Use the keywords feature with a free QxMD account.
Use Read by QxMD to access full text via your institution or open access sources.
Read also provides personalized recommendations to keep you up to date in your field.
Existing User
Sign InNew to Read
Sign Up#1
REVIEW
Hugo Zeberg, Mattias Jakobsson, Svante Pääbo
Modern human ancestors diverged from the ancestors of Neandertals and Denisovans about 600,000 years ago. Until about 40,000 years ago, these three groups existed in parallel, occasionally met, and exchanged genes. A critical question is why modern humans, and not the other two groups, survived, became numerous, and developed complex cultures. Here, we discuss genetic differences among the groups and some of their functional consequences. As more present-day genome sequences become available from diverse groups, we predict that very few, if any, differences will distinguish all modern humans from all Neandertals and Denisovans...
February 14, 2024: Cell
#2
JOURNAL ARTICLE
Margherita Piccardi, Manuel Gentiluomo, Stefania Bertoncini, Raffaele Pezzilli, Bálint Erőss, Stefania Bunduc, Faik G Uzunoglu, Renata Talar-Wojnarowska, Tomas Vanagas, Cosimo Sperti, Martin Oliverius, Mateus Nóbrega Aoki, Stefano Ermini, Tamás Hussein, Ugo Boggi, Krzysztof Jamroziak, Evaristo Maiello, Luca Morelli, Ludmila Vodickova, Gregorio Di Franco, Stefano Landi, Andrea Szentesi, Martin Lovecek, Marta Puzzono, Francesca Tavano, Hanneke W M van Laarhoven, Alessandro Zerbi, Beatrice Mohelnikova-Duchonova, Hannah Stocker, Eithne Costello, Gabriele Capurso, Laura Ginocchi, Rita T Lawlor, Giuseppe Vanella, Francesca Bazzocchi, Jakob R Izbicki, Anna Latiano, Bas Bueno-de-Mesquita, Ruggero Ponz de Leon Pisani, Ben Schöttker, Pavel Soucek, Péter Hegyi, Maria Gazouli, Thilo Hackert, Juozas Kupcinskas, Lina Poskiene, Matteo Tacelli, Susanne Roth, Silvia Carrara, Francesco Perri, Viktor Hlavac, George E Theodoropoulos, Olivier R Busch, Andrea Mambrini, Casper H J van Eijck, Paolo Arcidiacono, Aldo Scarpa, Claudio Pasquali, Daniela Basso, Maurizio Lucchesi, Anna Caterina Milanetto, John P Neoptolemos, Giulia Martina Cavestro, Dainius Janciauskas, Xuechen Chen, Roger Chammas, Mara Goetz, Hermann Brenner, Livia Archibugi, Michael Dannemann, Federico Canzian, Sergio Tofanelli, Daniele Campa
BACKGROUND: The genomes of present-day non-Africans are composed of 1-3% of Neandertal-derived DNA as a consequence of admixture events between Neandertals and anatomically modern humans about 50-60 thousand years ago. Neandertal-introgressed single nucleotide polymorphisms (aSNPs) have been associated with modern human disease-related traits, which are risk factors for pancreatic ductal adenocarcinoma (PDAC), such as obesity, type 2 diabetes, and inflammation. In this study, we aimed at investigating the role of aSNPs in PDAC in three Eurasian populations...
August 13, 2023: Biological Research
#3
JOURNAL ARTICLE
Richard Ågren, Snehal Patil, Xiang Zhou, Kristoffer Sahlholm, Svante Pääbo, Hugo Zeberg
Dupuytren's disease is characterized by fingers becoming permanently bent in a flexed position. Whereas people of African ancestry are rarely afflicted by Dupuytren's disease, up to ∼30% of men over 60 years suffer from this condition in northern Europe. Here, we meta-analyze 3 biobanks comprising 7,871 cases and 645,880 controls and find 61 genome-wide significant variants associated with Dupuytren's disease. We show that 3 of the 61 loci harbor alleles of Neandertal origin, including the second and third most strongly associated ones (P = 6...
June 1, 2023: Molecular Biology and Evolution
#4
JOURNAL ARTICLE
Jaime Garcia-Heras
The Nobel Assembly at the Karolinska Institute awarded the 2022 Nobel Prize in Physiology or Medicine to Svante Pääbo (Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany). This award acknowledged his discoveries about the genomes of extinct hominins (Neandertal man and the Denisovans), the molecular genetic insights of human origin and evolutionary history, and the understanding of phylogenetic relationships between archaic hominins and modern humans. The scientific advances included detection of Neandertal and Denisovan DNA carried by modern humans due to past admixture events, which in turn stimulated active research about the functional and phenotypic significance of such archaic ancestry on non-disease and disease phenotypic features in modern populations...
2023: Journal of the Association of Genetic Technologists
#5
JOURNAL ARTICLE
Julian Petersen, Lukas Englmaier, Artem V Artemov, Irina Poverennaya, Ruba Mahmoud, Thibault Bouderlique, Marketa Tesarova, Ruslan Deviatiiarov, Anett Szilvásy-Szabó, Evgeny E Akkuratov, David Pajuelo Reguera, Hugo Zeberg, Marketa Kaucka, Maria Eleni Kastriti, Jan Krivanek, Tomasz Radaszkiewicz, Kristína Gömöryová, Sarah Knauth, David Potesil, Zbynek Zdrahal, Ranjani Sri Ganji, Anna Grabowski, Miriam E Buhl, Tomas Zikmund, Michaela Kavkova, Håkan Axelson, David Lindgren, Rafael Kramann, Christoph Kuppe, Ferenc Erdélyi, Zoltán Máté, Gábor Szabó, Till Koehne, Tibor Harkany, Kaj Fried, Jozef Kaiser, Peter Boor, Csaba Fekete, Jan Rozman, Petr Kasparek, Jan Prochazka, Radislav Sedlacek, Vitezslav Bryja, Oleg Gusev, Igor Adameyko
In this study we use comparative genomics to uncover a gene with uncharacterized function (1700011H14Rik/C14orf105/CCDC198), which we hereby name FAME (Factor Associated with Metabolism and Energy). We observe that FAME shows an unusually high evolutionary divergence in birds and mammals. Through the comparison of single nucleotide polymorphisms, we identify gene flow of FAME from Neandertals into modern humans. We conduct knockout experiments on animals and observe altered body weight and decreased energy expenditure in Fame knockout animals, corresponding to genome-wide association studies linking FAME with higher body mass index in humans...
May 29, 2023: Nature Communications
#6
JOURNAL ARTICLE
Raymond Tobler, Yassine Souilmi, Christian D Huber, Nigel Bean, Chris S M Turney, Shane T Grey, Alan Cooper
The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA...
May 30, 2023: Proceedings of the National Academy of Sciences of the United States of America
#7
REVIEW
Danalaxshmi Shanen Ganapathee, Philipp Gunz
It has recently become possible to start exploring how the genotype translates into human brain morphology and behavior by combining detailed genomic and phenotypic data from thousands of present-day people with archaic genomes of extinct humans, and gene expression data. As a starting point into this emerging interdisciplinary domain, we highlight current debates about which aspects of the modern human brain are unique. We review recent developments from (1) comparative primate neuroscience-a fast-growing field offering an invaluable framework for understanding general mechanisms and the evolution of human-specific traits...
2023: Progress in Brain Research
#8
JOURNAL ARTICLE
Evelyn Jagoda, Davide Marnetto, Gayani Senevirathne, Victoria Gonzalez, Kaushal Baid, Francesco Montinaro, Daniel Richard, Darryl Falzarano, Emmanuelle V LeBlanc, Che C Colpitts, Arinjay Banerjee, Luca Pagani, Terence D Capellini
Individuals infected with the SARS-CoV-2 virus present with a wide variety of symptoms ranging from asymptomatic to severe and even lethal outcomes. Past research has revealed a genetic haplotype on chromosome 3 that entered the human population via introgression from Neanderthals as the strongest genetic risk factor for the severe response to COVID-19. However, the specific variants along this introgressed haplotype that contribute to this risk and the biological mechanisms that are involved remain unclear...
February 10, 2023: ELife
#9
JOURNAL ARTICLE
Danat Yermakovich, Vasili Pankratov, Urmo Võsa, Bayazit Yunusbayev, Michael Dannemann
The admixture between modern humans and Neandertals has resulted in ∼2% of the genomes of present-day non-Africans being composed of Neandertal DNA. Introgressed Neandertal DNA has been demonstrated to significantly affect the transcriptomic landscape in people today and via this molecular mechanism influence phenotype variation as well. However, little is known about how much of that regulatory impact is mediated through long-range regulatory effects that have been shown to explain ∼20% of expression variation...
December 23, 2022: Genetics
#10
JOURNAL ARTICLE
Olivier Gorgé, E Andrew Bennett, Diyendo Massilani, Julien Daligault, Eva-Maria Geigl, Thierry Grange
The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of ancient human skeletal remains have revolutionized our understanding of human evolution. This research led to the discovery of a new hominin lineage, and demonstrated multiple admixture events with more distantly related archaic human populations such as Neandertals and Denisovans over the last 100,000 years. Moreover, it has also yielded novel insights into the evolution of ancient pathogens...
2023: Methods in Molecular Biology
#11
JOURNAL ARTICLE
Michael Dannemann, Yuri Milaneschi, Danat Yermakovich, Victoria Stiglbauer, Hanna Maria Kariis, Kristi Krebs, Manuel A Friese, Christian Otte, Kelli Lehto, Brenda W J H Penninx, Janet Kelso, Stefan M Gold
Despite advances in identifying the genetic basis of psychiatric and neurological disorders, fundamental questions about their evolutionary origins remain elusive. Here, introgressed variants from archaic humans such as Neandertals can serve as an intriguing research paradigm. We compared the number of associations for Neandertal variants to the number of associations of frequency-matched non-archaic variants with regard to human CNS disorders (neurological and psychiatric), nervous system drug prescriptions (as a proxy for disease), and related, non-disease phenotypes in the UK biobank (UKBB)...
October 5, 2022: Translational Psychiatry
#12
JOURNAL ARTICLE
Steven E Churchill, Kamryn Keys, Ann H Ross
Ancient DNA from, Neandertal and modern human fossils, and comparative morphological analyses of them, reveal a complex history of interbreeding between these lineages and the introgression of Neandertal genes into modern human genomes. Despite substantial increases in our knowledge of these events, the timing and geographic location of hybridization events remain unclear. Six measures of facial size and shape, from regional samples of Neandertals and early modern humans, were used in a multivariate exploratory analysis to try to identify regions in which early modern human facial morphology was more similar to that of Neandertals, which might thus represent regions of greater introgression of Neandertal genes...
August 3, 2022: Biology
#13
JOURNAL ARTICLE
Stéphane Peyrégne, Janet Kelso, Benjamin M Peter, Svante Pääbo
Proteins associated with the spindle apparatus, a cytoskeletal structure that ensures the proper segregation of chromosomes during cell division, experienced an unusual number of amino acid substitutions in modern humans after the split from the ancestors of Neandertals and Denisovans. Here, we analyze the history of these substitutions and show that some of the genes in which they occur may have been targets of positive selection. We also find that the two changes in the kinetochore scaffold 1 (KNL1) protein, previously believed to be specific to modern humans, were present in some Neandertals...
July 11, 2022: ELife
#14
JOURNAL ARTICLE
Sigrid Haeggström, Magnus Ingelman-Sundberg, Svante Pääbo, Hugo Zeberg
Genetic variation in genes encoding cytochrome P450 enzymes influences the metabolism of drugs and endogenous compounds. The locus containing the cytochrome genes CYP2C8 and CYP2C9 on chromosome 10 exhibits linkage disequilibrium between the CYP2C8*3 and CYP2C9*2 alleles, forming a haplotype of ~300 kilobases. This haplotype is associated with altered metabolism of several drugs, most notably reduced metabolism of warfarin and phenytoin, leading to toxicity at otherwise therapeutic doses. Here we show that this haplotype is inherited from Neandertals...
July 2022: Pharmacogenomics Journal
#15
JOURNAL ARTICLE
Lorena Di Pietro, Marta Barba, Daniela Palacios, Federica Tiberio, Chiara Prampolini, Mirko Baranzini, Ornella Parolini, Alessandro Arcovito, Wanda Lattanzi
RUNX2 encodes the master bone transcription factor driving skeletal development in vertebrates, and playing a specific role in craniofacial and skull morphogenesis. The anatomically modern human (AMH) features sequence changes in the RUNX2 locus compared with archaic hominins' species. We aimed to understand how these changes may have contributed to human skull globularization occurred in recent evolution. We compared in silico AMH and archaic hominins' genomes, and used mesenchymal stromal cells isolated from skull sutures of craniosynostosis patients for in vitro functional assays...
October 29, 2021: Scientific Reports
#16
JOURNAL ARTICLE
Silvana Condemi, Stéphane Mazières, Pierre Faux, Caroline Costedoat, Andres Ruiz-Linares, Pascal Bailly, Jacques Chiaroni
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...
2021: PloS One
#17
A Rouf Banday, Megan L Stanifer, Oscar Florez-Vargas, Olusegun O Onabajo, Muhammad A Zahoor, Brenen W Papenberg, Timothy J Ring, Chia-Han Lee, Evangelos Andreakos, Evgeny Arons, Greg Barsh, Leslie G Biesecker, David L Boyle, Andrea Burnett-Hartman, Mary Carrington, Euijin Chang, Pyoeng Gyun Choe, Rex L Chrisholm, Clifton Dalgard, Jeff Edberg, Nathan Erdmann, Heather S Feigelson, Gary S Firestein, Adam J Gehring, Michelle Ho, Steven Holland, Amy A Hutchinson, Hogune Im, Michael G Ison, Hong Bin Kim, Robert J Kreitman, Bruce R Korf, Lisa Mirabello, Jennifer A Pacheco, Michael J Peluso, Daniel J Rader, David T Redden, Marylyn D Ritchie, Brooke Rosenbloom, Hanaisa P Sant Anna, Sharon Savage, Eleni Siouti, Vasiliki Triantafyllia, Joselin M Vargas, Anurag Verma, Vibha Vij, Duane R Wesemann, Meredith Yeager, Xu Yu, Yu Zhang, Steeve Boulant, Stephen J Chanock, Jordan J Feld, Ludmila Prokunina-Olsson
Genomic regions have been associated with COVID-19 susceptibility and outcomes, including the chr12q24.13 locus encoding antiviral proteins OAS1-3. Here, we report genetic, functional, and clinical insights into genetic associations within this locus. In Europeans, the risk of hospitalized vs. non-hospitalized COVID-19 was associated with a single 19Kb-haplotype comprised of 76 OAS1 variants included in a 95% credible set within a large genomic fragment introgressed from Neandertals. The risk haplotype was also associated with impaired spontaneous but not treatment-induced SARS-CoV-2 clearance in a clinical trial with pegIFN-λ1...
July 13, 2021: medRxiv
#18
JOURNAL ARTICLE
Leonardo N M Iasi, Harald Ringbauer, Benjamin M Peter
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...
July 12, 2021: Molecular Biology and Evolution
#19
JOURNAL ARTICLE
Vita Stepanova, Kaja Ewa Moczulska, Guido Vacano, Ilia Kurochkin, Xiangchun Ju, Stephan Riesenberg, Dominik Macak, Tomislav Maricic, Linda Dombrowski, Maria Schörnig, Konstantinos Anastassiadis, Oliver Baker, Ronald Naumann, Ekaterina Khrameeva, Anna Vanushkina, Elena Stekolshchikova, Alina Egorova, Anna Tkachev, Randall Mazzarino, Nathan Duval, Dmitri Zubkov, Patrick Giavalisco, Terry G Wilkinson Ii, David Patterson, Philipp Khaitovich, Svante Pääbo
We analyze the metabolomes of humans, chimpanzees and macaques in muscle, kidney and three different regions of the brain. Whereas 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...
May 4, 2021: ELife
#20
JOURNAL ARTICLE
Per Sjödin, James McKenna, Mattias Jakobsson
The patterns of genetic variation within and among individuals and populations can be used to make inferences about the evolutionary forces that generated those patterns. Numerous population genetic approaches have been developed in order to infer evolutionary history. Here, we present the "Two-Two (TT)" and the "Two-Two-outgroup (TTo)" methods; two closely related approaches for estimating divergence time based in coalescent theory. They rely on sequence data from two haploid genomes (or a single diploid individual) from each of two populations...
March 26, 2021: Genetics
Make the most of Read.
Download the mobile app.
Download the mobile app.
Fetching more papers... 
