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https://www.readbyqxmd.com/read/29165618/human-specific-mutations-and-positively-selected-sites-in-marco-confer-functional-changes
#1
Kyle E Novakowski, Nicholas V L Yap, Charles Yin, Kaori Sakamoto, Bryan Heit, G Brian Golding, Dawn M E Bowdish
Macrophage Receptor with COllagenous structure (MARCO) is a class A scavenger receptor that binds, phagocytoses, and modifies inflammatory responses to bacterial pathogens. Multiple candidate gene approach studies have shown that polymorphisms in MARCO are associated with susceptibility or resistance to Mycobacterium tuberculosis infection, but how these variants alter function is not known. To complement candidate gene approach studies, we previously used phylogenetic analyses to identify a residue, glutamine 452 (Q452), within the ligand-binding Scavenger Receptor Cysteine Rich (SRCR) domain as undergoing positive selection in humans...
November 20, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29040546/variation-and-functional-impact-of-neanderthal-ancestry-in-western-asia
#2
Recep Ozgur Taskent, Duha Alioglu, Evrim Fer, Handan Melike Donertas, Mehmet Somel, Omer Gokcumen
Neanderthals contributed genetic material to modern humans via multiple admixture events. Initial admixture events presumably occurred in Western Asia shortly after humans migrated out-of-Africa. Despite being a focal point of admixture, earlier studies indicate lower Neanderthal introgression rates in some Western Asian populations as compared to other Eurasian populations. To better understand the genome-wide and phenotypic impact of Neanderthal introgression in the region, we sequenced whole genomes of 10 present-day Europeans, Africans, and the Western Asian Druze at high depth, and analyzed available whole genome data from various other populations, including 16 genomes from present-day Turkey...
October 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29032037/ecocultural-range-expansion-scenarios-for-the-replacement-or-assimilation-of-neanderthals-by-modern-humans
#3
Joe Yuichiro Wakano, William Gilpin, Seiji Kadowaki, Marcus W Feldman, Kenichi Aoki
Recent archaeological records no longer support a simple dichotomous characterization of the cultures/behaviors of Neanderthals and modern humans, but indicate much cultural/behavioral variability over time and space. Thus, in modeling the replacement or assimilation of Neanderthals by modern humans, it is of interest to consider cultural dynamics and its relation to demographic change. The ecocultural framework for the competition between hominid species allows their carrying capacities to depend on some measure of the levels of culture they possess...
October 12, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/28902892/neanderthal-and-denisova-tooth-protein-variants-in-present-day-humans
#4
Clément Zanolli, Mathilde Hourset, Rémi Esclassan, Catherine Mollereau
Environment parameters, diet and genetic factors interact to shape tooth morphostructure. In the human lineage, archaic and modern hominins show differences in dental traits, including enamel thickness, but variability also exists among living populations. Several polymorphisms, in particular in the non-collagenous extracellular matrix proteins of the tooth hard tissues, like enamelin, are involved in dental structure variation and defects and may be associated with dental disorders or susceptibility to caries...
2017: PloS One
https://www.readbyqxmd.com/read/28855259/the-mobile-element-locator-tool-melt-population-scale-mobile-element-discovery-and-biology
#5
Eugene J Gardner, Vincent K Lam, Daniel N Harris, Nelson T Chuang, Emma C Scott, W Stephen Pittard, Ryan E Mills, Scott E Devine
Mobile element insertions (MEIs) represent ∼25% of all structural variants in human genomes. Moreover, when they disrupt genes, MEIs can influence human traits and diseases. Therefore, MEIs should be fully discovered along with other forms of genetic variation in whole genome sequencing (WGS) projects involving population genetics, human diseases, and clinical genomics. Here, we describe the Mobile Element Locator Tool (MELT), which was developed as part of the 1000 Genomes Project to perform MEI discovery on a population scale...
November 2017: Genome Research
https://www.readbyqxmd.com/read/28854627/the-mitonuclear-dimension-of-neanderthal-and-denisovan-ancestry-in-modern-human-genomes
#6
Joel Sharbrough, Justin C Havird, Gregory R Noe, Jessica M Warren, Daniel B Sloan
Some human populations interbred with Neanderthals and Denisovans, resulting in substantial contributions to modern-human genomes. Therefore, it is now possible to use genomic data to investigate mechanisms that shaped historical gene flow between humans and our closest hominin relatives. More generally, in eukaryotes, mitonuclear interactions have been argued to play a disproportionate role in generating reproductive isolation. There is no evidence of mtDNA introgression into modern human populations, which means that all introgressed nuclear alleles from archaic hominins must function on a modern-human mitochondrial background...
June 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28794033/ancient-evolution-and-dispersion-of-human-papillomavirus-58-variants
#7
Zigui Chen, Wendy C S Ho, Siaw Shi Boon, Priscilla T Y Law, Martin C W Chan, Rob DeSalle, Robert D Burk, Paul K S Chan
Human papillomavirus 58 (HPV58) is found in 10 to 18% of cervical cancers in East Asia but is rather uncommon elsewhere. The distribution and oncogenic potential of HPV58 variants appear to be heterogeneous, since the E7 T20I/G63S variant is more prevalent in East Asia and confers a 7- to 9-fold-higher risk of cervical precancer and cancer. However, the underlying genomic mechanisms that explain the geographic and carcinogenic diversity of HPV58 variants are still poorly understood. In this study, we used a combination of phylogenetic analyses and bioinformatics to investigate the deep evolutionary history of HPV58 complete genome variants...
November 1, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28740249/neanderthal-derived-genetic-variation-shapes-modern-human-cranium-and-brain
#8
Michael D Gregory, J Shane Kippenhan, Daniel P Eisenberg, Philip D Kohn, Dwight Dickinson, Venkata S Mattay, Qiang Chen, Daniel R Weinberger, Ziad S Saad, Karen F Berman
Before their disappearance from the fossil record approximately 40,000 years ago, Neanderthals, the ancient hominin lineage most closely related to modern humans, interbred with ancestors of present-day humans. The legacy of this gene flow persists through Neanderthal-derived variants that survive in modern human DNA; however, the neural implications of this inheritance are uncertain. Here, using MRI in a large cohort of healthy individuals of European-descent, we show that the amount of Neanderthal-originating polymorphism carried in living humans is related to cranial and brain morphology...
July 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28738867/q-a-what-is-human-language-when-did-it-evolve-and-why-should-we-care
#9
Mark Pagel
Human language is unique among all forms of animal communication. It is unlikely that any other species, including our close genetic cousins the Neanderthals, ever had language, and so-called sign 'language' in Great Apes is nothing like human language. Language evolution shares many features with biological evolution, and this has made it useful for tracing recent human history and for studying how culture evolves among groups of people with related languages. A case can be made that language has played a more important role in our species' recent (circa last 200,000 years) evolution than have our genes...
July 24, 2017: BMC Biology
https://www.readbyqxmd.com/read/28733602/distinct-selective-forces-and-neanderthal-introgression-shaped-genetic-diversity-at-genes-involved-in-neurodevelopmental-disorders
#10
Alessandra Mozzi, Diego Forni, Rachele Cagliani, Uberto Pozzoli, Mario Clerici, Manuela Sironi
In addition to high intelligence, humans evolved specialized social-cognitive skills, which are specifically affected in children with autism spectrum disorder (ASD). Genes affected in ASD represent suitable candidates to study the evolution of human social cognition. We performed an evolutionary analysis on 68 genes associated to neurodevelopmental disorders; our data indicate that genetic diversity was shaped by distinct selective forces, including natural selection and introgression from archaic hominins...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28675384/deeply-divergent-archaic-mitochondrial-genome-provides-lower-time-boundary-for-african-gene-flow-into-neanderthals
#11
Cosimo Posth, Christoph Wißing, Keiko Kitagawa, Luca Pagani, Laura van Holstein, Fernando Racimo, Kurt Wehrberger, Nicholas J Conard, Claus Joachim Kind, Hervé Bocherens, Johannes Krause
Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. Nuclear DNA indicated Neanderthals as a sister group of Denisovans after diverging from modern humans. However, the closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. Here we report the complete mtDNA of an archaic femur from the Hohlenstein-Stadel (HST) cave in southwestern Germany...
July 4, 2017: Nature Communications
https://www.readbyqxmd.com/read/28464262/a-tale-of-agriculturalists-and-hunter-gatherers-exploring-the-thrifty-genotype-hypothesis-in-native-south-americans
#12
Guillermo Reales, Diego L Rovaris, Vanessa C Jacovas, Tábita Hünemeier, José R Sandoval, Alcibiades Salazar-Granara, Darío A Demarchi, Eduardo Tarazona-Santos, Aline B Felkl, Michele A Serafini, Francisco M Salzano, Rafael Bisso-Machado, David Comas, Vanessa R Paixão-Côrtes, Maria Cátira Bortolini
OBJECTIVES: To determine genetic differences between agriculturalist and hunter-gatherer southern Native American populations for selected metabolism-related markers and to test whether Neel's thrifty genotype hypothesis (TGH) could explain the genetic patterns observed in these populations. MATERIALS AND METHODS: 375 Native South American individuals from 17 populations were genotyped using six markers (APOE rs429358 and rs7412; APOA2 rs5082; CD36 rs3211883; TCF7L2 rs11196205; and IGF2BP2 rs11705701)...
July 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28447043/comparative-genomics-of-human-stem-cell-factor-scf
#13
Moein Dehbashi, Elahe Kamali, Sadeq Vallian
Stem cell factor (SCF) is a critical protein with key roles in the cell such as hematopoiesis, gametogenesis and melanogenesis. In the present study a comparative analysis on nucleotide sequences of SCF was performed in Humanoids using bioinformatics tools including NCBI-BLAST, MEGA6, and JBrowse. Our analysis of nucleotide sequences to find closely evolved organisms with high similarity by NCBI-BLAST tools and MEGA6 showed that human and Chimpanzee (Pan troglodytes) were placed into the same cluster. By using JBrowse, we found that SCF in Neanderthal had a single copy number similar to modern human and partly conserved nucleotide sequences...
March 2017: Molecular Biology Research Communications
https://www.readbyqxmd.com/read/28444387/meiotic-genes-are-enriched-in-regions-of-reduced-archaic-ancestry
#14
B Jégou, S Sankararaman, A D Rolland, D Reich, F Chalmel
About 1-6% of the genetic ancestry of modern humans today originates from admixture with archaic humans. It has recently been shown that autosomal genomic regions with a reduced proportion of Neanderthal and Denisovan ancestries (NA and DA) are significantly enriched in genes that are more expressed in testis than in other tissues. To determine whether a cellular segregation pattern would exist, we combined maps of archaic introgression with a cross-analysis of three transcriptomic datasets deciphering the transcriptional landscape of human gonadal cell types...
August 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28376731/ad-libs-inferring-ancestry-across-hybrid-genomes-using-low-coverage-sequence-data
#15
Nathan K Schaefer, Beth Shapiro, Richard E Green
BACKGROUND: Inferring the ancestry of each region of admixed individuals' genomes is useful in studies ranging from disease gene mapping to speciation genetics. Current methods require high-coverage genotype data and phased reference panels, and are therefore inappropriate for many data sets. We present a software application, AD-LIBS, that uses a hidden Markov model to infer ancestry across hybrid genomes without requiring variant calling or phasing. This approach is useful for non-model organisms and in cases of low-coverage data, such as ancient DNA...
April 4, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28351985/living-in-an-adaptive-world-genomic-dissection-of-the-genus-homo-and-its-immune-response
#16
REVIEW
Hélène Quach, Lluis Quintana-Murci
More than a decade after the sequencing of the human genome, a deluge of genome-wide population data are generating a portrait of human genetic diversity at an unprecedented level of resolution. Genomic studies have provided new insight into the demographic and adaptive history of our species, Homo sapiens, including its interbreeding with other hominins, such as Neanderthals, and the ways in which natural selection, in its various guises, has shaped genome diversity. These studies, combined with functional genomic approaches, such as the mapping of expression quantitative trait loci, have helped to identify genes, functions, and mechanisms of prime importance for host survival and involved in phenotypic variation and differences in disease risk...
April 3, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28348941/cutting-the-stone-health-defined-in-the-era-of-value-based-care
#17
REVIEW
Ger Rijkers
The immune system contributes to the maintenance of health by preventing and limiting the clinical consequences of infections by pathogenic microorganisms. During the evolution of Homo sapiens, those with the fittest immune system survived. The immune system of Homo sapiens was further improved and adapted by admixture with Neanderthal genes. Nowadays, the human immune system provides adequate protection against the majority of infections. For some 20 infectious diseases, the immune system needs to be improved by vaccination...
February 10, 2017: Curēus
https://www.readbyqxmd.com/read/28185859/association-of-irf5-polymorphisms-with-increased-risk-for-systemic-lupus-erythematosus-in-population-of-crete-a-southern-eastern-european-greek-island
#18
M I Zervou, J M Dorschner, Y Ghodke-Puranik, D T Boumpas, T B Niewold, G N Goulielmos
Interferon regulatory factor 5 (IRF5) regulates type I interferon (IFN)-responsive genes, and has been one of the most consistently associated genes with systemic lupus erythematosus (SLE). We sought to investigate whether IRF5 haplotypes are associated with risk for SLE in the genetically homogeneous Greek population of the island of Crete, as well as whether these haplotypes are associated with increased type I IFN. 322 SLE patients and 247 healthy controls from Crete were genotyped for rs2004640, rs3807306, rs10488631 and rs2280714 SNPs of IRF5 gene by using Taqman primer-probe sets...
April 30, 2017: Gene
https://www.readbyqxmd.com/read/27853181/selective-sweep-on-human-amylase-genes-postdates-the-split-with-neanderthals
#19
Charlotte E Inchley, Cynthia D A Larbey, Nzar A A Shwan, Luca Pagani, Lauri Saag, Tiago Antão, Guy Jacobs, Georgi Hudjashov, Ene Metspalu, Mario Mitt, Christina A Eichstaedt, Boris Malyarchuk, Miroslava Derenko, Joseph Wee, Syafiq Abdullah, François-Xavier Ricaut, Maru Mormina, Reedik Mägi, Richard Villems, Mait Metspalu, Martin K Jones, John A L Armour, Toomas Kivisild
Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy...
November 17, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27569548/ancestral-origins-and-genetic-history-of-tibetan-highlanders
#20
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
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