keyword
https://read.qxmd.com/read/31975170/inference-of-ancestral-recombination-graphs-using-argweaver
#21
JOURNAL ARTICLE
Melissa Hubisz, Adam Siepel
This chapter describes the usage of the program ARGweaver, which estimates the ancestral recombination graph for as many as about 100 genome sequences. The ancestral recombination graph is a detailed description of the coalescence and recombination events that define the relationships among the sampled sequences. This rich description is useful for a wide variety of population genetic analyses. We describe the preparation of data and major considerations for running ARGweaver, as well as the interpretation of results...
2020: Methods in Molecular Biology
https://read.qxmd.com/read/30721683/brain-evolution-mapping-the-inner-neandertal
#22
COMMENT
Chet C Sherwood, Brenda J Bradley
Human populations that migrated out of Africa interbred with Neandertals. A new study assesses the effects of Neandertal gene variants on brain shape in modern humans, providing insights into the genomic basis of the uniquely globular human brain.
February 4, 2019: Current Biology: CB
https://read.qxmd.com/read/30647110/limits-of-long-term-selection-against-neandertal-introgression
#23
JOURNAL ARTICLE
Martin Petr, Svante Pääbo, Janet Kelso, Benjamin Vernot
Several studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45,000 years. Here, we show that this decline is an artifact likely caused by gene flow between modern human populations, which is not taken into account by statistics previously used to estimate Neandertal ancestry. When we apply a statistic that avoids assumptions about modern human demography by taking advantage of two high-coverage Neandertal genomes, we find no evidence for a change in Neandertal ancestry in Europe over the past 45,000 years...
January 29, 2019: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/30566634/immune-gene-diversity-in-archaic-and-present-day-humans
#24
COMPARATIVE STUDY
David Reher, Felix M Key, Aida M Andrés, Janet Kelso
Genome-wide analyses of two Neandertals and a Denisovan have shown that these archaic humans had lower genetic heterozygosity than present-day people. A similar reduction in genetic diversity of protein-coding genes (gene diversity) was found in exome sequences of three Neandertals. Reduced gene diversity, particularly in genes involved in immunity, may have important functional consequences. In fact, it has been suggested that reduced diversity in immune genes may have contributed to Neandertal extinction...
January 1, 2019: Genome Biology and Evolution
https://read.qxmd.com/read/30554901/neandertal-introgression-sheds-light-on-modern-human-endocranial-globularity
#25
JOURNAL ARTICLE
Philipp Gunz, Amanda K Tilot, Katharina Wittfeld, Alexander Teumer, Chin Yang Shapland, Theo G M van Erp, Michael Dannemann, Benjamin Vernot, Simon Neubauer, Tulio Guadalupe, Guillén Fernández, Han G Brunner, Wolfgang Enard, James Fallon, Norbert Hosten, Uwe Völker, Antonio Profico, Fabio Di Vincenzo, Giorgio Manzi, Janet Kelso, Beate St Pourcain, Jean-Jacques Hublin, Barbara Franke, Svante Pääbo, Fabio Macciardi, Hans J Grabe, Simon E Fisher
One of the features that distinguishes modern humans from our extinct relatives and ancestors is a globular shape of the braincase [1-4]. As the endocranium closely mirrors the outer shape of the brain, these differences might reflect altered neural architecture [4, 5]. However, in the absence of fossil brain tissue, the underlying neuroanatomical changes as well as their genetic bases remain elusive. To better understand the biological foundations of modern human endocranial shape, we turn to our closest extinct relatives: the Neandertals...
January 7, 2019: Current Biology: CB
https://read.qxmd.com/read/30278065/intragenus-homo-variation-in-a-chemokine-receptor-gene-ccr5
#26
JOURNAL ARTICLE
Kara C Hoover
Humans have a comparatively higher rate of more polymorphisms in regulatory regions of the primate CCR5 gene, an immune system gene with both general and specific functions. This has been interpreted as allowing flexibility and diversity of gene expression in response to varying disease loads. A broad expression repertoire is useful to humans-the only globally distributed primate-due to our unique adaptive pattern that increased pathogen exposure and disease loads (e.g., sedentism, subsistence practices). The main objective of the study was to determine if the previously observed human pattern of increased variation extended to other members of our genus, Homo...
2018: PloS One
https://read.qxmd.com/read/29608725/homo-sapiens-specific-binding-site-variants-within-brain-exclusive-enhancers-are-subject-to-accelerated-divergence-across-human-population
#27
JOURNAL ARTICLE
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://read.qxmd.com/read/29188235/precise-dating-of-the-middle-to-upper-paleolithic-transition-in-murcia-spain-supports-late-neandertal-persistence-in-iberia
#28
JOURNAL ARTICLE
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://read.qxmd.com/read/28757862/proteogenomic-review-of-the-changes-in-primate-apoc-i-during-evolution
#29
JOURNAL ARTICLE
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://read.qxmd.com/read/28366169/functional-implications-of-neandertal-introgression-in-modern-humans
#30
JOURNAL ARTICLE
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://read.qxmd.com/read/28044971/-innate-immunity-and-human-diseases-from-archaic-introgression-to-natural-selection
#31
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://read.qxmd.com/read/27899133/adaptively-introgressed-neandertal-haplotype-at-the-oas-locus-functionally-impacts-innate-immune-responses-in-humans
#32
JOURNAL ARTICLE
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://read.qxmd.com/read/27768888/genetic-adaptation-and-neandertal-admixture-shaped-the-immune-system-of-human-populations
#33
JOURNAL ARTICLE
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://read.qxmd.com/read/27708712/one-pedigree-we-all-may-have-come-from-did-adam-and-eve-have-the-chromosome-2-fusion
#34
JOURNAL ARTICLE
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://read.qxmd.com/read/27558013/hla-class-i-variation-in-iranian-lur-and-kurd-populations-high-haplotype-and-allotype-diversity-with-an-abundance-of-kir-ligands
#35
JOURNAL ARTICLE
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://read.qxmd.com/read/27486223/divergent-ah-receptor-ligand-selectivity-during-hominin-evolution
#36
JOURNAL ARTICLE
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://read.qxmd.com/read/27195518/the-mitogenome-of-a-35-000-year-old-homo-sapiens-from-europe-supports-a-palaeolithic-back-migration-to-africa
#37
JOURNAL ARTICLE
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://read.qxmd.com/read/27058445/the-divergence-of-neandertal-and-modern-human-y-chromosomes
#38
JOURNAL ARTICLE
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://read.qxmd.com/read/26979798/genetic-evidence-of-human-adaptation-to-a-cooked-diet
#39
JOURNAL ARTICLE
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://read.qxmd.com/read/26912836/human-evolution-neandertal-genes-linked-to-modern-diseases
#40
COMMENT
Ann Gibbons
No abstract text is available yet for this article.
February 12, 2016: Science
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