocyte expansion and tuberculosis severity in humans.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
pmid = {31637998},
issn = {2050-084X},
support = {G0D6817N//FWO/International ; Global Research Initiative Program TW008276/NH/NIH HHS/United States ; Early Career Scientist 55007412/HHMI/Howard Hughes Medical Institute/United States ; VLAIO IWT141614//Fonds Wetenschappelijk Onderzoek/International ; 23038.010048/2013-27//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/International ; PQ//Conselho Nacional de Desenvolvimento Científico e Tecnológico/International ; G0D6817N//Fonds Wetenschappelijk Onderzoek/International ; 23038.010048/2013-27//CAPES/International ; R01 TW008276/TW/FIC NIH HHS/United States ; },
abstract = {Monocyte counts are increased during human tuberculosis (TB) but it has not been determined whether Mycobacterium tuberculosis (Mtb) directly regulates myeloid commitment. We demonstrated that exposure to Mtb directs primary human CD34+ cells to differentiate into monocytes/macrophages. In vitro myeloid conversion did not require type I or type II IFN signaling. In contrast, Mtb enhanced IL-6 responses by CD34+ cell cultures and IL-6R neutralization inhibited myeloid differentiation and decreased mycobacterial growth in vitro. Integrated systems biology analysis of transcriptomic, proteomic and genomic data of large data sets of healthy controls and TB patients established the existence of a myeloid IL-6/IL6R/CEBP gene module associated with disease severity. Furthermore, genetic and functional analysis revealed the IL6/IL6R/CEBP gene module has undergone recent evolutionary selection, including Neanderthal introgression and human pathogen adaptation, connected to systemic monocyte counts. These results suggest Mtb co-opts an evolutionary recent IFN-IL6-CEBP feed-forward loop, increasing myeloid differentiation linked to severe TB in humans.},
}

@article {pmid31636186,
year = {2019},
author = {Niekus, MJLT and Kozowyk, PRB and Langejans, GHJ and Ngan-Tillard, D and van Keulen, H and van der Plicht, J and Cohen, KM and van Wingerden, W and van Os, B and Smit, BI and Amkreutz, LWSW and Johansen, L and Verbaas, A and Dusseldorp, GL},
title = {Middle Paleolithic complex technology and a Neandertal tar-backed tool from the Dutch North Sea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {44},
pages = {22081-22087},
pmid = {31636186},
issn = {1091-6490},
abstract = {We report the discovery of a 50,000-y-old birch tar-hafted flint tool found off the present-day coastline of The Netherlands. The production of adhesives and multicomponent tools is considered complex technology and has a prominent place in discussions about the evolution of human behavior. This find provides evidence on the technological capabilities of Neandertals and illuminates the currently debated conditions under which these technologies could be maintained. 14C-accelerator mass spectrometry dating and the geological provenance of the artifact firmly associates it with a host of Middle Paleolithic stone tools and a Neandertal fossil. The find was analyzed using pyrolysis-gas chromatography-mass spectrometry, X-ray micro-computed tomography, and optical light microscopy. The object is a piece of birch tar, encompassing one-third of a flint flake. This find is from northwestern Europe and complements a small set of well-dated and chemically identified adhesives from Middle Paleolithic/Middle Stone Age contexts. Together with data from experiments and other Middle Paleolithic adhesives, it demonstrates that Neandertals mastered complex adhesive production strategies and composite tool use at the northern edge of their range. Thus, a large population size is not a necessary condition for complex behavior and technology. The mitigation of ecological risk, as demonstrated by the challenging conditions during Marine Isotope Stage 4 and 3, provides a better explanation for the transmission and maintenance of technological complexity.},
}

@article {pmid31629539,
year = {2019},
author = {Borgel, S and Latimer, B and McDermott, Y and Sarig, R and Pokhojaev, A and Abulafia, T and Goder-Goldberger, M and Barzilai, O and May, H},
title = {Early Upper Paleolithic human foot bones from Manot Cave, Israel.},
journal = {Journal of human evolution},
volume = {},
number = {},
pages = {102668},
doi = {10.1016/j.jhevol.2019.102668},
pmid = {31629539},
issn = {1095-8606},
abstract = {The transition from the Middle Paleolithic to the Upper Paleolithic in the Levant represents a major event in human prehistory with regards to the dispersal of modern human populations. Unfortunately, the scarcity of human remains from this period has hampered our ability to study the anatomy of Upper Paleolithic populations. This study describes and examines pedal bones recovered from the Early Upper Paleolithic period at Manot Cave, Israel, from 2014 to 2017. The Manot Cave foot bones include a partial, left foot skeleton comprising a talus, a calcaneus, a cuboid, a first metatarsal, a second metatarsal, a fifth metatarsal, and a hallucal sesamoid. All these remains were found in the same archaeological unit of the cave and belong to a young adult. Shape and size comparisons with Neanderthals, Anatomically Modern Human and modern human foot bones indicate a modern human morphology. In some characteristics, however, the Manot Cave foot bones display a Neanderthal-like pattern. Notably, the Manot Cave foot is remarkable in its overall gracility. A healed traumatic injury in the second metatarsal (Lisfranc's fracture) is most likely due to a remote impact to the dorsum of the foot. This injury, its subsequent debility, and the individual's apparent recovery suggest that the members of the Manot Cave community had a supportive environment, one with mutual responsibilities among the members.},
}

@article {pmid31624180,
year = {2019},
author = {Hsieh, P and Vollger, MR and Dang, V and Porubsky, D and Baker, C and Cantsilieris, S and Hoekzema, K and Lewis, AP and Munson, KM and Sorensen, M and Kronenberg, ZN and Murali, S and Nelson, BJ and Chiatante, G and Maggiolini, FAM and Blanché, H and Underwood, JG and Antonacci, F and Deleuze, JF and Eichler, EE},
title = {Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes.},
journal = {Science (New York, N.Y.)},
volume = {366},
number = {6463},
pages = {},
pmid = {31624180},
issn = {1095-9203},
support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; },
abstract = {Copy number variants (CNVs) are subject to stronger selective pressure than single-nucleotide variants, but their roles in archaic introgression and adaptation have not been systematically investigated. We show that stratified CNVs are significantly associated with signatures of positive selection in Melanesians and provide evidence for adaptive introgression of large CNVs at chromosomes 16p11.2 and 8p21.3 from Denisovans and Neanderthals, respectively. Using long-read sequence data, we reconstruct the structure and complex evolutionary history of these polymorphisms and show that both encode positively selected genes absent from most human populations. Our results collectively suggest that large CNVs originating in archaic hominins and introgressed into modern humans have played an important role in local population adaptation and represent an insufficiently studied source of large-scale genetic variation.},
}

@article {pmid31621987,
year = {2019},
author = {Tryon, CA},
title = {The Middle/Later Stone Age transition and cultural dynamics of late Pleistocene East Africa.},
journal = {Evolutionary anthropology},
volume = {28},
number = {5},
pages = {267-282},
doi = {10.1002/evan.21802},
pmid = {31621987},
issn = {1520-6505},
abstract = {The Middle to Later Stone Age (MSA/LSA) transition is a prominent feature of the African archeological record that began in some places ~30,000-60,000 years ago, historically associated with the origin and/or dispersal of "modern" humans. Unlike the analogous Middle to Upper Paleolithic transition in Eurasia and associated Neanderthal extinction, the African MSA/LSA record remains poorly documented, with its potential role in explaining changes in the behavioral diversity and geographic range of Homo sapiens largely unexplored. I review archeological and biogeographic data from East Africa, show regionally diverse pathways to the MSA/LSA transition, and emphasize the need for analytical approaches that document potential ancestor-descendent relationships visible in the archeological record, needed to assess independent invention, population interaction, dispersal, and other potential mechanisms for behavioral change. Diversity within East Africa underscores the need for regional, rather than continental-scale narratives of the later evolutionary history of H. sapiens.},
}

@article {pmid31614276,
year = {2019},
author = {Pan, L and Dumoncel, J and Mazurier, A and Zanolli, C},
title = {Structural analysis of premolar roots in Middle Pleistocene hominins from China.},
journal = {Journal of human evolution},
volume = {136},
number = {},
pages = {102669},
doi = {10.1016/j.jhevol.2019.102669},
pmid = {31614276},
issn = {1095-8606},
abstract = {This study investigates permanent maxillary and mandibular premolar root structural organization in East Asian Middle Pleistocene hominins. In addition to reporting and analyzing the linear and volumetric properties of the roots, we used a landmark-free approach to both qualify and quantify in 3D premolar root shape variation of Middle Pleistocene hominins in East Asia. Moreover, we focus on some mid-to late East Asian Middle Pleistocene hominin specimens whose taxonomic attribution is unclear. We find considerable cementum in this sample of hominins, similar to other fossil groups, but clearly different from modern humans which have a very small amount of cementum. Additionally, a smaller root pulp cavity is found in later Homo (Neanderthals and modern humans). Our analyses on the crown-root surface area ratio show that East Asian Middle Pleistocene Homo erectus as well as one late Middle Pleistocene Homo sp. specimen (PA 81 P4 from Changyang site) are distinguished from other fossil and extant groups by a relatively larger root surface, stout root branches and thick cementum deposits. This may represent a distinct East Asian H. erectus dental pattern. Geometric morphometric analyses on the external root surface reveal a general trend of shape simplification along the Homo lineage examined here, and distinguish Early Pleistocene Homo, Middle Pleistocene H. erectus, Neanderthals and modern human morphologies. The late Middle Pleistocene teeth from Changyang site (PA 76 P3 and PA 81 P4) are close to East Asian H. erectus and Neanderthals, while the mid-Middle Pleistocene P3 from Panxian Dadong falls within the modern human distribution. Combined with dental crown morphology and root number/form reported in previous studies, our results show that the external root shape can be considered a taxonomically relevant indicator. In general, an evolutionary tendency towards modern human morphology is observed in part of the East Asian Middle Pleistocene specimens, while a retention of primitive, H. erectus-like features is expressed in some late Middle Pleistocene specimens, supporting a multi-lineage and discontinuous scenario of human settlements in East Asia.},
}

@article {pmid31611012,
year = {2019},
author = {Sarig, R and Fornai, C and Pokhojaev, A and May, H and Hans, M and Latimer, B and Barzilai, O and Quam, R and Weber, GW},
title = {The dental remains from the Early Upper Paleolithic of Manot Cave, Israel.},
journal = {Journal of human evolution},
volume = {},
number = {},
pages = {102648},
doi = {10.1016/j.jhevol.2019.102648},
pmid = {31611012},
issn = {1095-8606},
abstract = {This study presents the dental remains discovered at Manot Cave (MC), Western Galilee, Israel. The cave contains evidence for human occupation during the Early Upper Paleolithic period (46-33 ka) mainly of Early Ahmarian (∼46-42 ka) and Levantine Aurignacian (∼38-34 ka) cultural levels. Six teeth (three deciduous and three permanent) were found at the site, of which four could be thoroughly analyzed. The morphology of the teeth was qualitatively described and analyzed using traditional and geometric morphometric methods. A large comparative sample was used in order to assess the morphological affiliation of the Manot specimens with other Homo groups. The results provided equivocal signals: the upper first premolar (MC-9 P3) is probably modern human; the upper deciduous second molar (MC-10 dm2) and the upper second permanent molar (MC-8 M2) might be modern humans; the lower second deciduous molar (MC-7 dm2) might be Neanderthal. Owing to the small sample size and the almost total lack of distinctive characteristics, our outcome could not supply conclusive evidence to address the question of whether Manot Aurignacian population came from Europe or descended from the local Ahmarian population.},
}

@article {pmid31591491,
year = {2019},
author = {Colbran, LL and Gamazon, ER and Zhou, D and Evans, P and Cox, NJ and Capra, JA},
title = {Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences.},
journal = {Nature ecology & evolution},
volume = {3},
number = {11},
pages = {1598-1606},
doi = {10.1038/s41559-019-0996-x},
pmid = {31591491},
issn = {2397-334X},
support = {T32GM080178//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM127087//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01MH101820//U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)/ ; R01MH113362//U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)/ ; R01MH090937//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01GM115836//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; Preterm Birth Initiative//Burroughs Wellcome Fund (BWF)/ ; R35 HG010718/HG/NHGRI NIH HHS/United States ; },
abstract = {Sequencing DNA derived from archaic bones has enabled genetic comparison of Neanderthals and anatomically modern humans (AMHs), and revealed that they interbred. However, interpreting what genetic differences imply about their phenotypic differences remains challenging. Here, we introduce an approach for identifying divergent gene regulation between archaic hominins, such as Neanderthals, and AMH sequences, and find 766 genes that are likely to have been divergently regulated (DR) by Neanderthal haplotypes that do not remain in AMHs. DR genes include many involved in phenotypes known to differ between Neanderthals and AMHs, such as the structure of the rib cage and supraorbital ridge development. They are also enriched for genes associated with spontaneous abortion, polycystic ovary syndrome, myocardial infarction and melanoma. Phenotypes associated with modern human variation in these genes' regulation in ~23,000 biobank patients further support their involvement in immune and cardiovascular phenotypes. Comparing DR genes between two Neanderthals and a Denisovan revealed divergence in the immune system and in genes associated with skeletal and dental morphology that are consistent with the archaeological record. These results establish differences in gene regulatory architecture between AMHs and archaic hominins, and provide an avenue for exploring phenotypic differences between archaic groups from genomic information alone.},
}

@article {pmid31589589,
year = {2019},
author = {Eisová, S and Velemínský, P and Bruner, E},
title = {The Neanderthal endocast from Gánovce (Poprad, Slovak Republic).},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {97},
number = {},
pages = {},
doi = {10.4436/JASS.97005},
pmid = {31589589},
issn = {2037-0644},
abstract = {A Neanderthal endocast, naturally formed by travertine within the crater of a thermal spring, was found at Gánovce, near Poprad (Slovakia), in 1926, and dated to 105 ka. The endocast is partially covered by fragments of the braincase. The volume of the endocast was estimated to be 1320 cc. The endocast was first studied by the Czech paleoanthropologist Emanuel Vlček, who performed metric and morphological analyses which suggested its Neanderthal origin. Vlček published his works more than fifty years ago, but the fossil is scarcely known to the general paleoanthropological community, probably because of language barriers. Here, we review the historical and anatomical information available on the endocasts, providing additional paleoneurological assessments on its features. The endocast displays typical Neanderthal traits, and its overall appearance is similar to Guattari 1, mostly because of the pronounced frontal width and occipital bulging. The morphology of the Gánovce specimen suggests once more that the Neanderthal endocranial phenotype had already evolved at 100 ka.},
}

@article {pmid31586143,
year = {2019},
author = {Sánchez-Hernández, C and Gourichon, L and Pubert, E and Rendu, W and Montes, R and Rivals, F},
title = {Combined dental wear and cementum analyses in ungulates reveal the seasonality of Neanderthal occupations in Covalejos Cave (Northern Iberia).},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {14335},
pmid = {31586143},
issn = {2045-2322},
support = {HAR2016-76760-C3-1-P//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; BES-C-2014-0034//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; HAR2016-76760-C3-1-P//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; 2017-SGR-836//Generalitat de Catalunya (Government of Catalonia)/ ; 2017-SGR-836//Generalitat de Catalunya (Government of Catalonia)/ ; ANR-14-CE31-0011//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-14-CE31-0011//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-14-CE31-0011//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-14-CE31-0011//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {We propose for the first time the use of the combination of two high-resolution techniques, dental wear (meso- and microwear) and dental cementum analyses, to gain a better understanding of Neanderthal subsistence strategies and occupational patterns. Dental wear analysis provides information not only on ungulate palaeodiet and palaeoenvironments but also on hunting time and seasons. Dental cementum analysis allows the accurate determination of the age and season at death of a prey. Our study has focused on the Cantabrian region and has applied both methods to investigate the Mousterian faunal assemblages in Covalejos Cave. Identification of the ungulate palaeodiet reveals information on the environmental conditions of the studied region. Moreover, it may facilitate observation on the evolution of both palaeodiet and palaeoenvironment throughout the site sequence. Results show a general stability in the palaeoenvironmental conditions and in the ungulate palaeodiet throughout the Mousterian sequence; this finding may be attributed to the role of the area as a climate refuge, and slight differences in levels 8, 7 and 4 suggest long- or short-term but repeated Neanderthal occupations at different seasons in the annual cycle.},
}

@article {pmid31585375,
year = {2019},
author = {Davies, TW and Delezene, LK and Gunz, P and Hublin, JJ and Skinner, MM},
title = {Endostructural morphology in hominoid mandibular third premolars: Discrete traits at the enamel-dentine junction.},
journal = {Journal of human evolution},
volume = {136},
number = {},
pages = {102670},
doi = {10.1016/j.jhevol.2019.102670},
pmid = {31585375},
issn = {1095-8606},
abstract = {The mandibular third premolar (P3) exhibits substantial differences in size and shape among hominoid taxa, and displays a number of discrete traits that have proven to be useful in studies of hominin taxonomy and phylogeny. Discrete traits at the enamel-dentine junction (EDJ) can be accurately assessed on moderately worn specimens, and often appear sharper than at the outer-enamel surface (OES). Here we use microtomography to image the P3 EDJ of a broad sample of extant apes, extinct hominins and modern humans (n = 100). We present typologies for three important premolar discrete traits at the EDJ (transverse crest, marginal ridge and buccal grooves), and score trait frequencies within our sample. We find that the transverse crest is variable in extant apes, while the majority of hominins display a transverse crest which runs directly between the two major premolar cusps. Some Neanderthals display a unique form in which the transverse crest fails to reach the protoconid. We find that mesial marginal ridge discontinuity is common in Australopithecus anamensis and Australopithecus afarensis while continuous marginal ridges largely characterize Australopithecus africanus and Paranthropus. Interrupted mesial and distal marginal ridges are again seen in Homo sapiens and Neanderthals. Premolar buccal grooves, previously identified at the OES as important for hominin systematics, are again found to show a number of taxon-specific patterns at the EDJ, including a clear difference between Australopithecus and Paranthropus specimens. However, their appearance may be dependent on the morphology of other parts of the crown such as the protoconid crest, and the presence of accessory dentine horns. Finally, we discuss rare variations in the form of dentine horns that underlie premolar cusps, and their potential homology to similar morphologies in other tooth positions.},
}

@article {pmid31569005,
year = {2019},
author = {Conde-Valverde, M and Martínez, I and Quam, RM and Bonmatí, A and Lorenzo, C and Velez, AD and Martínez-Calvo, C and Arsuaga, JL},
title = {The cochlea of the Sima de los Huesos hominins (Sierra de Atapuerca, Spain): New insights into cochlear evolution in the genus Homo.},
journal = {Journal of human evolution},
volume = {136},
number = {},
pages = {102641},
doi = {10.1016/j.jhevol.2019.102641},
pmid = {31569005},
issn = {1095-8606},
abstract = {The cochlea contains taxonomic and phylogenetic information and its morphology is related with hearing abilities among fossil hominins. Data for the genus Homo is presently limited to early Homo and the early Neandertals from Krapina. The present study of the middle Pleistocene hominins from the Sima de los Huesos (SH) provides new evidence on cochlear evolution in the genus Homo. We compared the absolute length, proportional lengths of each turn, number of turns, size and shape of the cross-section of the basal turn, volume, curvature gradient, and thickness of the cochlea between extant Pan troglodytes, extant Homo sapiens, Homo neanderthalensis and the SH hominins. The SH hominins resemble P. troglodytes in the proportionally long basal turn, the small size and round shape of the cross-section of the basal turn, the small cochlear volume and the low cochlear thickness. The SH hominins resemble Neandertals and H. sapiens in their long cochlear length and in the proportionally short third turn. Homo neanderthalensis and H. sapiens share several features, not present in the SH hominins, and that likely represent homoplasies: a larger volume, larger size and oval shape of the cross-section of the basal turn and higher cochlear thickness. Later Neandertals show a derived proportionally shorter apical turn. Changes in cochlear volume in Homo cannot be fully explained by variation in body mass or cochlear length but are more directly related to changes in the cross-sectional area of the basal turn. Based on previous studies of the outer and middle ear in SH hominins, changes in the outer and middle ear preceded changes in the inner ear, and the cochlea and semicircular canals seem to have evolved independently in the Neandertal clade. Finally, the small cochlear volume in the SH hominins suggests a slightly higher upper limit of hearing compared with modern humans.},
}

@article {pmid31560950,
year = {2019},
author = {Mata, X and Renaud, G and Mollereau, C},
title = {The repertoire of family A-peptide GPCRs in archaic hominins.},
journal = {Peptides},
volume = {122},
number = {},
pages = {170154},
doi = {10.1016/j.peptides.2019.170154},
pmid = {31560950},
issn = {1873-5169},
abstract = {Given the importance of G-protein coupled receptors in the regulation of many physiological functions, deciphering the relationships between genotype and phenotype in past and present hominin GPCRs is of main interest to understand the evolutionary process that contributed to the present-day variability in human traits and health. Here, we carefully examined the publicly available genomic and protein sequence databases of the archaic hominins (Neanderthal and Denisova) to draw up the catalog of coding variations in GPCRs for peptide ligands, in comparison with living humans. We then searched in the literature the functional changes, phenotypes and risk of disease possibly associated with the detected variants. Our survey suggests that Neanderthal and Denisovan hominins were likely prone to lower risk of obesity, to enhanced platelet aggregation in response to thrombin, to better response to infection, to less anxiety and aggressiveness and to favorable sociability. While some archaic variants were likely advantageous in the past, they might be responsible for maladaptive disorders today in the context of modern life and/or specific regional distribution. For example, an archaic haplotype in the neuromedin receptor 2 is susceptible to confer risk of diabetic nephropathy in type 1 diabetes in present-day Europeans. Paying attention to the pharmacological properties of some of the archaic variants described in this study may be helpful to understand the variability of therapeutic efficacy between individuals or ethnic groups.},
}

@article {pmid31558742,
year = {2019},
author = {Morley, MW and Goldberg, P and Uliyanov, VA and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Jacobs, Z and Roberts, RG},
title = {Hominin and animal activities in the microstratigraphic record from Denisova Cave (Altai Mountains, Russia).},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {13785},
pmid = {31558742},
issn = {2045-2322},
abstract = {Denisova Cave in southern Siberia uniquely contains evidence of occupation by a recently discovered group of archaic hominins, the Denisovans, starting from the middle of the Middle Pleistocene. Artefacts, ancient DNA and a range of animal and plant remains have been recovered from the sedimentary deposits, along with a few fragmentary fossils of Denisovans, Neanderthals and a first-generation Neanderthal-Denisovan offspring. The deposits also contain microscopic traces of hominin and animal activities that can provide insights into the use of the cave over the last 300,000 years. Here we report the results of a micromorphological study of intact sediment blocks collected from the Pleistocene deposits in the Main and East Chambers of Denisova Cave. The presence of charcoal attests to the use of fire by hominins, but other evidence of their activities preserved in the microstratigraphic record are few. The ubiquitous occurrence of coprolites, which we attribute primarily to hyenas, indicates that the site was visited for much of its depositional history by cave-dwelling carnivores. Microscopic traces of post-depositional diagenesis, bioturbation and incipient cryoturbation are observed in only a few regions of the deposit examined here. Micromorphology can help identify areas of sedimentary deposit that are most conducive to ancient DNA preservation and could be usefully integrated with DNA analyses of sediments at archaeological sites to illuminate features of their human and environmental history that are invisible to the naked eye.},
}

@article {pmid31551725,
year = {2019},
author = {Benítez-Burraco, A and Murphy, E},
title = {Why Brain Oscillations Are Improving Our Understanding of Language.},
journal = {Frontiers in behavioral neuroscience},
volume = {13},
number = {},
pages = {190},
doi = {10.3389/fnbeh.2019.00190},
pmid = {31551725},
issn = {1662-5153},
abstract = {We explore the potential that brain oscillations have for improving our understanding of how language develops, is processed in the brain, and initially evolved in our species. The different synchronization patterns of brain rhythms can account for different perceptual and cognitive functions, and we argue that this includes language. We aim to address six distinct questions-the What, How, Where, Who, Why, and When questions-pertaining to oscillatory investigations of language. Language deficits found in clinical conditions like autism, schizophrenia and dyslexia can be satisfactorily construed in terms of an abnormal, disorder-specific pattern of brain rhythmicity. Lastly, an eco-evo-devo approach to language is defended with explicit reference to brain oscillations, embracing a framework that considers language evolution to be the result of a changing environment surrounding developmental paths of the primate brain.},
}

@article {pmid31539495,
year = {2019},
author = {Gokhman, D and Mishol, N and de Manuel, M and de Juan, D and Shuqrun, J and Meshorer, E and Marques-Bonet, T and Rak, Y and Carmel, L},
title = {Reconstructing Denisovan Anatomy Using DNA Methylation Maps.},
journal = {Cell},
volume = {179},
number = {1},
pages = {180-192.e10},
doi = {10.1016/j.cell.2019.08.035},
pmid = {31539495},
issn = {1097-4172},
abstract = {Denisovans are an extinct group of humans whose morphology remains unknown. Here, we present a method for reconstructing skeletal morphology using DNA methylation patterns. Our method is based on linking unidirectional methylation changes to loss-of-function phenotypes. We tested performance by reconstructing Neanderthal and chimpanzee skeletal morphologies and obtained >85% precision in identifying divergent traits. We then applied this method to the Denisovan and offer a putative morphological profile. We suggest that Denisovans likely shared with Neanderthals traits such as an elongated face and a wide pelvis. We also identify Denisovan-derived changes, such as an increased dental arch and lateral cranial expansion. Our predictions match the only morphologically informative Denisovan bone to date, as well as the Xuchang skull, which was suggested by some to be a Denisovan. We conclude that DNA methylation can be used to reconstruct anatomical features, including some that do not survive in the fossil record.},
}

@article {pmid31538229,
year = {2019},
author = {Hanke, B},
title = {[On the relationship between Neanderthal alleles and cytotoxicity].},
journal = {Der Pathologe},
volume = {40},
number = {6},
pages = {627-628},
pmid = {31538229},
issn = {1432-1963},
}

@article {pmid31517046,
year = {2019},
author = {Bennett, EA and Crevecoeur, I and Viola, B and Derevianko, AP and Shunkov, MV and Grange, T and Maureille, B and Geigl, EM},
title = {Morphology of the Denisovan phalanx closer to modern humans than to Neanderthals.},
journal = {Science advances},
volume = {5},
number = {9},
pages = {eaaw3950},
doi = {10.1126/sciadv.aaw3950},
pmid = {31517046},
issn = {2375-2548},
abstract = {A fully sequenced high-quality genome has revealed in 2010 the existence of a human population in Asia, the Denisovans, related to and contemporaneous with Neanderthals. Only five skeletal remains are known from Denisovans, mostly molars; the proximal fragment of a fifth finger phalanx used to generate the genome, however, was too incomplete to yield useful morphological information. Here, we demonstrate through ancient DNA analysis that a distal fragment of a fifth finger phalanx from the Denisova Cave is the larger, missing part of this phalanx. Our morphometric analysis shows that its dimensions and shape are within the variability of Homo sapiens and distinct from the Neanderthal fifth finger phalanges. Thus, unlike Denisovan molars, which display archaic characteristics not found in modern humans, the only morphologically informative Denisovan postcranial bone identified to date is suggested here to be plesiomorphic and shared between Denisovans and modern humans.},
}

@article {pmid31517044,
year = {2019},
author = {Raveane, A and Aneli, S and Montinaro, F and Athanasiadis, G and Barlera, S and Birolo, G and Boncoraglio, G and Di Blasio, AM and Di Gaetano, C and Pagani, L and Parolo, S and Paschou, P and Piazza, A and Stamatoyannopoulos, G and Angius, A and Brucato, N and Cucca, F and Hellenthal, G and Mulas, A and Peyret-Guzzon, M and Zoledziewska, M and Baali, A and Bycroft, C and Cherkaoui, M and Chiaroni, J and Di Cristofaro, J and Dina, C and Dugoujon, JM and Galan, P and Giemza, J and Kivisild, T and Mazieres, S and Melhaoui, M and Metspalu, M and Myers, S and Pereira, L and Ricaut, FX and Brisighelli, F and Cardinali, I and Grugni, V and Lancioni, H and Pascali, VL and Torroni, A and Semino, O and Matullo, G and Achilli, A and Olivieri, A and Capelli, C},
title = {Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe.},
journal = {Science advances},
volume = {5},
number = {9},
pages = {eaaw3492},
doi = {10.1126/sciadv.aaw3492},
pmid = {31517044},
issn = {2375-2548},
abstract = {European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.},
}

@article {pmid31506618,
year = {2019},
author = {Callaway, E},
title = {Lost Denisovan bone reveals surprisingly human-like finger.},
journal = {Nature},
volume = {573},
number = {7773},
pages = {175-176},
doi = {10.1038/d41586-019-02647-9},
pmid = {31506618},
issn = {1476-4687},
mesh = {Animals ; Archaeology ; Fingers ; *Hominidae ; Humans ; *Neanderthals ; },
}

Animals
Archaeology
Fingers
*Hominidae
Humans
*Neanderthals

@article {pmid31501334,
year = {2019},
author = {Duveau, J and Berillon, G and Verna, C and Laisné, G and Cliquet, D},
title = {The composition of a Neandertal social group revealed by the hominin footprints at Le Rozel (Normandy, France).},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {39},
pages = {19409-19414},
pmid = {31501334},
issn = {1091-6490},
abstract = {Footprints represent a unique snapshot of hominin life. They provide information on the size and composition of groups that differs from osteological and archeological remains, whose contemporaneity is difficult to establish. We report here on the discovery of 257 footprints dated to 80,000 y from the Paleolithic site at Le Rozel (Normandy, France), which represent the largest known Neandertal ichnological assemblage to date. We investigate the size and composition of a track-maker group from this large set by developing a morphometric method based on experimental footprints. Our analyses indicate that the footprints were made by a small group comprising different age classes, from early childhood to adult, with a majority of children. The Le Rozel footprints thus provide direct evidence for the size and composition of a Neandertal social group.},
}

@article {pmid31477933,
year = {2019},
author = {Speidel, L and Forest, M and Shi, S and Myers, SR},
title = {A method for genome-wide genealogy estimation for thousands of samples.},
journal = {Nature genetics},
volume = {51},
number = {9},
pages = {1321-1329},
doi = {10.1038/s41588-019-0484-x},
pmid = {31477933},
issn = {1546-1718},
support = {203141/Z/16/Z//Wellcome Trust (Wellcome)/ ; 098387/Z/12/Z//Wellcome Trust (Wellcome)/ ; 212284/Z/18/Z//Wellcome Trust (Wellcome)/ ; EP/G03706X/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; },
abstract = {Knowledge of genome-wide genealogies for thousands of individuals would simplify most evolutionary analyses for humans and other species, but has remained computationally infeasible. We have developed a method, Relate, scaling to >10,000 sequences while simultaneously estimating branch lengths, mutational ages and variable historical population sizes, as well as allowing for data errors. Application to 1,000 Genomes Project haplotypes produces joint genealogical histories for 26 human populations. Highly diverged lineages are present in all groups, but most frequent in Africa. Outside Africa, these mainly reflect ancient introgression from groups related to Neanderthals and Denisovans, while African signals instead reflect unknown events unique to that continent. Our approach allows more powerful inferences of natural selection than has previously been possible. We identify multiple regions under strong positive selection, and multi-allelic traits including hair color, body mass index and blood pressure, showing strong evidence of directional selection, varying among human groups.},
}

@article {pmid31472033,
year = {2019},
author = {Pagano, AS and Márquez, S and Laitman, JT},
title = {Reconstructing the Neanderthal Eustachian Tube: New Insights on Disease Susceptibility, Fitness Cost, and Extinction.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {302},
number = {12},
pages = {2109-2125},
doi = {10.1002/ar.24248},
pmid = {31472033},
issn = {1932-8494},
support = {1128901//Directorate for Social, Behavioral and Economic Sciences/ ; },
abstract = {Neanderthals are among the best studied and yet most enigmatic fossil human groups with aspects of their anatomy and functional morphology remaining poorly understood. We present the first anatomical reconstruction of the Neanderthal cartilaginous Eustachian tube (CET), a vital component of the upper respiratory tract and nexus for the middle ear and postnasal airway. The Eustachian (auditory, pharyngotympanic) tube, comprised of a bony and cartilaginous (CET) portion, is integral to normal physiological functions such as middle ear aeration and pressure equilibration. Findings indicate that Neanderthal tubal morphology may have predisposed them to high rates of middle ear disease (otitis media [OM]). In living humans, mechanical CET dysfunction underlies OM in infants and young children, with sequelae including hearing loss, meningitis, and pneumonia. Despite proven linkage of CET malfunction with OM, the role of CET morphology in Neanderthal health and disease remains unstudied. We reconstructed Neanderthal CET morphology, comparing their crania to a modern human growth series. Methods included geometric morphometrics and univariate measures among Procrustes-fitted coordinates. Results showed Neanderthal adults exhibiting primitively tall and narrow nasopharynges with infant-like horizontal CET and choanal orientation. As horizontal CET orientation is associated with increased OM incidence in infants and children until around age six, its appearance in Neanderthal adults strongly indicates persistence of high OM susceptibility at this time. This could have compromised fitness and disease load relative to sympatric modern humans, affecting Neanderthals' ability to compete within their ecological niche, and potentially contributing to their rapid extinction. Anat Rec, 302:2109-2125, 2019. © 2019 American Association for Anatomy.},
}

@article {pmid31469987,
year = {2019},
author = {Rosandić, M and Vlahović, I and Paar, V},
title = {Novel look at DNA and life-Symmetry as evolutionary forcing.},
journal = {Journal of theoretical biology},
volume = {483},
number = {},
pages = {109985},
doi = {10.1016/j.jtbi.2019.08.016},
pmid = {31469987},
issn = {1095-8541},
abstract = {After explanation of the Chargaff´s first parity rule in terms of the Watson-Crick base-pairing between the two DNA strands, the Chargaff´s second parity rule for each strand of DNA (also named strand symmetry), which cannot be explained by Watson-Crick base-pairing only, is still a challenging issue already fifty years. We show that during evolution DNA preserves its identity in the form of quadruplet A+T and C+G rich matrices based on purine-pyrimidine mirror symmetries of trinucleotides. Identical symmetries are present in our classification of trinucleotides and the genetic code table. All eukaryotes and almost all prokaryotes (bacteria and archaea) have quadruplet mirror symmetries in structural form and frequencies following the principle of Chargaff's second parity rule and Natural symmetry law of DNA creation and conservation. Some rare symbionts have mirror symmetry only in their structural form within each DNA strand. Based on our matrix analysis of closely related species, humans and Neanderthals, we find that the circular cycle of inverse proportionality between trinucleotides preserves identical relative frequencies of trinucleotides in each quadruplet and in the whole genome. According to our calculations, a change in frequencies in quadruplet matrices could lead to the creation of new species. Violation of quadruplet symmetries is practically inconsistent with life. DNA symmetries provide a key for understanding the restriction of disorder (entropy) due to mutations in the evolution of DNA.},
}

@article {pmid31427508,
year = {2019},
author = {Schmidt, P and Blessing, M and Rageot, M and Iovita, R and Pfleging, J and Nickel, KG and Righetti, L and Tennie, C},
title = {Birch tar production does not prove Neanderthal behavioral complexity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {36},
pages = {17707-17711},
doi = {10.1073/pnas.1911137116},
pmid = {31427508},
issn = {1091-6490},
abstract = {Birch tar production by Neanderthals-used for hafting tools-has been interpreted as one of the earliest manifestations of modern cultural behavior. This is because birch tar production per se was assumed to require a cognitively demanding setup, in which birch bark is heated in anaerobic conditions, a setup whose inherent complexity was thought to require modern levels of cognition and cultural transmission. Here we demonstrate that recognizable amounts of birch tar were likely a relatively frequent byproduct of burning birch bark (a natural tinder) under common, i.e., aerobic, conditions. We show that when birch bark burns close to a vertical to subvertical hard surface, such as an adjacent stone, birch tar is naturally deposited and can be easily scraped off the surface. The burning of birch bark near suitable surfaces provides useable quantities of birch tar in a single work session (3 h; including birch bark procurement). Chemical analysis of the resulting tar showed typical markers present in archaeological tar. Mechanical tests verify the tar's suitability for hafting and for hafted tools use. Given that similarly sized stones as in our experiment are frequently found in archaeological contexts associated with Neanderthals, the cognitively undemanding connection between burning birch bark and the production of birch tar would have been readily discoverable multiple times. Thus, the presence of birch tar alone cannot indicate the presence of modern cognition and/or cultural behaviors in Neanderthals.},
}

@article {pmid31421316,
year = {2019},
author = {Zanolli, C and Biglari, F and Mashkour, M and Abdi, K and Monchot, H and Debue, K and Mazurier, A and Bayle, P and Le Luyer, M and Rougier, H and Trinkaus, E and Macchiarelli, R},
title = {A Neanderthal from the Central Western Zagros, Iran. Structural reassessment of the Wezmeh 1 maxillary premolar.},
journal = {Journal of human evolution},
volume = {135},
number = {},
pages = {102643},
doi = {10.1016/j.jhevol.2019.102643},
pmid = {31421316},
issn = {1095-8606},
abstract = {Wezmeh Cave, in the Kermanshah region of Central Western Zagros, Iran, produced a Late Pleistocene faunal assemblage rich in carnivorans along with a human right maxillary premolar, Wezmeh 1, an unerupted tooth from an 8 ± 2 year-old individual. Uranium-series analyses of the fauna by alpha spectrometry provided age estimates between 70 and 11 ka. Crown dimensions place the tooth specimen at the upper limits of Late Pleistocene human ranges of variation. Wezmeh 1 metameric position (most likely a P3) remains uncertain and only its surficial morphology has been described so far. Accordingly, we used microfocus X-ray tomography (12.5 μm isotropic voxel size) to reassess the metameric position and taxonomic attribution of this specimen. We investigated its endostructural features and quantified crown tissue proportions. Topographic maps of enamel thickness (ET) distribution were also generated, and semilandmark-based geometric morphometric analyses of the enamel-dentine junction (EDJ) were performed. We compared Wezmeh 1 with unworn/slightly-moderately worn P3 and P4 of European Neanderthals, Middle Paleolithic modern humans from Qafzeh, an Upper Paleolithic premolar, and Holocene humans. The results confirm that Wezmeh 1 represents a P3. Based on its internal conformation and especially EDJ shape, Wezmeh 1 aligns closely with Neanderthals and is distinct from the fossil and extant modern human pattern of our comparative samples. Wezmeh 1 is thus the first direct evidence of Neanderthal presence on the western margin of the Iranian Plateau.},
}

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

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

@article {pmid31392716,
year = {2019},
author = {Garralda, MD and Maíllo-Fernández, JM and Higham, T and Neira, A and Bernaldo de Quirós, F},
title = {The Gravettian child mandible from El Castillo Cave (Puente Viesgo, Cantabria, Spain).},
journal = {American journal of physical anthropology},
volume = {170},
number = {3},
pages = {331-350},
doi = {10.1002/ajpa.23906},
pmid = {31392716},
issn = {1096-8644},
support = {HAR2015-70652-P//Spanish Ministry of Research and Science/ ; HAR2012-35214//Spanish Ministry of Research and Science/ ; },
abstract = {OBJECTIVES: This article documents an incomplete child's mandible found in H. Obermaier's excavation campaign (in 1912) in El Castillo Cave, Spain. This fossil was assigned to what was then considered a phase of the "Aurignacian-delta".

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

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

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

@article {pmid31368158,
year = {2019},
author = {Lieberman, P},
title = {The antiquity and evolution of the neural bases of rhythmic activity.},
journal = {Annals of the New York Academy of Sciences},
volume = {1453},
number = {1},
pages = {114-124},
doi = {10.1111/nyas.14199},
pmid = {31368158},
issn = {1749-6632},
abstract = {The evolution of the anatomy and neural circuits that regulate the rhythm of speech can be traced back to the Devonian age, 400 million years ago. Epigenetic processes 100 million years later modified these circuits. Natural selection on similar genetic processes occurred during the evolution of archaic hominins and humans. The lungs and larynx-anatomy that produces the rhythmic fundamental frequency patterns of speech-have a deep evolutionary history. Neural circuits linking the cortex, basal ganglia, and other subcortical structures plan, sequence, and execute motor as well as cognitive acts. These neural circuits generate the rhythm of speech, singing, and chanting. The human form of the transcription factor FOXP2 increased synaptic connectivity and plasticity in basal ganglia circuits, enhancing motor control and cognitive and linguistic capabilities in humans as well as Neanderthals. The archeological record also suggests that Neanderthals passed spoken language. Homologous circuits existed in amphibians. In songbirds, the avian form of FOXP2 acted on similar neural circuits allowing birds to learn and produce new songs. Current studies point to natural selection on genetic events enhancing these and other neural circuits to yield fully human rhythmic speech, and motor, cognitive, and linguistic capabilities, rather than the saltation proposed by Noam Chomsky.},
}

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

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

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

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

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

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

@article {pmid31308224,
year = {2019},
author = {Bokelmann, L and Hajdinjak, M and Peyrégne, S and Brace, S and Essel, E and de Filippo, C and Glocke, I and Grote, S and Mafessoni, F and Nagel, S and Kelso, J and Prüfer, K and Vernot, B and Barnes, I and Pääbo, S and Meyer, M and Stringer, C},
title = {A genetic analysis of the Gibraltar Neanderthals.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {31},
pages = {15610-15615},
doi = {10.1073/pnas.1903984116},
pmid = {31308224},
issn = {1091-6490},
support = {//Wellcome Trust/United Kingdom ; },
abstract = {The Forbes' Quarry and Devil's Tower partial crania from Gibraltar are among the first Neanderthal remains ever found. Here, we show that small amounts of ancient DNA are preserved in the petrous bones of the 2 individuals despite unfavorable climatic conditions. However, the endogenous Neanderthal DNA is present among an overwhelming excess of recent human DNA. Using improved DNA library construction methods that enrich for DNA fragments carrying deaminated cytosine residues, we were able to sequence 70 and 0.4 megabase pairs (Mbp) nuclear DNA of the Forbes' Quarry and Devil's Tower specimens, respectively, as well as large parts of the mitochondrial genome of the Forbes' Quarry individual. We confirm that the Forbes' Quarry individual was a female and the Devil's Tower individual a male. We also show that the Forbes' Quarry individual is genetically more similar to the ∼120,000-y-old Neanderthals from Scladina Cave in Belgium (Scladina I-4A) and Hohlenstein-Stadel Cave in Germany, as well as to a ∼60,000- to 70,000-y-old Neanderthal from Russia (Mezmaiskaya 1), than to a ∼49,000-y-old Neanderthal from El Sidrón (El Sidrón 1253) in northern Spain and other younger Neanderthals from Europe and western Asia. This suggests that the Forbes' Quarry fossil predates the latter Neanderthals. The preservation of archaic human DNA in the warm coastal climate of Gibraltar, close to the shores of Africa, raises hopes for the future recovery of archaic human DNA from regions in which climatic conditions are less than optimal for DNA preservation.},
}

@article {pmid31292546,
year = {2019},
author = {Harvati, K and Röding, C and Bosman, AM and Karakostis, FA and Grün, R and Stringer, C and Karkanas, P and Thompson, NC and Koutoulidis, V and Moulopoulos, LA and Gorgoulis, VG and Kouloukoussa, M},
title = {Apidima Cave fossils provide earliest evidence of Homo sapiens in Eurasia.},
journal = {Nature},
volume = {571},
number = {7766},
pages = {500-504},
doi = {10.1038/s41586-019-1376-z},
pmid = {31292546},
issn = {1476-4687},
mesh = {Animals ; Biological Evolution ; *Caves ; *Fossils ; Greece ; Humans ; Neanderthals/anatomy & histology/classification ; Principal Component Analysis ; Radiometric Dating ; Skull/*anatomy & histology ; Time Factors ; },
abstract = {Two fossilized human crania (Apidima 1 and Apidima 2) from Apidima Cave, southern Greece, were discovered in the late 1970s but have remained enigmatic owing to their incomplete nature, taphonomic distortion and lack of archaeological context and chronology. Here we virtually reconstruct both crania, provide detailed comparative descriptions and analyses, and date them using U-series radiometric methods. Apidima 2 dates to more than 170 thousand years ago and has a Neanderthal-like morphological pattern. By contrast, Apidima 1 dates to more than 210 thousand years ago and presents a mixture of modern human and primitive features. These results suggest that two late Middle Pleistocene human groups were present at this site-an early Homo sapiens population, followed by a Neanderthal population. Our findings support multiple dispersals of early modern humans out of Africa, and highlight the complex demographic processes that characterized Pleistocene human evolution and modern human presence in southeast Europe.},
}

Animals
Biological Evolution
*Caves
*Fossils
Greece
Humans
Neanderthals/anatomy & histology/classification
Principal Component Analysis
Radiometric Dating
Skull/*anatomy & histology
Time Factors

@article {pmid31278514,
year = {2019},
author = {Brzozowska, MM and Havula, E and Allen, RB and Cox, MP},
title = {Genetics, adaptation to environmental changes and archaic admixture in the pathogenesis of diabetes mellitus in Indigenous Australians.},
journal = {Reviews in endocrine & metabolic disorders},
volume = {20},
number = {3},
pages = {321-332},
pmid = {31278514},
issn = {1573-2606},
abstract = {Indigenous Australians are particularly affected by type 2 diabetes mellitus (T2D) due to both their genetic susceptibility and a range of environmental and lifestyle risk factors. Recent genetic studies link predisposition to some diseases, including T2D, to alleles acquired from archaic hominins, such as Neanderthals and Denisovans, which persist in the genomes of modern humans today. Indo-Pacific human populations, including Indigenous Australians, remain extremely underrepresented in genomic research with a paucity of data examining the impact of Denisovan or Neanderthal lineages on human phenotypes in Oceania. The few genetic studies undertaken emphasize the uniqueness and antiquity of Indigenous Australian genomes, with possibly the largest proportion of Denisovan ancestry of any population in the world. In this review, we focus on the potential contributions of ancient genes/pathways to modern human phenotypes, while also highlighting the evolutionary roles of genetic adaptation to dietary and environmental changes associated with an adopted Western lifestyle. We discuss the role of genetic and epigenetic factors in the pathogenesis of T2D in understudied Indigenous Australians, including the potential impact of archaic gene lineages on this disease. Finally, we propose that greater understanding of the underlying genetic predisposition may contribute to the clinical efficacy of diabetes management in Indigenous Australians. We suggest that improved identification of T2D risk variants in Oceania is needed. Such studies promise to clarify how genetic and phenotypic differences vary between populations and, crucially, provide novel targets for personalised medical therapies in currently marginalized groups.},
}

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

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

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

@article {pmid31222847,
year = {2019},
author = {Ackermann, RR and Arnold, ML and Baiz, MD and Cahill, JA and Cortés-Ortiz, L and Evans, BJ and Grant, BR and Grant, PR and Hallgrimsson, B and Humphreys, RA and Jolly, CJ and Malukiewicz, J and Percival, CJ and Ritzman, TB and Roos, C and Roseman, CC and Schroeder, L and Smith, FH and Warren, KA and Wayne, RK and Zinner, D},
title = {Hybridization in human evolution: Insights from other organisms.},
journal = {Evolutionary anthropology},
volume = {28},
number = {4},
pages = {189-209},
doi = {10.1002/evan.21787},
pmid = {31222847},
issn = {1520-6505},
support = {T32 GM007544/GM/NIGMS NIH HHS/United States ; //National Research Foundation of South Africa/ ; //DST/NRF Centre of Excellence in Palaeosciences (CoE-Pal)/ ; },
mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; Female ; Genome, Human/genetics ; *Hominidae/anatomy & histology/genetics ; Humans ; Hybridization, Genetic/*genetics ; Male ; Mice ; Neanderthals/anatomy & histology/genetics ; Phenotype ; Skull/anatomy & histology ; },
abstract = {During the late Pleistocene, isolated lineages of hominins exchanged genes thus influencing genomic variation in humans in both the past and present. However, the dynamics of this genetic exchange and associated phenotypic consequences through time remain poorly understood. Gene exchange across divergent lineages can result in myriad outcomes arising from these dynamics and the environmental conditions under which it occurs. Here we draw from our collective research across various organisms, illustrating some of the ways in which gene exchange can structure genomic/phenotypic diversity within/among species. We present a range of examples relevant to questions about the evolution of hominins. These examples are not meant to be exhaustive, but rather illustrative of the diverse evolutionary causes/consequences of hybridization, highlighting potential drivers of human evolution in the context of hybridization including: influences on adaptive evolution, climate change, developmental systems, sex-differences in behavior, Haldane's rule and the large X-effect, and transgressive phenotypic variation.},
}

Animals
Anthropology, Physical
*Biological Evolution
Female
Genome, Human/genetics
*Hominidae/anatomy & histology/genetics
Humans
Hybridization, Genetic/*genetics
Male
Mice
Neanderthals/anatomy & histology/genetics
Phenotype
Skull/anatomy & histology

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

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

@article {pmid31196864,
year = {2019},
author = {Haber, M and Jones, AL and Connell, BA and Asan, and Arciero, E and Yang, H and Thomas, MG and Xue, Y and Tyler-Smith, C},
title = {A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans Out of Africa.},
journal = {Genetics},
volume = {212},
number = {4},
pages = {1421-1428},
doi = {10.1534/genetics.119.302368},
pmid = {31196864},
issn = {1943-2631},
support = {//Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Present-day humans outside Africa descend mainly from a single expansion out ∼50,000-70,000 years ago, but many details of this expansion remain unclear, including the history of the male-specific Y chromosome at this time. Here, we reinvestigate a rare deep-rooting African Y-chromosomal lineage by sequencing the whole genomes of three Nigerian men described in 2003 as carrying haplogroup DE* Y chromosomes, and analyzing them in the context of a calibrated worldwide Y-chromosomal phylogeny. We confirm that these three chromosomes do represent a deep-rooting DE lineage, branching close to the DE bifurcation, but place them on the D branch as an outgroup to all other known D chromosomes, and designate the new lineage D0. We consider three models for the expansion of Y lineages out of Africa ∼50,000-100,000 years ago, incorporating migration back to Africa where necessary to explain present-day Y-lineage distributions. Considering both the Y-chromosomal phylogenetic structure incorporating the D0 lineage, and published evidence for modern humans outside Africa, the most favored model involves an origin of the DE lineage within Africa with D0 and E remaining there, and migration out of the three lineages (C, D, and FT) that now form the vast majority of non-African Y chromosomes. The exit took place 50,300-81,000 years ago (latest date for FT lineage expansion outside Africa - earliest date for the D/D0 lineage split inside Africa), and most likely 50,300-59,400 years ago (considering Neanderthal admixture). This work resolves a long-running debate about Y-chromosomal out-of-Africa/back-to-Africa migrations, and provides insights into the out-of-Africa expansion more generally.},
}

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

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

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

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

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

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

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

@article {pmid31163991,
year = {2019},
author = {Santander, C and Montinaro, F and Capelli, C},
title = {Searching for archaic contribution in Africa.},
journal = {Annals of human biology},
volume = {46},
number = {2},
pages = {129-139},
doi = {10.1080/03014460.2019.1624823},
pmid = {31163991},
issn = {1464-5033},
mesh = {Africa ; African Continental Ancestry Group/*genetics ; Animals ; DNA, Ancient/*analysis ; Genome, Human ; Hominidae/*genetics ; Humans ; *Hybridization, Genetic ; },
abstract = {Context: Africa's role in the narrative of human evolution is indisputably emphasised in the emergence of Homo sapiens. However, once humans dispersed beyond Africa, the history of those who stayed remains vastly under-studied, lacking the proper attention the birthplace of both modern and archaic humans deserves. The sequencing of Neanderthal and Denisovan genomes has elucidated evidence of admixture between archaic and modern humans outside of Africa, but has not aided efforts in answering whether archaic admixture happened within Africa. Objectives: This article reviews the state of research for archaic introgression in African populations and discusses recent insights into this topic. Methods: Gathering published sources and recently released preprints, this review reports on the different methods developed for detecting archaic introgression. Particularly it discusses how relevant these are when implemented on African populations and what findings these studies have shown so far. Results: Methods for detecting archaic introgression have been predominantly developed and implemented on non-African populations. Recent preprints present new methods considering African populations. While a number of studies using these methods suggest archaic introgression in Africa, without an African archaic genome to validate these results, such findings remain as putative archaic introgression. Conclusion: In light of the caveats with implementing current archaic introgression detection methods in Africa, we recommend future studies to concentrate on unravelling the complicated demographic history of Africa through means of ancient DNA where possible and through more focused efforts to sequence modern DNA from more representative populations across the African continent.},
}

Africa
African Continental Ancestry Group/*genetics
Animals
DNA, Ancient/*analysis
Genome, Human
Hominidae/*genetics
Humans
*Hybridization, Genetic

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

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

@article {pmid31136573,
year = {2019},
author = {Durvasula, A and Sankararaman, S},
title = {A statistical model for reference-free inference of archaic local ancestry.},
journal = {PLoS genetics},
volume = {15},
number = {5},
pages = {e1008175},
doi = {10.1371/journal.pgen.1008175},
pmid = {31136573},
issn = {1553-7404},
support = {R35 GM125055/GM/NIGMS NIH HHS/United States ; R00 GM111744/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Genetics, Population/*methods ; Genome, Human/genetics ; Genomics/*methods ; Hominidae/*genetics ; Humans ; Models, Statistical ; Neanderthals/genetics ; },
abstract = {Statistical analyses of genomic data from diverse human populations have demonstrated that archaic hominins, such as Neanderthals and Denisovans, interbred or admixed with the ancestors of present-day humans. Central to these analyses are methods for inferring archaic ancestry along the genomes of present-day individuals (archaic local ancestry). Methods for archaic local ancestry inference rely on the availability of reference genomes from the ancestral archaic populations for accurate inference. However, several instances of archaic admixture lack reference archaic genomes, making it difficult to characterize these events. We present a statistical method that combines diverse population genetic summary statistics to infer archaic local ancestry without access to an archaic reference genome. We validate the accuracy and robustness of our method in simulations. When applied to genomes of European individuals, our method recovers segments that are substantially enriched for Neanderthal ancestry, even though our method did not have access to any Neanderthal reference genomes.},
}

Animals
Genetics, Population/*methods
Genome, Human/genetics
Genomics/*methods
Hominidae/*genetics
Humans
Models, Statistical
Neanderthals/genetics

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

@article {pmid31113254,
year = {2019},
author = {Ham, E and Underdown, SJ and Houldcroft, CJ},
title = {The relative roles of maternal survival and inter-personal violence as selection pressures on the persistence of Neanderthal hypercoagulability alleles in modern Europeans.},
journal = {Annals of human biology},
volume = {46},
number = {2},
pages = {99-108},
doi = {10.1080/03014460.2019.1622038},
pmid = {31113254},
issn = {1464-5033},
mesh = {Alleles ; Animals ; Europe ; European Continental Ancestry Group ; Gene Frequency ; Humans ; Longevity/*genetics ; Mothers/*statistics & numerical data ; Neanderthals/genetics ; P-Selectin/*genetics/metabolism ; Physical Abuse/*statistics & numerical data ; Polymorphism, Single Nucleotide/*genetics ; *Selection, Genetic ; Tanzania ; Thrombophilia/genetics ; },
abstract = {Background: Simonti et al. reported variation in the frequency of Neanderthal alleles found in modern humans and argued that they may have provided an evolutionary advantage. One such allele is SNP rs3917862, associated with hypercoagulability. rs3917862 can be deleterious, but can also help prevent blood loss. Aim: To investigate two possible selective pressure hypotheses for rs3917862 surviving to higher frequencies: deaths from interpersonal violent trauma and childbirth. Subjects and methods: Mortality data from modern hunter-gatherers models the living conditions and causes of death of humans and Neanderthals at the point of admixture. Results: National census data indicates a positive correlation between the presence of rs3917862 and decreased maternal mortality ratios. When the maternal mortality ratio is modelled using GDP, births attended by skilled assistants and the presence of rs3917862, women are 0.1% more likely to die in childbirth in populations lacking rs3917862. Deaths due to violence show no correlation with rs3917862. Conclusion: These findings challenge the idea that Neanderthal admixture has negatively impacted the overall health of modern humans. Maternal survival may have acted as a selective pressure for the persistence of hypercoagulability alleles in modern Europeans. Understanding the role of hypercoagulability in childbirth, and the role of rs3917862, could help to reduce maternal mortality ratios.},
}

Alleles
Animals
Europe
European Continental Ancestry Group
Gene Frequency
Humans
Longevity/*genetics
Mothers/*statistics & numerical data
Neanderthals/genetics
P-Selectin/*genetics/metabolism
Physical Abuse/*statistics & numerical data
Polymorphism, Single Nucleotide/*genetics
*Selection, Genetic
Tanzania
Thrombophilia/genetics

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

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

@article {pmid31068377,
year = {2019},
author = {Vangenot, C and Gagneux, P and de Groot, NG and Baumeyer, A and Mouterde, M and Crouau-Roy, B and Darlu, P and Sanchez-Mazas, A and Sabbagh, A and Poloni, ES},
title = {Humans and Chimpanzees Display Opposite Patterns of Diversity in Arylamine N-Acetyltransferase Genes.},
journal = {G3 (Bethesda, Md.)},
volume = {9},
number = {7},
pages = {2199-2224},
doi = {10.1534/g3.119.400223},
pmid = {31068377},
issn = {2160-1836},
abstract = {Among the many genes involved in the metabolism of therapeutic drugs, human arylamine N-acetyltransferases (NATs) genes have been extensively studied, due to their medical importance both in pharmacogenetics and disease epidemiology. One member of this small gene family, NAT2, is established as the locus of the classic human acetylation polymorphism in drug metabolism. Current hypotheses hold that selective processes favoring haplotypes conferring lower NAT2 activity have been operating in modern humans' recent history as an adaptation to local chemical and dietary environments. To shed new light on such hypotheses, we investigated the genetic diversity of the three members of the NAT gene family in seven hominid species, including modern humans, Neanderthals and Denisovans. Little polymorphism sharing was found among hominids, yet all species displayed high NAT diversity, but distributed in an opposite fashion in chimpanzees and bonobos (Pan genus) compared to modern humans, with higher diversity in Pan species at NAT1 and lower at NAT2, while the reverse is observed in humans. This pattern was also reflected in the results returned by selective neutrality tests, which suggest, in agreement with the predicted functional impact of mutations detected in non-human primates, stronger directional selection, presumably purifying selection, at NAT1 in modern humans, and at NAT2 in chimpanzees. Overall, the results point to the evolution of divergent functions of these highly homologous genes in the different primate species, possibly related to their specific chemical/dietary environment (exposome) and we hypothesize that this is likely linked to the emergence of controlled fire use in the human lineage.},
}

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

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

@article {pmid31025315,
year = {2019},
author = {Bosman, AM and Harvati, K},
title = {A virtual assessment of the proposed suprainiac fossa on the early modern European calvaria from Cioclovina, Romania.},
journal = {American journal of physical anthropology},
volume = {169},
number = {3},
pages = {567-574},
doi = {10.1002/ajpa.23844},
pmid = {31025315},
issn = {1096-8644},
support = {//German Research Foundation/ ; },
abstract = {OBJECTIVES: The calvaria from Cioclovina (Romania) has been argued to possess some traits commonly ascribed to individuals belonging to the Neanderthal lineage, including a suprainiac fossa. However, its supranuchal morphology has only been evaluated with a qualitative analysis of the ectocranial surface. We evaluate whether the morphology of the supranuchal area of this specimen is homologous to the Neanderthal condition.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid30942856,
year = {2019},
author = {Harris, DN and Ruczinski, I and Yanek, LR and Becker, LC and Becker, DM and Guio, H and Cui, T and Chilton, FH and Mathias, RA and O'Connor, TD},
title = {Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World.},
journal = {Genome biology and evolution},
volume = {11},
number = {5},
pages = {1417-1430},
doi = {10.1093/gbe/evz071},
pmid = {30942856},
issn = {1759-6653},
support = {R01 AT008621/AT/NCCIH NIH HHS/United States ; },
mesh = {Animals ; *Evolution, Molecular ; Fatty Acid Desaturases/*genetics/metabolism ; Fatty Acids, Unsaturated/*metabolism ; Hominidae/*genetics/metabolism ; Humans ; Indians, North American/genetics ; Selection, Genetic ; Siberia ; },
abstract = {The metabolic conversion of dietary omega-3 and omega-6 18 carbon (18C) to long chain (>20 carbon) polyunsaturated fatty acids (LC-PUFAs) is vital for human life. The rate-limiting steps of this process are catalyzed by fatty acid desaturase (FADS) 1 and 2. Therefore, understanding the evolutionary history of the FADS genes is essential to our understanding of hominin evolution. The FADS genes have two haplogroups, ancestral and derived, with the derived haplogroup being associated with more efficient LC-PUFA biosynthesis than the ancestral haplogroup. In addition, there is a complex global distribution of these haplogroups that is suggestive of Neanderthal introgression. We confirm that Native American ancestry is nearly fixed for the ancestral haplogroup, and replicate a positive selection signal in Native Americans. This positive selection potentially continued after the founding of the Americas, although simulations suggest that the timing is dependent on the allele frequency of the ancestral Beringian population. We also find that the Neanderthal FADS haplotype is more closely related to the derived haplogroup and the Denisovan clusters closer to the ancestral haplogroup. Furthermore, the derived haplogroup has a time to the most recent common ancestor of 688,474 years before present. These results support an ancient polymorphism, as opposed to Neanderthal introgression, forming in the FADS region during the Pleistocene with possibly differential selection pressures on both haplogroups. The near fixation of the ancestral haplogroup in Native American ancestry calls for future studies to explore the potential health risk of associated low LC-PUFA levels in these populations.},
}

Animals
*Evolution, Molecular
Fatty Acid Desaturases/*genetics/metabolism
Fatty Acids, Unsaturated/*metabolism
Hominidae/*genetics/metabolism
Humans
Indians, North American/genetics
Selection, Genetic
Siberia

@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},
mesh = {Body Remains/chemistry ; Carbon Radioisotopes/*analysis ; Fossils/*history ; History, Ancient ; Humans ; Italy ; Radiometric Dating/*methods ; Tooth/chemistry ; },
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.},
}

Body Remains/chemistry
Carbon Radioisotopes/*analysis
Fossils/*history
History, Ancient
Humans
Italy
Radiometric Dating/*methods
Tooth/chemistry

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

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

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

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

@article {pmid30875039,
year = {2019},
author = {Korlević, P and Meyer, M},
title = {Pretreatment: Removing DNA Contamination from Ancient Bones and Teeth Using Sodium Hypochlorite and Phosphate.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {15-19},
doi = {10.1007/978-1-4939-9176-1_2},
pmid = {30875039},
issn = {1940-6029},
mesh = {Animals ; Bone and Bones/*metabolism ; DNA/*analysis/chemistry/*isolation & purification ; *DNA Contamination ; Decontamination ; Neanderthals ; Phosphates/*chemistry ; Polymerase Chain Reaction ; Sodium Hypochlorite/*chemistry ; Specimen Handling/methods ; Tooth/*metabolism ; },
abstract = {DNA isolated from ancient bones and teeth comprises a mixture of microbial contamination and DNA from the organism under study. In addition, analyses of ancient human remains are often complicated by contamination with present-day human DNA, which can be introduced during excavation and subsequent handling of the specimens. In most cases, the relative abundance of contaminant DNA is much greater than that of the target organism. Here we present two techniques for reducing the proportion of contaminant DNA in bones and teeth. The first and most efficient technique uses a sodium hypochlorite (bleach) pretreatment to destroy contaminant DNA that may be bound or otherwise attached to the surface of bone/tooth powder. The second, less destructive pretreatment uses a phosphate buffer to release surface-bound DNA.},
}

Animals
Bone and Bones/*metabolism
DNA/*analysis/chemistry/*isolation & purification
*DNA Contamination
Decontamination
Neanderthals
Phosphates/*chemistry
Polymerase Chain Reaction
Sodium Hypochlorite/*chemistry
Specimen Handling/methods
Tooth/*metabolism

@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.},
}