keyword
MENU ▼
Read by QxMD icon Read
search

neandertal genome

keyword
https://www.readbyqxmd.com/read/27768888/genetic-adaptation-and-neandertal-admixture-shaped-the-immune-system-of-human-populations
#1
Hélène Quach, Maxime Rotival, Julien Pothlichet, Yong-Hwee Eddie Loh, Michael Dannemann, Nora Zidane, Guillaume Laval, Etienne Patin, Christine Harmant, Marie Lopez, Matthieu Deschamps, Nadia Naffakh, Darragh Duffy, Anja Coen, Geert Leroux-Roels, Frederic Clément, Anne Boland, Jean-François Deleuze, Janet Kelso, Matthew L Albert, Lluis Quintana-Murci
Humans differ in the outcome that follows exposure to life-threatening pathogens, yet the extent of population differences in immune responses and their genetic and evolutionary determinants remain undefined. Here, we characterized, using RNA sequencing, the transcriptional response of primary monocytes from Africans and Europeans to bacterial and viral stimuli-ligands activating Toll-like receptor pathways (TLR1/2, TLR4, and TLR7/8) and influenza virus-and mapped expression quantitative trait loci (eQTLs)...
October 20, 2016: Cell
https://www.readbyqxmd.com/read/27708712/one-pedigree-we-all-may-have-come-from-did-adam-and-eve-have-the-chromosome-2-fusion
#2
Paweł Stankiewicz
BACKGROUND: In contrast to Great Apes, who have 48 chromosomes, modern humans and likely Neandertals and Denisovans have and had, respectively, 46 chromosomes. The reduction in chromosome number was caused by the head-to-head fusion of two ancestral chromosomes to form human chromosome 2 (HSA2) and may have contributed to the reproductive barrier with Great Apes. RESULTS: Next generation sequencing and molecular clock analyses estimated that this fusion arose prior to our last common ancestor with Neandertal and Denisovan hominins ~ 0...
2016: Molecular Cytogenetics
https://www.readbyqxmd.com/read/27486223/divergent-ah-receptor-ligand-selectivity-during-hominin-evolution
#3
Troy D Hubbard, Iain A Murray, William H Bisson, Alexis P Sullivan, Aswathy Sebastian, George H Perry, Nina G Jablonski, Gary H Perdew
We have identified a fixed nonsynonymous sequence difference between humans (Val381; derived variant) and Neandertals (Ala381; ancestral variant) in the ligand-binding domain of the aryl hydrocarbon receptor (AHR) gene. In an exome sequence analysis of four Neandertal and Denisovan individuals compared with nine modern humans, there are only 90 total nucleotide sites genome-wide for which archaic hominins are fixed for the ancestral nonsynonymous variant and the modern humans are fixed for the derived variant...
October 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27423248/chromosome-specific-centromere-sequences-provide-an-estimate-of-the-ancestral-chromosome-2-fusion-event-in-hominin-genomes
#4
Karen H Miga
Human chromosome 2 is a product of a telomere fusion of two ancestral chromosomes and loss/degeneration of one of the two original centromeres. Genomic signatures of this event are limited to inverted telomeric repeats at the precise site of chromosomal fusion and to the small amount of relic centromeric sequences that remain on 2q21.2. Unlike the site of fusion, which is enriched for sequences that are shared elsewhere in the human genome, the region of the nonfunctioning and degenerate ancestral centromere appears to share limited similarity with other sites in the human genome, thereby providing an opportunity to study this genomic arrangement in short, fragmented ancient DNA genomic datasets...
July 16, 2016: Journal of Heredity
https://www.readbyqxmd.com/read/27058445/the-divergence-of-neandertal-and-modern-human-y-chromosomes
#5
Fernando L Mendez, G David Poznik, Sergi Castellano, Carlos D Bustamante
Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes-including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447-806 kya)...
April 7, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/26989198/excavating-neandertal-and-denisovan-dna-from-the-genomes-of-melanesian-individuals
#6
Benjamin Vernot, Serena Tucci, Janet Kelso, Joshua G Schraiber, Aaron B Wolf, Rachel M Gittelman, Michael Dannemann, Steffi Grote, Rajiv C McCoy, Heather Norton, Laura B Scheinfeldt, David A Merriwether, George Koki, Jonathan S Friedlaender, Jon Wakefield, Svante Pääbo, Joshua M Akey
Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown Island Melanesian genomes. In aggregate, we recovered 1.34 gigabases and 303 megabases of the Neandertal and Denisovan genome, respectively...
April 8, 2016: Science
https://www.readbyqxmd.com/read/26979798/genetic-evidence-of-human-adaptation-to-a-cooked-diet
#7
Rachel N Carmody, Michael Dannemann, Adrian W Briggs, Birgit Nickel, Emily E Groopman, Richard W Wrangham, Janet Kelso
Humans have been argued to be biologically adapted to a cooked diet, but this hypothesis has not been tested at the molecular level. Here, we combine controlled feeding experiments in mice with comparative primate genomics to show that consumption of a cooked diet influences gene expression and that affected genes bear signals of positive selection in the human lineage. Liver gene expression profiles in mice fed standardized diets of meat or tuber were affected by food type and cooking, but not by caloric intake or consumer energy balance...
April 13, 2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/26937625/ancient-hybridization-and-genomic-stabilization-in-a-swordtail-fish
#8
Molly Schumer, Rongfeng Cui, Daniel L Powell, Gil G Rosenthal, Peter Andolfatto
A rapidly increasing body of work is revealing that the genomes of distinct species often exhibit hybrid ancestry, presumably due to postspeciation hybridization between closely related species. Despite the growing number of documented cases, we still know relatively little about how genomes evolve and stabilize following hybridization, and to what extent hybridization is functionally relevant. Here, we examine the case of Xiphophorus nezahualcoyotl, a teleost fish whose genome exhibits significant hybrid ancestry...
June 2016: Molecular Ecology
https://www.readbyqxmd.com/read/26912863/the-phenotypic-legacy-of-admixture-between-modern-humans-and-neandertals
#9
Corinne N Simonti, Benjamin Vernot, Lisa Bastarache, Erwin Bottinger, David S Carrell, Rex L Chisholm, David R Crosslin, Scott J Hebbring, Gail P Jarvik, Iftikhar J Kullo, Rongling Li, Jyotishman Pathak, Marylyn D Ritchie, Dan M Roden, Shefali S Verma, Gerard Tromp, Jeffrey D Prato, William S Bush, Joshua M Akey, Joshua C Denny, John A Capra
Many modern human genomes retain DNA inherited from interbreeding with archaic hominins, such as Neandertals, yet the influence of this admixture on human traits is largely unknown. We analyzed the contribution of common Neandertal variants to over 1000 electronic health record (EHR)-derived phenotypes in ~28,000 adults of European ancestry. We discovered and replicated associations of Neandertal alleles with neurological, psychiatric, immunological, and dermatological phenotypes. Neandertal alleles together explained a significant fraction of the variation in risk for depression and skin lesions resulting from sun exposure (actinic keratosis), and individual Neandertal alleles were significantly associated with specific human phenotypes, including hypercoagulation and tobacco use...
February 12, 2016: Science
https://www.readbyqxmd.com/read/26885854/tlrs-of-our-fathers
#10
COMMENT
Mihai G Netea, Leo A B Joosten
Two new studies published in The American Journal of Human Genetics (Dannemann et al., 2016; Deschamps et al., 2016) show that introgression of innate immune genes from Neandertals and Denisovans contributed to the modern genome of European and Asian, but not African, populations, and this might partly explain differences in susceptibility to immune-mediated diseases.
February 16, 2016: Immunity
https://www.readbyqxmd.com/read/26852813/virtual-ancestor-reconstruction-revealing-the-ancestor-of-modern-humans-and-neandertals
#11
Aurélien Mounier, Marta Mirazón Lahr
The timing and geographic origin of the common ancestor of modern humans and Neandertals remain controversial. A poor Pleistocene hominin fossil record and the evolutionary complexities introduced by dispersals and regionalisation of lineages have fuelled taxonomic uncertainty, while new ancient genomic data have raised completely new questions. Here, we use maximum likelihood and 3D geometric morphometric methods to predict possible morphologies of the last common ancestor of modern humans and Neandertals from a simplified, fully resolved phylogeny...
February 2016: Journal of Human Evolution
https://www.readbyqxmd.com/read/26849112/a-burden-of-rare-variants-associated-with-extremes-of-gene-expression-in-human-peripheral-blood
#12
Jing Zhao, Idowu Akinsanmi, Dalia Arafat, T J Cradick, Ciaran M Lee, Samridhi Banskota, Urko M Marigorta, Gang Bao, Greg Gibson
In order to evaluate whether rare regulatory variants in the vicinity of promoters are likely to impact gene expression, we conducted a novel burden test for enrichment of rare variants at the extremes of expression. After sequencing 2-kb promoter regions of 472 genes in 410 healthy adults, we performed a quadratic regression of rare variant count on bins of peripheral blood transcript abundance from microarrays, summing over ranks of all genes. After adjusting for common eQTLs and the major axes of gene expression covariance, a highly significant excess of variants with minor allele frequency less than 0...
February 4, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/26819241/mapping-the-genomic-architecture-of-adaptive-traits-with-interspecific-introgressive-origin-a-coalescent-based-approach
#13
Hussein A Hejase, Kevin J Liu
Recent studies of eukaryotes including human and Neandertal, mice, and butterflies have highlighted the major role that interspecific introgression has played in adaptive trait evolution. A common question arises in each case: what is the genomic architecture of the introgressed traits? One common approach that can be used to address this question is association mapping, which looks for genotypic markers that have significant statistical association with a trait. It is well understood that sample relatedness can be a confounding factor in association mapping studies if not properly accounted for...
2016: BMC Genomics
https://www.readbyqxmd.com/read/26791510/analysis-of-ancient-dna-in-microbial-ecology
#14
Olivier Gorgé, E Andrew Bennett, Diyendo Massilani, Julien Daligault, Melanie Pruvost, 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 the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as Neandertals and Denisovans. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes allows the study of their recent evolution, presently over the last several millennia...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/26630009/nuclear-and-mitochondrial-dna-sequences-from-two-denisovan-individuals
#15
Susanna Sawyer, Gabriel Renaud, Bence Viola, Jean-Jacques Hublin, Marie-Theres Gansauge, Michael V Shunkov, Anatoly P Derevianko, Kay Prüfer, Janet Kelso, Svante Pääbo
Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010...
December 22, 2015: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/26072518/global-survey-of-variation-in-a-human-olfactory-receptor-gene-reveals-signatures-of-non-neutral-evolution
#16
Kara C Hoover, Omer Gokcumen, Zoya Qureshy, Elise Bruguera, Aulaphan Savangsuksa, Matthew Cobb, Hiroaki Matsunami
Allelic variation at 4 loci in the human olfactory receptor gene OR7D4 is associated with perceptual variation in the sex steroid-derived odorants, androstenone, and androstadienone. Androstadienone has been linked with chemosensory identification whereas androstenone makes pork from uncastrated pigs distasteful ("boar taint"). In a sample of 2224 individuals from 43 populations, we identified 45 OR7D4 single nucleotide polymorphisms. Coalescent modeling of frequency-site-spectrum-based statistics identified significant deviation from neutrality in human OR7D4; individual populations with statistically significant deviations from neutrality include Gujarati, Beijing Han, Great Britain, Iberia, and Puerto Rico...
September 2015: Chemical Senses
https://www.readbyqxmd.com/read/25908660/archaeology-the-makers-of-the-protoaurignacian-and-implications-for-neandertal-extinction
#17
S Benazzi, V Slon, S Talamo, F Negrino, M Peresani, S E Bailey, S Sawyer, D Panetta, G Vicino, E Starnini, M A Mannino, P A Salvadori, M Meyer, S Pääbo, J-J Hublin
The Protoaurignacian culture is pivotal to the debate about the timing of the arrival of modern humans in western Europe and the demise of Neandertals. However, which group is responsible for this culture remains uncertain. We investigated dental remains associated with the Protoaurignacian. The lower deciduous incisor from Riparo Bombrini is modern human, based on its morphology. The upper deciduous incisor from Grotta di Fumane contains ancient mitochondrial DNA of a modern human type. These teeth are the oldest human remains in an Aurignacian-related archaeological context, confirming that by 41,000 calendar years before the present, modern humans bearing Protoaurignacian culture spread into southern Europe...
May 15, 2015: Science
https://www.readbyqxmd.com/read/25683122/selection-and-reduced-population-size-cannot-explain-higher-amounts-of-neandertal-ancestry-in-east-asian-than-in-european-human-populations
#18
Bernard Y Kim, Kirk E Lohmueller
It has been hypothesized that the greater proportion of Neandertal ancestry in East Asians than in Europeans is due to the fact that purifying selection is less effective at removing weakly deleterious Neandertal alleles from East Asian populations. Using simulations of a broad range of models of selection and demography, we have shown that this hypothesis cannot account for the higher proportion of Neandertal ancestry in East Asians than in Europeans. Instead, more complex demographic scenarios, most likely involving multiple pulses of Neandertal admixture, are required to explain the data...
March 5, 2015: American Journal of Human Genetics
https://www.readbyqxmd.com/read/25683119/complex-history-of-admixture-between-modern-humans-and-neandertals
#19
Benjamin Vernot, Joshua M Akey
Recent analyses have found that a substantial amount of the Neandertal genome persists in the genomes of contemporary non-African individuals. East Asians have, on average, higher levels of Neandertal ancestry than do Europeans, which might be due to differences in the efficiency of purifying selection, an additional pulse of introgression into East Asians, or other unexplored scenarios. To better define the scope of plausible models of archaic admixture between Neandertals and anatomically modern humans, we analyzed patterns of introgressed sequence in whole-genome data of 379 Europeans and 286 East Asians...
March 5, 2015: American Journal of Human Genetics
https://www.readbyqxmd.com/read/25563409/insights-into-hominin-phenotypic-and-dietary-evolution-from-ancient-dna-sequence-data
#20
George H Perry, Logan Kistler, Mary A Kelaita, Aaron J Sams
Nuclear genome sequence data from Neandertals, Denisovans, and archaic anatomically modern humans can be used to complement our understanding of hominin evolutionary biology and ecology through i) direct inference of archaic hominin phenotypes, ii) indirect inference of those phenotypes by identifying the effects of previously-introgressed alleles still present among modern humans, or iii) determining the evolutionary timing of relevant hominin-specific genetic changes. Here we review and reanalyze published Neandertal and Denisovan genome sequence data to illustrate an example of the third approach...
February 2015: Journal of Human Evolution
keyword
keyword
84173
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"