@article {pmid34534904,
year = {2021},
author = {Keller, M and Hagag, IT and Balzer, J and Beyer, K and Kersebohm, JC and Sadeghi, B and Wernike, K and Höper, D and Wylezich, C and Beer, M and Groschup, MH},
title = {Detection of SARS-CoV-2 variant B.1.1.7 in a cat in Germany.},
journal = {Research in veterinary science},
volume = {140},
number = {},
pages = {229-232},
doi = {10.1016/j.rvsc.2021.09.008},
pmid = {34534904},
issn = {1532-2661},
abstract = {Several non-variant of concern SARS-CoV-2 infections in pets have been reported as documented in the OIE and GISAID databases and there is only one fully documented case of an alpha variant of concern (VOC)(B.1.1.7) in the United States so far. Here, we describe the first case in a cat infected with the alpha SARS-CoV-2 variant in Germany. A cat suffering from pneumonia was presented to a veterinary practice. The pneumonia was treated symptomatically, but 16 days later the cat was presented again. Since the owner had been tested positive for a SARS-CoV-2 infection in the meantime, swab samples were taken from the cat and analyzed for SARS-CoV-2 specific nucleic acids. The various RT-qPCR analyses and whole-genome sequencing revealed the presence of the SARS-CoV-2 B.1.1.7 variant in this cat. This study shows that pets living in close contact with SARS-CoV-2 B.1.1.7 infected owners can contract this virus and also suffer from a respiratory disease. It is not clear yet whether onward transmissions to other cats and humans can occur. To minimize transmission risks, pet owners and veterinarians should comply to the hygienic rules published by OIE and others. It must be stated, that infections of cats with SARS-CoV-2 is still a rare event. Cats with clinical signs of a respiratory disease should be presented to a veterinarian, who will decide on further steps.},
}

@article {pmid34531420,
year = {2021},
author = {Neto de Carvalho, C and Belaústegui, Z and Toscano, A and Muñiz, F and Belo, J and Galán, JM and Gómez, P and Cáceres, LM and Rodríguez-Vidal, J and Cunha, PP and Cachão, M and Ruiz, F and Ramirez-Cruzado, S and Giles-Guzmán, F and Finlayson, G and Finlayson, S and Finlayson, C},
title = {First tracks of newborn straight-tusked elephants (Palaeoloxodon antiquus).},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {17311},
pmid = {34531420},
issn = {2045-2322},
support = {RNM 238//Junta de Andalucía/ ; RNM 293//Junta de Andalucía/ ; UIDB/MAR/04292/2020//Fundação para a Ciência e Tecnologia/ ; },
abstract = {Tracks and trackways of newborns, calves and juveniles attributed to straight-tusked elephants were found in the MIS 5 site (Upper Pleistocene) known as the Matalascañas Trampled Surface (MTS) at Huelva, SW Spain. Evidence of a snapshot of social behaviour, especially parental care, can be determined from the concentration of elephant tracks and trackways, and especially from apparently contemporaneous converging trackways, of small juvenile and larger, presumably young adult female tracks. The size frequency of the tracks enabled us to infer body mass and age distribution of the animals that crossed the MTS. Comparisons of the MTS demographic frequency with the morphology of the fore- and hind limbs of extant and fossil proboscideans shed light into the reproductive ecology of the straight-tusked elephant, Palaeloxodon antiquus. The interdune pond habitat appeared to have been an important water and food resource for matriarchal herds of straight-tusked elephants and likely functioned as a reproductive habitat, with only the rare presence of adult and older males in the MTS. The preservation of this track record in across a paleosol surface, although heavily trampled by different animals, including Neanderthals, over a short time frame, permitted an exceptional view into short-term intraspecific trophic interactions occurring in the Last Interglacial coastal habitat. Therefore, it is hypothesized that Neanderthals visited MTS for hunting or scavenging on weakened or dead elephants, and more likely calves.},
}

@article {pmid34528508,
year = {2021},
author = {Yan, SM and Sherman, RM and Taylor, DJ and Nair, DR and Bortvin, AN and Schatz, MC and McCoy, RC},
title = {Local adaptation and archaic introgression shape global diversity at human structural variant loci.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
doi = {10.7554/eLife.67615},
pmid = {34528508},
issn = {2050-084X},
support = {R35GM133747/NH/NIH HHS/United States ; DBI-1350041//National Science Foundation/ ; },
abstract = {Large genomic insertions and deletions are a potent source of functional variation, but are challenging to resolve with short-read sequencing, limiting knowledge of the role of such structural variants (SVs) in human evolution. Here, we used a graph-based method to genotype long-read-discovered SVs in short-read data from diverse human genomes. We then applied an admixture-aware method to identify 220 SVs exhibiting extreme patterns of frequency differentiation-a signature of local adaptation. The top two variants traced to the immunoglobulin heavy chain locus, tagging a haplotype that swept to near fixation in certain Southeast Asian populations, but is rare in other global populations. Further investigation revealed evidence that the haplotype traces to gene flow from Neanderthals, corroborating the role of immune-related genes as prominent targets of adaptive introgression. Our study demonstrates how recent technical advances can help resolve signatures of key evolutionary events that remained obscured within technically challenging regions of the genome.},
}

@article {pmid34521476,
year = {2021},
author = {Árnason, Ú},
title = {The unidirectional phylogeny of Homo sapiens anchors the origin of modern humans in Eurasia.},
journal = {Hereditas},
volume = {158},
number = {1},
pages = {36},
pmid = {34521476},
issn = {1601-5223},
abstract = {BACKGROUND: The Out of Africa hypothesis, OOAH, was challenged recently in an extended mtDNA analysis, PPA (Progressive Phylogenetic Analysis), that identified the African human populations as paraphyletic, a finding that contradicted the common OOAH understanding that Hss had originated in Africa and invaded Eurasia from there. The results were consistent with the molecular Out of Eurasia hypothesis, OOEH, and Eurasian palaeontology, a subject that has been largely disregarded in the discussion of OOAH.

RESULTS: In the present study the mtDNA tree, a phylogeny based on maternal inheritance, was compared to the nuclear DNA tree of the paternally transmitted Y-chromosome haplotypes, Y-DNAs. The comparison showed full phylogenetic coherence between these two separate sets of data. The results were consistent with potentially four translocations of modern humans from Eurasia into Africa, the earliest taking place ≈ 250,000 years before present, YBP. The results were in accordance with the postulates behind OOEH at the same time as they lent no support to the OOAH.

CONCLUSIONS: The conformity between the mtDNA and Y-DNA phylogenies of Hss is consistent with the understanding that Eurasia was the donor and not the receiver in human evolution. The evolutionary problems related to OOAH became similarly exposed by the mtDNA introgression that took place from Hss into Neanderthals ≈ 500,000 YBP, a circumstance that demonstrated the early coexistence of the two lineages in Eurasia.},
}

@article {pmid34493715,
year = {2021},
author = {Coll Macià, M and Skov, L and Peter, BM and Schierup, MH},
title = {Different historical generation intervals in human populations inferred from Neanderthal fragment lengths and mutation signatures.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {5317},
pmid = {34493715},
issn = {2041-1723},
support = {NNF18OC0031004//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 6108-00385//Det Frie Forskningsråd (Danish Council for Independent Research)/ ; },
abstract = {After the main Out-of-Africa event, humans interbred with Neanderthals leaving 1-2% of Neanderthal DNA scattered in small fragments in all non-African genomes today. Here we investigate what can be learned about human demographic processes from the size distribution of these fragments. We observe differences in fragment length across Eurasia with 12% longer fragments in East Asians than West Eurasians. Comparisons between extant populations with ancient samples show that these differences are caused by different rates of decay in length by recombination since the Neanderthal admixture. In concordance, we observe a strong correlation between the average fragment length and the mutation accumulation, similar to what is expected by changing the ages at reproduction as estimated from trio studies. Altogether, our results suggest differences in the generation interval across Eurasia, by up 10-20%, over the past 40,000 years. We use sex-specific mutation signatures to infer whether these changes were driven by shifts in either male or female age at reproduction, or both. We also find that previously reported variation in the mutational spectrum may be largely explained by changes to the generation interval. We conclude that Neanderthal fragment lengths provide unique insight into differences among human populations over recent history.},
}

@article {pmid34487600,
year = {2021},
author = {Gregory, MD and Eisenberg, DP and Hamborg, M and Kippenhan, JS and Kohn, P and Kolachana, B and Dickinson, D and Berman, KF},
title = {Neanderthal-derived genetic variation in living humans relates to schizophrenia diagnosis, to psychotic symptom severity, and to dopamine synthesis.},
journal = {American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajmg.b.32872},
pmid = {34487600},
issn = {1552-485X},
support = {//the Hebrew University Genetic Resource/ ; //the North Shore-LIJ Health System Foundation/ ; R01 MH084098/MH/NIMH NIH HHS/United States ; RC2MH089964//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; U01 MH79470//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; U01 MH79469//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; U01 MH46318//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; U01 MH46289//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; U01 MH46276//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; R01 MH81800//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; R01 MH60879//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; R01 MH61675//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; R01 MH59586//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; R01 MH59566//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; R01 MH60870//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; R01 MH59587//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; R01 MH59565//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; R01 MH59571//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; R01 MH59588//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; R01 MH67257//National Institute of Mental Health, National Institutes of Health, Bethesda, MD/ ; ZIAMH002652//Intramural Research Program/ ; ZIAMH002717//Intramural Research Program/ ; ZIAMH002942//Intramural Research Program/ ; },
abstract = {Schizophrenia has been hypothesized to be a human-specific condition, but experimental approaches to testing this idea have been limited. Because Neanderthals, our closest evolutionary relatives, interbred with modern humans prior to their disappearance from the fossil record, leaving a residual echo that survives in our DNA today, we leveraged new discoveries about ancient hominid DNA to explore this hypothesis in living people in three converging ways. First, in four independent case-control datasets totaling 9,362 individuals, individuals with schizophrenia had less Neanderthal-derived genetic variation than controls (p = .044). Second, in 49 unmedicated inpatients with schizophrenia, having more Neanderthal admixture predicted less severe positive symptoms (p = .046). Finally, using 18 F-fluorodopa PET scanning in 172 healthy individuals, having greater Neanderthal introgression was significantly associated with lower dopamine synthesis capacity in the striatum and pons (p's < 2 × 10-5), which is fundamentally important in the pathophysiology and treatment of psychosis. These results may help to elucidate the evolutionary history of a devastating neuropsychiatric disease by supporting the notion of schizophrenia as a human-specific condition. Additionally, the relationship between Neanderthal admixture and dopamine function suggests a potential mechanism whereby Neanderthal admixture may have affected our gene pool to alter schizophrenia risk and/or course.},
}

@article {pmid34480555,
year = {2021},
author = {Ferreira, JC and Alshamali, F and Montinaro, F and Cavadas, B and Torroni, A and Pereira, L and Raveane, A and Fernandes, V},
title = {Projecting ancient ancestry in modern-day Arabians and Iranians: a key role of the past exposed Arabo-Persian Gulf on human migrations.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evab194},
pmid = {34480555},
issn = {1759-6653},
abstract = {The Arabian Peninsula is strategic for investigations centred on the early structuring of modern humans in the wake of the out-of-Africa migration. Despite its poor climatic conditions for the recovery of ancient human DNA evidence, the availability of both genomic data from neighbouring ancient specimens and informative statistical tools allow modelling the ancestry of local modern populations. We applied this approach to a dataset of 741,000 variants screened in 291 Arabians and 78 Iranians, and obtained insightful evidence. The west-east axis was a strong forcer of population structure in the Peninsula, and, more importantly, there were clear continuums throughout time linking western Arabia with the Levant, and eastern Arabia with Iran and the Caucasus. Eastern Arabians also displayed the highest levels of the basal Eurasian lineage of all tested modern-day populations, a signal that was maintained even after correcting for a possible bias due to a recent sub-Saharan African input in their genomes. Not surprisingly, eastern Arabians were also the ones with highest similarity with Iberomaurusians, who were, so far, the best proxy for the basal Eurasians amongst the known ancient specimens. The basal Eurasian lineage is the signature of ancient non-Africans who diverged from the common European-Eastern Asian pool before 50 thousand years ago, prior to the later interbred with Neanderthals. Our results appear to indicate that the exposed basin of the Arabo-Persian Gulf was the possible home of basal Eurasians, a scenario to be further investigated by searching ancient Arabian human specimens.},
}

@article {pmid34475260,
year = {2021},
author = {Warinner, C and Velsko, IM and Fellows Yates, JA},
title = {Reply to Ben-Dor et al.: Oral bacteria of Neanderthals and modern humans exhibit evidence of starch adaptation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {37},
pages = {},
doi = {10.1073/pnas.2112526118},
pmid = {34475260},
issn = {1091-6490},
}

@article {pmid34471286,
year = {2021},
author = {Groucutt, HS and White, TS and Scerri, EML and Andrieux, E and Clark-Wilson, R and Breeze, PS and Armitage, SJ and Stewart, M and Drake, N and Louys, J and Price, GJ and Duval, M and Parton, A and Candy, I and Carleton, WC and Shipton, C and Jennings, RP and Zahir, M and Blinkhorn, J and Blockley, S and Al-Omari, A and Alsharekh, AM and Petraglia, MD},
title = {Multiple hominin dispersals into Southwest Asia over the past 400,000 years.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {34471286},
issn = {1476-4687},
abstract = {Pleistocene hominin dispersals out of, and back into, Africa necessarily involved traversing the diverse and often challenging environments of Southwest Asia1-4. Archaeological and palaeontological records from the Levantine woodland zone document major biological and cultural shifts, such as alternating occupations by Homo sapiens and Neanderthals. However, Late Quaternary cultural, biological and environmental records from the vast arid zone that constitutes most of Southwest Asia remain scarce, limiting regional-scale insights into changes in hominin demography and behaviour1,2,5. Here we report a series of dated palaeolake sequences, associated with stone tool assemblages and vertebrate fossils, from the Khall Amayshan 4 and Jubbah basins in the Nefud Desert. These findings, including the oldest dated hominin occupations in Arabia, reveal at least five hominin expansions into the Arabian interior, coinciding with brief 'green' windows of reduced aridity approximately 400, 300, 200, 130-75 and 55 thousand years ago. Each occupation phase is characterized by a distinct form of material culture, indicating colonization by diverse hominin groups, and a lack of long-term Southwest Asian population continuity. Within a general pattern of African and Eurasian hominin groups being separated by Pleistocene Saharo-Arabian aridity, our findings reveal the tempo and character of climatically modulated windows for dispersal and admixture.},
}

@article {pmid34455262,
year = {2021},
author = {Buck, LT and Katz, DC and Ackermann, RR and Hlusko, LJ and Kanthaswamy, S and Weaver, TD},
title = {Effects of hybridization on pelvic morphology: A macaque model.},
journal = {Journal of human evolution},
volume = {159},
number = {},
pages = {103049},
doi = {10.1016/j.jhevol.2021.103049},
pmid = {34455262},
issn = {1095-8606},
abstract = {Ancient DNA analyses have shown that interbreeding between hominin taxa occurred multiple times. Although admixture is often reflected in skeletal phenotype, the relationship between the two remains poorly understood, hampering interpretation of the hominin fossil record. Direct study of this relationship is often impossible due to the paucity of hominin fossils and difficulties retrieving ancient genetic material. Here, we use a sample of known ancestry hybrids between two closely related nonhuman primate taxa (Indian and Chinese Macaca mulatta) to investigate the effect of admixture on skeletal morphology. We focus on pelvic shape, which has potential fitness implications in hybrids, as mismatches between maternal pelvic and fetal cranial morphology are often fatal to mother and offspring. As the pelvis is also one of the skeletal regions that differs most between Homo sapiens and Neanderthals, investigating the pelvic consequences of interbreeding could be informative regarding the viability of their hybrids. We find that the effect of admixture in M. mulatta is small and proportional to the relatively small morphological difference between the parent taxa. Sexual dimorphism appears to be the main determinant of pelvic shape in M. mulatta. The lack of difference in pelvic shape between Chinese and Indian M. mulatta is in contrast to that between Neanderthals and H. sapiens, despite a similar split time (in generations) between the hybridizing pairs. Greater phenotypic divergence between hominins may relate to adaptations to disparate environments but may also highlight how the unique degree of cultural buffering in hominins allowed for greater neutral divergence. In contrast to some previous work identifying extreme morphologies in first- and second-generation hybrids, here the relationship between pelvic shape and admixture is linear. This linearity may be because most sampled animals have a multigenerational admixture history or because of relatively high constraints on the pelvis compared with other skeletal regions.},
}

@article {pmid34437543,
year = {2021},
author = {Heydari-Guran, S and Benazzi, S and Talamo, S and Ghasidian, E and Hariri, N and Oxilia, G and Asiabani, S and Azizi, F and Naderi, R and Safaierad, R and Hublin, JJ and Foley, RA and Lahr, MM},
title = {The discovery of an in situ Neanderthal remain in the Bawa Yawan Rockshelter, West-Central Zagros Mountains, Kermanshah.},
journal = {PloS one},
volume = {16},
number = {8},
pages = {e0253708},
doi = {10.1371/journal.pone.0253708},
pmid = {34437543},
issn = {1932-6203},
abstract = {Neanderthal extinction has been a matter of debate for many years. New discoveries, better chronologies and genomic evidence have done much to clarify some of the issues. This evidence suggests that Neanderthals became extinct around 40,000-37,000 years before present (BP), after a period of coexistence with Homo sapiens of several millennia, involving biological and cultural interactions between the two groups. However, the bulk of this evidence relates to Western Eurasia, and recent work in Central Asia and Siberia has shown that there is considerable local variation. Southwestern Asia, despite having a number of significant Neanderthal remains, has not played a major part in the debate over extinction. Here we report a Neanderthal deciduous canine from the site of Bawa Yawan in the West-Central Zagros Mountains of Iran. The tooth is associated with Zagros Mousterian lithics, and its context is preliminary dated to between ~43,600 and ~41,500 years ago.},
}

@article {pmid34433829,
year = {2021},
author = {Hsieh, P and Dang, V and Vollger, MR and Mao, Y and Huang, TH and Dishuck, PC and Baker, C and Cantsilieris, S and Lewis, AP and Munson, KM and Sorensen, M and Welch, AE and Underwood, JG and Eichler, EE},
title = {Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {5118},
pmid = {34433829},
issn = {2041-1723},
support = {K99 HG011041/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
abstract = {TRP channel-associated factor 1/2 (TCAF1/TCAF2) proteins antagonistically regulate the cold-sensor protein TRPM8 in multiple human tissues. Understanding their significance has been complicated given the locus spans a gap-ridden region with complex segmental duplications in GRCh38. Using long-read sequencing, we sequence-resolve the locus, annotate full-length TCAF models in primate genomes, and show substantial human-specific TCAF copy number variation. We identify two human super haplogroups, H4 and H5, and establish that TCAF duplications originated ~1.7 million years ago but diversified only in Homo sapiens by recurrent structural mutations. Conversely, in all archaic-hominin samples the fixation for a specific H4 haplotype without duplication is likely due to positive selection. Here, our results of TCAF copy number expansion, selection signals in hominins, and differential TCAF2 expression between haplogroups and high TCAF2 and TRPM8 expression in liver and prostate in modern-day humans imply TCAF diversification among hominins potentially in response to cold or dietary adaptations.},
}

@article {pmid34428206,
year = {2021},
author = {Richards, MP and Mannino, MA and Jaouen, K and Dozio, A and Hublin, JJ and Peresani, M},
title = {Strontium isotope evidence for Neanderthal and modern human mobility at the upper and middle palaeolithic site of Fumane Cave (Italy).},
journal = {PloS one},
volume = {16},
number = {8},
pages = {e0254848},
doi = {10.1371/journal.pone.0254848},
pmid = {34428206},
issn = {1932-6203},
abstract = {To investigate the mobility patterns of Neanderthals and modern humans in Europe during the Middle-to-Upper Palaeolithic transition period, we applied strontium isotope analysis to Neanderthal (n = 3) and modern human (n = 2) teeth recovered from the site of Fumane Cave in the Monti Lessini region of Northern Italy. We also measured a large number of environmental samples from the region, to establish a strontium 'baseline', and also micromammals (vole teeth) from the levels associated with the hominin teeth. We found that the modern humans and Neanderthals had similar strontium isotope values, and these values match the local baseline values we obtained for the site and the surrounding region. We conclude that both groups were utilizing the local mountainous region where Fumane Cave is situated, and likely the nearby Lessini highlands and Adige plains, and therefore the strontium evidence does not show differening mobility patterns between Neanderthals and modern humans at the Fumane site.},
}

@article {pmid34413328,
year = {2021},
author = {Bensusan, K and Holmes, TL and Perez, C and Finlayson, G and Finlayson, S and Guillem, R and Finlayson, C},
title = {Crag Martin neontology complements taphonomy at the Gorham's Cave Complex.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {16851},
pmid = {34413328},
issn = {2045-2322},
abstract = {Species present in the fossil record may continue to exist at an archaeological site, allowing study that fine-tunes our picture of the ecological past. A large wintering population of Eurasian Crag Martins Ptyonoprogne rupestris (ECM) roosts at the 'Gorham's Cave Complex' UNESCO World Heritage site in Gibraltar, which is best known for its occupation by Neanderthals at times when ECMs were also present. Its complex geomorphology allows the study of use of different micro-sites (caves) within the roost. We used mark-recapture to test whether birds showed fidelity to micro-sites for roosting, and for differences in condition of birds across micro-sites. ECM showed very high fidelity towards micro-sites, within and between years, with > 90% chance of recapture at caves where they were first caught. Condition of birds differed between micro-sites, suggesting differences in roost quality between caves; birds were more likely to be recaptured at the micro-site where birds were in best condition, indicating higher survivorship. Our results demonstrate extremely fine-scale fidelity at the largest roosting site documented for ECM globally. Implications for conservation are discussed. The study provides current knowledge of a bird that has been using these caves since the Pleistocene and more generally on these caves as refuges.},
}

@article {pmid34386877,
year = {2021},
author = {Paar, V and Vlahović, I and Rosandić, M and Glunčić, M},
title = {Global Repeat Map (GRM): Advantageous Method for Discovery of Largest Higher-Order Repeats (HORs) in Neuroblastoma Breakpoint Family (NBPF) Genes, in Hornerin Exon and in Chromosome 21 Centromere.},
journal = {Progress in molecular and subcellular biology},
volume = {60},
number = {},
pages = {203-234},
pmid = {34386877},
issn = {0079-6484},
abstract = {Here we present three interesting novel human Higher-Order Repeats (HORs) discovered using the HOR-searching method with GRM algorithm: (a) The novel Neuroblastoma Breakpoint Family gene (NBPF) 3mer HOR, discovered applying GRM algorithm to human chromosome 1 (Paar et al., Mol Biol Evol 28:1877-1892, 2011). NBPF 3mer HOR is based on previously known ~1.6 kb NBPF primary repeat monomers (known as DUF1220 domain) in human chromosome 1, but the NBPF HOR was not known before its discovery by using GRM. It should be stressed that the NBPF HOR presents a unique human-specific pattern, distinguishing human from nonhuman primates. (b) The novel quartic HOR (2mer⊃2mer⊃9mer) discovered using the GRM algorithm for analysis of hornerin genes in human chromosome 1 (Paar et al., Mol Biol Evol 28:1877-1892, 2011). This quartic HOR is based on 39 bp hornerin primary repeat monomer in human chromosome 1. To our knowledge, this is the first known case of quartic HOR, with four levels of hierarchy of HOR organization. (c) The novel 33mer alpha satellite HOR in human chromosome 21, discovered using the GRM algorithm (Glunčić et al., Sci Rep 9:12629, 2019). This 33mer HOR in the smallest human chromosome is the largest alpha satellite HOR copy among all 22 somatic human chromosomes. Moreover, the same 33mer HOR is present in the hg38 human genome assembly of four human chromosomes: 21, 22, 13, and 14. We point out that the DUF1220 encoding genomic structures in NBPF genes in human chromosome 1, recently studied and related to the brain evolution and pathologies and cognitive aptitude, can be considered in the framework of the general concept of HORs, already extensively studied in genomics, especially in the centromeric region.},
}

@article {pmid34352227,
year = {2021},
author = {Almarri, MA and Haber, M and Lootah, RA and Hallast, P and Al Turki, S and Martin, HC and Xue, Y and Tyler-Smith, C},
title = {The genomic history of the Middle East.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2021.07.013},
pmid = {34352227},
issn = {1097-4172},
abstract = {The Middle East region is important to understand human evolution and migrations but is underrepresented in genomic studies. Here, we generated 137 high-coverage physically phased genome sequences from eight Middle Eastern populations using linked-read sequencing. We found no genetic traces of early expansions out-of-Africa in present-day populations but found Arabians have elevated Basal Eurasian ancestry that dilutes their Neanderthal ancestry. Population sizes within the region started diverging 15-20 kya, when Levantines expanded while Arabians maintained smaller populations that derived ancestry from local hunter-gatherers. Arabians suffered a population bottleneck around the aridification of Arabia 6 kya, while Levantines had a distinct bottleneck overlapping the 4.2 kya aridification event. We found an association between movement and admixture of populations in the region and the spread of Semitic languages. Finally, we identify variants that show evidence of selection, including polygenic selection. Our results provide detailed insights into the genomic and selective histories of the Middle East.},
}

@article {pmid34350666,
year = {2021},
author = {Madison, P},
title = {Brutish Neanderthals: History of a merciless characterization.},
journal = {Evolutionary anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/evan.21918},
pmid = {34350666},
issn = {1520-6505},
support = {60669//John Templeton Foundation/ ; //School of Life Sciences, Arizona State University/ ; },
abstract = {The idea that Neanderthals were brutish and unintelligent is often traced back to Marcellin Boule, a French paleontologist who examined the specimen known as the Old Man in the first decades of the 20th century. This article examines the work of Boule's predecessors and aggregate a variety of literature to underline an argument that this idea has much earlier origins and is rooted in the first recognized specimen discovered in the Neander Valley in 1856. Reorienting our understanding of the brutish Neanderthal to account for its 19th-century origins, allows for a reexamination of the factors in 19th-century culture, science, and society which contributed to this caricature, especially the concepts of race and species' extinction. Such a reexamination dismantles the narrative of Boule's error while providing a new vantage point to think about Neanderthals in the present.},
}

@article {pmid34341069,
year = {2021},
author = {Pitarch Martí, A and Zilhão, J and d'Errico, F and Cantalejo-Duarte, P and Domínguez-Bella, S and Fullola, JM and Weniger, GC and Ramos-Muñoz, J},
title = {The symbolic role of the underground world among Middle Paleolithic Neanderthals.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {33},
pages = {},
doi = {10.1073/pnas.2021495118},
pmid = {34341069},
issn = {1091-6490},
abstract = {Cueva de Ardales in Málaga, Spain, is one of the richest and best-preserved Paleolithic painted caves of southwestern Europe, containing over a thousand graphic representations. Here, we study the red pigment in panel II.A.3 of "Sala de las Estrellas," dated by U-Th to the Middle Paleolithic, to determine its composition, verify its anthropogenic nature, infer the associated behaviors, and discuss their implications. Using optical microscopy, scanning electron microscopy coupled with energy dispersive X-ray spectroscopy, micro-Raman spectroscopy, and X-ray diffraction, we analyzed a set of samples from the panel and compared them to natural coloring materials collected from the floor and walls of the cave. The conspicuously different texture and composition of the geological samples indicates that the pigments used in the paintings do not come from the outcrops of colorant material known in the cave. We confirm that the paintings are not the result of natural processes and show that the composition of the paint is consistent with the artistic activity being recurrent. Our results strengthen the hypothesis that Neanderthals symbolically used these paintings and the large stalagmitic dome harboring them over an extended time span.},
}

@article {pmid34340120,
year = {2021},
author = {Bowland, LA and Scott, JE and Kivell, TL and Patel, BA and Tocheri, MW and Orr, CM},
title = {Homo naledi pollical metacarpal shaft morphology is distinctive and intermediate between that of australopiths and other members of the genus Homo.},
journal = {Journal of human evolution},
volume = {158},
number = {},
pages = {103048},
doi = {10.1016/j.jhevol.2021.103048},
pmid = {34340120},
issn = {1095-8606},
abstract = {Homo naledi fossils from the Rising Star cave system provide important insights into the diversity of hand morphology within the genus Homo. Notably, the pollical (thumb) metacarpal (Mc1) displays an unusual suite of characteristics including a median longitudinal crest, a narrow proximal base, and broad flaring intrinsic muscle flanges. The present study evaluates the affinities of H. naledi Mc1 morphology via 3D geometric morphometric analysis of shaft shape using a broader comparative sample (n = 337) of fossil hominins, recent humans, apes, and cercopithecoid monkeys than in prior work. Results confirm that the H. naledi Mc1 is distinctive from most other hominins in being narrow at the proximal end but surmounted by flaring muscle flanges distally. Only StW 418 (Australopithecus cf. africanus) is similar in these aspects of shape. The gracile proximal shaft is most similar to cercopithecoids, Pan, Pongo, Australopithecus afarensis, and Australopithecus sediba, suggesting that H. naledi retains the condition primitive for the genus Homo. In contrast, Neandertal Mc1s are characterized by wide proximal bases and shafts, pinched midshafts, and broad distal flanges, while those of recent humans generally have straight shafts, less robust muscle flanges, and wide proximal shafts/bases. Although uncertainties remain regarding character polarity, the morphology of the H. naledi thumb might be interpreted as a retained intermediate state in a transformation series between the overall gracility of the shaft and the robust shafts of later hominins. Such a model suggests that the addition of broad medial and lateral muscle flanges to a primitively slender shaft was the first modification in transforming the Mc1 into the overall more robust structure exhibited by other Homo taxa including Neandertals and recent Homo sapiens in whose shared lineage the bases and proximal shafts became expanded, possibly as an adaptation to the repeated recruitment of powerful intrinsic pollical muscles.},
}

@article {pmid34335974,
year = {2021},
author = {Zhang, Q and Wadgaonkar, P and Xu, L and Thakur, C and Fu, Y and Bi, Z and Qiu, Y and Almutairy, B and Zhang, W and Stemmer, P and Chen, F},
title = {Environmentally-induced mdig contributes to the severity of COVID-19 through fostering expression of SARS-CoV-2 receptor NRPs and glycan metabolism.},
journal = {Theranostics},
volume = {11},
number = {16},
pages = {7970-7983},
pmid = {34335974},
issn = {1838-7640},
mesh = {Alveolar Epithelial Cells/metabolism ; Animals ; COVID-19/epidemiology/*metabolism/*virology ; Cathepsins/metabolism ; Cell Line ; Cells, Cultured ; Dioxygenases/biosynthesis/genetics/*metabolism ; Environmental Exposure ; Histone Demethylases/biosynthesis/genetics/*metabolism ; Histones/metabolism ; Humans ; Neuropilin-1/*metabolism ; Nuclear Proteins/biosynthesis/genetics/*metabolism ; Pandemics ; Polysaccharides/*metabolism ; Rats ; SARS-CoV-2/*metabolism/pathogenicity ; Spike Glycoprotein, Coronavirus/metabolism ; },
abstract = {The novel β-coronavirus, SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19), has infected more than 177 million people and resulted in 3.84 million death worldwide. Recent epidemiological studies suggested that some environmental factors, such as air pollution, might be the important contributors to the mortality of COVID-19. However, how environmental exposure enhances the severity of COVID-19 remains to be fully understood. In the present report, we provided evidence showing that mdig, a previously reported environmentally-induced oncogene that antagonizes repressive trimethylation of histone proteins, is an important regulator for SARS-CoV-2 receptors neuropilin-1 (NRP1) and NRP2, cathepsins, glycan metabolism and inflammation, key determinants for viral infection and cytokine storm of the patients. Depletion of mdig in bronchial epithelial cells by CRISPR-Cas-9 gene editing resulted in a decreased expression of NRP1, NRP2, cathepsins, and genes involved in protein glycosylation and inflammation, largely due to a substantial enrichment of lysine 9 and/or lysine 27 trimethylation of histone H3 (H3K9me3/H3K27me3) on these genes as determined by ChIP-seq. Meanwhile, we also validated that environmental factor arsenic is able to induce mdig, NRP1 and NRP2, and genetic disruption of mdig lowered expression of NRP1 and NRP2. Furthermore, mdig may coordinate with the Neanderthal variants linked to an elevated mortality of COVID-19. These data, thus, suggest that mdig is a key mediator for the severity of COVID-19 in response to environmental exposure and targeting mdig may be the one of the effective strategies in ameliorating the symptom and reducing the mortality of COVID-19.},
}

Alveolar Epithelial Cells/metabolism
Animals
COVID-19/epidemiology/*metabolism/*virology
Cathepsins/metabolism
Cell Line
Cells, Cultured
Dioxygenases/biosynthesis/genetics/*metabolism
Environmental Exposure
Histone Demethylases/biosynthesis/genetics/*metabolism
Histones/metabolism
Humans
Neuropilin-1/*metabolism
Nuclear Proteins/biosynthesis/genetics/*metabolism
Pandemics
Polysaccharides/*metabolism
Rats
SARS-CoV-2/*metabolism/pathogenicity
Spike Glycoprotein, Coronavirus/metabolism

@article {pmid34320013,
year = {2021},
author = {Condemi, S and Mazières, S and Faux, P and Costedoat, C and Ruiz-Linares, A and Bailly, P and Chiaroni, J},
title = {Blood groups of Neandertals and Denisova decrypted.},
journal = {PloS one},
volume = {16},
number = {7},
pages = {e0254175},
pmid = {34320013},
issn = {1932-6203},
abstract = {Blood group systems were the first phenotypic markers used in anthropology to decipher the origin of populations, their migratory movements, and their admixture. The recent emergence of new technologies based on the decoding of nucleic acids from an individual's entire genome has relegated them to their primary application, blood transfusion. Thus, despite the finer mapping of the modern human genome in relation to Neanderthal and Denisova populations, little is known about red cell blood groups in these archaic populations. Here we analyze the available high-quality sequences of three Neanderthals and one Denisovan individuals for 7 blood group systems that are used today in transfusion (ABO including H/Se, Rh (Rhesus), Kell, Duffy, Kidd, MNS, Diego). We show that Neanderthal and Denisova were polymorphic for ABO and shared blood group alleles recurrent in modern Sub-Saharan populations. Furthermore, we found ABO-related alleles currently preventing from viral gut infection and Neanderthal RHD and RHCE alleles nowadays associated with a high risk of hemolytic disease of the fetus and newborn. Such a common blood group pattern across time and space is coherent with a Neanderthal population of low genetic diversity exposed to low reproductive success and with their inevitable demise. Lastly, we connect a Neanderthal RHD allele to two present-day Aboriginal Australian and Papuan, suggesting that a segment of archaic genome was introgressed in this gene in non-Eurasian populations. While contributing to both the origin and late evolutionary history of Neanderthal and Denisova, our results further illustrate that blood group systems are a relevant piece of the puzzle helping to decipher it.},
}

@article {pmid34312431,
year = {2021},
author = {Alcaraz-Castaño, M and Alcolea-González, JJ and de Andrés-Herrero, M and Castillo-Jiménez, S and Cuartero, F and Cuenca-Bescós, G and Kehl, M and López-Sáez, JA and Luque, L and Pérez-Díaz, S and Piqué, R and Ruiz-Alonso, M and Weniger, GC and Yravedra, J},
title = {First modern human settlement recorded in the Iberian hinterland occurred during Heinrich Stadial 2 within harsh environmental conditions.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {15161},
pmid = {34312431},
issn = {2045-2322},
support = {805478//H2020 European Research Council/ ; HAR2017-82483-C3-3-P//Spanish Ministry of Science and Innovation/ ; CRC 806 (C1)//German Research Foundation/ ; 628179//FP7 People: Marie-Curie Actions/ ; },
abstract = {As the south-westernmost region of Europe, the Iberian Peninsula stands as a key area for understanding the process of modern human dispersal into Eurasia. However, the precise timing, ecological setting and cultural context of this process remains controversial concerning its spatiotemporal distribution within the different regions of the peninsula. While traditional models assumed that the whole Iberian hinterland was avoided by modern humans due to ecological factors until the retreat of the Last Glacial Maximum, recent research has demonstrated that hunter-gatherers entered the Iberian interior at least during Solutrean times. We provide a multi-proxy geoarchaeological, chronometric and paleoecological study on human-environment interactions based on the key site of Peña Capón (Guadalajara, Spain). Results show (1) that this site hosts the oldest modern human presence recorded to date in central Iberia, associated to pre-Solutrean cultural traditions around 26,000 years ago, and (2) that this presence occurred during Heinrich Stadial 2 within harsh environmental conditions. These findings demonstrate that this area of the Iberian hinterland was recurrently occupied regardless of climate and environmental variability, thus challenging the widely accepted hypothesis that ecological risk hampered the human settlement of the Iberian interior highlands since the first arrival of modern humans to Southwest Europe.},
}

@article {pmid34294692,
year = {2021},
author = {McArthur, E and Rinker, DC and Capra, JA},
title = {Quantifying the contribution of Neanderthal introgression to the heritability of complex traits.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {4481},
pmid = {34294692},
issn = {2041-1723},
support = {F30 HG011200/HG/NHGRI NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; T32 GM007347/GM/NIGMS NIH HHS/United States ; },
mesh = {Adaptation, Physiological/genetics ; Alleles ; Animals ; Cognition ; Female ; *Genetic Introgression ; Genetic Variation ; Genome, Human ; Genome-Wide Association Study ; Hair/anatomy & histology ; Humans ; Linkage Disequilibrium ; Male ; *Models, Genetic ; *Multifactorial Inheritance ; Neanderthals/anatomy & histology/*genetics/physiology ; Phenotype ; Selection, Genetic ; },
abstract = {Eurasians have ~2% Neanderthal ancestry, but we lack a comprehensive understanding of the genome-wide influence of Neanderthal introgression on modern human diseases and traits. Here, we quantify the contribution of introgressed alleles to the heritability of more than 400 diverse traits. We show that genomic regions in which detectable Neanderthal ancestry remains are depleted of heritability for all traits considered, except those related to skin and hair. Introgressed variants themselves are also depleted for contributions to the heritability of most traits. However, introgressed variants shared across multiple Neanderthal populations are enriched for heritability and have consistent directions of effect on several traits with potential relevance to human adaptation to non-African environments, including hair and skin traits, autoimmunity, chronotype, bone density, lung capacity, and menopause age. Integrating our results, we propose a model in which selection against introgressed functional variation was the dominant trend (especially for cognitive traits); however, for a few traits, introgressed variants provided beneficial variation via uni-directional (e.g., lightening skin color) or bi-directional (e.g., modulating immune response) effects.},
}

Adaptation, Physiological/genetics
Alleles
Animals
Cognition
Female
*Genetic Introgression
Genetic Variation
Genome, Human
Genome-Wide Association Study
Hair/anatomy & histology
Humans
Linkage Disequilibrium
Male
*Models, Genetic
*Multifactorial Inheritance
Neanderthals/anatomy & histology/*genetics/physiology
Phenotype
Selection, Genetic

@article {pmid34285394,
year = {2021},
author = {Leder, D and Hermann, R and Hüls, M and Russo, G and Hoelzmann, P and Nielbock, R and Böhner, U and Lehmann, J and Meier, M and Schwalb, A and Tröller-Reimer, A and Koddenberg, T and Terberger, T},
title = {Publisher Correction: A 51,000-year-old engraved bone reveals Neanderthals' capacity for symbolic behaviour.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41559-021-01537-6},
pmid = {34285394},
issn = {2397-334X},
}

@article {pmid34272242,
year = {2021},
author = {Schaefer, NK and Shapiro, B and Green, RE},
title = {An ancestral recombination graph of human, Neanderthal, and Denisovan genomes.},
journal = {Science advances},
volume = {7},
number = {29},
pages = {},
pmid = {34272242},
issn = {2375-2548},
abstract = {Many humans carry genes from Neanderthals, a legacy of past admixture. Existing methods detect this archaic hominin ancestry within human genomes using patterns of linkage disequilibrium or direct comparison to Neanderthal genomes. Each of these methods is limited in sensitivity and scalability. We describe a new ancestral recombination graph inference algorithm that scales to large genome-wide datasets and demonstrate its accuracy on real and simulated data. We then generate a genome-wide ancestral recombination graph including human and archaic hominin genomes. From this, we generate a map within human genomes of archaic ancestry and of genomic regions not shared with archaic hominins either by admixture or incomplete lineage sorting. We find that only 1.5 to 7% of the modern human genome is uniquely human. We also find evidence of multiple bursts of adaptive changes specific to modern humans within the past 600,000 years involving genes related to brain development and function.},
}

@article {pmid34254144,
year = {2021},
author = {Iasi, LNM and Ringbauer, H and Peter, BM},
title = {An Extended Admixture Pulse Model Reveals the Limitations to Human-Neandertal Introgression Dating.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msab210},
pmid = {34254144},
issn = {1537-1719},
abstract = {Neandertal DNA makes up 2-3% of the genomes of all non-African individuals. The patterns of Neandertal ancestry in modern humans have been used to estimate that this is the result of gene flow that occurred during the expansion of modern humans into Eurasia, but the precise dates of this event remain largely unknown. Here, we introduce an extended admixture pulse model that allows joint estimation of the timing and duration of gene flow. This model leads to simple expressions for both the admixture segment distribution and the decay curve of ancestry linkage disequilibrium, and we show that these two statistics are closely related. In simulations, we find that estimates of the mean time of admixture are largely robust to details in gene flow models, but that the duration of the gene flow can only be recovered if gene flow is very recent and the exact recombination map is known. These results imply that gene flow from Neandertals into modern humans could have happened over hundreds of generations. Ancient genomes from the time around the admixture event are thus likely required to resolve the question when, where, and for how long humans and Neandertals interacted.},
}

@article {pmid34226702,
year = {2021},
author = {Leder, D and Hermann, R and Hüls, M and Russo, G and Hoelzmann, P and Nielbock, R and Böhner, U and Lehmann, J and Meier, M and Schwalb, A and Tröller-Reimer, A and Koddenberg, T and Terberger, T},
title = {A 51,000-year-old engraved bone reveals Neanderthals' capacity for symbolic behaviour.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {34226702},
issn = {2397-334X},
abstract = {While there is substantial evidence for art and symbolic behaviour in early Homo sapiens across Africa and Eurasia, similar evidence connected to Neanderthals is sparse and often contested in scientific debates. Each new discovery is thus crucial for our understanding of Neanderthals' cognitive capacity. Here we report on the discovery of an at least 51,000-year-old engraved giant deer phalanx found at the former cave entrance of Einhornhöhle, northern Germany. The find comes from an apparent Middle Palaeolithic context that is linked to Neanderthals. The engraved bone demonstrates that conceptual imagination, as a prerequisite to compose individual lines into a coherent design, was present in Neanderthals. Therefore, Neanderthal's awareness of symbolic meaning is very likely. Our findings show that Neanderthals were capable of creating symbolic expressions before H. sapiens arrived in Central Europe.},
}

@article {pmid34226701,
year = {2021},
author = {Bello, SM},
title = {Boning up on Neanderthal art.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {34226701},
issn = {2397-334X},
}

@article {pmid34214909,
year = {2021},
author = {Bergmann, I and Hublin, JJ and Gunz, P and Freidline, SE},
title = {How did modern morphology evolve in the human mandible? The relationship between static adult allometry and mandibular variability in Homo sapiens.},
journal = {Journal of human evolution},
volume = {157},
number = {},
pages = {103026},
doi = {10.1016/j.jhevol.2021.103026},
pmid = {34214909},
issn = {1095-8606},
abstract = {Key to understanding human origins are early Homo sapiens fossils from Jebel Irhoud, as well as from the early Late Pleistocene sites Tabun, Border Cave, Klasies River Mouth, Skhul, and Qafzeh. While their upper facial shape falls within the recent human range of variation, their mandibles display a mosaic morphology. Here we quantify how mandibular shape covaries with mandible size and how static allometry differs between Neanderthals, early H. sapiens, and modern humans from the Upper Paleolithic/Later Stone Age and Holocene (= later H. sapiens). We use 3D (semi)landmark geometric morphometric methods to visualize allometric trends and to explore how gracilization affects the expression of diagnostic shape features. Early H. sapiens were highly variable in mandible size, exhibiting a unique allometric trajectory that explains aspects of their 'archaic' appearance. At the same time, early H. sapiens share a suite of diagnostic features with later H. sapiens that are not related to mandibular sizes, such as an incipient chin and an anteroposteriorly decreasing corpus height. The mandibular morphology, often referred to as 'modern', can partly be explained by gracilization owing to size reduction. Despite distinct static allometric shape changes in each group studied, bicondylar and bigonial breadth represent important structural constraints for the expression of shape features in most Middle to Late Pleistocene hominin mandibles.},
}

@article {pmid34166582,
year = {2021},
author = {Schwartz, JH and Pantoja-Pérez, A and Arsuaga, JL},
title = {The nasal region of the ~417 ka Sima de los Huesos (Sierra de Atapuerca, Spain) Hominin: New terminology and implications for later human evolution.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.24698},
pmid = {34166582},
issn = {1932-8494},
support = {//Fundación Atapuerca/ ; //Junta de Castilla y León/ ; PGC2018-093925-B-C33//Ministerio de Ciencia e Innovación of the government of Spain/ ; },
abstract = {Circum-nasal and nasal cavity morphology add to the picture of the Sima de los Huesos specimens as, at one level, representing a distinct morph and, at another, displaying individual variation. They developed a robust, midline-grooved, three-dimensional spinal ridge lying anteriorly in the nasal cavity floor that was distended posteriorly over the nasal cavity floor, and, typically, an expansive, three-dimensional patch of rugose bone on the nasal cavity wall where a conchal crest would otherwise lie. They vary, for example, in degree of topographic relief of the nasal cavity wall, expression of the spinal ridge, and development of nasal crests and fossae. Lacking an anterior nasal spine, Sima specimens differ from extant and most fossil Homo sapiens, some specimens attributed to H. heidelbergensis, and the Gran Dolina partial face, whose anterior nasal spine is a superoanterior distention of the nasoalveolar clivus, and also from Neanderthals, whose anterior nasal spine projects anteriorly away from the nasoalveolar clivus. Comparison of Neanderthals, the Sima hominin, and specimens regarded as H. heidelbergensis calls for re-evaluating the integrity of "heidelbergensis" and rethinking the phylogenetic relationships of them all. To precisely describe the numerous features and combinations thereof of the nasal region in Sima specimens, and compare them with Neandertals and "H. heidelbergensis", we developed terminology that is applicable not only to hominins, but to mammals in general.},
}

@article {pmid34163072,
year = {2021},
author = {Zavala, EI and Jacobs, Z and Vernot, B and Shunkov, MV and Kozlikin, MB and Derevianko, AP and Essel, E and de Fillipo, C and Nagel, S and Richter, J and Romagné, F and Schmidt, A and Li, B and O'Gorman, K and Slon, V and Kelso, J and Pääbo, S and Roberts, RG and Meyer, M},
title = {Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave.},
journal = {Nature},
volume = {595},
number = {7867},
pages = {399-403},
pmid = {34163072},
issn = {1476-4687},
abstract = {Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals1-4. The dozen hominin remains recovered from the deposits also include Neanderthals5,6 and the child of a Neanderthal and a Denisovan7, which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages5,8-11. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly-possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments.},
}

@article {pmid34155120,
year = {2021},
author = {Devièse, T and Abrams, G and Hajdinjak, M and Pirson, S and De Groote, I and Di Modica, K and Toussaint, M and Fischer, V and Comeskey, D and Spindler, L and Meyer, M and Semal, P and Higham, T},
title = {Reply to Van Peer: Direct radiocarbon dating and ancient genomic analysis reveal the true age of the Neanderthals at Spy Cave.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {26},
pages = {},
pmid = {34155120},
issn = {1091-6490},
}

@article {pmid34155119,
year = {2021},
author = {Van Peer, P},
title = {The stratigraphic context of Spy Cave and the timing of Neanderthal disappearance in Northwest Europe.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {26},
pages = {},
pmid = {34155119},
issn = {1091-6490},
}

@article {pmid34150310,
year = {2021},
author = {Amos, W},
title = {Correlated and geographically predictable Neanderthal and Denisovan legacies are difficult to reconcile with a simple model based on inter-breeding.},
journal = {Royal Society open science},
volume = {8},
number = {6},
pages = {201229},
pmid = {34150310},
issn = {2054-5703},
abstract = {Although the presence of archaic hominin legacies in humans is taken for granted, little attention has been given as to how the data fit with how humans colonized the world. Here, I show that Neanderthal and Denisovan legacies are strongly correlated and that inferred legacy size, like heterozygosity, exhibits a strong correlation with distance from Africa. Simulations confirm that, once created, legacy size is extremely stable: it may reduce through admixture with lower legacy populations but cannot increase significantly through neutral drift. Consequently, populations carrying the highest legacies are likely to be those whose ancestors inter-bred most with archaics. However, the populations with the highest legacies are globally scattered and are unified, not by having origins within the known Neanderthal range, but instead by living in locations that lie furthest from Africa. Furthermore, the Simons Genome Diversity Project data reveal two distinct correlations between Neanderthal and Denisovan legacies, one that starts in North Africa and increases west to east across Eurasia and into some parts of Oceania, and a second, much steeper trend that starts in Africa, peaking with the San and Ju/'hoansi and which, if extrapolated, predicts the large inferred legacies of both archaics found in Oceania/Australia. Similar 'double' trends are observed for the introgression statistic f 4 in a second large dataset published by Qin and Stoneking (Qin & Stoneking 2015 Mol. Biol. Evol. 32, 2665-2674 (doi:10.1093/molbev/msv141)). These trends appear at odds with simple models of how introgression occurred though more complicated patterns of introgression could potentially generate better fits. Moreover, substituting archaic genomes with those of great apes yields similar but biologically impossible signals of introgression, suggesting that the signals these metrics capture arise within humans and are largely independent of the test group. Interestingly, the data do appear to fit a speculative model in which the loss of diversity that occurred when humans moved further from Africa created a gradient in heterozygosity that in turn progressively reduced mutation rate such that populations furthest from Africa have diverged less from our common ancestor and hence from the archaics. In this light, the two distinct trends could be interpreted in terms of two 'out of Africa' events, an early one ending in Oceania and Australia and a later one that colonized Eurasia and the Americas.},
}

@article {pmid34148308,
year = {2021},
author = {Jeworutzki, E and Tüttelmann, F and Rothenberg, I and Pusch, M and Schreiber, JA and Kliesch, S and Wünsch, B and Strutz-Seebohm, N and Seebohm, G},
title = {Can Unlikely Neanderthal Chloride Channel CLC-2 Gene Variants Provide Insights in Modern Human Infertility?.},
journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology},
volume = {55},
number = {3},
pages = {301-310},
doi = {10.33594/000000376},
pmid = {34148308},
issn = {1421-9778},
support = {CRU326//Deutsche Forschungsgemeinschaft (DFG)/Germany ; GRK2515//Deutsche Forschungsgemeinschaft (DFG)/Germany ; #IG21558//Fondazione AIRC per la Ricerca sul Cancro/Italy ; PRIN 20174TB8KW//Italian Research Ministry/Italy ; },
abstract = {BACKGROUND/AIMS: Neanderthals, although well adapted to local environments, were rapidly replaced by anatomically modern humans (AMH) for unknown reasons. Genetic information on Neanderthals is limited restricting applicability of standard population genetics.

METHODS: Here, we apply a novel combination of restricted genetic analyses on preselected physiological key players (ion channels), electrophysiological analyses of gene variants of unclear significance expressed in Xenopus laevis oocytes using two electrode voltage clamp and transfer of results to AMH genetics. Using genetic screening in infertile men identified a loss of CLC-2 associated with sperm deficiency.

RESULTS: Increased genetic variation caused functionally impaired Neanderthals CLC-2 channels.

CONCLUSION: Increased genetic variation could reflect an adaptation to different local salt supplies at the cost of reduced sperm density. Interestingly and consistent with this hypothesis, lack of CLC-2 protein in a patient associates with high blood K+ concentration and azoospermia.},
}

@article {pmid34140364,
year = {2021},
author = {Gibbons, A},
title = {Genomes offer rare glimpse of Neanderthal family groups.},
journal = {Science (New York, N.Y.)},
volume = {372},
number = {6548},
pages = {1251-1252},
doi = {10.1126/science.372.6548.1251},
pmid = {34140364},
issn = {1095-9203},
mesh = {Animals ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Family ; Female ; *Genome ; Male ; Neanderthals/*genetics ; Sociological Factors ; Y Chromosome ; },
}

Animals
DNA, Ancient/*analysis
DNA, Mitochondrial/*analysis
Family
Female
*Genome
Male
Neanderthals/*genetics
Sociological Factors
Y Chromosome

@article {pmid34132815,
year = {2021},
author = {Levi, G and de Lombares, C and Giuliani, C and Iannuzzi, V and Aouci, R and Garagnani, P and Franceschi, C and Grimaud-Hervé, D and Narboux-Nême, N},
title = {DLX5/6 GABAergic expression affects social vocalization: implications for human evolution.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msab181},
pmid = {34132815},
issn = {1537-1719},
abstract = {DLX5 and DLX6 are two closely related transcription factors involved in brain development and in GABAergic differentiation. The DLX5/6 locus is regulated by FoxP2, a gene involved in language evolution and has been associated to neurodevelopmental disorders and mental retardation. Targeted inactivation of Dlx5/6 in mouse GABAergic neurons (Dlx5/6VgatCre mice) results in behavioural and metabolic phenotypes notably increasing lifespan by 33%. Here, we show that Dlx5/6VgatCre mice present a hyper-vocalization and hyper-socialization phenotype. While only 7% of control mice emitted more than 700 vocalizations/10min, 30% and 56% of heterozygous or homozygous Dlx5/6VgatCre mice emitted more than 700 and up to 1400 calls/10min with a higher proportion of complex and modulated calls. Hyper-vocalizing animals were more sociable: the time spent in dynamic interactions with an unknown visitor was more than doubled compared to low-vocalizing individuals. The characters affected by Dlx5/6 in the mouse (sociability, vocalization, skull and brain shape…) overlap those affected in the "domestication syndrome". We therefore explored the possibility that DLX5/6 played a role in human evolution and "self-domestication" comparing DLX5/6 genomic regions from Neanderthal and modern humans. We identified an introgressed Neanderthal haplotype (DLX5/6-N-Haplotype) present in 12.6% of European individuals that covers DLX5/6 coding and regulatory sequences. The DLX5/6-N-Haplotype includes the binding site for GTF2I, a gene associated to Williams-Beuren syndrome, a hyper-sociability and hyper-vocalization neurodevelopmental disorder. The DLX5/6-N-Haplotype is significantly underrepresented in semi-supercentenarians (>105y of age), a well-established human model of healthy ageing and longevity, suggesting their involvement in the co-evolution of longevity, sociability and speech.},
}

@article {pmid34117635,
year = {2021},
author = {Antonio, P and Costantino, B and Silvia, C and Marina, M and Paolo, P and Alessio, V and Pasquale, R},
title = {Arothron: An R package for geometric morphometric methods and virtual anthropology applications.},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24340},
pmid = {34117635},
issn = {1096-8644},
abstract = {OBJECTIVES: The statistical analysis of fossil remains is essential to understand the evolution of the genus Homo. Unfortunately, the human fossil record is straight away scarce and plagued with severe loss of information caused by taphonomic processes. The recently developed field of Virtual Anthropology helps to ameliorate this situation by using digital techniques to restore damaged and incomplete fossils.

MATERIALS AND METHODS: We present the package Arothron, an R software suite meant to process and analyze digital models of skeletal elements. Arothron includes tools to digitally extract virtual cavities such as cranial endocasts, to statistically align disarticulated or broken bony elements, and to visualize local variations between surface meshes and landmark configurations.

RESULTS: We describe the main functionalities of Arothron and illustrate their usage through reproducible case studies. We describe a tool for segmentation of skeletal cavities by showing its application on a malleus bone, a Neanderthal tooth, and a modern human cranium, reproducing their shape and calculating their volume. We illustrate how to digitally align a disarticulated model of a modern human cranium, and how to combine piecemeal shape information on individual specimens into one. In addition, we present useful visualization tools by comparing the morphological differences between the right hemisphere of the Neanderthal and the modern human brain.

CONCLUSIONS: The Arothron R package is designed to study digital models of fossil specimens. By using Arothron, scientists can handle digital models with ease, investigate the inner morphology of 3D skeletal models, gain a full representation of the original shapes of damaged specimens, and compare shapes across specimens.},
}

@article {pmid34117310,
year = {2021},
author = {Singh, PP and Srivastava, A and Sultana, GNN and Khanam, N and Pathak, A and Suravajhala, P and Singh, R and Shrivastava, P and van Driem, G and Thangaraj, K and Chaubey, G},
title = {The major genetic risk factor for severe COVID-19 does not show any association among South Asian populations.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {12346},
pmid = {34117310},
issn = {2045-2322},
mesh = {Angiotensin-Converting Enzyme 2/genetics ; Asian Continental Ancestry Group/*genetics ; COVID-19/*pathology/virology ; Gene Frequency ; Genetic Loci ; Haplotypes ; Humans ; Polymorphism, Single Nucleotide ; Risk Factors ; SARS-CoV-2/isolation & purification ; },
abstract = {With the growing evidence on the variable human susceptibility against COVID-19, it is evident that some genetic loci modulate the severity of the infection. Recent studies have identified several loci associated with greater severity. More recently, a study has identified a 50 kb genomic segment introgressed from Neanderthal adding a risk for COVID-19, and this genomic segment is present among 16% and 50% people of European and South Asian descent, respectively. Our studies on ACE2 identified a haplotype present among 20% and 60% of European and South Asian populations, respectively, which appears to be responsible for the low case fatality rate among South Asian populations. This result was also consistent with the real-time infection rate and case fatality rate among various states of India. We readdressed this issue using both of the contrasting datasets and compared them with the real-time infection rates and case fatality rate in India. We found that the polymorphism present in the 50 kb introgressed genomic segment (rs10490770) did not show any significant correlation with the infection and case fatality rate in India.},
}

Angiotensin-Converting Enzyme 2/genetics
Asian Continental Ancestry Group/*genetics
COVID-19/*pathology/virology
Gene Frequency
Genetic Loci
Haplotypes
Humans
Polymorphism, Single Nucleotide
Risk Factors
SARS-CoV-2/isolation & purification

@article {pmid34095864,
year = {2021},
author = {Zhou, Y and Browning, SR},
title = {Protocol for detecting introgressed archaic variants with SPrime.},
journal = {STAR protocols},
volume = {2},
number = {2},
pages = {100550},
pmid = {34095864},
issn = {2666-1667},
abstract = {The SPrime program detects the variants in current-day populations that were introgressed from an archaic source in the past. It is optimized for detecting introgression from Neanderthals and Denisovans in modern humans. We provide a protocol for detecting Neanderthal and Denisovan introgression in 1000 Genomes Project data, specifically focusing on the CHB (Han Chinese in Beijing) population. For complete details on the use and execution of this protocol, please refer to Browning et al. (2018).},
}

@article {pmid34079134,
year = {2021},
author = {Barras, C},
title = {How did Neanderthals and other ancient humans learn to count?.},
journal = {Nature},
volume = {594},
number = {7861},
pages = {22-25},
pmid = {34079134},
issn = {1476-4687},
mesh = {Animals ; *Archaeology ; *Bone and Bones ; Cognition ; Cultural Evolution/*history ; History, Ancient ; Humans ; Inventions/history ; Mathematics/*history ; Neanderthals/*psychology ; Pan troglodytes/psychology ; Selection, Genetic ; },
}

Animals
*Archaeology
*Bone and Bones
Cognition
Cultural Evolution/*history
History, Ancient
Humans
Inventions/history
Mathematics/*history
Neanderthals/*psychology
Pan troglodytes/psychology
Selection, Genetic

@article {pmid34073168,
year = {2021},
author = {Folgerø, PO and Johansson, C and Stokkedal, LH},
title = {The Superior Visual Perception Hypothesis: Neuroaesthetics of Cave Art.},
journal = {Behavioral sciences (Basel, Switzerland)},
volume = {11},
number = {6},
pages = {},
pmid = {34073168},
issn = {2076-328X},
abstract = {Cave Art in the Upper Paleolithic presents a boost of creativity and visual thinking. What can explain these savant-like paintings? The normal brain function in modern man rarely supports the creation of highly detailed paintings, particularly the convincing representation of animal movement, without extensive training and access to modern technology. Differences in neuro-signaling and brain anatomy between modern and archaic Homo sapiens could also cause differences in perception. The brain of archaic Homo sapiens could perceive raw detailed information without using pre-established top-down concepts, as opposed to the common understanding of the normal modern non-savant brain driven by top-down control. Some ancient genes preserved in modern humans may be expressed in rare disorders. Researchers have compared Cave Art with art made by people with autism spectrum disorder. We propose that archaic primary consciousness, as opposed to modern secondary consciousness, included a savant-like perception with a superior richness of details compared to modern man. Modern people with high frequencies of Neanderthal genes, have notable anatomical features such as increased skull width in the occipital and parietal visual areas. We hypothesize that the anatomical differences are functional and may allow a different path to visual perception.},
}

@article {pmid34066804,
year = {2021},
author = {Yamamoto, N and Yamamoto, R and Ariumi, Y and Mizokami, M and Shimotohno, K and Yoshikura, H},
title = {Does Genetic Predisposition Contribute to the Exacerbation of COVID-19 Symptoms in Individuals with Comorbidities and Explain the Huge Mortality Disparity between the East and the West?.},
journal = {International journal of molecular sciences},
volume = {22},
number = {9},
pages = {},
pmid = {34066804},
issn = {1422-0067},
support = {JP19fk0108104//Japan Agency for Medical Research and Development/ ; },
mesh = {Aged ; Alleles ; Angiotensin-Converting Enzyme 2/genetics/metabolism ; Animals ; COVID-19/*genetics/metabolism/physiopathology/virology ; Comorbidity ; *Genetic Predisposition to Disease ; HLA Antigens/genetics/metabolism ; Haplotypes ; Humans ; Inflammation/genetics/metabolism ; Neanderthals/genetics ; Peptidyl-Dipeptidase A/*genetics/metabolism ; Polymorphism, Genetic ; Risk Factors ; Severity of Illness Index ; },
abstract = {The elderly and patients with several comorbidities experience more severe cases of coronavirus disease 2019 (COVID-19) than healthy patients without underlying medical conditions. However, it is unclear why these people are prone to developing alveolar pneumonia, rapid exacerbations, and death. Therefore, we hypothesized that people with comorbidities may have a genetic predisposition that makes them more vulnerable to various factors; for example, they are likely to become more severely ill when infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To test this hypothesis, we searched the literature extensively. Polymorphisms of genes, such as those that encode angiotensin-converting enzyme 1 (ACE1), have been associated with numerous comorbidities, such as cardiovascular disease, hypertension, diabetes, chronic kidney disease, and obesity, and there are potential mechanisms to explain these associations (e.g., DD-type carriers have greater ACE1 activity, and patients with a genetic alpha-1 anti-trypsin (AAT) deficiency lack control over inflammatory mediators). Since comorbidities are associated with chronic inflammation and are closely related to the renin-angiotensin-aldosterone system (RAAS), these individuals may already have a mild ACE1/ACE2 imbalance before viral infection, which increases their risk for developing severe cases of COVID-19. However, there is still much debate about the association between ACE1 D/I polymorphism and comorbidities. The best explanation for this discrepancy could be that the D allele and DD subtypes are associated with comorbidities, but the DD genotype alone does not have an exceptionally large effect. This is also expected since the ACE1 D/I polymorphism is only an intron marker. We also discuss how polymorphisms of AAT and other genes are involved in comorbidities and the severity of SARS-CoV-2 infection. Presumably, a combination of multiple genes and non-genetic factors is involved in the establishment of comorbidities and aggravation of COVID-19.},
}

Aged
Alleles
Angiotensin-Converting Enzyme 2/genetics/metabolism
Animals
COVID-19/*genetics/metabolism/physiopathology/virology
Comorbidity
*Genetic Predisposition to Disease
HLA Antigens/genetics/metabolism
Haplotypes
Humans
Inflammation/genetics/metabolism
Neanderthals/genetics
Peptidyl-Dipeptidase A/*genetics/metabolism
Polymorphism, Genetic
Risk Factors
Severity of Illness Index

@article {pmid34051612,
year = {2021},
author = {Salazar-García, DC and Power, RC and Rudaya, N and Kolobova, K and Markin, S and Krivoshapkin, A and Henry, AG and Richards, MP and Viola, B},
title = {Dietary evidence from Central Asian Neanderthals: A combined isotope and plant microremains approach at Chagyrskaya Cave (Altai, Russia).},
journal = {Journal of human evolution},
volume = {156},
number = {},
pages = {102985},
doi = {10.1016/j.jhevol.2021.102985},
pmid = {34051612},
issn = {1095-8606},
abstract = {Neanderthals are known primarily from their habitation of Western Eurasia, but they also populated large expanses of Northern Asia for thousands of years. Owing to a sparse archaeological record, relatively little is known about these eastern Neanderthal populations. Unlike in their western range, there are limited zooarchaeological and paleobotanical studies that inform us about the nature of their subsistence. Here, we perform a combined analysis of carbon and nitrogen stable isotopes on bone collagen and microbotanical remains in dental calculus to reconstruct the diet of eastern Neanderthals at Chagyrskaya Cave in the Altai Mountains of Southern Siberia, Russia. Stable isotopes identify one individual as possessing a high trophic level due to the hunting of large- and medium-sized ungulates, while the analysis of dental calculus also indicates the presence of plants in the diet of this individual and others from the site. These findings indicate eastern Neanderthals may have had broadly similar subsistence patterns to those elsewhere in their range.},
}

@article {pmid34028527,
year = {2021},
author = {Ahlquist, KD and Bañuelos, MM and Funk, A and Lai, J and Rong, S and Villanea, FA and Witt, KE},
title = {Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture.},
journal = {Genome biology and evolution},
volume = {13},
number = {7},
pages = {},
doi = {10.1093/gbe/evab115},
pmid = {34028527},
issn = {1759-6653},
support = {R35 GM128946/GM/NIGMS NIH HHS/United States ; },
abstract = {The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: 1) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; 2) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; 3) how these novel methods can detect archaic introgression in modern African populations; and 4) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.},
}

@article {pmid34020296,
year = {2021},
author = {Spindler, L and Comeskey, D and Chabai, V and Uthmeier, T and Buckley, M and Devièse, T and Higham, T},
title = {Dating the last Middle Palaeolithic of the Crimean Peninsula: New hydroxyproline AMS dates from the site of Kabazi II.},
journal = {Journal of human evolution},
volume = {156},
number = {},
pages = {102996},
doi = {10.1016/j.jhevol.2021.102996},
pmid = {34020296},
issn = {1095-8606},
abstract = {Radiocarbon dating of bone and charcoal from sites dating to the Middle and Upper Paleolithic is challenging due to low residual levels of radiocarbon. This means that small amounts of contaminating carbon can wield a great influence over accuracy unless they are fully removed. The site of Kabazi II in the Crimea is important because radiocarbon dates previously obtained from bones in archaeological horizons that date to the Western Crimean Mousterian (WCM) are surprisingly young. We redated the same samples using a single compound dating method that focuses on extracting and dating the amino acid hydroxyproline. We show that single amino acid dates produce significantly older determinations than those that use bulk collagen pretreatment procedures. Our results suggest that instead of dating to 35,000-40,000 cal BP, the bones actually date to >50,000 cal BP. This implies that the WCM at this site is much older than previously thought. In light of these current findings, we considered the dates of other key Crimean sites and concluded that in the absence of reliable pretreatment methods, it would be wise to consider many of them minimum ages. We conclude that there is little robust evidence to suggest Neanderthals were present in the Crimea after 40,000 cal BP.},
}

@article {pmid34010592,
year = {2021},
author = {Svensson, E and Günther, T and Hoischen, A and Hervella, M and Munters, AR and Ioana, M and Ridiche, F and Edlund, H and van Deuren, RC and Soficaru, A and de-la-Rua, C and Netea, MG and Jakobsson, M},
title = {Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe.},
journal = {Current biology : CB},
volume = {31},
number = {14},
pages = {2973-2983.e9},
doi = {10.1016/j.cub.2021.04.045},
pmid = {34010592},
issn = {1879-0445},
abstract = {Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from "Peştera Muierii," Romania who lived ∼34,000 years ago to 13.5× coverage. The genome shows similarities to modern-day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture (∼3.1%) to most EUP humans but only half compared to the ∼40,000-year-old Peştera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans.},
}

@article {pmid33992907,
year = {2021},
author = {Kerner, G and Patin, E and Quintana-Murci, L},
title = {New insights into human immunity from ancient genomics.},
journal = {Current opinion in immunology},
volume = {72},
number = {},
pages = {116-125},
doi = {10.1016/j.coi.2021.04.006},
pmid = {33992907},
issn = {1879-0372},
abstract = {Population genetic studies have clearly indicated that immunity and host defense are among the functions most frequently subject to natural selection, and increased our understanding of the biological relevance of the corresponding genes and their contribution to variable immune traits and diseases. Herein, we will focus on some recently studied forms of human adaptation to infectious agents, including hybridization with now-extinct hominins, such as Neanderthals and Denisovans, and admixture between modern human populations. These studies, which are partly enabled by the technological advances in the sequencing of DNA from ancient remains, provide new insight into the sources of immune response variation in contemporary humans, such as the recently reported link between Neanderthal heritage and susceptibility to severe COVID-19 disease. Furthermore, ancient DNA analyses, in both humans and pathogens, allow to measure the action of natural selection on immune genes across time and to reconstruct the impact of past epidemics on the evolution of human immunity.},
}

@article {pmid33990781,
year = {2021},
author = {},
title = {Microbes in Neanderthals' mouths reveal their carb-laden diet.},
journal = {Nature},
volume = {593},
number = {7859},
pages = {316},
doi = {10.1038/d41586-021-01260-z},
pmid = {33990781},
issn = {1476-4687},
}

@article {pmid33974862,
year = {2021},
author = {Harvati, K},
title = {Katerina Harvati.},
journal = {Current biology : CB},
volume = {31},
number = {9},
pages = {R418-R419},
doi = {10.1016/j.cub.2021.04.003},
pmid = {33974862},
issn = {1879-0445},
abstract = {Interview with paleoanthropologist Katerina Harvati, who studies Neanderthal evolution and modern human origins at the Eberhard Karls University of Tübingen.},
}

@article {pmid33972424,
year = {2021},
author = {Fellows Yates, JA and Velsko, IM and Aron, F and Posth, C and Hofman, CA and Austin, RM and Parker, CE and Mann, AE and Nägele, K and Arthur, KW and Arthur, JW and Bauer, CC and Crevecoeur, I and Cupillard, C and Curtis, MC and Dalén, L and Díaz-Zorita Bonilla, M and Díez Fernández-Lomana, JC and Drucker, DG and Escribano Escrivá, E and Francken, M and Gibbon, VE and González Morales, MR and Grande Mateu, A and Harvati, K and Henry, AG and Humphrey, L and Menéndez, M and Mihailović, D and Peresani, M and Rodríguez Moroder, S and Roksandic, M and Rougier, H and Sázelová, S and Stock, JT and Straus, LG and Svoboda, J and Teßmann, B and Walker, MJ and Power, RC and Lewis, CM and Sankaranarayanan, K and Guschanski, K and Wrangham, RW and Dewhirst, FE and Salazar-García, DC and Krause, J and Herbig, A and Warinner, C},
title = {The evolution and changing ecology of the African hominid oral microbiome.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {20},
pages = {},
pmid = {33972424},
issn = {1091-6490},
abstract = {The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine-platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.},
}

@article {pmid33951239,
year = {2021},
author = {Gopalan, S and Atkinson, EG and Buck, LT and Weaver, TD and Henn, BM},
title = {Inferring archaic introgression from hominin genetic data.},
journal = {Evolutionary anthropology},
volume = {30},
number = {3},
pages = {199-220},
doi = {10.1002/evan.21895},
pmid = {33951239},
issn = {1520-6505},
support = {K12-GM102778/NH/NIH HHS/United States ; K01-MH121659/NH/NIH HHS/United States ; R35-GM133531/NH/NIH HHS/United States ; K01 MH121659/MH/NIMH NIH HHS/United States ; K12 GM102778/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Genetic Introgression/*genetics ; Hominidae/classification/genetics ; Humans ; Neanderthals/classification/*genetics ; },
abstract = {Questions surrounding the timing, extent, and evolutionary consequences of archaic admixture into human populations have a long history in evolutionary anthropology. More recently, advances in human genetics, particularly in the field of ancient DNA, have shed new light on the question of whether or not Homo sapiens interbred with other hominin groups. By the late 1990s, published genetic work had largely concluded that archaic groups made no lasting genetic contribution to modern humans; less than a decade later, this conclusion was reversed following the successful DNA sequencing of an ancient Neanderthal. This reversal of consensus is noteworthy, but the reasoning behind it is not widely understood across all academic communities. There remains a communication gap between population geneticists and paleoanthropologists. In this review, we endeavor to bridge this gap by outlining how technological advancements, new statistical methods, and notable controversies ultimately led to the current consensus.},
}

Animals
Anthropology, Physical
*Biological Evolution
DNA, Ancient/*analysis
DNA, Mitochondrial/genetics
Genetic Introgression/*genetics
Hominidae/classification/genetics
Humans
Neanderthals/classification/*genetics

@article {pmid33942714,
year = {2021},
author = {Stepanova, V and Moczulska, KE and Vacano, GN and Kurochkin, I and Ju, X and Riesenberg, S and Macak, D and Maricic, T and Dombrowski, L and Schörnig, M and Anastassiadis, K and Baker, O and Naumann, R and Khrameeva, E and Vanushkina, A and Stekolshchikova, E and Egorova, A and Tkachev, A and Mazzarino, R and Duval, N and Zubkov, D and Giavalisco, P and Wilkinson, TG and Patterson, D and Khaitovich, P and Pääbo, S},
title = {Reduced purine biosynthesis in humans after their divergence from Neandertals.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {33942714},
issn = {2050-084X},
abstract = {We analyze the metabolomes of humans, chimpanzees, and macaques in muscle, kidney and three different regions of the brain. Although several compounds in amino acid metabolism occur at either higher or lower concentrations in humans than in the other primates, metabolites downstream of adenylosuccinate lyase, which catalyzes two reactions in purine synthesis, occur at lower concentrations in humans. This enzyme carries an amino acid substitution that is present in all humans today but absent in Neandertals. By introducing the modern human substitution into the genomes of mice, as well as the ancestral, Neandertal-like substitution into the genomes of human cells, we show that this amino acid substitution contributes to much or all of the reduction of de novo synthesis of purines in humans.},
}

@article {pmid33934123,
year = {2021},
author = {Mualim, K and Theunert, C and Slatkin, M},
title = {Estimation of coalescence probabilities and population divergence times from SNP data.},
journal = {Heredity},
volume = {127},
number = {1},
pages = {1-9},
pmid = {33934123},
issn = {1365-2540},
support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; },
abstract = {We present a method called the G(A|B) method for estimating coalescence probabilities within population lineages from genome sequences when one individual is sampled from each population. Population divergence times can be estimated from these coalescence probabilities if additional assumptions about the history of population sizes are made. Our method is based on a method presented by Rasmussen et al. (2014) to test whether an archaic genome is from a population directly ancestral to a present-day population. The G(A|B) method does not require distinguishing ancestral from derived alleles or assumptions about demographic history before population divergence. We discuss the relationship of our method to two similar methods, one introduced by Green et al. (2010) and called the F(A|B) method and the other introduced by Schlebusch et al. (2017) and called the TT method. When our method is applied to individuals from three or more populations, it provides a test of whether the population history is treelike because coalescence probabilities are additive on a tree. We illustrate the use of our method by applying it to three high-coverage archaic genomes, two Neanderthals (Vindija and Altai) and a Denisovan.},
}

@article {pmid33892510,
year = {2021},
author = {Villanea, FA and Huerta-Sanchez, E and Fox, K},
title = {ABO Genetic Variation in Neanderthals and Denisovans.},
journal = {Molecular biology and evolution},
volume = {38},
number = {8},
pages = {3373-3382},
pmid = {33892510},
issn = {1537-1719},
support = {R35 GM128946/GM/NIGMS NIH HHS/United States ; R35GM128946//U.S. National Institute of Health/ ; },
abstract = {Variation at the ABO locus was one of the earliest sources of data in the study of human population identity and history, and to this day remains widely genotyped due to its importance in blood and tissue transfusions. Here, we look at ABO blood type variants in our archaic relatives: Neanderthals and Denisovans. Our goal is to understand the genetic landscape of the ABO gene in archaic humans, and how it relates to modern human ABO variation. We found two Neanderthal variants of the O allele in the Siberian Neanderthals (O1 and O2), one of these variants is shared with an European Neanderthal, who is a heterozygote for this O1 variant and a rare cis-AB variant. The Denisovan individual is heterozygous for two variants of the O1 allele, functionally similar to variants found widely in modern humans. Perhaps more surprisingly, the O2 allele variant found in Siberian Neanderthals can be found at low frequencies in modern Europeans and Southeast Asians, and the O1 allele variant found in Siberian and European Neanderthal is also found at very low frequency in modern East Asians. Our genetic distance analyses suggest both alleles survive in modern humans due to inbreeding with Neanderthals. We find that the sequence backgrounds of the surviving Neanderthal-like O alleles in modern humans retain a higher sequence divergence than other surviving Neanderthal genome fragments, supporting a view of balancing selection operating in the Neanderthal ABO alleles by retaining highly diverse haplotypes compared with portions of the genome evolving neutrally.},
}

@article {pmid33885362,
year = {2021},
author = {Weiss, CV and Harshman, L and Inoue, F and Fraser, HB and Petrov, DA and Ahituv, N and Gokhman, D},
title = {The cis-regulatory effects of modern human-specific variants.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {33885362},
issn = {2050-084X},
support = {F31 HG011568/HG/NHGRI NIH HHS/United States ; 1R01MH109907/MH/NIMH NIH HHS/United States ; 1U01MH116438/MH/NIMH NIH HHS/United States ; 1UM1HG009408/HG/NHGRI NIH HHS/United States ; },
abstract = {The Neanderthal and Denisovan genomes enabled the discovery of sequences that differ between modern and archaic humans, the majority of which are noncoding. However, our understanding of the regulatory consequences of these differences remains limited, in part due to the decay of regulatory marks in ancient samples. Here, we used a massively parallel reporter assay in embryonic stem cells, neural progenitor cells, and bone osteoblasts to investigate the regulatory effects of the 14,042 single-nucleotide modern human-specific variants. Overall, 1791 (13%) of sequences containing these variants showed active regulatory activity, and 407 (23%) of these drove differential expression between human groups. Differentially active sequences were associated with divergent transcription factor binding motifs, and with genes enriched for vocal tract and brain anatomy and function. This work provides insight into the regulatory function of variants that emerged along the modern human lineage and the recent evolution of human gene expression.},
}

@article {pmid33882583,
year = {2021},
author = {Spiegelhalder, P and Bögemann, M},
title = {[Non-metastatic castration-resistant prostate cancer (M0CRPC) - Apalutamide in high-risk M0CRPC: case reports from the SPARTAN study and the apalutamide compassionate use program].},
journal = {Aktuelle Urologie},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-1338-0202},
pmid = {33882583},
issn = {1438-8820},
abstract = {The occurrence of distant metastases represents a prognostically unfavourable turning point in non-metastatic castration-resistant prostate cancer (M0CRPC). M0CRPC patients with a short PSA doubling time have a particularly high risk of progression. For a long time, there was no further treatment option for these patients apart from watchful waiting while maintaining classic androgen deprivation therapy (ADT). Apalutamide, a next-generation anti-androgen available since January 2019, significantly increased metastasis-free survival compared with placebo in the pivotal SPARTAN trial in patients with high-risk M0CRPC. The presented patient cases from SPARTAN and the apalutamide compassionate use program are examples of the beneficial effects that apalutamide can achieve in the M0CRPC setting.},
}

@article {pmid33879864,
year = {2021},
author = {Zwir, I and Del-Val, C and Hintsanen, M and Cloninger, KM and Romero-Zaliz, R and Mesa, A and Arnedo, J and Salas, R and Poblete, GF and Raitoharju, E and Raitakari, O and Keltikangas-Järvinen, L and de Erausquin, GA and Tattersall, I and Lehtimäki, T and Cloninger, CR},
title = {Evolution of genetic networks for human creativity.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {33879864},
issn = {1476-5578},
abstract = {The genetic basis for the emergence of creativity in modern humans remains a mystery despite sequencing the genomes of chimpanzees and Neanderthals, our closest hominid relatives. Data-driven methods allowed us to uncover networks of genes distinguishing the three major systems of modern human personality and adaptability: emotional reactivity, self-control, and self-awareness. Now we have identified which of these genes are present in chimpanzees and Neanderthals. We replicated our findings in separate analyses of three high-coverage genomes of Neanderthals. We found that Neanderthals had nearly the same genes for emotional reactivity as chimpanzees, and they were intermediate between modern humans and chimpanzees in their numbers of genes for both self-control and self-awareness. 95% of the 267 genes we found only in modern humans were not protein-coding, including many long-non-coding RNAs in the self-awareness network. These genes may have arisen by positive selection for the characteristics of human well-being and behavioral modernity, including creativity, prosocial behavior, and healthy longevity. The genes that cluster in association with those found only in modern humans are over-expressed in brain regions involved in human self-awareness and creativity, including late-myelinating and phylogenetically recent regions of neocortex for autobiographical memory in frontal, parietal, and temporal regions, as well as related components of cortico-thalamo-ponto-cerebellar-cortical and cortico-striato-cortical loops. We conclude that modern humans have more than 200 unique non-protein-coding genes regulating co-expression of many more protein-coding genes in coordinated networks that underlie their capacities for self-awareness, creativity, prosocial behavior, and healthy longevity, which are not found in chimpanzees or Neanderthals.},
}

@article {pmid33860534,
year = {2021},
author = {Yi, Z and Zanolli, C and Liao, W and Wang, W},
title = {A deep-learning-based workflow to assess taxonomic affinity of hominid teeth with a test on discriminating Pongo and Homo upper molars.},
journal = {American journal of physical anthropology},
volume = {175},
number = {4},
pages = {931-942},
doi = {10.1002/ajpa.24286},
pmid = {33860534},
issn = {1096-8644},
support = {40772011//National Natural Science Foundation of China/ ; 41572023//National Natural Science Foundation of China/ ; //Bagui Scholar of Guangxi/ ; },
abstract = {OBJECTIVES: Convolutional neural network (CNN) is a state-of-art deep learning (DL) method with superior performance in image classification. Here, a CNN-based workflow is proposed to discriminate hominid teeth. Our hope is that this method could help confirm otherwise questionable records of Homo from Pleistocene deposits where there is a standing risk of mis-attributing molars of Pongo to Homo.

METHODS AND MATERIALS: A two-step workflow was designed. The first step is converting the enamel-dentine junction (EDJ) into EDJ card, that is, a two-dimensional image conversion of the three-dimensional EDJ surface. In this step, researchers must carefully orient the teeth according to the cervical plane. The second step is training the CNN learner with labeled EDJ cards. A sample consisting of 53 fossil Pongo and 53 Homo (modern human and Neanderthal) was adopted to generate EDJ cards, which were then separated into training set (n = 84) and validation set (n = 22). To assess the feasibility of this workflow, a Pongo-Homo classifier was trained from the aforementioned EDJ card set, and then the classifier was used to predict the taxonomic affinities of six samples (test set) from von Koenigswald's Chinese Apothecary collection.

RESULTS: Results show that EDJ cards in validation set are classified accurately by the CNN learner. More importantly, taxonomic predictions for six specimens in test set match well with the diagnosis results deduced from multiple lines of evidence, implying the great potential of CNN method.

DISCUSSION: This workflow paves a way for future studies using CNN to address taxonomic complexity (e.g., distinguishing Pongo and Homo teeth from the Pleistocene of Asia). Further improvements include visual interpretation and extending the applicability to moderately worn teeth.},
}

@article {pmid33859012,
year = {2021},
author = {Gibbons, A},
title = {DNA from cave dirt traces Neanderthal upheaval.},
journal = {Science (New York, N.Y.)},
volume = {372},
number = {6539},
pages = {222-223},
doi = {10.1126/science.372.6539.222},
pmid = {33859012},
issn = {1095-9203},
mesh = {Animals ; Caves ; DNA ; *Hominidae/genetics ; *Neanderthals/genetics ; },
}

Animals
Caves
DNA
*Hominidae/genetics
*Neanderthals/genetics

@article {pmid33858989,
year = {2021},
author = {Vernot, B and Zavala, EI and Gómez-Olivencia, A and Jacobs, Z and Slon, V and Mafessoni, F and Romagné, F and Pearson, A and Petr, M and Sala, N and Pablos, A and Aranburu, A and de Castro, JMB and Carbonell, E and Li, B and Krajcarz, MT and Krivoshapkin, AI and Kolobova, KA and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Viola, B and Grote, S and Essel, E and Herráez, DL and Nagel, S and Nickel, B and Richter, J and Schmidt, A and Peter, B and Kelso, J and Roberts, RG and Arsuaga, JL and Meyer, M},
title = {Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments.},
journal = {Science (New York, N.Y.)},
volume = {372},
number = {6542},
pages = {},
doi = {10.1126/science.abf1667},
pmid = {33858989},
issn = {1095-9203},
mesh = {Animals ; Caves/chemistry ; Cell Nucleus/*genetics ; DNA, Mitochondrial/analysis/*genetics/isolation & purification ; Geologic Sediments/chemistry ; Neanderthals/*classification/*genetics ; Phylogeny ; Population/genetics ; Sequence Analysis, DNA ; Siberia ; Spain ; },
abstract = {Bones and teeth are important sources of Pleistocene hominin DNA, but are rarely recovered at archaeological sites. Mitochondrial DNA (mtDNA) has been retrieved from cave sediments but provides limited value for studying population relationships. We therefore developed methods for the enrichment and analysis of nuclear DNA from sediments and applied them to cave deposits in western Europe and southern Siberia dated to between 200,000 and 50,000 years ago. We detected a population replacement in northern Spain about 100,000 years ago, which was accompanied by a turnover of mtDNA. We also identified two radiation events in Neanderthal history during the early part of the Late Pleistocene. Our work lays the ground for studying the population history of ancient hominins from trace amounts of nuclear DNA in sediments.},
}

Animals
Caves/chemistry
Cell Nucleus/*genetics
DNA, Mitochondrial/analysis/*genetics/isolation & purification
Geologic Sediments/chemistry
Neanderthals/*classification/*genetics
Phylogeny
Population/genetics
Sequence Analysis, DNA
Siberia
Spain

@article {pmid33854233,
year = {2021},
author = {Choin, J and Mendoza-Revilla, J and Arauna, LR and Cuadros-Espinoza, S and Cassar, O and Larena, M and Ko, AM and Harmant, C and Laurent, R and Verdu, P and Laval, G and Boland, A and Olaso, R and Deleuze, JF and Valentin, F and Ko, YC and Jakobsson, M and Gessain, A and Excoffier, L and Stoneking, M and Patin, E and Quintana-Murci, L},
title = {Genomic insights into population history and biological adaptation in Oceania.},
journal = {Nature},
volume = {592},
number = {7855},
pages = {583-589},
pmid = {33854233},
issn = {1476-4687},
abstract = {The Pacific region is of major importance for addressing questions regarding human dispersals, interactions with archaic hominins and natural selection processes1. However, the demographic and adaptive history of Oceanian populations remains largely uncharacterized. Here we report high-coverage genomes of 317 individuals from 20 populations from the Pacific region. We find that the ancestors of Papuan-related ('Near Oceanian') groups underwent a strong bottleneck before the settlement of the region, and separated around 20,000-40,000 years ago. We infer that the East Asian ancestors of Pacific populations may have diverged from Taiwanese Indigenous peoples before the Neolithic expansion, which is thought to have started from Taiwan around 5,000 years ago2-4. Additionally, this dispersal was not followed by an immediate, single admixture event with Near Oceanian populations, but involved recurrent episodes of genetic interactions. Our analyses reveal marked differences in the proportion and nature of Denisovan heritage among Pacific groups, suggesting that independent interbreeding with highly structured archaic populations occurred. Furthermore, whereas introgression of Neanderthal genetic information facilitated the adaptation of modern humans related to multiple phenotypes (for example, metabolism, pigmentation and neuronal development), Denisovan introgression was primarily beneficial for immune-related functions. Finally, we report evidence of selective sweeps and polygenic adaptation associated with pathogen exposure and lipid metabolism in the Pacific region, increasing our understanding of the mechanisms of biological adaptation to island environments.},
}

@article {pmid33850254,
year = {2021},
author = {Vaesen, K and Dusseldorp, GL and Brandt, MJ},
title = {Author Correction: An emerging consensus in palaeoanthropology: demography was the main factor responsible for the disappearance of Neanderthals.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {8450},
doi = {10.1038/s41598-021-88189-5},
pmid = {33850254},
issn = {2045-2322},
}

@article {pmid33833103,
year = {2021},
author = {Gibbons, A},
title = {When modern humans met Neanderthals.},
journal = {Science (New York, N.Y.)},
volume = {372},
number = {6538},
pages = {115-116},
doi = {10.1126/science.372.6538.115},
pmid = {33833103},
issn = {1095-9203},
mesh = {Animals ; Bulgaria ; Czech Republic ; *DNA, Ancient ; Female ; Genetics, Population ; *Genome, Human ; Hominidae/*genetics ; Humans ; Male ; Neanderthals/*genetics ; Sexual Behavior ; Sexual Behavior, Animal ; },
}

Animals
Bulgaria
Czech Republic
*DNA, Ancient
Female
Genetics, Population
*Genome, Human
Hominidae/*genetics
Humans
Male
Neanderthals/*genetics
Sexual Behavior
Sexual Behavior, Animal

@article {pmid33828320,
year = {2021},
author = {Hajdinjak, M and Mafessoni, F and Skov, L and Vernot, B and Hübner, A and Fu, Q and Essel, E and Nagel, S and Nickel, B and Richter, J and Moldovan, OT and Constantin, S and Endarova, E and Zahariev, N and Spasov, R and Welker, F and Smith, GM and Sinet-Mathiot, V and Paskulin, L and Fewlass, H and Talamo, S and Rezek, Z and Sirakova, S and Sirakov, N and McPherron, SP and Tsanova, T and Hublin, JJ and Peter, BM and Meyer, M and Skoglund, P and Kelso, J and Pääbo, S},
title = {Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry.},
journal = {Nature},
volume = {592},
number = {7853},
pages = {253-257},
pmid = {33828320},
issn = {1476-4687},
support = {FC001595/MRC_/Medical Research Council/United Kingdom ; 852558/ERC_/European Research Council/International ; 694707/ERC_/European Research Council/International ; FC001595/WT_/Wellcome Trust/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; },
mesh = {Alleles ; Americas/ethnology ; Animals ; Archaeology ; Bulgaria/ethnology ; Caves ; DNA, Ancient/*analysis ; Far East/ethnology ; Female ; Genome, Human/*genetics ; History, Ancient ; Humans ; Male ; Neanderthals/*genetics ; Phylogeny ; },
abstract = {Modern humans appeared in Europe by at least 45,000 years ago1-5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania7 and Siberia8 who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.},
}

Alleles
Americas/ethnology
Animals
Archaeology
Bulgaria/ethnology
Caves
DNA, Ancient/*analysis
Far East/ethnology
Female
Genome, Human/*genetics
History, Ancient
Humans
Male
Neanderthals/*genetics
Phylogeny

@article {pmid33828282,
year = {2021},
author = {Callaway, E},
title = {Oldest DNA from a Homo sapiens reveals surprisingly recent Neanderthal ancestry.},
journal = {Nature},
volume = {592},
number = {7854},
pages = {339},
pmid = {33828282},
issn = {1476-4687},
}

@article {pmid33828250,
year = {2021},
author = {Lalueza-Fox, C},
title = {Neanderthal assimilation?.},
journal = {Nature ecology & evolution},
volume = {5},
number = {6},
pages = {711-712},
pmid = {33828250},
issn = {2397-334X},
mesh = {Animals ; Czech Republic ; Genome ; *Hominidae/genetics ; Humans ; Infant, Newborn ; *Neanderthals/genetics ; Skull ; },
}

Animals
Czech Republic
Genome
*Hominidae/genetics
Humans
Infant, Newborn
*Neanderthals/genetics
Skull

@article {pmid33828249,
year = {2021},
author = {Prüfer, K and Posth, C and Yu, H and Stoessel, A and Spyrou, MA and Deviese, T and Mattonai, M and Ribechini, E and Higham, T and Velemínský, P and Brůžek, J and Krause, J},
title = {A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia.},
journal = {Nature ecology & evolution},
volume = {5},
number = {6},
pages = {820-825},
pmid = {33828249},
issn = {2397-334X},
mesh = {Africa ; Czech Republic ; Europe ; Female ; Humans ; Infant, Newborn ; Middle East ; Siberia ; *Skull ; },
abstract = {Modern humans expanded into Eurasia more than 40,000 years ago following their dispersal out of Africa. These Eurasians carried ~2-3% Neanderthal ancestry in their genomes, originating from admixture with Neanderthals that took place sometime between 50,000 and 60,000 years ago, probably in the Middle East. In Europe, the modern human expansion preceded the disappearance of Neanderthals from the fossil record by 3,000-5,000 years. The genetic makeup of the first Europeans who colonized the continent more than 40,000 years ago remains poorly understood since few specimens have been studied. Here, we analyse a genome generated from the skull of a female individual from Zlatý kůň, Czechia. We found that she belonged to a population that appears to have contributed genetically neither to later Europeans nor to Asians. Her genome carries ~3% Neanderthal ancestry, similar to those of other Upper Palaeolithic hunter-gatherers. However, the lengths of the Neanderthal segments are longer than those observed in the currently oldest modern human genome of the ~45,000-year-old Ust'-Ishim individual from Siberia, suggesting that this individual from Zlatý kůň is one of the earliest Eurasian inhabitants following the expansion out of Africa.},
}

Africa
Czech Republic
Europe
Female
Humans
Infant, Newborn
Middle East
Siberia
*Skull

@article {pmid33798098,
year = {2021},
author = {Devièse, T and Abrams, G and Hajdinjak, M and Pirson, S and De Groote, I and Di Modica, K and Toussaint, M and Fischer, V and Comeskey, D and Spindler, L and Meyer, M and Semal, P and Higham, T},
title = {Reevaluating the timing of Neanderthal disappearance in Northwest Europe.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {12},
pages = {},
pmid = {33798098},
issn = {1091-6490},
abstract = {Elucidating when Neanderthal populations disappeared from Eurasia is a key question in paleoanthropology, and Belgium is one of the key regions for studying the Middle to Upper Paleolithic transition. Previous radiocarbon dating placed the Spy Neanderthals among the latest surviving Neanderthals in Northwest Europe with reported dates as young as 23,880 ± 240 B.P. (OxA-8912). Questions were raised, however, regarding the reliability of these dates. Soil contamination and carbon-based conservation products are known to cause problems during the radiocarbon dating of bulk collagen samples. Employing a compound-specific approach that is today the most efficient in removing contamination and ancient genomic analysis, we demonstrate here that previous dates produced on Neanderthal specimens from Spy were inaccurately young by up to 10,000 y due to the presence of unremoved contamination. Our compound-specific radiocarbon dates on the Neanderthals from Spy and those from Engis and Fonds-de-Forêt demonstrate that they disappeared from Northwest Europe at 44,200 to 40,600 cal B.P. (at 95.4% probability), much earlier than previously suggested. Our data contribute significantly to refining models for Neanderthal disappearance in Europe and, more broadly, show that chronometric models regarding the appearance or disappearance of animal or hominin groups should be based only on radiocarbon dates obtained using robust pretreatment methods.},
}

@article {pmid33797824,
year = {2021},
author = {Ocobock, C and Lacy, S and Niclou, A},
title = {Between a rock and a cold place: Neanderthal biocultural cold adaptations.},
journal = {Evolutionary anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/evan.21894},
pmid = {33797824},
issn = {1520-6505},
abstract = {A large body of work focuses on the unique aspects of Neanderthal anatomy, inferred physiology, and behavior to test the assumption that Neanderthals were hyper-adapted to living in cold environments. This research has expanded over the years to include previously unexplored and potentially adaptive features such as brown adipose tissue and fire-usage. Here we review the current state of knowledge of Neanderthal cold adaptations along morphological, physiological, and behavioral lines. While highlighting foundational as well as recent work, we also emphasize key areas for future research. Despite thriving in a variety of climates, it is well-accepted that Neanderthals appear to be the most cold-adapted of known fossil hominin groups; however, there are still many unknowns. There is a great deal yet to be uncovered about the nature and manifestation of Neanderthal adaptation and how the synergy of biology and culture helped buffer them against extreme and variable environments.},
}

@article {pmid33794419,
year = {2021},
author = {Baab, KL and Nesbitt, A and Hublin, JJ and Neubauer, S},
title = {Assessing the status of the KNM-ER 42700 fossil using Homo erectus neurocranial development.},
journal = {Journal of human evolution},
volume = {154},
number = {},
pages = {102980},
doi = {10.1016/j.jhevol.2021.102980},
pmid = {33794419},
issn = {1095-8606},
abstract = {Based on ontogenetic data of endocranial shape, it has been proposed that a younger than previously assumed developmental status of the 1.5-Myr-old KNM-ER 42700 calvaria could explain why the calvaria of this fossil does not conform to the shape of other Homo erectus individuals. Here, we investigate (ecto)neurocranial ontogeny in H. erectus and assess the proposed juvenile status of this fossil using recent Homo sapiens, chimpanzees (Pan troglodytes), and Neanderthals (Homo neanderthalensis) to model and discuss changes in neurocranial shape from the juvenile to adult stages. We show that all four species share common patterns of developmental shape change resulting in a relatively lower cranial vault and expanded supraorbital torus at later developmental stages. This finding suggests that ectoneurocranial data from extant hominids can be used to model the ontogenetic trajectory for H. erectus, for which only one well-preserved very young individual is known. However, our study also reveals differences in the magnitudes and, to a lesser extent, directions of the species-specific trajectories that add to the overall shared pattern of neurocranial shape changes. We demonstrate that the very young H. erectus juvenile from Mojokerto together with subadult and adult H. erectus individuals cannot be accommodated within the pattern of the postnatal neurocranial trajectory for humans. Instead, the chimpanzee pattern might be a better 'fit' for H. erectus despite their more distant phylogenetic relatedness. The data are also compatible with an ontogenetic shape trajectory that is in some regards intermediate between that of recent H. sapiens and chimpanzees, implying a unique trajectory for H. erectus that combines elements of both extant species. Based on this new knowledge, neurocranial shape supports the assessment that KNM-ER 42700 is a young juvenile H. erectus if H. erectus followed an ontogenetic shape trajectory that was more similar to chimpanzees than humans.},
}

@article {pmid33791713,
year = {2021},
author = {Huffman, J and Butler-Laporte, G and Khan, A and Drivas, TG and Peloso, GM and Nakanishi, T and Verma, A and Kiryluk, K and Richards, JB and Zeberg, H},
title = {Alternative splicing of OAS1 alters the risk for severe COVID-19.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {33791713},
support = {UL1 TR001873/TR/NCATS NIH HHS/United States ; UL1 TR001878/TR/NCATS NIH HHS/United States ; },
abstract = {A locus containing OAS1/2/3 has been identified as a risk locus for severe COVID-19 among Europeans ancestry individuals, with a protective haplotype of ∼75 kilobases derived from Neanderthals. Here, we show that among several potentially causal variants at this locus, a splice variant of OAS1 occurs in people of African ancestry independently of the Neanderthal haplotype and confers protection against COVID-19 of a magnitude similar to that seen in individuals without African ancestry.},
}

@article {pmid33787889,
year = {2021},
author = {Yair, S and Lee, KM and Coop, G},
title = {The timing of human adaptation from Neanderthal introgression.},
journal = {Genetics},
volume = {218},
number = {1},
pages = {},
pmid = {33787889},
issn = {1943-2631},
support = {R01 GM108779/GM/NIGMS NIH HHS/United States ; R01 GM121372/GM/NIGMS NIH HHS/United States ; R35 GM136290/GM/NIGMS NIH HHS/United States ; },
abstract = {Admixture has the potential to facilitate adaptation by providing alleles that are immediately adaptive in a new environment or by simply increasing the long-term reservoir of genetic diversity for future adaptation. A growing number of cases of adaptive introgression are being identified in species across the tree of life, however the timing of selection, and therefore the importance of the different evolutionary roles of admixture, is typically unknown. Here, we investigate the spatio-temporal history of selection favoring Neanderthal-introgressed alleles in modern human populations. Using both ancient and present-day samples of modern humans, we integrate the known demographic history of populations, namely population divergence and migration, with tests for selection. We model how a sweep placed along different branches of an admixture graph acts to modify the variance and covariance in neutral allele frequencies among populations at linked loci. Using a method based on this model of allele frequencies, we study previously identified cases of adaptive Neanderthal introgression. From these, we identify cases in which Neanderthal-introgressed alleles were quickly beneficial and other cases in which they persisted at low frequency for some time. For some of the alleles that persisted at low frequency, we show that selection likely independently favored them later on in geographically separated populations. Our work highlights how admixture with ancient hominins has contributed to modern human adaptation and contextualizes observed levels of Neanderthal ancestry in present-day and ancient samples.},
}

@article {pmid33774376,
year = {2021},
author = {Chevalier, T and Colard, T and Colombo, A and Golovanova, L and Doronichev, V and Hublin, JJ},
title = {Early ontogeny of humeral trabecular bone in Neandertals and recent modern humans.},
journal = {Journal of human evolution},
volume = {154},
number = {},
pages = {102968},
doi = {10.1016/j.jhevol.2021.102968},
pmid = {33774376},
issn = {1095-8606},
abstract = {Trabecular bone ontogeny is well known in modern humans and unknown in Neandertals. Yet the bone developmental pattern is useful for interpreting fossils from evolutionary and functional perspectives. Interestingly, microstructure in early ontogeny is supposedly not influenced by high and specific mechanical loading related to the lifestyle of a human group and consequently does not directly depend on the activities of hunter-gatherers. Here, we specifically explored the early growth trajectories of the trabecular bone structure of the humerus and emphasized in particular how bone fraction (bone volume/total volume [BV/TV]) was built up in Neandertals, given the specific modern human bone loss after birth and the use of BV/TV in functional studies. Six Neandertals and 26 recent modern humans ranging from perinates to adolescents were included in this study. Six trabecular parameters were measured within a cubic region of interest extracted from the proximal metaphysis of the humerus. We found that the microstructural changes in Neandertals during early ontogeny (<1 year) fit with modern human growth trajectories for each parameter. The specific bone loss occurring immediately after birth in modern humans also occurred in Neandertals (but not in chimpanzees). However, the early childhood fossil Ferrassie 6 presented unexpectedly high BV/TV, whereas the high BV/TV in the Crouzade I adolescent was predictable. These results suggest that Neandertals and modern humans shared predetermined early growth trajectories and developmental mechanisms. We assume that the close relationship between skeletal characteristics in early ontogeny and adults in modern humans also existed in Neandertals. However, it was difficult to ensure that the high BV/TV in Neandertal early childhood, represented by only one individual, was at the origin of the high BV/TV observed in adults. Consequently, our study does not challenge the mechanical hypothesis that explains the trabecular gracilization of the humerus during the Holocene.},
}

@article {pmid33753899,
year = {2021},
author = {Teixeira, JC and Jacobs, GS and Stringer, C and Tuke, J and Hudjashov, G and Purnomo, GA and Sudoyo, H and Cox, MP and Tobler, R and Turney, CSM and Cooper, A and Helgen, KM},
title = {Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture.},
journal = {Nature ecology & evolution},
volume = {5},
number = {5},
pages = {616-624},
pmid = {33753899},
issn = {2397-334X},
mesh = {Animals ; Asia, Southeastern ; Fossils ; *Hominidae/genetics ; Humans ; Islands ; *Neanderthals ; },
abstract = {The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic 'super-archaic' species-Homo luzonensis and H. floresiensis-were present around the time anatomically modern humans arrived in the region >50,000 years ago. Intriguingly, contemporary human populations across ISEA carry distinct genomic traces of ancient interbreeding events with Denisovans-a separate hominin lineage that currently lacks a fossil record in ISEA. To query this apparent disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes, including >200 from ISEA. Our results corroborate widespread Denisovan ancestry in ISEA populations, but fail to detect any substantial super-archaic admixture signals compatible with the endemic fossil record of ISEA. We discuss the implications of our findings for the understanding of hominin history in ISEA, including future research directions that might help to unlock more details about the prehistory of the enigmatic Denisovans.},
}

Animals
Asia, Southeastern
Fossils
*Hominidae/genetics
Humans
Islands
*Neanderthals

@article {pmid33707474,
year = {2021},
author = {Mayoral, E and Díaz-Martínez, I and Duveau, J and Santos, A and Ramírez, AR and Morales, JA and Morales, LA and Díaz-Delgado, R},
title = {Tracking late Pleistocene Neandertals on the Iberian coast.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {4103},
pmid = {33707474},
issn = {2045-2322},
support = {PID2019-104625RB-100//Ministry of Science and Innovation of Spain/ ; RNM276//Andalusian Government to the Research Group/ ; EJ IT1418-19.//Basque Government to the Research Group/ ; },
abstract = {Here, we report the recent discovery of 87 Neandertal footprints on the Southwest of the Iberian Peninsula (Doñana shoreline, Spain) located on an upper Pleistocene aeolian littoral setting (about 106 ± 19 kyr). Morphometric comparisons, high resolution digital photogrammetric 3D models and detailed sedimentary analysis have been provided to characterized the footprints and the palaeoenvironment. The footprints were impressed in the shoreline of a hypersaline swamped area related to benthic microbial mats, close to the coastline. They have a rounded heel, a longitudinal arch, relatively short toes, and adducted hallux, and represent the oldest upper Pleistocene record of Neandertal footprints in the world. Among these 87 footprints, 31 are longitudinally complete and measure from 14 to 29 cm. The calculated statures range from 104 to 188 cm, with half of the data between 130 and 150 cm. The wide range of sizes of the footprints suggests the existence of a social group integrated by individuals of different age classes but dominated, however, by non-adult individuals. The footprints, which are outside the flooded area are oriented perpendicular to the shoreline. These 87 footprints reinforce the ecological scenario of Neandertal groups established in coastal areas.},
}

@article {pmid33707343,
year = {2021},
author = {García-Campos, C and Martinén-Torres, M and Modesto-Mata, M and Martín-Francés, L and Martínez de Pinillos, M and Bermúdez de Castro, JM},
title = {Indicators of sexual dimorphism in Homo antecessor permanent canines.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {99},
number = {},
pages = {},
doi = {10.4436/JASS.99001},
pmid = {33707343},
issn = {2037-0644},
abstract = {One of the main concerns of paleoanthropologists is to make a correct interpretation of the variability observed in the fossil record. However, the current knowledge about sexual dimorphism in the human lineage comes mainly from the study of modern human, Neanderthal and pre-Neanderthal populations, whereas information available about the intrapopulation variability of the groups that preceded these taxa is still ambiguous. In this preliminary study, Homo antecessor dental sample was assessed with the aim of trying to evaluate the degree of variability of their permanent canines` dental tissue proportions. Microtomographic techniques were here employed in order to measure and compare the crown volumes and surface areas of their enamel caps and dentine-pulp complexes. Then, the Pearson`s Coefficient of Variation and the Euclidean Distance were assessed to evaluate of intrapopulation variability of Gran Dolina TD6.2 dental sample. The values obtained were also compared with those of the dental samples from Sima de los Huesos site (Spain), the Neanderthal site of Krapina (Croatia), as well as from a broad forensic collection of known sex. Our results showed a marked intrapopulation variability in the dental tissues measurements of the canines of the individuals H1 and H3 from this site. This variability may be interpreted as an indicator of sexual dimorphism. If this is the case, H1 may be considered as a male individual, whereas H3 would be a female. Future discoveries of new fossils in the level TD6.2 of Gran Dolina site might help to confirm or refute this hypothesis.},
}

@article {pmid33674720,
year = {2021},
author = {Banks, WE and Moncel, MH and Raynal, JP and Cobos, ME and Romero-Alvarez, D and Woillez, MN and Faivre, JP and Gravina, B and d'Errico, F and Locht, JL and Santos, F},
title = {An ecological niche shift for Neanderthal populations in Western Europe 70,000 years ago.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {5346},
pmid = {33674720},
issn = {2045-2322},
support = {ANR-10-LABX-52//Agence Nationale de la Recherche/ ; ANR-19-CE27-0011-03//Agence Nationale de la Recherche/ ; 2010-159, 2011-61, 2014-142//Ministère de la Culture et de la Communication/ ; FP7/2007-2013: 249587/ERC_/European Research Council/International ; PIA IdEx//Université de Bordeaux/ ; SapienCE project 262618//Research Council of Norway/ ; },
abstract = {Middle Paleolithic Neanderthal populations occupied Eurasia for at least 250,000 years prior to the arrival of anatomically modern humans. While a considerable body of archaeological research has focused on Neanderthal material culture and subsistence strategies, little attention has been paid to the relationship between regionally specific cultural trajectories and their associated existing fundamental ecological niches, nor to how the latter varied across periods of climatic variability. We examine the Middle Paleolithic archaeological record of a naturally constrained region of Western Europe between 82,000 and 60,000 years ago using ecological niche modeling methods. Evaluations of ecological niche estimations, in both geographic and environmental dimensions, indicate that 70,000 years ago the range of suitable habitats exploited by these Neanderthal populations contracted and shifted. These ecological niche dynamics are the result of groups continuing to occupy habitual territories that were characterized by new environmental conditions during Marine Isotope Stage 4. The development of original cultural adaptations permitted this territorial stability.},
}

@article {pmid33649543,
year = {2021},
author = {Conde-Valverde, M and Martínez, I and Quam, RM and Rosa, M and Velez, AD and Lorenzo, C and Jarabo, P and Bermúdez de Castro, JM and Carbonell, E and Arsuaga, JL},
title = {Neanderthals and Homo sapiens had similar auditory and speech capacities.},
journal = {Nature ecology & evolution},
volume = {5},
number = {5},
pages = {609-615},
pmid = {33649543},
issn = {2397-334X},
mesh = {Animals ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; Speech ; },
abstract = {The study of audition in fossil hominins is of great interest given its relationship with intraspecific vocal communication. While the auditory capacities have been studied in early hominins and in the Middle Pleistocene Sima de los Huesos hominins, less is known about the hearing abilities of the Neanderthals. Here, we provide a detailed approach to their auditory capacities. Relying on computerized tomography scans and a comprehensive model from the field of auditory bioengineering, we have established sound power transmission through the outer and middle ear and calculated the occupied bandwidth in Neanderthals. The occupied bandwidth is directly related to the efficiency of the vocal communication system of a species. Our results show that the occupied bandwidth of Neanderthals was greater than the Sima de los Huesos hominins and similar to extant humans, implying that Neanderthals evolved the auditory capacities to support a vocal communication system as efficient as modern human speech.},
}

Animals
Fossils
*Hominidae
Humans
*Neanderthals
Speech

@article {pmid33649483,
year = {2021},
author = {Vaesen, K and Dusseldorp, GL and Brandt, MJ},
title = {An emerging consensus in palaeoanthropology: demography was the main factor responsible for the disappearance of Neanderthals.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {4925},
pmid = {33649483},
issn = {2045-2322},
abstract = {The causes of Neanderthal disappearance about 40,000 years ago remain highly contested. Over a dozen serious hypotheses are currently endorsed to explain this enigmatic event. Given the relatively large number of contending explanations and the relatively large number of participants in the debate, it is unclear how strongly each contender is supported by the research community. What does the community actually believe about the demise of Neanderthals? To address this question, we conducted a survey among practicing palaeo-anthropologists (total number of respondents = 216). It appears that received wisdom is that demography was the principal cause of the demise of Neanderthals. In contrast, there is no received wisdom about the role that environmental factors and competition with modern humans played in the extinction process; the research community is deeply divided about these issues. Finally, we tested the hypothesis that palaeo-anthropologists' stand in the debate co-varies with their socio-political views and attitudes. We found no evidence for such a correlation.},
}

@article {pmid33644865,
year = {2021},
author = {Richards, GD and Guipert, G and Jabbour, RS and Defleur, AR},
title = {Neanderthal cranial remains from Baume Moula-Guercy (Soyons, Ardèche, France).},
journal = {American journal of physical anthropology},
volume = {175},
number = {1},
pages = {201-226},
doi = {10.1002/ajpa.24256},
pmid = {33644865},
issn = {1096-8644},
mesh = {Adult ; Animals ; Anthropology, Physical ; Female ; France ; Humans ; Male ; Neanderthals/*anatomy & histology ; Skull/*anatomy & histology ; },
abstract = {OBJECTIVES: We provide the first comparative description of the Guercy 1 cranium and isolated cranial fragments from Baume Moula-Guercy and examine their affinities to European Preneanderthals, Neanderthals, and Homo sapiens.

MATERIALS AND METHODS: The Moula-Guercy hominins derive from deposits chronostratigraphically and biostratigraphically dated to the Eemian Interglacial (MIS 5e). For comparisons we compiled a sample of European and Southwest Asian subadult-adult Middle-to-Late Pleistocene hominins (≈MIS 14-MIS 2; N = 184). This sample represents a Preneanderthal-Neanderthal group and a H. sapiens group, both of which were further divided into three time-successive subgroups defined by associated marine isotope stages (MIS). Metric and morphological observations were made on the original fossils and a virtual reconstruction of Guercy 1. Developmental age and sex and the minimum-maximum number of individuals were assessed.

RESULTS: Guercy 1 represents the remains of a late stage adolescent (≈15-16.0 years) female. Morphological and metric data combine to associate the total morphological pattern expressed in Guercy 1 with our MIS 7-MIS 5e ("Early Neanderthal") subgroup. Some features, especially those related to the frontal, suggest linkage to a paleodeme comprising the Moula-Guercy, Artenac, La Chaise Abri Suard and, possibly, the Biache-Saint-Vaast samples.

DISCUSSION: Remains of MIS 7-MIS 5e Neanderthals are rare and fragmentary, especially those dated to the Last Interglacial. The Baume Moula-Guercy sample provides new insights into the total morphological pattern expressed in MIS 5e Neanderthals. Further, our results support earlier suggestions that MIS 7-MIS 5e European hominins represent a morphotype that is distinct from both earlier and later members of the Preneanderthal-Neanderthal group.},
}

Adult
Animals
Anthropology, Physical
Female
France
Humans
Male
Neanderthals/*anatomy & histology
Skull/*anatomy & histology

@article {pmid33638923,
year = {2021},
author = {Mora-Bermúdez, F and Taverna, E and Huttner, WB},
title = {From stem and progenitor cells to neurons in the developing neocortex: key differences among hominids.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.15793},
pmid = {33638923},
issn = {1742-4658},
abstract = {Comparing the biology of humans to that of other primates, and notably other hominids, is a useful path to learn more about what makes us human. Some of the most interesting differences among hominids are closely related to brain development and function, for example behaviour and cognition. This makes it particularly interesting to compare the hominid neural cells of the neocortex, a part of the brain that plays central roles in those processes. However, well-preserved tissue from great apes is usually extremely difficult to obtain. A variety of new alternative tools, for example brain organoids, are now beginning to make it possible to search for such differences and analyse their potential biological and biomedical meaning. Here, we present an overview of recent findings from comparisons of the neural stem and progenitor cells (NSPCs) and neurons of hominids. In addition to differences in proliferation and differentiation of NSPCs, and maturation of neurons, we highlight that the regulation of the timing of these processes is emerging as a general foundational difference in the development of the neocortex of hominids.},
}

@article {pmid33633408,
year = {2021},
author = {Zhou, S and Butler-Laporte, G and Nakanishi, T and Morrison, DR and Afilalo, J and Afilalo, M and Laurent, L and Pietzner, M and Kerrison, N and Zhao, K and Brunet-Ratnasingham, E and Henry, D and Kimchi, N and Afrasiabi, Z and Rezk, N and Bouab, M and Petitjean, L and Guzman, C and Xue, X and Tselios, C and Vulesevic, B and Adeleye, O and Abdullah, T and Almamlouk, N and Chen, Y and Chassé, M and Durand, M and Paterson, C and Normark, J and Frithiof, R and Lipcsey, M and Hultström, M and Greenwood, CMT and Zeberg, H and Langenberg, C and Thysell, E and Pollak, M and Mooser, V and Forgetta, V and Kaufmann, DE and Richards, JB},
title = {A Neanderthal OAS1 isoform protects individuals of European ancestry against COVID-19 susceptibility and severity.},
journal = {Nature medicine},
volume = {27},
number = {4},
pages = {659-667},
pmid = {33633408},
issn = {1546-170X},
mesh = {2',5'-Oligoadenylate Synthetase/genetics/*physiology ; Aged ; Aged, 80 and over ; Animals ; COVID-19/*etiology/genetics ; Case-Control Studies ; European Continental Ancestry Group ; Female ; *Genetic Predisposition to Disease ; Humans ; Interleukin-10 Receptor beta Subunit/genetics ; Male ; Mendelian Randomization Analysis ; Middle Aged ; Neanderthals ; Protein Isoforms/physiology ; Quantitative Trait Loci ; *SARS-CoV-2 ; Severity of Illness Index ; },
abstract = {To identify circulating proteins influencing Coronavirus Disease 2019 (COVID-19) susceptibility and severity, we undertook a two-sample Mendelian randomization (MR) study, rapidly scanning hundreds of circulating proteins while reducing bias due to reverse causation and confounding. In up to 14,134 cases and 1.2 million controls, we found that an s.d. increase in OAS1 levels was associated with reduced COVID-19 death or ventilation (odds ratio (OR) = 0.54, P = 7 × 10-8), hospitalization (OR = 0.61, P = 8 × 10-8) and susceptibility (OR = 0.78, P = 8 × 10-6). Measuring OAS1 levels in 504 individuals, we found that higher plasma OAS1 levels in a non-infectious state were associated with reduced COVID-19 susceptibility and severity. Further analyses suggested that a Neanderthal isoform of OAS1 in individuals of European ancestry affords this protection. Thus, evidence from MR and a case-control study support a protective role for OAS1 in COVID-19 adverse outcomes. Available pharmacological agents that increase OAS1 levels could be prioritized for drug development.},
}

2',5'-Oligoadenylate Synthetase/genetics/*physiology
Aged
Aged, 80 and over
Animals
COVID-19/*etiology/genetics
Case-Control Studies
European Continental Ancestry Group
Female
*Genetic Predisposition to Disease
Humans
Interleukin-10 Receptor beta Subunit/genetics
Male
Mendelian Randomization Analysis
Middle Aged
Neanderthals
Protein Isoforms/physiology
Quantitative Trait Loci
*SARS-CoV-2
Severity of Illness Index

@article {pmid33620372,
year = {2021},
author = {Baldoni, M and Al-Hashmi, M and Bianchi, AE and Sakal, F and Al-Naimi, F and Leisten, T and Martínez-Labarga, C and Tomei, S},
title = {Bioarchaeology-related studies in the Arabian Gulf: potentialities and shortcomings.},
journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen},
volume = {72},
number = {1},
pages = {17-32},
doi = {10.1127/homo/2021/1282},
pmid = {33620372},
issn = {1618-1301},
abstract = {Archaeological studies provide a powerful tool to understand the prehistoric societies, especially when combined to cutting-edge morphological and molecular anthropological analyses, allowing reconstructing past population dynamics, admixture events, and socio-cultural changes. Despite the advances achieved in the last decades by archaeological studies worldwide, several regions of the World have been spared from this scientific improvement due to various reasons. The Arabian Gulf represents a unique ground to investigate, being the passageway for human migrations and one of the hypothesized areas in which Neanderthal introgression occurred. A number of archaeological sites are currently present in the Arabian Gulf and have witnessed the antiquity and the intensiveness of the human settlements in the region. Nevertheless, the archaeological and anthropological investigation in the Gulf is still in its infancy. Data collected through archaeological studies in the area have the potential to help answering adamant questions of human history from the beginning of the structuring of genetic diversity in human species to the Neolithisation process. This review aims at providing an overview of the archaeological studies in the Arabian Gulf with special focus to Qatar, highlighting potentialities and shortcomings.},
}

@article {pmid33619340,
year = {2021},
author = {Zilio, L and Hammond, H and Karampaglidis, T and Sánchez-Romero, L and Blasco, R and Rivals, F and Rufà, A and Picin, A and Chacón, MG and Demuro, M and Arnold, LJ and Rosell, J},
title = {Examining Neanderthal and carnivore occupations of Teixoneres Cave (Moià, Barcelona, Spain) using archaeostratigraphic and intra-site spatial analysis.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {4339},
pmid = {33619340},
issn = {2045-2322},
abstract = {Teixoneres Cave (Moià, Barcelona, Spain) is a reference site for Middle Palaeolithic studies of the Iberian Peninsula. The cave preserves an extensive stratigraphic sequence made up of eight units, which is presented in depth in this work. The main goal of this study is to undertake an initial spatial examination of Unit III, formed during Marine Isotope Stage 3, with the aim of understanding spatial organization and past activities developed by Neanderthals and carnivores (bears, hyenas and smaller carnivores). The total sample analysed includes 38,244 archaeological items and 5888 limestone blocks. The application of GIS tools allows us to clearly distinguish three geologically-defined stratigraphic subunits. Unit III has been previously interpreted as a palimpsest resulting from alternating occupation of the cave by human groups and carnivores. The distribution study shows that faunal specimens, lithic artefacts, hearths and charcoal fragments are significantly concentrated at the entrance of the cave where, it is inferred, hominins carried out different activities, while carnivores preferred the sheltered zones in the inner areas of the cave. The results obtained reveal a spatial pattern characterized by fire use related zones, and show that the site was occupied by Neanderthals in a similar and consistent way throughout the ˃ 7000 years range covered by the analysed subunits. This spatial pattern is interpreted as resulting from repeated short-term human occupations.},
}

@article {pmid33616898,
year = {2021},
author = {González-Urquijo, J and Bailey, SE and Lazuen, T},
title = {Axlor's level IV human remains are convincingly Neanderthals: A reply to Gómez-Olivencia et al.},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24252},
pmid = {33616898},
issn = {1096-8644},
support = {PID2019-107260GB-I00//Ministerio de Ciencia e Innovación, Spain/ ; },
}

@article {pmid33595856,
year = {2021},
author = {Lee, JW and Lee, IH and Sato, T and Kong, SW and Iimura, T},
title = {Genetic variation analyses indicate conserved SARS-CoV-2-host interaction and varied genetic adaptation in immune response factors in modern human evolution.},
journal = {Development, growth & differentiation},
volume = {63},
number = {3},
pages = {219-227},
pmid = {33595856},
issn = {1440-169X},
support = {U01 TR002623/TR/NCATS NIH HHS/United States ; R24OD024622//National Institution of Health/ ; R01MH107205//National Institution of Health/ ; R01 MH107205/MH/NIMH NIH HHS/United States ; 18H02983//Grant-in-Aids for Scientific Research from the Japan Society for the Promotion of Science (JSPS KAKENHI)/ ; PK43200005//Takeda Science Foundation/ ; 18K19649//Grant-in-Aids for Scientific Research from the Japan Society for the Promotion of Science (JSPS KAKENHI)/ ; U01TR002623//National Institution of Health/ ; 19K10044//Grant-in-Aids for Scientific Research from the Japan Society for the Promotion of Science (JSPS KAKENHI)/ ; R24 OD024622/OD/NIH HHS/United States ; },
mesh = {*Adaptive Immunity/genetics/immunology ; Animals ; *COVID-19/epidemiology/genetics/immunology ; Conserved Sequence ; *Evolution, Molecular ; *Genetic Variation ; Genome-Wide Association Study ; Host Adaptation/genetics/immunology ; *Host-Pathogen Interactions/genetics/immunology ; Humans ; Pandemics ; SARS-CoV-2/*genetics/immunology ; Sequence Analysis, RNA ; },
abstract = {Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a pandemic as of early 2020. Upon infection, SARS-CoV-2 attaches to its receptor, that is, angiotensin-converting enzyme 2 (ACE2), on the surface of host cells and is then internalized into host cells via enzymatic machineries. This subsequently stimulates immune response factors. Since the host immune response and severity of COVID-19 vary among individuals, genetic risk factors for severe COVID-19 cases have been investigated. Our research group recently conducted a survey of genetic variants among SARS-CoV-2-interacting molecules across populations, noting near absence of difference in allele frequency spectrum between populations in these genes. Recent genome-wide association studies have identified genetic risk factors for severe COVID-19 cases in a segment of chromosome 3 that involves six genes encoding three immune-regulatory chemokine receptors and another three molecules. The risk haplotype seemed to be inherited from Neanderthals, suggesting genetic adaptation against pathogens in modern human evolution. Therefore, SARS-CoV-2 uses highly conserved molecules as its virion interaction, whereas its immune response appears to be genetically biased in individuals to some extent. We herein review the molecular process of SARS-CoV-2 infection as well as our further survey of genetic variants of its related immune effectors. We also discuss aspects of modern human evolution.},
}

*Adaptive Immunity/genetics/immunology
Animals
*COVID-19/epidemiology/genetics/immunology
Conserved Sequence
*Evolution, Molecular
*Genetic Variation
Genome-Wide Association Study
Host Adaptation/genetics/immunology
*Host-Pathogen Interactions/genetics/immunology
Humans
Pandemics
SARS-CoV-2/*genetics/immunology
Sequence Analysis, RNA

@article {pmid33593941,
year = {2021},
author = {Zeberg, H and Pääbo, S},
title = {A genomic region associated with protection against severe COVID-19 is inherited from Neandertals.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {9},
pages = {},
pmid = {33593941},
issn = {1091-6490},
mesh = {Animals ; COVID-19/*genetics/immunology ; Chromosomes, Human, Pair 12/*genetics ; *Evolution, Molecular ; *Genetic Predisposition to Disease ; Haplotypes ; Humans ; Neanderthals/*genetics ; Quantitative Trait Loci ; },
abstract = {It was recently shown that the major genetic risk factor associated with becoming severely ill with COVID-19 when infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is inherited from Neandertals. New, larger genetic association studies now allow additional genetic risk factors to be discovered. Using data from the Genetics of Mortality in Critical Care (GenOMICC) consortium, we show that a haplotype at a region on chromosome 12 associated with requiring intensive care when infected with the virus is inherited from Neandertals. This region encodes proteins that activate enzymes that are important during infections with RNA viruses. In contrast to the previously described Neandertal haplotype that increases the risk for severe COVID-19, this Neandertal haplotype is protective against severe disease. It also differs from the risk haplotype in that it has a more moderate effect and occurs at substantial frequencies in all regions of the world outside Africa. Among ancient human genomes in western Eurasia, the frequency of the protective Neandertal haplotype may have increased between 20,000 and 10,000 y ago and again during the past 1,000 y.},
}

Animals
COVID-19/*genetics/immunology
Chromosomes, Human, Pair 12/*genetics
*Evolution, Molecular
*Genetic Predisposition to Disease
Haplotypes
Humans
Neanderthals/*genetics
Quantitative Trait Loci

@article {pmid33589653,
year = {2021},
author = {Blinkhorn, J and Zanolli, C and Compton, T and Groucutt, HS and Scerri, EML and Crété, L and Stringer, C and Petraglia, MD and Blockley, S},
title = {Nubian Levallois technology associated with southernmost Neanderthals.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {2869},
pmid = {33589653},
issn = {2045-2322},
support = {RPG-2017-087//Leverhulme Trust/ ; },
abstract = {Neanderthals occurred widely across north Eurasian landscapes, but between ~ 70 and 50 thousand years ago (ka) they expanded southwards into the Levant, which had previously been inhabited by Homo sapiens. Palaeoanthropological research in the first half of the twentieth century demonstrated alternate occupations of the Levant by Neanderthal and Homo sapiens populations, yet key early findings have largely been overlooked in later studies. Here, we present the results of new examinations of both the fossil and archaeological collections from Shukbah Cave, located in the Palestinian West Bank, presenting new quantitative analyses of a hominin lower first molar and associated stone tool assemblage. The hominin tooth shows clear Neanderthal affinities, making it the southernmost known fossil specimen of this population/species. The associated Middle Palaeolithic stone tool assemblage is dominated by Levallois reduction methods, including the presence of Nubian Levallois points and cores. This is the first direct association between Neanderthals and Nubian Levallois technology, demonstrating that this stone tool technology should not be considered an exclusive marker of Homo sapiens.},
}

@article {pmid33584703,
year = {2020},
author = {Bach, JF},
title = {Revisiting the Hygiene Hypothesis in the Context of Autoimmunity.},
journal = {Frontiers in immunology},
volume = {11},
number = {},
pages = {615192},
pmid = {33584703},
issn = {1664-3224},
mesh = {Animals ; Autoimmune Diseases/etiology/genetics/immunology/prevention & control ; *Autoimmunity ; Bacteria/immunology ; Biological Evolution ; Causality ; Child ; Cytokines/physiology ; Disease Models, Animal ; Dysbiosis/complications ; Environmental Exposure ; Epidemiologic Methods ; Gastrointestinal Microbiome/immunology ; Host-Pathogen Interactions/immunology ; Humans ; *Hygiene Hypothesis ; Hypersensitivity/etiology/genetics/immunology/prevention & control ; Immunity, Innate ; Neanderthals/genetics/immunology ; Parasites/immunology ; Stochastic Processes ; *Symbiosis ; Toll-Like Receptors/physiology ; Viruses/immunology ; },
abstract = {Initially described for allergic diseases, the hygiene hypothesis was extended to autoimmune diseases in the early 2000s. A historical overview allows appreciation of the development of this concept over the last two decades and its discussion in the context of evolution. While the epidemiological data are convergent, with a few exceptions, the underlying mechanisms are multiple and complex. A major question is to determine what is the respective role of pathogens, bacteria, viruses, and parasites, versus commensals. The role of the intestinal microbiota has elicited much interest, but is it a cause or a consequence of autoimmune-mediated inflammation? Our hypothesis is that both pathogens and commensals intervene. Another question is to dissect what are the underlying cellular and molecular mechanisms. The role of immunoregulatory cytokines, in particular interleukin-10 and TGF beta is probably essential. An important place should also be given to ligands of innate immunity receptors present in bacteria, viruses or parasites acting independently of their immunogenicity. The role of Toll-Like Receptor (TLR) ligands is well documented including via TLR ligand desensitization.},
}

Animals
Autoimmune Diseases/etiology/genetics/immunology/prevention & control
*Autoimmunity
Bacteria/immunology
Biological Evolution
Causality
Child
Cytokines/physiology
Disease Models, Animal
Dysbiosis/complications
Environmental Exposure
Epidemiologic Methods
Gastrointestinal Microbiome/immunology
Host-Pathogen Interactions/immunology
Humans
*Hygiene Hypothesis
Hypersensitivity/etiology/genetics/immunology/prevention & control
Immunity, Innate
Neanderthals/genetics/immunology
Parasites/immunology
Stochastic Processes
*Symbiosis
Toll-Like Receptors/physiology
Viruses/immunology

@article {pmid33574596,
year = {2021},
author = {Remmel, A},
title = {Neanderthal-like 'mini-brains' created in lab with CRISPR.},
journal = {Nature},
volume = {590},
number = {7846},
pages = {376-377},
pmid = {33574596},
issn = {1476-4687},
mesh = {Brain ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA ; Humans ; *Neanderthals/genetics ; Stem Cells ; },
}

Brain
Clustered Regularly Interspaced Short Palindromic Repeats
DNA
Humans
*Neanderthals/genetics
Stem Cells

@article {pmid33574182,
year = {2021},
author = {Trujillo, CA and Rice, ES and Schaefer, NK and Chaim, IA and Wheeler, EC and Madrigal, AA and Buchanan, J and Preissl, S and Wang, A and Negraes, PD and Szeto, RA and Herai, RH and Huseynov, A and Ferraz, MSA and Borges, FS and Kihara, AH and Byrne, A and Marin, M and Vollmers, C and Brooks, AN and Lautz, JD and Semendeferi, K and Shapiro, B and Yeo, GW and Smith, SEP and Green, RE and Muotri, AR},
title = {Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment.},
journal = {Science (New York, N.Y.)},
volume = {371},
number = {6530},
pages = {},
pmid = {33574182},
issn = {1095-9203},
support = {R01 HL137223/HL/NHLBI NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; R01 MH121487/MH/NIMH NIH HHS/United States ; U41 HG009889/HG/NHGRI NIH HHS/United States ; S10 OD026929/OD/NIH HHS/United States ; R01 HG004659/HG/NHGRI NIH HHS/United States ; R01 MH113545/MH/NIMH NIH HHS/United States ; K01 AA026911/AA/NIAAA NIH HHS/United States ; U19 MH107367/MH/NIMH NIH HHS/United States ; },
mesh = {Alleles ; Alternative Splicing ; Amino Acid Substitution ; Animals ; Binding Sites ; Biological Evolution ; CRISPR-Cas Systems ; Cell Proliferation ; Cerebral Cortex/cytology/*growth & development/*physiology ; Gene Expression Regulation, Developmental ; Genetic Variation ; Genome ; Genome, Human ; Haplotypes ; Hominidae/genetics ; Humans ; Induced Pluripotent Stem Cells ; Neanderthals/*genetics ; Nerve Net/physiology ; Nerve Tissue Proteins/genetics/metabolism ; Neurons/*physiology ; Organoids ; RNA-Binding Proteins/*genetics/*metabolism ; Synapses/physiology ; },
abstract = {The evolutionarily conserved splicing regulator neuro-oncological ventral antigen 1 (NOVA1) plays a key role in neural development and function. NOVA1 also includes a protein-coding difference between the modern human genome and Neanderthal and Denisovan genomes. To investigate the functional importance of an amino acid change in humans, we reintroduced the archaic allele into human induced pluripotent cells using genome editing and then followed their neural development through cortical organoids. This modification promoted slower development and higher surface complexity in cortical organoids with the archaic version of NOVA1 Moreover, levels of synaptic markers and synaptic protein coassociations correlated with altered electrophysiological properties in organoids expressing the archaic variant. Our results suggest that the human-specific substitution in NOVA1, which is exclusive to modern humans since divergence from Neanderthals, may have had functional consequences for our species' evolution.},
}

Alleles
Alternative Splicing
Amino Acid Substitution
Animals
Binding Sites
Biological Evolution
CRISPR-Cas Systems
Cell Proliferation
Cerebral Cortex/cytology/*growth & development/*physiology
Gene Expression Regulation, Developmental
Genetic Variation
Genome
Genome, Human
Haplotypes
Hominidae/genetics
Humans
Induced Pluripotent Stem Cells
Neanderthals/*genetics
Nerve Net/physiology
Nerve Tissue Proteins/genetics/metabolism
Neurons/*physiology
Organoids
RNA-Binding Proteins/*genetics/*metabolism
Synapses/physiology

@article {pmid33568824,
year = {2021},
author = {Bergström, A and Stringer, C and Hajdinjak, M and Scerri, EML and Skoglund, P},
title = {Origins of modern human ancestry.},
journal = {Nature},
volume = {590},
number = {7845},
pages = {229-237},
pmid = {33568824},
issn = {1476-4687},
support = {/ERC_/European Research Council/International ; /WT_/Wellcome Trust/United Kingdom ; 217223/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Africa/ethnology ; Animals ; Fossils ; Gene Flow/genetics ; History, Ancient ; Human Migration/*history ; Humans ; Neanderthals/genetics ; *Pedigree ; },
abstract = {New finds in the palaeoanthropological and genomic records have changed our view of the origins of modern human ancestry. Here we review our current understanding of how the ancestry of modern humans around the globe can be traced into the deep past, and which ancestors it passes through during our journey back in time. We identify three key phases that are surrounded by major questions, and which will be at the frontiers of future research. The most recent phase comprises the worldwide expansion of modern humans between 40 and 60 thousand years ago (ka) and their last known contacts with archaic groups such as Neanderthals and Denisovans. The second phase is associated with a broadly construed African origin of modern human diversity between 60 and 300 ka. The oldest phase comprises the complex separation of modern human ancestors from archaic human groups from 0.3 to 1 million years ago. We argue that no specific point in time can currently be identified at which modern human ancestry was confined to a limited birthplace, and that patterns of the first appearance of anatomical or behavioural traits that are used to define Homo sapiens are consistent with a range of evolutionary histories.},
}

Africa/ethnology
Animals
Fossils
Gene Flow/genetics
History, Ancient
Human Migration/*history
Humans
Neanderthals/genetics
*Pedigree

@article {pmid33564646,
year = {2021},
author = {Mortazavi, SAR and Kaveh-Ahangar, K and Mortazavi, SMJ and Firoozi, D and Haghani, M},
title = {How Our Neanderthal Genes Affect the COVID-19 Mortality: Iran and Mongolia, Two Countries with the Same SARS-CoV-2 Mutation Cluster but Different Mortality Rates.},
journal = {Journal of biomedical physics & engineering},
volume = {11},
number = {1},
pages = {109-114},
pmid = {33564646},
issn = {2251-7200},
abstract = {Neanderthal genes possibly gave modern human protection against viruses. However, a recent study revealed that that a long sequence of DNA that is inherited from our Neanderthal ancestors can be linked to severe COVID-19 infection and hospitalization. Substantial evidence now indicates that our genetic background may be involved in the transmissibility of SARS-CoV-2 and the rapid progress of COVID-19 in some infected individuals. Although both morbidity and mortality of COVID-19 strongly depends on key factors such as age and co-existing health conditions, potential classes of human genomic variants possibly affect the likelihood of SARS-CoV-2 infection and its progress. Despite Iran and Mongolia seem to share the same SARS-CoV-2 mutation cluster, the COVID-19 mortality rates in these two countries are drastically different. While the population in Iran is 25.8 times higher than that of Mongolia, the number of confirmed cases is 1170 times higher. Moreover, the death rate shows a drastic difference. Since Neanderthals interbred with modern humans in Middle East between 47,000 and 65,000 years ago before going extinct 40,000 years ago, some Iranians have much more Neanderthal DNA than other people. Although neither genetic background nor environmental factors alone can determine our risk of developing severe COVID-19, our genes clearly affect both the development and progression of infectious diseases including COVID-19. Given these considerations, we believe that these great differences, at least to some extent, can be due to the proportion of Neanderthal genes among the people of these two countries.},
}

@article {pmid33556445,
year = {2021},
author = {Reinscheid, RK and Mafessoni, F and Lüttjohann, A and Jüngling, K and Pape, HC and Schulz, S},
title = {Neandertal introgression and accumulation of hypomorphic mutations in the neuropeptide S (NPS) system promote attenuated functionality.},
journal = {Peptides},
volume = {138},
number = {},
pages = {170506},
doi = {10.1016/j.peptides.2021.170506},
pmid = {33556445},
issn = {1873-5169},
abstract = {The neuropeptide S (NPS) system plays an important role in fear and fear memory processing but has also been associated with allergic and inflammatory diseases. Genes for NPS and its receptor NPSR1 are found in all tetrapods. Compared to non-human primates, several non-synonymous single-nucleotide polymorphisms (SNPs) occur in both human genes that collectively result in functional attenuation, suggesting adaptive mechanisms in a human context. To investigate historic and geographic origins of these hypomorphic mutations and explore genetic signs of selection, we analyzed ancient genomes and worldwide genotype frequencies of four prototypic SNPs in the NPS system. Neandertal and Denisovan genomes contain exclusively ancestral alleles for NPSR1 while all derived alleles occur in ancient genomes of anatomically modern humans, indicating that they arose in modern Homo sapiens. Worldwide genotype frequencies for three hypomorphic NPSR1 SNPs show significant regional homogeneity but follow a gradient towards increasing derived allele frequencies that supports an out-of-Africa scenario. Increased density of high-frequency polymorphisms around the three NPSR1 loci suggests weak or possibly balancing selection. A hypomorphic mutation in the NPS precursor, however, was detected at high frequency in Eurasian Neandertal genomes and shows genetic signatures indicating that it was introgressed into the human gene pool, particularly in Southern Europe, by interbreeding with Neandertals. We discuss potential evolutionary scenarios including behavior and immune-based natural selection.},
}

@article {pmid33547403,
year = {2021},
author = {Rampelli, S and Turroni, S and Mallol, C and Hernandez, C and Galván, B and Sistiaga, A and Biagi, E and Astolfi, A and Brigidi, P and Benazzi, S and Lewis, CM and Warinner, C and Hofman, CA and Schnorr, SL and Candela, M},
title = {Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {169},
pmid = {33547403},
issn = {2399-3642},
support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; },
abstract = {A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.},
}

@article {pmid33543780,
year = {2021},
author = {Selig, KR and Kupczik, K and Silcox, MT},
title = {The effect of high wear diets on the relative pulp volume of the lower molars.},
journal = {American journal of physical anthropology},
volume = {174},
number = {4},
pages = {804-811},
doi = {10.1002/ajpa.24242},
pmid = {33543780},
issn = {1096-8644},
mesh = {Animals ; Anthropology, Physical ; *Dental Pulp/anatomy & histology/physiology ; Diet/*veterinary ; *Hominidae/anatomy & histology/physiology ; Molar/anatomy & histology/physiology ; Tooth Wear/*pathology ; },
abstract = {OBJECTIVES: One role of dental pulp is in the upkeep and maintenance of dentine. Under wear, odontoblasts in the pulp deposit tertiary dentine to ensure the sensitive internal dental tissues are not exposed and vulnerable to infection. It follows that there may be an adaptive advantage for increasing molar pulp volume in anthropoid primate taxa that are prone to high levels of wear. The relative volume of dental pulp is therefore predicted to covary with dietary abrasiveness (in the sense of including foods that cause high degrees of wear).

MATERIALS AND METHODS: We examined relatively unworn lower second molars in pairs of species of extant hominoids, cebids, and pitheciids that vary in the abrasiveness of their diet (n = 36). Using micro-CT scans, we measured the percent of tooth that is pulp (PTP) as the ratio of pulp volume to that of the total volume of the tooth.

RESULTS: We found that in each pair of species, the taxa that consume a more abrasive diet had a significantly higher PTP than the closely related taxa that consume a softer diet.

CONCLUSIONS: Our results point to an adaptive mechanism in the molars of taxa that consume abrasive diets and are thus subject to higher levels of wear. Our results provide additional understanding of the relationship between dental pulp and diet and may offer insight into the diet of extinct taxa such as Paranthropus boisei or into the adaptive context of the taurodont molars of Neanderthals.},
}

Animals
Anthropology, Physical
*Dental Pulp/anatomy & histology/physiology
Diet/*veterinary
*Hominidae/anatomy & histology/physiology
Molar/anatomy & histology/physiology
Tooth Wear/*pathology

@article {pmid33524842,
year = {2021},
author = {Lacy, SA},
title = {Evidence of dental agenesis in late pleistocene Homo.},
journal = {International journal of paleopathology},
volume = {32},
number = {},
pages = {103-110},
doi = {10.1016/j.ijpp.2021.01.001},
pmid = {33524842},
issn = {1879-9825},
abstract = {OBJECTIVE: Differential diagnosis and tabulation of cases of dental agenesis in Middle and Upper Paleolithic Western Eurasian humans to synthesize this data and to test previous hypotheses about when recent human patterns of third molar agenesis were established.

MATERIALS: 139 Late Pleistocene human remains and 149 individuals from three Epi-Paleolithic/ Holocene non-agricultural comparative collections.

METHODS: All remains were visually and radiographically recorded by the author.

RESULTS: In addition to establishing that third molar agenesis was common during the Late Upper Paleolithic (22,500-10,000 years BP), this study suggests a pattern of increasing prevalence through time.

CONCLUSIONS: An increase in the prevalence of third molar agenesis in the Late Upper Paleolithic could indicate selection for dental size reduction and orthognathy, but also bio-cultural changes from more intensive food preparation techniques.

SIGNIFICANCE: Third molar agenesis, a well-known developmental defect, is often reported for recent human skeletal collections, but the prevalence of the condition for Pleistocene hominins had not been previously quantified in order to consider patterns through time. Hypotheses posited for the high prevalence of third molar agenesis, or hypodontia in general, in some recent human groups require an understanding of the prevalence of these traits in the past.

LIMITATIONS: Paleolithic skeletal remains are incomplete, so these values are under-estimations. Individuals are also separated diachronically and geographically and should not be assumed to represent a single population sample.

Hypotheses on some of the potential selective forces acting on dental size reduction and subsequent agenesis could be tested in recent humans.},
}

@article {pmid33517134,
year = {2021},
author = {Compton, T and Skinner, MM and Humphrey, L and Pope, M and Bates, M and Davies, TW and Parfitt, SA and Plummer, WP and Scott, B and Shaw, A and Stringer, C},
title = {The morphology of the Late Pleistocene hominin remains from the site of La Cotte de St Brelade, Jersey (Channel Islands).},
journal = {Journal of human evolution},
volume = {152},
number = {},
pages = {102939},
doi = {10.1016/j.jhevol.2020.102939},
pmid = {33517134},
issn = {1095-8606},
mesh = {Animals ; Biological Evolution ; Channel Islands ; Female ; Fossils/*anatomy & histology ; Neanderthals/*anatomy & histology ; Paleodontology ; Tooth/*anatomy & histology ; },
abstract = {Thirteen permanent fully erupted teeth were excavated at the Paleolithic site of La Cotte de St Brelade in Jersey in 1910 and 1911. These were all found in the same location, on a ledge behind a hearth in a Mousterian occupation level. They were originally identified as being Neanderthal. A fragment of occipital bone was found in a separate locality in a later season. Recent dating of adjacent sediments gives a probable age of <48 ka. The purpose of this article is to provide an updated description of the morphology of this material and consider its likely taxonomic assignment from comparison with Neanderthal and Homo sapiens samples. One of the original teeth has been lost, and we identify one as nonhominin. At least two adult individuals are represented. Cervix shape and the absence of common Neanderthal traits in several teeth suggest affinities with H. sapiens in both individuals, while crown and root dimensions and root morphology of all the teeth are entirely consistent with a Neanderthal attribution, pointing toward a possible shared Neanderthal and H. sapiens ancestry (the likely date of this material corresponds with the time in which both Neanderthals and H. sapiens were present in Europe). The occipital fragment is stratigraphically more recent and does not exhibit any diagnostic Neanderthal features.},
}

Animals
Biological Evolution
Channel Islands
Female
Fossils/*anatomy & histology
Neanderthals/*anatomy & histology
Paleodontology
Tooth/*anatomy & histology

@article {pmid33486494,
year = {2021},
author = {Kliesch, S and Schmidt, S and Wilborn, D and Aigner, C and Albrecht, W and Bedke, J and Beintker, M and Beyersdorff, D and Bokemeyer, C and Busch, J and Classen, J and de Wit, M and Dieckmann, KP and Diemer, T and Dieing, A and Gockel, M and Göckel-Beining, B and Hakenberg, OW and Heidenreich, A and Heinzelbecker, J and Herkommer, K and Hermanns, T and Kaufmann, S and Kornmann, M and Kotzerke, J and Krege, S and Kristiansen, G and Lorch, A and Müller, AC and Oechsle, K and Ohloff, T and Oing, C and Otto, U and Pfister, D and Pichler, R and Recken, H and Rick, O and Rudolph, Y and Ruf, C and Schirren, J and Schmelz, H and Schmidberger, H and Schrader, M and Schweyer, S and Seeling, S and Souchon, R and Winter, C and Wittekind, C and Zengerling, F and Zermann, DH and Zillmann, R and Albers, P},
title = {Management of Germ Cell Tumours of the Testes in Adult Patients: German Clinical Practice Guideline, PART II - Recommendations for the Treatment of Advanced, Recurrent, and Refractory Disease and Extragonadal and Sex Cord/Stromal Tumours and for the Management of Follow-Up, Toxicity, Quality of Life, Palliative Care, and Supportive Therapy.},
journal = {Urologia internationalis},
volume = {105},
number = {3-4},
pages = {181-191},
pmid = {33486494},
issn = {1423-0399},
mesh = {Adult ; Aftercare ; Humans ; Male ; Neoplasm Metastasis ; Neoplasm Recurrence, Local/therapy ; Neoplasm Staging ; Neoplasms, Germ Cell and Embryonal/pathology/*therapy ; Palliative Care ; Practice Guidelines as Topic ; Quality of Life ; Sex Cord-Gonadal Stromal Tumors/*therapy ; Testicular Neoplasms/pathology/*therapy ; },
abstract = {OBJECTIVES: We developed the first German evidence- and consensus-based clinical guideline on diagnosis, treatment, and follow-up of germ cell tumours (GCT) of the testes in adult patients. We present the guideline content in 2 separate publications. The present second part summarizes therecommendations for the treatment of advanced disease stages and for the management of follow-up and late effects.

MATERIALS AND METHODS: An interdisciplinary panel of 42 experts including 1 patient representative developed the guideline content. Clinical recommendations and statements were based on scientific evidence and expert consensus. For this purpose, evidence tables for several review questions, which were based on systematic literature searches (last search in March 2018), were provided. Thirty-one experts, who were entitled to vote, rated the final clinical recommendations and statements.

RESULTS: Here we present the treatment recommendations separately for patients with metastatic seminoma and non-seminomatous GCT (stages IIA/B and IIC/III), for restaging and treatment of residual masses, and for relapsed and refractory disease stages. The recommendations also cover extragonadal and sex cord/stromal tumours, the management of follow-up and toxicity, quality-of-life aspects, palliative care, and supportive therapy.

CONCLUSION: Physicians and other medical service providers who are involved in the diagnostics, treatment, and follow-up of GCT (all stages, outpatient and inpatient care as well as rehabilitation) are the users of the present guideline. The guideline also comprises quality indicators for measuring the implementation of the guideline recommendations in routine clinical care; these data will be presented in a future publication.},
}

Adult
Aftercare
Humans
Male
Neoplasm Metastasis
Neoplasm Recurrence, Local/therapy
Neoplasm Staging
Neoplasms, Germ Cell and Embryonal/pathology/*therapy
Palliative Care
Practice Guidelines as Topic
Quality of Life
Sex Cord-Gonadal Stromal Tumors/*therapy
Testicular Neoplasms/pathology/*therapy