@article {pmid32217711,
year = {2020},
author = {Will, M},
title = {Neanderthal surf and turf.},
journal = {Science (New York, N.Y.)},
volume = {367},
number = {6485},
pages = {1422-1423},
doi = {10.1126/science.abb3568},
pmid = {32217711},
issn = {1095-9203},
}

@article {pmid32217702,
year = {2020},
author = {Zilhão, J and Angelucci, DE and Igreja, MA and Arnold, LJ and Badal, E and Callapez, P and Cardoso, JL and d'Errico, F and Daura, J and Demuro, M and Deschamps, M and Dupont, C and Gabriel, S and Hoffmann, DL and Legoinha, P and Matias, H and Monge Soares, AM and Nabais, M and Portela, P and Queffelec, A and Rodrigues, F and Souto, P},
title = {Last Interglacial Iberian Neandertals as fisher-hunter-gatherers.},
journal = {Science (New York, N.Y.)},
volume = {367},
number = {6485},
pages = {},
doi = {10.1126/science.aaz7943},
pmid = {32217702},
issn = {1095-9203},
abstract = {Marine food-reliant subsistence systems such as those in the African Middle Stone Age (MSA) were not thought to exist in Europe until the much later Mesolithic. Whether this apparent lag reflects taphonomic biases or behavioral distinctions between archaic and modern humans remains much debated. Figueira Brava cave, in the Arrábida range (Portugal), provides an exceptionally well preserved record of Neandertal coastal resource exploitation on a comparable scale to the MSA and dated to ~86 to 106 thousand years ago. The breadth of the subsistence base-pine nuts, marine invertebrates, fish, marine birds and mammals, tortoises, waterfowl, and hoofed game-exceeds that of regional early Holocene sites. Fisher-hunter-gatherer economies are not the preserve of anatomically modern people; by the Last Interglacial, they were in place across the Old World in the appropriate settings.},
}

@article {pmid31604218,
year = {2019},
author = {Price, M},
title = {Face of the mysterious Denisovans emerges.},
journal = {Science (New York, N.Y.)},
volume = {365},
number = {6459},
pages = {1232},
doi = {10.1126/science.365.6459.1232},
pmid = {31604218},
issn = {1095-9203},
mesh = {Animals ; Asia ; *Biological Evolution ; DNA Methylation ; Epigenesis, Genetic ; Extinction, Biological ; Hominidae/*classification ; Neanderthals ; },
}

Animals
Asia
*Biological Evolution
DNA Methylation
Epigenesis, Genetic
Extinction, Biological
Hominidae/*classification
Neanderthals

@article {pmid31636221,
year = {2019},
author = {Zilhão, J},
title = {Tar adhesives, Neandertals, and the tyranny of the discontinuous mind.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {44},
pages = {21966-21968},
pmid = {31636221},
issn = {1091-6490},
mesh = {Adhesives ; Fossils ; Humans ; *Neanderthals ; North Sea ; Technology ; },
}

Adhesives
Fossils
Humans
*Neanderthals
North Sea
Technology

@article {pmid31296750,
year = {2019},
author = {Wade, L},
title = {Was our species in Europe 210,000 years ago?.},
journal = {Science (New York, N.Y.)},
volume = {365},
number = {6449},
pages = {111},
doi = {10.1126/science.365.6449.111},
pmid = {31296750},
issn = {1095-9203},
mesh = {Animals ; Anthropology ; Caves ; *Extinction, Biological ; Fossils/anatomy & histology ; Greece ; Humans ; Neanderthals/*anatomy & histology ; Skull/*anatomy & histology ; },
}

Animals
Anthropology
Caves
*Extinction, Biological
Fossils/anatomy & histology
Greece
Humans
Neanderthals/*anatomy & histology
Skull/*anatomy & histology

@article {pmid32199301,
year = {2020},
author = {Hunt, KD},
title = {Obituary of Charles Loring Brace, IV (1930-2019).},
journal = {Journal of human evolution},
volume = {142},
number = {},
pages = {102743},
doi = {10.1016/j.jhevol.2020.102743},
pmid = {32199301},
issn = {1095-8606},
}

@article {pmid32193295,
year = {2020},
author = {Bergström, A and McCarthy, SA and Hui, R and Almarri, MA and Ayub, Q and Danecek, P and Chen, Y and Felkel, S and Hallast, P and Kamm, J and Blanché, H and Deleuze, JF and Cann, H and Mallick, S and Reich, D and Sandhu, MS and Skoglund, P and Scally, A and Xue, Y and Durbin, R and Tyler-Smith, C},
title = {Insights into human genetic variation and population history from 929 diverse genomes.},
journal = {Science (New York, N.Y.)},
volume = {367},
number = {6484},
pages = {},
doi = {10.1126/science.aay5012},
pmid = {32193295},
issn = {1095-9203},
support = {/WT_/Wellcome Trust/United Kingdom ; /CRUK_/Cancer Research UK/United Kingdom ; //Medical Research Council,/International ; /ERC_/European Research Council/International ; /HHMI/Howard Hughes Medical Institute/United States ; },
abstract = {Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.},
}

@article {pmid32170098,
year = {2020},
author = {Modesto-Mata, M and Dean, MC and Lacruz, RS and Bromage, TG and García-Campos, C and Martínez de Pinillos, M and Martín-Francés, L and Martinón-Torres, M and Carbonell, E and Arsuaga, JL and Bermúdez de Castro, JM},
title = {Short and long period growth markers of enamel formation distinguish European Pleistocene hominins.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {4665},
doi = {10.1038/s41598-020-61659-y},
pmid = {32170098},
issn = {2045-2322},
support = {BOCYL-D-02102014-10//ConsejerÍa de EducaciÓn, Junta de Castilla y LeÓn/ ; BOCYL-D-02102014-10//ConsejerÍa de EducaciÓn, Junta de Castilla y LeÓn/ ; BOCYL-D-20052013-14//ConsejerÍa de EducaciÓn, Junta de Castilla y LeÓn/ ; },
abstract = {Characterizing dental development in fossil hominins is important for distinguishing between them and for establishing where and when the slow overall growth and development of modern humans appeared. Dental development of australopiths and early Homo was faster than modern humans. The Atapuerca fossils (Spain) fill a barely known gap in human evolution, spanning ~1.2 to ~0.4 million years (Ma), during which H. sapiens and Neandertal dental growth characteristics may have developed. We report here perikymata counts, perikymata distributions and periodicities of all teeth belonging to the TE9 level of Sima del Elefante, level TD6.2 of Gran Dolina (H. antecessor) and Sima de los Huesos. We found some components of dental growth in the Atapuerca fossils resembled more recent H. sapiens. Mosaic evolution of perikymata counts and distribution generate three distinct clusters: H. antecessor, Sima de los Huesos and H. sapiens.},
}

@article {pmid32163763,
year = {2020},
author = {Belcastro, MG and Mariotti, V and Pietrobelli, A and Sorrentino, R and García-Tabernero, A and Estalrrich, A and Rosas, A},
title = {The study of the lower limb entheses in the Neanderthal sample from El Sidrón (Asturias, Spain): How much musculoskeletal variability did Neanderthals accumulate?.},
journal = {Journal of human evolution},
volume = {141},
number = {},
pages = {102746},
doi = {10.1016/j.jhevol.2020.102746},
pmid = {32163763},
issn = {1095-8606},
abstract = {Entheses have rarely been systematically studied in the field of human evolution. However, the investigation of their morphological variability (e.g., robusticity) could provide new insight into their evolutionary significance in the European Neanderthal populations. The aim of this work is to study the entheses and joint features of the lower limbs of El Sidrón Neanderthals (Spain; 49 ka), using standardized scoring methods developed on modern samples. Paleobiology, growth, and development of both juveniles and adults from El Sidrón are studied and compared with those of Krapina Neanderthals (Croatia, 130 ka) and extant humans. The morphological patterns of the gluteus maximus and vastus intermedius entheses in El Sidrón, Krapina, and modern humans differ from one another. Both Neanderthal groups show a definite enthesis design for the gluteus maximus, with little intrapopulation variability with respect to modern humans, who are characterized by a wider range of morphological variability. The gluteus maximus enthesis in the El Sidrón sample shows the osseous features of fibrous entheses, as in modern humans, whereas the Krapina sample shows the aspects of fibrocartilaginous ones. The morphology and anatomical pattern of this enthesis has already been established during growth in all three human groups. One of two and three of five adult femurs from El Sidrón and from Krapina, respectively, show the imprint of the vastus intermedius, which is absent among juveniles from those Neanderthal samples and in modern samples. The scant intrapopulation and the high interpopulation variability in the two Neanderthal samples is likely due to a long-term history of small, isolated populations with high levels of inbreeding, who also lived in different ecological conditions. The comparison of different anatomical entheseal patterns (fibrous vs. fibrocartilaginous) in the Neanderthals and modern humans provides additional elements in the discussion of their functional and genetic origin.},
}

@article {pmid32146203,
year = {2020},
author = {Rosas, A and Losada Agustina, B and García-Martínez, D and Torres-Tamayo, N and García-Tabernero, A and Pastor, JF and Rasilla, M and Bastir, M},
title = {Analyses of the neandertal patellae from El Sidrón (Asturias, Spain) with implications for the evolution of body form in Homo.},
journal = {Journal of human evolution},
volume = {141},
number = {},
pages = {102738},
doi = {10.1016/j.jhevol.2019.102738},
pmid = {32146203},
issn = {1095-8606},
abstract = {The evolution of the body form in Homo and its potential morphological connection to the arrangement of different skeletal systems is of major interest in human evolution. Patella morphology as part of the knee is potentially influenced by body form. Here, we describe for the first time the patellae remains recovered at El Sidrón Neandertal site and analyze them in a comparative evolutionary framework. We aim to clarify whether morphometric features frequently observed in Neandertal and modern human patellae are retained from a primitive anatomical arrangement or whether they represent derived features (apomorphies). For this purpose, we combine analyses of discrete features, classic anthropological measurements, and 3D geometric morphometrics based on generalized Procrustes analysis, mean size and shape comparisons, and principal components analysis. We found a size increment of the patella in hominin evolution, with large species showing a larger patella. Modern humans and Neandertals exhibit overall larger patellae, with maximum values observed in the latter, likely as a consequence of their broader body shape. Also, some Neandertals display a thicker patella, which has been linked to larger quadriceps muscles. However, Neandertals retain a primitive morphology in their patellar articular surfaces, with similar-sized lateral and medial articular facets, leading to a more symmetrical internal face. This feature is inherited from a primitive Homo ancestor and suggests a different configuration of the knee in Neandertals. Conversely, Homo sapiens exhibits an autoapomorphic patellar anatomy with expanded lateral articular facets. We propose that these distinct configurations of the patella within Homo may be a consequence of different body forms rather than specific functional adaptations of the knee. Thus, the slender body form of modern humans may entail a medial reorientation of the tibial tuberosity (patellar ligament), allowing lateral surface expansion. These anatomical evolutionary variations may involve subtle secondary differences in bipedalism within Homo.},
}

@article {pmid32132541,
year = {2020},
author = {Gokhman, D and Nissim-Rafinia, M and Agranat-Tamir, L and Housman, G and García-Pérez, R and Lizano, E and Cheronet, O and Mallick, S and Nieves-Colón, MA and Li, H and Alpaslan-Roodenberg, S and Novak, M and Gu, H and Osinski, JM and Ferrando-Bernal, M and Gelabert, P and Lipende, I and Mjungu, D and Kondova, I and Bontrop, R and Kullmer, O and Weber, G and Shahar, T and Dvir-Ginzberg, M and Faerman, M and Quillen, EE and Meissner, A and Lahav, Y and Kandel, L and Liebergall, M and Prada, ME and Vidal, JM and Gronostajski, RM and Stone, AC and Yakir, B and Lalueza-Fox, C and Pinhasi, R and Reich, D and Marques-Bonet, T and Meshorer, E and Carmel, L},
title = {Differential DNA methylation of vocal and facial anatomy genes in modern humans.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {1189},
doi = {10.1038/s41467-020-15020-6},
pmid = {32132541},
issn = {2041-1723},
abstract = {Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that likely emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes associated with face and vocal tract anatomy went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-associated genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.},
}

@article {pmid32128408,
year = {2020},
author = {Rogers, AR and Harris, NS and Achenbach, AA},
title = {Neanderthal-Denisovan ancestors interbred with a distantly related hominin.},
journal = {Science advances},
volume = {6},
number = {8},
pages = {eaay5483},
doi = {10.1126/sciadv.aay5483},
pmid = {32128408},
issn = {2375-2548},
abstract = {Previous research has shown that modern Eurasians interbred with their Neanderthal and Denisovan predecessors. We show here that hundreds of thousands of years earlier, the ancestors of Neanderthals and Denisovans interbred with their own Eurasian predecessors-members of a "superarchaic" population that separated from other humans about 2 million years ago. The superarchaic population was large, with an effective size between 20 and 50 thousand individuals. We confirm previous findings that (i) Denisovans also interbred with superarchaics, (ii) Neanderthals and Denisovans separated early in the middle Pleistocene, (iii) their ancestors endured a bottleneck of population size, and (iv) the Neanderthal population was large at first but then declined in size. We provide qualified support for the view that (v) Neanderthals interbred with the ancestors of modern humans.},
}

@article {pmid31462783,
year = {2019},
author = {Fox, K and Hawks, J},
title = {Use ancient remains more wisely.},
journal = {Nature},
volume = {572},
number = {7771},
pages = {581-583},
doi = {10.1038/d41586-019-02516-5},
pmid = {31462783},
issn = {1476-4687},
mesh = {Animals ; Archaeology/*ethics/*methods ; DNA, Ancient/*analysis/*isolation & purification ; Female ; Genomics/*ethics/*methods ; Hawaii/ethnology ; History, 18th Century ; History, Ancient ; Humans ; Male ; Neanderthals/genetics ; Stakeholder Participation ; },
}

Animals
Archaeology/*ethics/*methods
DNA, Ancient/*analysis/*isolation & purification
Female
Genomics/*ethics/*methods
Hawaii/ethnology
History, 18th Century
History, Ancient
Humans
Male
Neanderthals/genetics
Stakeholder Participation

@article {pmid32095519,
year = {2020},
author = {Durvasula, A and Sankararaman, S},
title = {Recovering signals of ghost archaic introgression in African populations.},
journal = {Science advances},
volume = {6},
number = {7},
pages = {eaax5097},
doi = {10.1126/sciadv.aax5097},
pmid = {32095519},
issn = {2375-2548},
abstract = {While introgression from Neanderthals and Denisovans has been documented in modern humans outside Africa, the contribution of archaic hominins to the genetic variation of present-day Africans remains poorly understood. We provide complementary lines of evidence for archaic introgression into four West African populations. Our analyses of site frequency spectra indicate that these populations derive 2 to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans. Using a method that can identify segments of archaic ancestry without the need for reference archaic genomes, we built genome-wide maps of archaic ancestry in the Yoruba and the Mende populations. Analyses of these maps reveal segments of archaic ancestry at high frequency in these populations that represent potential targets of adaptive introgression. Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day West African populations.},
}

@article {pmid31276507,
year = {2019},
author = {Centi, L and Groman-Yaroslavski, I and Friedman, N and Oron, M and Prévost, M and Zaidner, Y},
title = {The bulb retouchers in the Levant: New insights into Middle Palaeolithic retouching techniques and mobile tool-kit composition.},
journal = {PloS one},
volume = {14},
number = {7},
pages = {e0218859},
doi = {10.1371/journal.pone.0218859},
pmid = {31276507},
issn = {1932-6203},
mesh = {Animals ; Archaeology/*methods ; Bone and Bones/*anatomy & histology ; *Fossils ; Geography ; Humans ; Mediterranean Region ; *Neanderthals ; Problem Solving/physiology ; Time Factors ; Tool Use Behavior/physiology ; },
abstract = {In this paper we describe two assemblages of flint retouchers or "bulb retouchers" retrieved from Nesher Ramla and Quneitra, two Middle Palaeolithic, open-air sites in the Levant. The site of Nesher Ramla yielded the largest assemblage of bulb retouchers (n = 159) currently known, allowing a detailed investigation of this poorly known phenomenon. An extensive experimental program and use-wear analysis enabled us to characterize the different sets of traces related to the retouching activity and to identify different motions applied by the knappers in the course of this action. In both sites, blanks used as bulb retouchers were almost exclusively retouched items, with a special emphasis on convergent morphotypes in Nesher Ramla. The use of retouched items as bulb retouchers is a common trait over different time spans and geographical areas. Our data suggests that bulb retouchers were versatile, multi-purpose tools with a long use-life, transported over long distances as components of the hunter-gatherer mobile tool kit. The high frequencies of bulb retouchers within some archaeological units of Nesher Ramla appear to be connected to the highly curated nature of the lithic assemblages, in turn reflecting a high mobility of the human groups that produced them.},
}

Animals
Archaeology/*methods
Bone and Bones/*anatomy & histology
*Fossils
Geography
Humans
Mediterranean Region
*Neanderthals
Problem Solving/physiology
Time Factors
Tool Use Behavior/physiology

@article {pmid32080391,
year = {2017},
author = {},
title = {Ancient encounters of the Neanderthal kind.},
journal = {Nature},
volume = {550},
number = {7675},
pages = {161-162},
doi = {10.1038/d41586-017-04376-3},
pmid = {32080391},
issn = {1476-4687},
}

@article {pmid32080432,
year = {2017},
author = {},
title = {Neanderthal brains were slow to grow.},
journal = {Nature},
volume = {549},
number = {7673},
pages = {435},
doi = {10.1038/d41586-017-03796-5},
pmid = {32080432},
issn = {1476-4687},
}

@article {pmid32078934,
year = {2020},
author = {Moncel, MH and Ashton, N and Arzarello, M and Fontana, F and Lamotte, A and Scott, B and Muttillo, B and Berruti, G and Nenzioni, G and Tuffreau, A and Peretto, C},
title = {Early Levallois core technology between Marine Isotope Stage 12 and 9 in Western Europe.},
journal = {Journal of human evolution},
volume = {139},
number = {},
pages = {102735},
doi = {10.1016/j.jhevol.2019.102735},
pmid = {32078934},
issn = {1095-8606},
abstract = {Early Levallois core technology is usually dated in Europe to the end of Marine Isotope Stage (MIS) 9 and particularly from the beginning of MIS 8 to MIS 6. This technology is considered as one of the markers of the transition from lower to Middle Paleolithic or from Mode 2 to Mode 3. Recent discoveries show that some lithic innovations actually appeared earlier in western Europe, from MIS 12 to MIS 9, contemporaneous with changes in subsistence strategies and the first appearance of early Neanderthal anatomical features. Among these discoveries, there is the iconic Levallois core technology. A selection of well-dated assemblages in the United Kingdom, France, and Italy dated from MIS 12 to 9, which include both cores and flakes with Levallois features, has been described and compared with the aim of characterizing this technology. The conclusion supports the interpretation that several technical features may be attributed to a Levallois technology similar to those observed in younger Middle Paleolithic sites, distinct from the main associated core technologies in each level. Some features in the sample of sites suggest a gradual transformation of existing core technologies. The small evidence of Levallois could indicate occasional local innovations from different technological backgrounds and would explain the diversity of Levallois methods that is observed from MIS 12. The technological roots of Levallois technology in the Middle Pleistocene would suggest a multiregional origin and diffusion in Europe and early evidence of regionalization of local traditions through Europe from MIS 12 to 9. The relationships of Levallois technology with new needs and behaviors are discussed, such as flake preference, functional reasons related to hunting and hafting, an increase in the use of mental templates in European populations, and changes in the structure of hominin groups adapting to climatic and environmental changes.},
}

@article {pmid32062432,
year = {2020},
author = {Weissbrod, L and Weinstein-Evron, M},
title = {Climate variability in early expansions of Homo sapiens in light of the new record of micromammals in Misliya Cave, Israel.},
journal = {Journal of human evolution},
volume = {139},
number = {},
pages = {102741},
doi = {10.1016/j.jhevol.2020.102741},
pmid = {32062432},
issn = {1095-8606},
abstract = {In this study, we provide the first taphonomic and taxonomic descriptions of the micromammals from Misliya Cave, where recently a Homo sapiens hemimaxilla has been reported. This finding significantly extends the time frame for the out-of-Africa presence of anatomically modern humans. It also provides an opportunity to reassess variation in early modern human population responses to climate change in the Levantine sequence. Information on species ranking and diversity estimations (Shannon functions) is obtained from quantitative data across 31 Levantine assemblages and investigated in a broad comparative frame using multivariate analyses. Recent models of human-climate interactions in the late Early-Middle Paleolithic of the southern Levant have drawn heavily on on-site associations of human fossils with remains of micromammals. However, there has been little, if any, attempt to examine the long-term picture of how paleocommunities of micromammals responded qualitatively and quantitatively to climatic oscillations of the region by altering their compositional complexity. Consequently, our understanding is vastly limited in regard to the paleoecosystem functions that linked past precipitation shifts to changes in primary producers and consumers or as to the background climatic conditions that allowed for the development of highly nonanalog ancient communities in the region. Although previous studies argued for a correspondence between alternations in H. sapiens and Neanderthal occupations of the Levant and faunal shifts in key biostratigraphic indicator taxa (such as Euro-Siberian Ellobius versus Saharo-Arabian Mastomys and Arvicanthis), our data indicate the likelihood that early H. sapiens populations (Misliya and Qafzeh hominins) persisted through high amplitudes of paleoecological and climatic oscillations. It is unlikely, given these results, that climate functioned as a significant filter of early modern human persistence and genetic interactions with Neanderthals in the Levant.},
}

@article {pmid31898502,
year = {2020},
author = {Rotival, M and Quintana-Murci, L},
title = {Functional consequences of archaic introgression and their impact on fitness.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {3},
pmid = {31898502},
issn = {1474-760X},
mesh = {Adaptation, Biological ; Alleles ; Animals ; Epistasis, Genetic ; *Genetic Fitness ; *Genetic Introgression ; *Genome, Human ; Haplotypes ; Humans ; Neanderthals/*genetics ; },
}

Adaptation, Biological
Alleles
Animals
Epistasis, Genetic
*Genetic Fitness
*Genetic Introgression
*Genome, Human
Haplotypes
Humans
Neanderthals/*genetics

@article {pmid32031468,
year = {2020},
author = {Le Tortorec, A and Matusali, G and Mahé, D and Aubry, F and Mazaud-Guittot, S and Houzet, L and Dejucq-Rainsford, N},
title = {From Ancient to Emerging Infections: The Odyssey of Viruses in the Male Genital Tract.},
journal = {Physiological reviews},
volume = {},
number = {},
pages = {},
doi = {10.1152/physrev.00021.2019},
pmid = {32031468},
issn = {1522-1210},
abstract = {The male genital tract (MGT) is the target of a number of viral infections that can have deleterious consequences at the individual, offspring and population levels. These consequences include infertility, cancers of male organs, transmission to the embryo/fetal development abnormalities and sexual dissemination of major viral pathogens such as human immunodeficiency virus (HIV) and hepatitis B virus (HBV). Lately, two emerging viruses, Zika and Ebola, have additionally revealed that the human MGT can constitute a reservoir for viruses cleared from peripheral circulation by the immune system, leading to their sexual transmission by cured men. This represents a concern for future epidemics and further underlines the need for a better understanding of the interplay between viruses and the MGT. We review here how viruses, from ancient viruses that integrated the germ line during evolution through old viruses (e.g. papillomaviruses originating from Neanderthals) and more modern sexually-transmitted infections (e.g. simian zoonotic HIV) to emerging viruses (e.g. Ebola and Zika) take advantage of genital tract colonization for horizontal dissemination, viral persistence, vertical transmission and endogenization. The MGT immune responses to viruses and the impact of these infections are discussed. We summarize the latest data regarding the sources of viruses in semen and the complex role of this body fluid in sexual transmission. Finally, we introduce key animal findings that are relevant for our understanding of viral infection and persistence in the human MGT and suggest future research directions.},
}

@article {pmid32004458,
year = {2020},
author = {Chen, L and Wolf, AB and Fu, W and Li, L and Akey, JM},
title = {Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2020.01.012},
pmid = {32004458},
issn = {1097-4172},
abstract = {Admixture has played a prominent role in shaping patterns of human genomic variation, including gene flow with now-extinct hominins like Neanderthals and Denisovans. Here, we describe a novel probabilistic method called IBDmix to identify introgressed hominin sequences, which, unlike existing approaches, does not use a modern reference population. We applied IBDmix to 2,504 individuals from geographically diverse populations to identify and analyze Neanderthal sequences segregating in modern humans. Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date.},
}

@article {pmid32001636,
year = {2020},
author = {Price, M},
title = {Africans, too, carry Neanderthal genetic legacy.},
journal = {Science (New York, N.Y.)},
volume = {367},
number = {6477},
pages = {497},
doi = {10.1126/science.367.6477.497},
pmid = {32001636},
issn = {1095-9203},
}

@article {pmid31988114,
year = {2020},
author = {Kolobova, KA and Roberts, RG and Chabai, VP and Jacobs, Z and Krajcarz, MT and Shalagina, AV and Krivoshapkin, AI and Li, B and Uthmeier, T and Markin, SV and Morley, MW and O'Gorman, K and Rudaya, NA and Talamo, S and Viola, B and Derevianko, AP},
title = {Archaeological evidence for two separate dispersals of Neanderthals into southern Siberia.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1918047117},
pmid = {31988114},
issn = {1091-6490},
abstract = {Neanderthals were once widespread across Europe and western Asia. They also penetrated into the Altai Mountains of southern Siberia, but the geographical origin of these populations and the timing of their dispersal have remained elusive. Here we describe an archaeological assemblage from Chagyrskaya Cave, situated in the Altai foothills, where around 90,000 Middle Paleolithic artifacts and 74 Neanderthal remains have been recovered from deposits dating to between 59 and 49 thousand years ago (age range at 95.4% probability). Environmental reconstructions suggest that the Chagyrskaya hominins were adapted to the dry steppe and hunted bison. Their distinctive toolkit closely resembles Micoquian assemblages from central and eastern Europe, including the northern Caucasus, more than 3,000 kilometers to the west of Chagyrskaya Cave. At other Altai sites, evidence of earlier Neanderthal populations lacking associated Micoquian-like artifacts implies two or more Neanderthal incursions into this region. We identify eastern Europe as the most probable ancestral source region for the Chagyrskaya toolmakers, supported by DNA results linking the Neanderthal remains with populations in northern Croatia and the northern Caucasus, and providing a rare example of a long-distance, intercontinental population movement associated with a distinctive Paleolithic toolkit.},
}

@article {pmid31975170,
year = {2020},
author = {Hubisz, M and Siepel, A},
title = {Inference of Ancestral Recombination Graphs Using ARGweaver.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2090},
number = {},
pages = {231-266},
doi = {10.1007/978-1-0716-0199-0_10},
pmid = {31975170},
issn = {1940-6029},
abstract = {This chapter describes the usage of the program ARGweaver, which estimates the ancestral recombination graph for as many as about 100 genome sequences. The ancestral recombination graph is a detailed description of the coalescence and recombination events that define the relationships among the sampled sequences. This rich description is useful for a wide variety of population genetic analyses. We describe the preparation of data and major considerations for running ARGweaver, as well as the interpretation of results. We then demonstrate an analysis using the DARC (Duffy) gene as an example, and show how ARGweaver can be used to detect signatures of natural selection and Neandertal introgression, as well as to estimate the dates of mutation events. This chapter provides sufficient detail to get a new user up and running with this complex but powerful analysis tool.},
}

@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},
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 {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},
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 {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},
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},
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},
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 = {2020},
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 (15-12 Ma: 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 (12-5 Ma), and fossil apes and early hominins were both adapted for life on ground and in trees. Around 2.5 Ma, 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 1.8 Ma with the origin of Homo erectus. Homo erectus had increased body size, greater hunting skills, a diet rich in meat, control of fire and understanding about cooking food, and moved from woodland to savannah. 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 300 kyr, but they had separated from Neanderthals by 480 kyr or earlier. Their diet shifted towards grain-based foods about 100 kyr ago, and settled agriculture developed about 10 kyr 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 = {2020},
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 = {171},
number = {2},
pages = {242-259},
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},
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},
mesh = {Africa, Eastern ; Animals ; *Archaeology ; *Biological Evolution ; *Cultural Evolution ; History, Ancient ; Humans ; Neanderthals ; Technology/history ; Tool Use Behavior ; },
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.},
}

Africa, Eastern
Animals
*Archaeology
*Biological Evolution
*Cultural Evolution
History, Ancient
Humans
Neanderthals
Technology/history
Tool Use Behavior

@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 = {R01 MH101820/MH/NIMH NIH HHS/United States ; R01 GM115836/GM/NIGMS NIH HHS/United States ; R01 MH090937/MH/NIMH NIH HHS/United States ; R01 MH113362/MH/NIMH NIH HHS/United States ; T32 GM080178/GM/NIGMS NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; R35 HG010718/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Female ; Genome, Human ; Haplotypes ; *Hominidae ; Humans ; *Neanderthals ; Phenotype ; },
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.},
}

Animals
Female
Genome, Human
Haplotypes
*Hominidae
Humans
*Neanderthals
Phenotype

@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 = {96},
number = {},
pages = {139-149},
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 {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 {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 {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 {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},
mesh = {*Alleles ; Animals ; Humans ; *Neanderthals/genetics ; },
}

*Alleles
Animals
Humans
*Neanderthals/genetics

@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)/International ; 098387/Z/12/Z//Wellcome Trust (Wellcome)/International ; 212284/Z/18/Z//Wellcome Trust (Wellcome)/International ; },
mesh = {Animals ; *Evolution, Molecular ; *Genetics, Population ; *Genome, Human ; Genome-Wide Association Study/*methods ; Haplotypes ; Humans ; Mutation ; Neanderthals ; *Pedigree ; Polymorphism, Single Nucleotide ; Population Density ; *Selection, Genetic ; },
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.},
}

Animals
*Evolution, Molecular
*Genetics, Population
*Genome, Human
Genome-Wide Association Study/*methods
Haplotypes
Humans
Mutation
Neanderthals
*Pedigree
Polymorphism, Single Nucleotide
Population Density
*Selection, Genetic

@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},
mesh = {Animals ; Brain ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; },
}

Animals
Brain
Fossils
*Hominidae
Humans
*Neanderthals

@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},
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},
mesh = {Animals ; Fossils/*anatomy & histology ; Israel ; Mollusca/anatomy & histology/classification ; Neanderthals/*anatomy & histology ; },
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.},
}

Animals
Fossils/*anatomy & histology
Israel
Mollusca/anatomy & histology/classification
Neanderthals/*anatomy & histology

@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},
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 {pmid31220106,
year = {2019},
author = {Degano, I and Soriano, S and Villa, P and Pollarolo, L and Lucejko, JJ and Jacobs, Z and Douka, K and Vitagliano, S and Tozzi, C},
title = {Hafting of Middle Paleolithic tools in Latium (central Italy): New data from Fossellone and Sant'Agostino caves.},
journal = {PloS one},
volume = {14},
number = {6},
pages = {e0213473},
doi = {10.1371/journal.pone.0213473},
pmid = {31220106},
issn = {1932-6203},
mesh = {Adhesives ; Animals ; Fires ; History, Ancient ; Hominidae ; *Neanderthals ; Resins, Plant ; Technology/*methods ; *Tool Use Behavior ; },
abstract = {Hafting of stone tools was an important advance in the technology of the Paleolithic. Evidence of hafting in the Middle Paleolithic is growing and is not limited to points hafted on spears for thrusting or throwing. This article describes the identification of adhesive used for hafting on a variety of stone tools from two Middle Paleolithic caves in Latium, Fossellone Cave and Sant'Agostino Cave. Analysis of the organic residue by gas chromatography/mass spectrometry shows that a conifer resin adhesive was used, in one case mixed with beeswax. Contrary to previous suggestions that the small Middle Paleolithic tools of Latium could be used by hand and that hafting was not needed since it did not improve their functionality, our evidence shows that hafting was used by Neandertals in central Italy. Ethnographic evidence indicates that resin, which dries when exposed to air, is generally warmed by exposure to a small fire thus softened to be molded and pushed in position in the haft. The use of resin at both sites suggests regular fire use, as confirmed by moderate frequencies of burnt lithics in both assemblages. Lithic analysis shows that hafting was applied to a variety of artifacts, irrespective of type, size and technology. Prior to our study evidence of hafting in the Middle Paleolithic of Italy was limited to one case only.},
}

Adhesives
Animals
Fires
History, Ancient
Hominidae
*Neanderthals
Resins, Plant
Technology/*methods
*Tool Use Behavior

@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 ; },
mesh = {Chromosomes, Human, Y/*genetics ; *Evolution, Molecular ; *Haplotypes ; *Human Migration ; Humans ; Male ; Nigeria ; Phylogeny ; Polymorphism, Genetic ; },
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.},
}

Chromosomes, Human, Y/*genetics
*Evolution, Molecular
*Haplotypes
*Human Migration
Humans
Male
Nigeria
Phylogeny
Polymorphism, Genetic

@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},
mesh = {DNA Copy Number Variations/*genetics ; *Gene Dosage ; Genome, Human/genetics ; Genomics/methods ; Humans ; Polymerase Chain Reaction/*methods ; Receptors, Neuropeptide Y/*genetics ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; },
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.},
}

DNA Copy Number Variations/*genetics
*Gene Dosage
Genome, Human/genetics
Genomics/methods
Humans
Polymerase Chain Reaction/*methods
Receptors, Neuropeptide Y/*genetics
Reproducibility of Results
Sequence Analysis, DNA/*methods