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https://www.readbyqxmd.com/read/29914355/motifome-comparison-between-modern-human-neanderthal-and-denisovan
#1
Matyas F Cserhati, Mary-Ellen Mooter, Lauren Peterson, Benjamin Wicks, Peng Xiao, Mark Pauley, Chittibabu Guda
BACKGROUND: The availability of the genomes of two archaic humans, Neanderthal and Denisovan, and that of modern humans provides researchers an opportunity to investigate genetic differences between these three subspecies on a genome-wide scale. Here we describe an algorithm that predicts statistically significant motifs based on the difference between a given motif's actual and expected distributions. The algorithm was previously applied to plants but was modified for this work. RESULTS: The result of applying the algorithm to the human, Neanderthal, and Denisovan genomes is a catalog of potential regulatory motifs in these three human subspecies...
June 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29894925/something-old-something-borrowed-admixture-and-adaptation-in-human-evolution
#2
REVIEW
Michael Dannemann, Fernando Racimo
The sequencing of ancient DNA from archaic humans-Neanderthals and Denisovans-has revealed that modern and archaic humans interbred at least twice during the Pleistocene. The field of human paleogenomics has now turned its attention towards understanding the nature of this genetic legacy in the gene pool of present-day humans. What exactly did modern humans obtain from interbreeding with Neanderthals and Denisovans? Was the introgressed genetic material beneficial, neutral or maladaptive? Can differences in phenotypes among present-day human populations be explained by archaic human introgression? These questions are of prime importance for our understanding of recent human evolution, but will require careful computational modeling and extensive functional assays before they can be answered in full...
June 9, 2018: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/29747567/recently-evolved-human-specific-methylated-regions-are-enriched-in-schizophrenia-signals
#3
Niladri Banerjee, Tatiana Polushina, Francesco Bettella, Sudheer Giddaluru, Vidar M Steen, Ole A Andreassen, Stephanie Le Hellard
BACKGROUND: One explanation for the persistence of schizophrenia despite the reduced fertility of patients is that it is a by-product of recent human evolution. This hypothesis is supported by evidence suggesting that recently-evolved genomic regions in humans are involved in the genetic risk for schizophrenia. Using summary statistics from genome-wide association studies (GWAS) of schizophrenia and 11 other phenotypes, we tested for enrichment of association with GWAS traits in regions that have undergone methylation changes in the human lineage compared to Neanderthals and Denisovans, i...
May 11, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29739306/neanderthal-and-denisovan-ancestry-in-papuans-a-functional-study
#4
Evgeny E Akkuratov, Mikhail S Gelfand, Ekaterina E Khrameeva
Sequencing of complete nuclear genomes of Neanderthal and Denisovan stimulated studies about their relationship with modern humans demonstrating, in particular, that DNA alleles from both Neanderthal and Denisovan genomes are present in genomes of modern humans. The Papuan genome is a unique object because it contains both Neanderthal and Denisovan alleles. Here, we have shown that the Papuan genomes contain different gene functional groups inherited from each of the ancient people. The Papuan genomes demonstrate a relative prevalence of Neanderthal alleles in genes responsible for the regulation of transcription and neurogenesis...
April 2018: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29658973/searching-for-ancient-balanced-polymorphisms-shared-between-neanderthals-and-modern-humans
#5
Lucas Henriques Viscardi, Vanessa Rodrigues Paixão-Côrtes, David Comas, Francisco Mauro Salzano, Diego Rovaris, Claiton Dotto Bau, Carlos Eduardo G Amorim, Maria Cátira Bortolini
Hominin evolution is characterized by adaptive solutions often rooted in behavioral and cognitive changes. If balancing selection had an important and long-lasting impact on the evolution of these traits, it can be hypothesized that genes associated with them should carry an excess of shared polymorphisms (trans- SNPs) across recent Homo species. In this study, we investigate the role of balancing selection in human evolution using available exomes from modern (Homo sapiens) and archaic humans (H. neanderthalensis and Denisovan) for an excess of trans-SNP in two gene sets: one associated with the immune system (IMMS) and another one with behavioral system (BEHS)...
January 2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29603507/model-based-detection-and-analysis-of-introgressed-neanderthal-ancestry-in-modern-humans
#6
Matthias Steinrücken, Jeffrey P Spence, John A Kamm, Emilia Wieczorek, Yun S Song
Genetic evidence has revealed that the ancestors of modern human populations outside Africa and their hominin sister groups, notably Neanderthals, exchanged genetic material in the past. The distribution of these introgressed sequence tracts along modern-day human genomes provides insight into the selective forces acting on them and the role of introgression in the evolutionary history of hominins. Studying introgression patterns on the X-chromosome is of particular interest, as sex chromosomes are thought to play a special role in speciation...
March 30, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29562232/reconstructing-the-genetic-history-of-late-neanderthals
#7
Mateja Hajdinjak, Qiaomei Fu, Alexander Hübner, Martin Petr, Fabrizio Mafessoni, Steffi Grote, Pontus Skoglund, Vagheesh Narasimham, Hélène Rougier, Isabelle Crevecoeur, Patrick Semal, Marie Soressi, Sahra Talamo, Jean-Jacques Hublin, Ivan Gušić, Željko Kućan, Pavao Rudan, Liubov V Golovanova, Vladimir B Doronichev, Cosimo Posth, Johannes Krause, Petra Korlević, Sarah Nagel, Birgit Nickel, Montgomery Slatkin, Nick Patterson, David Reich, Kay Prüfer, Matthias Meyer, Svante Pääbo, Janet Kelso
Although it has previously been shown that Neanderthals contributed DNA to modern humans, not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared. Our ability to retrieve DNA from a larger number of Neanderthal individuals has been limited by poor preservation of endogenous DNA and contamination of Neanderthal skeletal remains by large amounts of microbial and present-day human DNA...
March 29, 2018: Nature
https://www.readbyqxmd.com/read/29409727/ancestral-variations-of-the-pcdhg-gene-cluster-predispose-to-dyslexia-in-a-multiplex-family
#8
Teesta Naskar, Mohammed Faruq, Priyajit Banerjee, Massarat Khan, Rashi Midha, Renu Kumari, Subhashree Devasenapathy, Bharat Prajapati, Sanghamitra Sengupta, Deepti Jain, Mitali Mukerji, Nandini Chatterjee Singh, Subrata Sinha
Dyslexia is a heritable neurodevelopmental disorder characterized by difficulties in reading and writing. In this study, we describe the identification of a set of 17 polymorphisms located across 1.9Mb region on chromosome 5q31.3, encompassing genes of the PCDHG cluster, TAF7, PCDH1 and ARHGAP26, dominantly inherited with dyslexia in a multi-incident family. Strikingly, the non-risk form of seven variations of the PCDHG cluster, are preponderant in the human lineage, while risk alleles are ancestral and conserved across Neanderthals to non-human primates...
February 2018: EBioMedicine
https://www.readbyqxmd.com/read/29383489/genomic-structure-of-the-native-inhabitants-of-peninsular-malaysia-and-north-borneo-suggests-complex-human-population-history-in-southeast-asia
#9
Chee-Wei Yew, Dongsheng Lu, Lian Deng, Lai-Ping Wong, Rick Twee-Hee Ong, Yan Lu, Xiaoji Wang, Yushimah Yunus, Farhang Aghakhanian, Siti Shuhada Mokhtar, Mohammad Zahirul Hoque, Christopher Lok-Yung Voo, Thuhairah Abdul Rahman, Jong Bhak, Maude E Phipps, Shuhua Xu, Yik-Ying Teo, Subbiah Vijay Kumar, Boon-Peng Hoh
Southeast Asia (SEA) is enriched with a complex history of peopling. Malaysia, which is located at the crossroads of SEA, has been recognized as one of the hubs for early human migration. To unravel the genomic complexity of the native inhabitants of Malaysia, we sequenced 12 samples from 3 indigenous populations from Peninsular Malaysia and 4 native populations from North Borneo to a high coverage of 28-37×. We showed that the Negritos from Peninsular Malaysia shared a common ancestor with the East Asians, but exhibited some level of gene flow from South Asia, while the North Borneo populations exhibited closer genetic affinity towards East Asians than the Malays...
February 2018: Human Genetics
https://www.readbyqxmd.com/read/29284020/health-status-by-gender-hair-color-and-eye-color-red-haired-women-are-the-most-divergent
#10
Peter Frost, Karel Kleisner, Jaroslav Flegr
Red hair is associated in women with pain sensitivity. This medical condition, and perhaps others, seems facilitated by the combination of being red-haired and female. We tested this hypothesis by questioning a large sample of Czech and Slovak respondents about the natural redness and darkness of their hair, their natural eye color, their physical and mental health (24 categories), and other personal attributes (height, weight, number of children, lifelong number of sexual partners, frequency of smoking). Red-haired women did worse than other women in ten health categories and better in only three, being particularly prone to colorectal, cervical, uterine, and ovarian cancer...
2017: PloS One
https://www.readbyqxmd.com/read/29234166/the-iicr-inverse-instantaneous-coalescence-rate-as-a-summary-of-genomic-diversity-insights-into-demographic-inference-and-model-choice
#11
Lounès Chikhi, Willy Rodríguez, Simona Grusea, Patrícia Santos, Simon Boitard, Olivier Mazet
Several inferential methods using genomic data have been proposed to quantify and date population size changes in the history of species. At the same time an increasing number of studies have shown that population structure can generate spurious signals of population size change. Recently, Mazet et al. (2016) introduced, for a sample size of two, a time-dependent parameter, which they called the IICR (inverse instantaneous coalescence rate). The IICR is equivalent to a population size in panmictic models, but not necessarily in structured models...
January 2018: Heredity
https://www.readbyqxmd.com/read/29165618/human-specific-mutations-and-positively-selected-sites-in-marco-confer-functional-changes
#12
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 domain as undergoing positive selection in humans...
February 1, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29040546/variation-and-functional-impact-of-neanderthal-ancestry-in-western-asia
#13
Recep Ozgur Taskent, Nursen 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 with other Eurasian populations. To better understand the genome-wide and phenotypic impact of Neanderthal introgression in the region, we sequenced whole genomes of nine 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...
December 1, 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
#14
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 their 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...
February 2018: Theoretical Population Biology
https://www.readbyqxmd.com/read/28902892/neanderthal-and-denisova-tooth-protein-variants-in-present-day-humans
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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