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https://www.readbyqxmd.com/read/29603507/model-based-detection-and-analysis-of-introgressed-neanderthal-ancestry-in-modern-humans
#1
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
#2
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 21, 2018: Nature
https://www.readbyqxmd.com/read/29409727/ancestral-variations-of-the-pcdhg-gene-cluster-predispose-to-dyslexia-in-a-multiplex-family
#3
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...
January 9, 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
#4
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...
January 30, 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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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