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Neandertal genes

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https://www.readbyqxmd.com/read/29608725/homo-sapiens-specific-binding-site-variants-within-brain-exclusive-enhancers-are-subject-to-accelerated-divergence-across-human-population
#1
Rabail Zehra, Amir Ali Abbasi
Empirical assessments of human accelerated noncoding DNA frgaments have delineated presence of many cis-regulatory elements. Enhancers make up an important category of such accelerated cis-regulatory elements that efficiently control the spatiotemporal expression of many developmental genes. Establishing plausible reasons for accelerated enhancer sequence divergence in Homo sapiens has been termed significant in various previously published studies. This acceleration by including closely related primates and archaic human data has the potential to open up evolutionary avenues for deducing present-day brain structure...
March 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29188235/precise-dating-of-the-middle-to-upper-paleolithic-transition-in-murcia-spain-supports-late-neandertal-persistence-in-iberia
#2
João Zilhão, Daniela Anesin, Thierry Aubry, Ernestina Badal, Dan Cabanes, Martin Kehl, Nicole Klasen, Armando Lucena, Ignacio Martín-Lerma, Susana Martínez, Henrique Matias, Davide Susini, Peter Steier, Eva Maria Wild, Diego E Angelucci, Valentín Villaverde, Josefina Zapata
The late persistence in Southern Iberia of a Neandertal-associated Middle Paleolithic is supported by the archeological stratigraphy and the radiocarbon and luminescence dating of three newly excavated localities in the Mula basin of Murcia (Spain). At Cueva Antón, Mousterian layer I-k can be no more than 37,100 years-old. At La Boja, the basal Aurignacian can be no less than 36,500 years-old. The regional Middle-to-Upper Paleolithic transition process is thereby bounded to the first half of the 37th millennium Before Present, in agreement with evidence from Andalusia, Gibraltar and Portugal...
November 2017: Heliyon
https://www.readbyqxmd.com/read/28757862/proteogenomic-review-of-the-changes-in-primate-apoc-i-during-evolution
#3
Donald Puppione, Julian P Whitelegge
Apolipoprotein C-I has evolved more rapidly than any of the other soluble apolipoproteins. During the course of primate evolution, the gene for this apolipoprotein was duplicated. Prompted by our observation that the two resulting genes encode two distinct forms of apoC-I in great apes, we have reviewed both the genomic and proteomic data to examine what changes have occurred during the course of primate evolution. We have found data showing that one of the duplicated genes, known to be a pseudogene in humans, was also a pseudogene in Denisovans and Neandertals...
October 2013: Frontiers in Biology
https://www.readbyqxmd.com/read/28366169/functional-implications-of-neandertal-introgression-in-modern-humans
#4
Michael Dannemann, Kay Prüfer, Janet Kelso
BACKGROUND: Admixture between early modern humans and Neandertals approximately 50,000-60,000 years ago has resulted in 1.5-4% Neandertal ancestry in the genomes of present-day non-Africans. Evidence is accumulating that some of these archaic alleles are advantageous for modern humans, while others are deleterious; however, the major mechanism by which these archaic alleles act has not been fully explored. RESULTS: Here we assess the contributions of introgressed non-synonymous and regulatory variants to modern human protein and gene expression variation...
April 3, 2017: Genome Biology
https://www.readbyqxmd.com/read/28044971/-innate-immunity-and-human-diseases-from-archaic-introgression-to-natural-selection
#5
REVIEW
Matthieu Deschamps, Lluís Quintana-Murci
Throughout evolution, humans have had to face strong variation in environmental conditions, with pathogens being among the strongest threats that our species has encountered. The use of population genetic approaches provides novel insights into how natural selection imposed by pathogen pressures, in its different forms and intensities, has shaped the patterns of diversity of the human genome at the population level. These studies help to distinguish genes playing essential, non-redundant functions in host defence from genes variation in which has conferred selective advantages to specific human populations and/or has been acquired through admixture with archaic hominins, such as Neandertals...
December 2016: Médecine Sciences: M/S
https://www.readbyqxmd.com/read/27899133/adaptively-introgressed-neandertal-haplotype-at-the-oas-locus-functionally-impacts-innate-immune-responses-in-humans
#6
Aaron J Sams, Anne Dumaine, Yohann Nédélec, Vania Yotova, Carolina Alfieri, Jerome E Tanner, Philipp W Messer, Luis B Barreiro
BACKGROUND: The 2'-5' oligoadenylate synthetase (OAS) locus encodes for three OAS enzymes (OAS1-3) involved in innate immune response. This region harbors high amounts of Neandertal ancestry in non-African populations; yet, strong evidence of positive selection in the OAS region is still lacking. RESULTS: Here we used a broad array of selection tests in concert with neutral coalescent simulations to demonstrate a signal of adaptive introgression at the OAS locus...
November 29, 2016: Genome Biology
https://www.readbyqxmd.com/read/27768888/genetic-adaptation-and-neandertal-admixture-shaped-the-immune-system-of-human-populations
#7
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
#8
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/27558013/hla-class-i-variation-in-iranian-lur-and-kurd-populations-high-haplotype-and-allotype-diversity-with-an-abundance-of-kir-ligands
#9
E Ashouri, P J Norman, L A Guethlein, A S Han, N Nemat-Gorgani, S J Norberg, A Ghaderi, P Parham
HLA-A, -B and -C alleles of 285 individuals, representing three Iranian Lur populations and one Iranian Kurd population were sequenced completely, yielding human leukocyte antigen (HLA) class I genotypes at high resolution and filling four fields of the official HLA nomenclature. Each population has 87-99 alleles, evenly distributed between the three HLA class I genes, 145 alleles being identified in total. These alleles were already known, named and deposited in the HLA database. The alleles form 316 different HLA A-B-C haplotypes, with each population having between 80 and 112 haplotypes...
September 2016: HLA
https://www.readbyqxmd.com/read/27486223/divergent-ah-receptor-ligand-selectivity-during-hominin-evolution
#10
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/27195518/the-mitogenome-of-a-35-000-year-old-homo-sapiens-from-europe-supports-a-palaeolithic-back-migration-to-africa
#11
M Hervella, E M Svensson, A Alberdi, T Günther, N Izagirre, A R Munters, S Alonso, M Ioana, F Ridiche, A Soficaru, M Jakobsson, M G Netea, C de-la-Rua
After the dispersal of modern humans (Homo sapiens) Out of Africa, hominins with a similar morphology to that of present-day humans initiated the gradual demographic expansion into Eurasia. The mitogenome (33-fold coverage) of the Peştera Muierii 1 individual (PM1) from Romania (35 ky cal BP) we present in this article corresponds fully to Homo sapiens, whilst exhibiting a mosaic of morphological features related to both modern humans and Neandertals. We have identified the PM1 mitogenome as a basal haplogroup U6*, not previously found in any ancient or present-day humans...
May 19, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27058445/the-divergence-of-neandertal-and-modern-human-y-chromosomes
#12
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/26979798/genetic-evidence-of-human-adaptation-to-a-cooked-diet
#13
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/26912836/human-evolution-neandertal-genes-linked-to-modern-diseases
#14
COMMENT
Ann Gibbons
No abstract text is available yet for this article.
February 12, 2016: Science
https://www.readbyqxmd.com/read/26885854/tlrs-of-our-fathers
#15
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/26849112/a-burden-of-rare-variants-associated-with-extremes-of-gene-expression-in-human-peripheral-blood
#16
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
#17
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...
January 11, 2016: BMC Genomics
https://www.readbyqxmd.com/read/26748514/introgression-of-neandertal-and-denisovan-like-haplotypes-contributes-to-adaptive-variation-in-human-toll-like-receptors
#18
Michael Dannemann, Aida M Andrés, Janet Kelso
Pathogens and the diseases they cause have been among the most important selective forces experienced by humans during their evolutionary history. Although adaptive alleles generally arise by mutation, introgression can also be a valuable source of beneficial alleles. Archaic humans, who lived in Europe and Western Asia for more than 200,000 years, were probably well adapted to this environment and its local pathogens. It is therefore conceivable that modern humans entering Europe and Western Asia who admixed with them obtained a substantial immune advantage from the introgression of archaic alleles...
January 7, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/26748513/genomic-signatures-of-selective-pressures-and-introgression-from-archaic-hominins-at-human-innate-immunity-genes
#19
Matthieu Deschamps, Guillaume Laval, Maud Fagny, Yuval Itan, Laurent Abel, Jean-Laurent Casanova, Etienne Patin, Lluis Quintana-Murci
Human genes governing innate immunity provide a valuable tool for the study of the selective pressure imposed by microorganisms on host genomes. A comprehensive, genome-wide study of how selective constraints and adaptations have driven the evolution of innate immunity genes is missing. Using full-genome sequence variation from the 1000 Genomes Project, we first show that innate immunity genes have globally evolved under stronger purifying selection than the remainder of protein-coding genes. We identify a gene set under the strongest selective constraints, mutations in which are likely to predispose individuals to life-threatening disease, as illustrated by STAT1 and TRAF3...
January 7, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/26454764/functional-analyses-of-transcription-factor-binding-sites-that-differ-between-present-day-and-archaic-humans
#20
Sven Weyer, Svante Pääbo
We analyze 25 previously identified transcription factor binding sites that carry DNA sequence changes that are present in all or nearly all present-day humans, yet occur in the ancestral state in Neandertals and Denisovans, the closest evolutionary relatives of humans. When the ancestral and derived forms of the transcription factor binding sites are tested using reporter constructs in 3 neuronal cell lines, the activity of 12 of the derived versions of transcription factor binding sites differ from the respective ancestral variants...
February 2016: Molecular Biology and Evolution
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