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Neanderthal genes

Dongsheng Lu, Haiyi Lou, Kai Yuan, Xiaoji Wang, Yuchen Wang, Chao Zhang, Yan Lu, Xiong Yang, Lian Deng, Ying Zhou, Qidi Feng, Ya Hu, Qiliang Ding, Yajun Yang, Shilin Li, Li Jin, Yaqun Guan, Bing Su, Longli Kang, Shuhua Xu
The origin of Tibetans remains one of the most contentious puzzles in history, anthropology, and genetics. Analyses of deeply sequenced (30×-60×) genomes of 38 Tibetan highlanders and 39 Han Chinese lowlanders, together with available data on archaic and modern humans, allow us to comprehensively characterize the ancestral makeup of Tibetans and uncover their origins. Non-modern human sequences compose ∼6% of the Tibetan gene pool and form unique haplotypes in some genomic regions, where Denisovan-like, Neanderthal-like, ancient-Siberian-like, and unknown ancestries are entangled and elevated...
September 1, 2016: American Journal of Human Genetics
John S Taylor, Thomas E Reimchen
The Neanderthals' northern distribution, hunting techniques, and orbit breadths suggest that they were more active in dim light than modern humans. We surveyed visual opsin genes from four Neanderthals and two other archaic hominids to see if they provided additional support for this hypothesis. This analysis was motivated by the observation that alleles responsible for anomalous trichromacy in humans are more common in northern latitudes, by data suggesting that these variants might enhance vision in mesopic conditions, and by the observation that dim light active species often have fewer opsin genes than diurnal relatives...
August 2016: Genome Génome / Conseil National de Recherches Canada
Laurent Abi-Rached, Didier Raoult
With the advent of next-generation sequencing, paleogenetics has considerably expanded over the past few years and notably encompassed the characterization of the genomes of archaic humans who lived more than 30,000 years ago. These paleogenetics investigations have revealed that admixture between modern and archaic humans occurred, with Neanderthals having contributed to 1.5% to 2.1% of modern Eurasian genomes, and Denisovans to 3% to 6% of modern Melanesian genomes and to approximately 0.2% of modern Asian genomes...
June 2016: Microbiology Spectrum
Chris Stringer
If we restrict the use of Homo sapiens in the fossil record to specimens which share a significant number of derived features in the skeleton with extant H. sapiens, the origin of our species would be placed in the African late middle Pleistocene, based on fossils such as Omo Kibish 1, Herto 1 and 2, and the Levantine material from Skhul and Qafzeh. However, genetic data suggest that we and our sister species Homo neanderthalensis shared a last common ancestor in the middle Pleistocene approximately 400-700 ka, which is at least 200 000 years earlier than the species origin indicated from the fossils already mentioned...
July 5, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Kaleigh Anne Eichel, Rebecca Rogers Ackermann
Hybridization is increasingly proving to be an important force shaping human evolution. Comparisons of both ancient and modern genomes have provided support for a complex evolutionary scenario over the past million years, with evidence for multiple incidents of gene exchange. However, to date, genetic evidence is still limited in its ability to pinpoint the precise time and place of ancient admixture. For that we must rely on evidence of admixture from the skeleton. The research presented here builds on previous work on the crania of baboon hybrids, focusing on the nasal cavity of olive baboons, yellow baboons, and first generation (F1) hybrids...
May 2016: Journal of Human Evolution
Priya Moorjani, Sriram Sankararaman, Qiaomei Fu, Molly Przeworski, Nick Patterson, David Reich
The study of human evolution has been revolutionized by inferences from ancient DNA analyses. Key to these studies is the reliable estimation of the age of ancient specimens. High-resolution age estimates can often be obtained using radiocarbon dating, and, while precise and powerful, this method has some biases, making it of interest to directly use genetic data to infer a date for samples that have been sequenced. Here, we report a genetic method that uses the recombination clock. The idea is that an ancient genome has evolved less than the genomes of present-day individuals and thus has experienced fewer recombination events since the common ancestor...
May 17, 2016: Proceedings of the National Academy of Sciences of the United States of America
Nashaiman Pervaiz, Amir Ali Abbasi
Human brain evolution is characterized by dramatic expansion in cerebral cortex size. WDR62 (WD repeat domain 62) is one of the important gene in controlling human cortical development. Mutations in WDR62 lead to primary microcephaly, a neurodevelopmental disease characterized by three to four fold reduction in cerebral cortex size of affected individuals. This study analyzes comparative protein evolutionary rate to provide a useful insight into the molecular evolution of WDR62 and hence pinpointed human specific amino acid replacements...
September 2016: Meta Gene
Kelley Harris, Rasmus Nielsen
Approximately 2-4% of genetic material in human populations outside Africa is derived from Neanderthals who interbred with anatomically modern humans. Recent studies have shown that this Neanderthal DNA is depleted around functional genomic regions; this has been suggested to be a consequence of harmful epistatic interactions between human and Neanderthal alleles. However, using published estimates of Neanderthal inbreeding and the distribution of mutational fitness effects, we infer that Neanderthals had at least 40% lower fitness than humans on average; this increased load predicts the reduction in Neanderthal introgression around genes without the need to invoke epistasis...
June 2016: Genetics
Sriram Sankararaman, Swapan Mallick, Nick Patterson, David Reich
Some present-day humans derive up to ∼5% [1] of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals [2]. We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry [3]. In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0...
May 9, 2016: Current Biology: CB
Matthias Meyer, Juan-Luis Arsuaga, Cesare de Filippo, Sarah Nagel, Ayinuer Aximu-Petri, Birgit Nickel, Ignacio Martínez, Ana Gracia, José María Bermúdez de Castro, Eudald Carbonell, Bence Viola, Janet Kelso, Kay Prüfer, Svante Pääbo
A unique assemblage of 28 hominin individuals, found in Sima de los Huesos in the Sierra de Atapuerca in Spain, has recently been dated to approximately 430,000 years ago. An interesting question is how these Middle Pleistocene hominins were related to those who lived in the Late Pleistocene epoch, in particular to Neanderthals in western Eurasia and to Denisovans, a sister group of Neanderthals so far known only from southern Siberia. While the Sima de los Huesos hominins share some derived morphological features with Neanderthals, the mitochondrial genome retrieved from one individual from Sima de los Huesos is more closely related to the mitochondrial DNA of Denisovans than to that of Neanderthals...
March 24, 2016: Nature
Silvia Ghirotto, Francesca Tassi, Guido Barbujani, Linda Pattini, Caroline Hayward, Peter Vollenweider, Murielle Bochud, Luca Rampoldi, Olivier Devuyst
Common variants in the UMOD gene encoding uromodulin, associated with risk of hypertension and CKD in the general population, increase UMOD expression and urinary excretion of uromodulin, causing salt-sensitive hypertension and renal lesions. To determine the effect of selective pressure on variant frequency, we investigated the allelic frequency of the lead UMOD variant rs4293393 in 156 human populations, in eight ancient human genomes, and in primate genomes. The T allele of rs4293393, associated with CKD risk, has high frequency in most modern populations and was the one detected in primate genomes...
March 10, 2016: Journal of the American Society of Nephrology: JASN
Alessandra Mozzi, Diego Forni, Mario Clerici, Uberto Pozzoli, Sara Mascheretti, Franca R Guerini, Stefania Riva, Nereo Bresolin, Rachele Cagliani, Manuela Sironi
Humans possess a communication system based on spoken and written language. Other animals can learn vocalization by imitation, but this is not equivalent to human language. Many genes were described to be implicated in language impairment (LI) and developmental dyslexia (DD), but their evolutionary history has not been thoroughly analyzed. Herein we analyzed the evolution of ten genes involved in DD and LI. Results show that the evolutionary history of LI genes for mammals and aves was comparable in vocal-learner species and non-learners...
2016: Scientific Reports
PingHsun Hsieh, August E Woerner, Jeffrey D Wall, Joseph Lachance, Sarah A Tishkoff, Ryan N Gutenkunst, Michael F Hammer
Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in Eurasia. Within Africa, fossil evidence suggests that anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr; however, the absence of ancient DNA in Africa has limited our ability to make a direct comparison between archaic and modern human genomes...
March 2016: Genome Research
Martin Kuhlwilm, Ilan Gronau, Melissa J Hubisz, Cesare de Filippo, Javier Prado-Martinez, Martin Kircher, Qiaomei Fu, Hernán A Burbano, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Pavao Rudan, Dejana Brajkovic, Željko Kucan, Ivan Gušic, Tomas Marques-Bonet, Aida M Andrés, Bence Viola, Svante Pääbo, Matthias Meyer, Adam Siepel, Sergi Castellano
It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000-65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals...
February 25, 2016: Nature
Virginia Savova, Sung Chun, Mashaal Sohail, Ruth B McCole, Robert Witwicki, Lisa Gai, Tobias L Lenz, C-ting Wu, Shamil R Sunyaev, Alexander A Gimelbrant
An unexpectedly large number of human autosomal genes are subject to monoallelic expression (MAE). Our analysis of 4,227 such genes uncovers surprisingly high genetic variation across human populations. This increased diversity is unlikely to reflect relaxed purifying selection. Remarkably, MAE genes exhibit an elevated recombination rate and an increased density of hypermutable sequence contexts. However, these factors do not fully account for the increased diversity. We find that the elevated nucleotide diversity of MAE genes is also associated with greater allelic age: variants in these genes tend to be older and are enriched in polymorphisms shared by Neanderthals and chimpanzees...
March 2016: Nature Genetics
Saurabh Srinivasan, Francesco Bettella, Morten Mattingsdal, Yunpeng Wang, Aree Witoelar, Andrew J Schork, Wesley K Thompson, Verena Zuber, Bendik S Winsvold, John-Anker Zwart, David A Collier, Rahul S Desikan, Ingrid Melle, Thomas Werge, Anders M Dale, Srdjan Djurovic, Ole A Andreassen
BACKGROUND: Why schizophrenia has accompanied humans throughout our history despite its negative effect on fitness remains an evolutionary enigma. It is proposed that schizophrenia is a by-product of the complex evolution of the human brain and a compromise for humans' language, creative thinking, and cognitive abilities. METHODS: We analyzed recent large genome-wide association studies of schizophrenia and a range of other human phenotypes (anthropometric measures, cardiovascular disease risk factors, immune-mediated diseases) using a statistical framework that draws on polygenic architecture and ancillary information on genetic variants...
August 15, 2016: Biological Psychiatry
Aleksandar M Mikić
Ancient DNA (aDNA) is any DNA extracted from ancient specimens, important for diverse evolutionary researches. The major obstacles in aDNA studies are mutations, contamination and fragmentation. Its studies may be crucial for crop history if integrated with human aDNA research and historical linguistics, both general and relating to agriculture. Legumes (Fabaceae) are one of the richest end economically most important plant families, not only from Neolithic onwards, since they were used as food by Neanderthals and Paleolithic modern man...
2015: Frontiers in Plant Science
Maurizio Serva
We propose and solve a stochastic mathematical model of general applicability to interbreeding populations which share the same habitat. Resources are limited so that the total population size is fixed by environmental factors. Interbreeding occurs during all the time of coexistence until one of the two population disappears by a random fluctuation. None of the two populations has a selective advantage. We answer the following questions: How long the two populations coexist and how genetically similar they become before the extinction of one of the two? how much the genetic makeup of the surviving population changes by the contribution of the disappearing one? what it is the number of interbreeding events given the observed introgression of genetic material? The model was originally motivated by a paleoanthropological problem concerning the interbreeding of Neanderthals and African modern humans in Middle East which is responsible for the fraction of Neanderthal genes (1-4%) in present Eurasian population...
December 2015: Bulletin of Mathematical Biology
Rebekah L Rogers
Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure that occurred recently in human evolution. Hundreds of rearrangements indicate genomic trafficking between the sex chromosomes and autosomes, raising the possibility of sex-specific changes. Additionally, genes adjacent to genome structure changes in Neanderthals are associated with testis-specific expression, consistent with evolutionary theory that new genes commonly form with expression in the testes...
December 2015: Molecular Biology and Evolution
Ya Hu, Qiliang Ding, Yungang He, Shuhua Xu, Li Jin
In this study, we present an analysis of Neanderthal introgression at the dipeptidase 1 gene, DPEP1. A Neanderthal origin for the putative introgressive haplotypes was demonstrated using an established three-step approach. This introgression was under positive natural selection, reached a frequency of >50%, and introduced a homocysteine level- and pigmentation-associated allele (rs460879-T) into East Asians. However, the same allele was also found in non-East Asians, but not from Neanderthal introgression...
December 2015: Molecular Biology and Evolution
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