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Human evolutionary genetics

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https://www.readbyqxmd.com/read/29790964/evidence-of-evolutionary-history-and-selective-sweeps-in-the-genome-of-meishan-pig-reveals-its-genetic-and-phenotypic-characterization
#1
Pengju Zhao, Ying Yu, Wen Feng, Heng Du, Jian Yu, Huimin Kang, Xianrui Zheng, Zhiquan Wang, George E Liu, Catherine W Ernst, Xueqin Ran, Jiafu Wang, Jian-Feng Liu
Background: Meishan is a pig breed indigenous to China and famous for its high fecundity. The traits of Meishan are strongly associated with its distinct evolutionary history and domestication. However, the genomic evidence linking the domestication of Meishan pigs with the unique features are still poorly understood. The goal of this study is to investigate the genomic signatures and evolutionary evidence related to phenotypic traits of Meishan by large-scale sequencing. Results: We found the unique domestication of Meishan pigs happened at the Taihu Basin area between the Majiabang and the Liangzhu culture, during which 300 protein-coding genes have undergone positive selection...
May 22, 2018: GigaScience
https://www.readbyqxmd.com/read/29788909/whole-genome-analysis-reveals-the-diversity-and-evolutionary-relationships-between-necrotic-enteritis-causing-strains-of-clostridium-perfringens
#2
Jake A Lacey, Theodore R Allnutt, Ben Vezina, Thi Thu Hao Van, Thomas Stent, Xiaoyan Han, Julian I Rood, Ben Wade, Anthony L Keyburn, Torsten Seemann, Honglei Chen, Volker Haring, Priscilla A Johanesen, Dena Lyras, Robert J Moore
BACKGROUND: Clostridium perfringens causes a range of diseases in animals and humans including necrotic enteritis in chickens and food poisoning and gas gangrene in humans. Necrotic enteritis is of concern in commercial chicken production due to the cost of the implementation of infection control measures and to productivity losses. This study has focused on the genomic analysis of a range of chicken-derived C. perfringens isolates, from around the world and from different years. The genomes were sequenced and compared with 20 genomes available from public databases, which were from a diverse collection of isolates from chickens, other animals, and humans...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29788292/biological-processes-modulating-longevity-across-primates-a-phylogenetic-genome-phenome-analysis
#3
Gerard Muntané, Xavier Farré, Juan Antonio Rodríguez, Cinta Pegueroles, David A Hughes, João Pedro de Magalhães, Toni Gabaldón, Arcadi Navarro
Aging is a complex process affecting different species and individuals in different ways. Comparing genetic variation across species with their aging phenotypes will help understanding the molecular basis of aging and longevity. Although most studies on aging have so far focused on short-lived model organisms, recent comparisons of genomic, transcriptomic, and metabolomic data across lineages with different lifespans are unveiling molecular signatures associated with longevity. Here, we examine the relationship between genomic variation and maximum lifespan (MLS) across primate species...
May 21, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29787621/recent-evolution-of-the-human-skin-barrier
#4
REVIEW
Erin A Brettmann, Cristina de Guzman Strong
The skin is the first line of defense against the environment, with the epidermis as the outermost tissue providing much of the barrier function. Given its direct exposure to and encounters with the environment, the epidermis must evolve to provide an optimal barrier for the survival of an organism. Recent advances in genomics have identified a number of genes for the human skin barrier that have undergone evolutionary changes since humans diverged from chimpanzees. Here we highlight a selection of key and innovative genetic findings for skin barrier evolution in our divergence from our primate ancestors and among modern human populations...
May 22, 2018: Experimental Dermatology
https://www.readbyqxmd.com/read/29785944/-overview-of-the-genetic-control-of-horse-coat-color-patterns
#5
Ruo Yang Zhao, Yi Ping Zhao, Bei Li, Gerelchimeg Bou, Xin Zhuang Zhang, Togtokh Mongke, Tugeqin Bao, Shurenchimeg Gereliin, Tsimbai Gereltuuin, Chao Li, Dong Yi Bai, Mang Lai Dugarjaviin
Mammalian coat color is one of the first phenotypic changes resulting from positive selection by humans, and it serves important roles in genetic and evolutionary processes. Among them, horses show a broad variety of coat color patterns, based on which it is difficult to distinguish the real phenotypes, resulting in confused records in horse breed registration. Thus, research in the genetic mechanisms on the development of coat color patterns is significant in horse reproduction and breeding. With the recent establishment of genomics and sequencing technologies, there are significant advances in research in the genetics of horse coat colors, which demonstrate that special coat colors could be associated with certain diseases...
May 20, 2018: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/29784979/pervasive-introgression-facilitated-domestication-and-adaptation-in-the-bos-species-complex
#6
Dong-Dong Wu, Xiang-Dong Ding, Sheng Wang, Jan M Wójcik, Yi Zhang, Małgorzata Tokarska, Yan Li, Ming-Shan Wang, Omar Faruque, Rasmus Nielsen, Qin Zhang, Ya-Ping Zhang
Species of the Bos genus, including taurine cattle, zebu, gayal, gaur, banteng, yak, wisent and bison, have been domesticated at least four times and have been an important source of meat, milk and power for many human cultures. We sequence the genomes of gayal, gaur, banteng, wisent and bison, and provide population genomic sequencing of an additional 98 individuals. We use these data to determine the phylogeny and evolutionary history of these species and show that the threatened gayal is an independent species or subspecies...
May 21, 2018: Nature Ecology & Evolution
https://www.readbyqxmd.com/read/29784759/of-what-use-is-connectomics-a-personal-perspective-on-the-drosophila-connectome
#7
REVIEW
Ian A Meinertzhagen
The brain is a network of neurons and its biological output is behaviour. This is an exciting age, with a growing acknowledgement that the comprehensive compilation of synaptic circuits densely reconstructed in the brains of model species is now both technologically feasible and a scientifically enabling possibility in neurobiology, much as 30 years ago genomics was in molecular biology and genetics. Implemented by huge advances in electron microscope technology, especially focused ion beam-scanning electron microscope (FIB-SEM) milling (see Glossary), image capture and alignment, and computer-aided reconstruction of neuron morphologies, enormous progress has been made in the last decade in the detailed knowledge of the actual synaptic circuits formed by real neurons, in various brain regions of the fly Drosophila It is useful to distinguish synaptic pathways that are major, with 100 or more presynaptic contacts, from those that are minor, with fewer than about 10; most neurites are both presynaptic and postsynaptic, and all synaptic sites have multiple postsynaptic dendrites...
May 20, 2018: Journal of Experimental Biology
https://www.readbyqxmd.com/read/29782933/whole-genome-sequencing-and-analyses-identify-high-genetic-heterogeneity-and-diversity-of-rotavirus-genotype-p-6-strains-circulating-in-africa
#8
Martin M Nyaga, Yi Tan, Mapaseka L Seheri, Rebecca A Halpin, Asmik Akopov, Karla M Stucker, Nadia B Fedorova, Susmita Shrivastava, A Duncan Steele, Jason M Mwenda, Brett E Pickett, Suman R Das, M Jeffery Mphahlele
Rotavirus A (RVA) exhibits a wide genotype diversity globally. Little is known about the genetic composition of genotype P[6] from Africa. This study investigated possible evolutionary mechanisms leading to genetic diversity of genotype P[6] VP4 sequences. Phylogenetic analyses on 167 P[6] VP4 full-length sequences were conducted, which included six porcine-origin sequences. Of the 167 sequences, 57 were newly acquired through whole genome sequencing as part of this study. The other 110 sequences were all publicly-available global P[6] VP4 full-length sequences downloaded from GenBank...
May 18, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29782925/the-developmental-genetics-of-canalization
#9
REVIEW
Benedikt Hallgrimsson, Rebecca M Green, David Katz, Jennifer L Fish, Francois P J Bernier, Charles C Roseman, Nathan M Young, James M Cheverud, Ralph S Marcucio
Canalization, or robustness to genetic or environmental perturbations, is fundamental to complex organisms. While there is strong evidence for canalization as an evolved property that varies among genotypes, the developmental and genetic mechanisms that produce this phenomenon are very poorly understood. For evolutionary biology, understanding how canalization arises is important because, by modulating the phenotypic variation that arises in response to genetic differences, canalization is a determinant of evolvability...
May 18, 2018: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29781421/molecular-phylogeny-based-on-six-nuclear-genes-suggests-that-echinococcus-granulosus-sensu-lato-genotypes-g6-g7-and-g8-g10-can-be-regarded-as-two-distinct-species
#10
Teivi Laurimäe, Liina Kinkar, Epp Moks, Thomas Romig, Rihab A Omer, Adriano Casulli, Gérald Umhang, Guna Bagrade, Malik Irshadullah, Mitra Sharbatkhori, Hossein Mirhendi, Francisco Ponce-Gordo, Silvia V Soriano, Antonio Varcasia, Mohammad Rostami-Nejad, Vanessa Andresiuk, Urmas Saarma
Tapeworms of the species complex of Echinococcus granulosus sensu lato (s. l.) are the cause of a severe zoonotic disease - cystic echinococcosis, which is listed among the most severe parasitic diseases in humans and is prioritized by the World Health Organization. A stable taxonomy of E. granulosus s. l. is essential to the medical and veterinary communities for accurate and effective communication of the role of different species in this complex on human and animal health. E. granulosus s. l. displays high genetic diversity and has been divided into different species and genotypes...
May 21, 2018: Parasitology
https://www.readbyqxmd.com/read/29778197/genetic-analysis-and-biological-characteristics-of-different-internal-gene-origin-h5n6-reassortment-avian-influenza-virus-in-china-in-2016
#11
Wenqiang Sun, Jiaxin Li, Jiao Hu, Daxiu Jiang, Chaonan Xing, Tiansong Zhan, Xiufan Liu
Clade 2.3.4.4 of H5N6 subtype Avian Influenza Viruses (AIVs) has become dominant clade in South-East Asia. So far, a total of 16 cases of human infection, including 6 deaths, have been confirmed since 2014. In this study, we systematically investigated the genetic evolution and biological characteristics of these viruses. We first carried out phylogenetic and statistical analysis of all H5N6 viruses that were downloaded from Influenza Research Database, GISAID and isolates from our lab. We found that H5N6 AIVs continued to reassort with other AIVs subtypes since 2014...
June 2018: Veterinary Microbiology
https://www.readbyqxmd.com/read/29776375/range-wide-genetic-analysis-of-dermacentor-variabilis-and-its-francisella-like-endosymbionts-demonstrates-phylogeographic-concordance-between-both-taxa
#12
Emily L Kaufman, Nathan E Stone, Glen A Scoles, Crystal M Hepp, Joseph D Busch, David M Wagner
BACKGROUND: The American dog tick, Dermacentor variabilis, is an important vector of pathogens to humans, wildlife and domestic animals in North America. Although this tick species is widely distributed in the USA and Canada, knowledge of its range-wide phylogeographic patterns remains incomplete. METHODS: We carried out a phylogenetic analysis of D. variabilis using samples collected from 26 USA states and five Canadian provinces. Tick samples (n = 1053 in total) originated from two main sources: existing archives (2000-2011), and new collections made from 2012 to 2013...
May 18, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29774232/multiple-origins-of-green-blood-in-new-guinea-lizards
#13
Zachary B Rodriguez, Susan L Perkins, Christopher C Austin
Several species of lizards from the megadiverse island of New Guinea have evolved green blood. An unusually high concentration of the green bile pigment biliverdin in the circulatory system of these lizards makes the blood, muscles, bones, tongue, and mucosal tissues bright green in color, eclipsing the crimson color from their red blood cells. This is a remarkable physiological feature because bile pigments are toxic physiological waste products of red blood cell catabolism and, when chronically elevated, cause jaundice in humans and all other vertebrates...
May 2018: Science Advances
https://www.readbyqxmd.com/read/29770663/-in-silico-cloning-and-comparative-analysis-of-nad1-gene-in-three-common-human-parasites
#14
Xie Jian, Zhao Yong-Xia, Yang Ming-Li, Zhang Zhi-Min, Jia Qi
OBJECTIVE: To in silico clone the NAD1 gene of three common parasites and analyze their bioinformatics, so as to lay the foundation for further research on the NAD gene. METHODS: By using the in silico cloning method, the full length cDNA (s) of NAD 1 genes of Clonorchis sinensis , Ascaris lumbricoides and Schistosoma japonicum were got, then their physical and chemical properties, compositions of amino acids, subcellular localizations, binary and ternary structures were contrastively analyzed...
April 25, 2018: Zhongguo Xue Xi Chong Bing Fang Zhi za Zhi, Chinese Journal of Schistosomiasis Control
https://www.readbyqxmd.com/read/29769347/avian-influenza-viruses-in-wild-birds-virus-evolution-in-a-multi-host-ecosystem
#15
Divya Venkatesh, Marjolein J Poen, Theo M Bestebroer, Rachel D Scheuer, Oanh Vuong, Mzia Chkhaidze, Anna Machablishvili, Jimsher Mamuchadze, Levan Ninua, Nadia B Fedorova, Rebecca A Halpin, Xudong Lin, Amy Ransier, Timothy B Stockwell, David E Wentworth, Divya Kriti, Jayeeta Dutta, Harm van Bakel, Anita Puranik, Marek J Slomka, Steve Essen, Ian H Brown, Ron A M Fouchier, Nicola S Lewis
Wild ducks and gulls are the major reservoirs for avian influenza A viruses (AIVs). The mechanisms that drive AIV evolution are complex at sites where various duck and gull species from multiple flyways breed, winter or stage. The Republic of Georgia is located at the intersection of three migratory flyways: Central Asian Flyway, East Asian/East African Flyway and Black Sea/Mediterranean Flyway. For six consecutive years (2010-2016), we collected AIV samples from various duck and gull species that breed, migrate and overwinter in Georgia...
May 16, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29765366/evolutionary-analysis-provides-insight-into-the-origin-and-adaptation-of-hcv
#16
Diego Forni, Rachele Cagliani, Chiara Pontremoli, Uberto Pozzoli, Jacopo Vertemara, Luca De Gioia, Mario Clerici, Manuela Sironi
Hepatitis C virus (HCV) belongs to the Hepacivirus genus and is genetically heterogeneous, with seven major genotypes further divided into several recognized subtypes. HCV origin was previously dated in a range between ∼200 and 1000 years ago. Hepaciviruses have been identified in several domestic and wild mammals, the largest viral diversity being observed in bats and rodents. The closest relatives of HCV were found in horses/donkeys (equine hepaciviruses, EHV). However, the origin of HCV as a human pathogen is still an unsolved puzzle...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29763671/searching-for-signals-of-recent-natural-selection-in-genes-of-the-innate-immune-response-ancient-dna-study
#17
Magda Lewandowska, Krystyna Jędrychowska-Dańska, Tomasz Płoszaj, Piotr Witas, Alicja Zamerska, Hanna Mańkowska-Pliszka, Henryk W Witas
The last decade has seen sharp progress in the field of human evolutionary genetics and a great amount of genetic evidence of natural selection has been provided so far. Since host-pathogen co-evolution is difficult to trace due to the polygenic nature of human susceptibility to microbial diseases, of particular interest is any signal of natural selection in response to the strong selective pressure exerted by pathogens. Analysis of ancient DNA allows for the direct insight into changes of a gene pool content over time and enables monitoring allele frequency fluctuations...
May 12, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29761492/c7-vertebra-homeotic-transformation-in-domestic-dogs-are-pug-dogs-breaking-mammalian-evolutionary-constraints
#18
J Brocal, S De Decker, R José-López, E G Manzanilla, J Penderis, C Stalin, S Bertram, J J Schoenebeck, C Rusbridge, N Fitzpatrick, R Gutierrez-Quintana
The number of cervical vertebrae in mammals is almost constant at seven, regardless of their neck length, implying that there is selection against variation in this number. Homebox (Hox) genes are involved in this evolutionary mammalian conservation, and homeotic transformation of cervical into thoracic vertebrae (cervical ribs) is a common phenotypic abnormality when Hox gene expression is altered. This relatively benign phenotypic change can be associated with fatal traits in humans. Mutations in genes upstream of Hox, inbreeding and stressors during organogenesis can also cause cervical ribs...
May 14, 2018: Journal of Anatomy
https://www.readbyqxmd.com/read/29757366/a-systematic-review-and-meta-analysis-reveals-pervasive-effects-of-germline-mitochondrial-replacement-on-components-of-health
#19
Ralph Dobler, Damian K Dowling, Edward H Morrow, Klaus Reinhardt
BACKGROUND: Mitochondrial replacement, a form of nuclear transfer, has been proposed as a germline therapy to prevent the transmission of mitochondrial diseases. Mitochondrial replacement therapy has been licensed for clinical application in the UK, and already carried out in other countries, but little is known about negative or unintended effects on the health of offspring born using this technique. OBJECTIVE AND RATIONALE: Studies in invertebrate models have used techniques that achieve mitochondrial replacement to create offspring with novel combinations of mitochondrial and nuclear genotype...
May 11, 2018: Human Reproduction Update
https://www.readbyqxmd.com/read/29755620/human-genomic-loci-important-in-common-infectious-diseases-role-of-high-throughput-sequencing-and-genome-wide-association-studies
#20
REVIEW
Gerald Mboowa, Ivan Sserwadda, Marion Amujal, Norah Namatovu
HIV/AIDS, tuberculosis (TB), and malaria are 3 major global public health threats that undermine development in many resource-poor settings. Recently, the notion that positive selection during epidemics or longer periods of exposure to common infectious diseases may have had a major effect in modifying the constitution of the human genome is being interrogated at a large scale in many populations around the world. This positive selection from infectious diseases increases power to detect associations in genome-wide association studies (GWASs)...
2018: Canadian Journal of Infectious Diseases & Medical Microbiology
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