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Human evolutionary genetics

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https://www.readbyqxmd.com/read/28102248/tracing-the-peopling-of-the-world-through-genomics
#1
Rasmus Nielsen, Joshua M Akey, Mattias Jakobsson, Jonathan K Pritchard, Sarah Tishkoff, Eske Willerslev
Advances in the sequencing and the analysis of the genomes of both modern and ancient peoples have facilitated a number of breakthroughs in our understanding of human evolutionary history. These include the discovery of interbreeding between anatomically modern humans and extinct hominins; the development of an increasingly detailed description of the complex dispersal of modern humans out of Africa and their population expansion worldwide; and the characterization of many of the genetic adaptions of humans to local environmental conditions...
January 18, 2017: Nature
https://www.readbyqxmd.com/read/28101534/pathogenicity-determinants-of-the-human-malaria-parasite-plasmodium-falciparum-have-ancient-origins
#2
Andrew J Brazier, Marion Avril, Maria Bernabeu, Maxwell Benjamin, Joseph D Smith
Plasmodium falciparum, the most deadly of the human malaria parasites, is a member of the Laverania subgenus that also infects African Great Apes. The virulence of P. falciparum is related to cytoadhesion of infected erythrocytes in microvasculature, but the origin of dangerous parasite adhesion traits is poorly understood. To investigate the evolutionary history of the P. falciparum cytoadhesion pathogenicity determinant, we studied adhesion domains from the chimpanzee malaria parasite P. reichenowi. We demonstrate that the P...
January 2017: MSphere
https://www.readbyqxmd.com/read/28100614/human-rhinovirus-diversity-and-evolution-how-strange-the-change-from-major-to-minor
#3
Nicole Lewis-Rogers, Jon Seger, Frederick R Adler
: Rhinoviruses are the most common cause of the common cold. Their many distinct lineages fall into "major" and "minor" groups that use different cell-surface receptors to enter host cells. Minor-group rhinoviruses are more immunogenic in laboratory studies, although their patterns of transmission and their cold symptoms are broadly similar to those of the major group. Here we present evolutionary evidence that minor-group viruses are also more immunogenic in humans. A key finding is that rates of amino-acid substitution at exposed sites in the capsid proteins VP2, VP3 and VP1 tend to be elevated in minor-group relative to major-group viruses, while rates at buried sites show no consistent differences...
January 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28100184/cnvs-into-the-wild-screening-the-genomes-of-conifer-trees-picea-spp-reveals-fewer-gene-copy-number-variations-in-hybrids-and-links-to-adaptation
#4
Julien Prunier, Sébastien Caron, John MacKay
BACKGROUND: Copy number variations (CNVs) have been linked to different phenotypes in human, including many diseases. A genome-scale understanding of CNVs is available in a few plants but none are wild species, leaving a knowledge gap regarding their genome biology and evolutionary role. We developed a reliable CNV detection method for species lacking contiguous reference genome. We selected multiple probes within 14,078 gene sequences and developed comparative genome hybridization on arrays...
January 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28100168/effects-of-pleistocene-sea-level-fluctuations-on-mangrove-population-dynamics-a-lesson-from-sonneratia-alba
#5
Yuchen Yang, Jianfang Li, Shuhuan Yang, Xinnian Li, Lu Fang, Cairong Zhong, Norman C Duke, Renchao Zhou, Suhua Shi
BACKGROUND: A large-scale systematical investigation of the influence of Pleistocene climate oscillation on mangrove population dynamics could enrich our knowledge about the evolutionary history during times of historical climate change, which in turn may provide important information for their conservation. RESULTS: In this study, phylogeography of a mangrove tree Sonneratia alba was studied by sequencing three chloroplast fragments and seven nuclear genes. A low level of genetic diversity at the population level was detected across its range, especially at the range margins, which was mainly attributed to the steep sea-level drop and associated climate fluctuations during the Pleistocene glacial periods...
January 18, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28099513/the-tetraspanin-associated-uroplakins-family-upk2-3-is-evolutionarily-related-to-ptprq-a-phosphotyrosine-phosphatase-receptor
#6
Javier U Chicote, Rob DeSalle, José Segarra, Tung-Tien Sun, Antonio García-España
Uroplakins are a widespread group of vertebrate integral membrane proteins that belong to two different families: UPK1a and UPK1b belong to the large tetraspanin (TSPAN) gene family, and UPK3a, UPK3b, UPK3c, UPK3d, UPK2a and UPK2b form a family of their own, the UPK2/3 tetraspanin-associated family. In a previous study, we reported that uroplakins first appeared in vertebrates, and that uroplakin tetraspanins (UPK1a and UPK1b) should have originated by duplication of an ancestor tetraspanin gene. However, the evolutionary origin of the UPK2/3 family remains unclear...
2017: PloS One
https://www.readbyqxmd.com/read/28098149/characterising-private-and-shared-signatures-of-positive-selection-in-37-asian-populations
#7
Xuanyao Liu, Dongsheng Lu, Woei-Yuh Saw, Philip J Shaw, Pongsakorn Wangkumhang, Chumpol Ngamphiw, Suthat Fucharoen, Worachart Lert-Itthiporn, Kwanrutai Chin-Inmanu, Tran Nguyen Bich Chau, Katie Anders, Anuradhani Kasturiratne, H Janaka de Silva, Tomohiro Katsuya, Ryosuke Kimura, Toru Nabika, Takayoshi Ohkubo, Yasuharu Tabara, Fumihiko Takeuchi, Ken Yamamoto, Mitsuhiro Yokota, Dolikun Mamatyusupu, Wenjun Yang, Yeun-Jun Chung, Li Jin, Boon-Peng Hoh, Ananda R Wickremasinghe, RickTwee-Hee Ong, Chiea-Chuen Khor, Sarah J Dunstan, Cameron Simmons, Sissades Tongsima, Prapat Suriyaphol, Norihiro Kato, Shuhua Xu, Yik-Ying Teo
The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified...
January 18, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28096484/evolutionary-dynamics-of-pandemic-methicillin-sensitive-staphylococcus-aureus-st398-and-its-international-spread-via-routes-of-human-migration
#8
Anne-Catrin Uhlemann, Paul R McAdam, Sean B Sullivan, Justin R Knox, Hossein Khiabanian, Raul Rabadan, Peter R Davies, J Ross Fitzgerald, Franklin D Lowy
: Methicillin-susceptible Staphylococcus aureus (MSSA) accounts for the majority of S. aureus infections globally, and yet surprisingly little is known about its clonal evolution. We applied comparative whole-genome sequencing (WGS) analyses to epidemiologically and geographically diverse ST398-MSSA, a pandemic lineage affecting both humans and livestock. Bayesian phylogenetic analysis predicted divergence of human-associated ST398-MSSA ~40 years ago. Isolates from Midwestern pigs and veterinarians differed substantially from those in New York City (NYC)...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28093611/a-highly-divergent-puumala-virus-lineage-in-southern-poland
#9
Ulrike M Rosenfeld, Stephan Drewes, Hanan Sheikh Ali, Edyta T Sadowska, Magdalena Mikowska, Gerald Heckel, Paweł Koteja, Rainer G Ulrich
Puumala virus (PUUV) represents one of the most important hantaviruses in Central Europe. Phylogenetic analyses of PUUV strains indicate a strong genetic structuring of this hantavirus. Recently, PUUV sequences were identified in the natural reservoir, the bank vole (Myodes glareolus), collected in the northern part of Poland. The objective of this study was to evaluate the presence of PUUV in bank voles from southern Poland. A total of 72 bank voles were trapped in 2009 at six sites in this part of Poland...
January 16, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28092658/mutation-effects-predicted-from-sequence-co-variation
#10
Thomas A Hopf, John B Ingraham, Frank J Poelwijk, Charlotta P I Schärfe, Michael Springer, Chris Sander, Debora S Marks
Many high-throughput experimental technologies have been developed to assess the effects of large numbers of mutations (variation) on phenotypes. However, designing functional assays for these methods is challenging, and systematic testing of all combinations is impossible, so robust methods to predict the effects of genetic variation are needed. Most prediction methods exploit evolutionary sequence conservation but do not consider the interdependencies of residues or bases. We present EVmutation, an unsupervised statistical method for predicting the effects of mutations that explicitly captures residue dependencies between positions...
January 16, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28092606/molecular-characterization-and-expression-analysis-of-the-nlr-family-card-containing-five-transcripts-in-the-pig
#11
Q Y Yang, T Chen, Y B Chen, D L Lan
The NOD-like receptor (NLR) family caspase recruitment domain-containing 5 (NLRC5) is one of the newly discovered and largest NLR family members. The NLRC5 has recently received extensive attention because of its important role in regulating innate and adaptive immune responses. The NLRC5 in many vertebrates, such as humans, mice, cattle, and horses, has already been proven and studied. However, the NLRC5 gene characteristics of pigs remain unclear. Thus, we completely cloned the NLRC5 cDNA sequence of the pig using the rapid amplification of cDNA ends(RACE) technology...
December 1, 2016: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/28086750/a-genome-wide-scan-for-genes-under-balancing-selection-in-drosophila-melanogaster
#12
Myriam Croze, Andreas Wollstein, Vedran Božičević, Daniel Živković, Wolfgang Stephan, Stephan Hutter
BACKGROUND: In the history of population genetics balancing selection has been considered as an important evolutionary force, yet until today little is known about its abundance and its effect on patterns of genetic diversity. Several well-known examples of balancing selection have been reported from humans, mice, plants, and parasites. However, only very few systematic studies have been carried out to detect genes under balancing selection. We performed a genome scan in Drosophila melanogaster to find signatures of balancing selection in a derived (European) and an ancestral (African) population...
January 13, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28081145/probing-the-association-between-early-evolutionary-markers-and-schizophrenia
#13
Saurabh Srinivasan, Francesco Bettella, Sahar Hassani, Yunpeng Wang, Aree Witoelar, Andrew J Schork, Wesley K Thompson, David A Collier, Rahul S Desikan, Ingrid Melle, Anders M Dale, Srdjan Djurovic, Ole A Andreassen
Schizophrenia is suggested to be a by-product of the evolution in humans, a compromise for our language, creative thinking and cognitive abilities, and thus, essentially, a human disorder. The time of its origin during the course of human evolution remains unclear. Here we investigate several markers of early human evolution and their relationship to the genetic risk of schizophrenia. We tested the schizophrenia evolutionary hypothesis by analyzing genome-wide association studies of schizophrenia and other human phenotypes in a statistical framework suited for polygenic architectures...
2017: PloS One
https://www.readbyqxmd.com/read/28080995/rapid-emergence-of-pathogens-in-agro-ecosystems-global-threats-to-agricultural-sustainability-and-food-security
#14
REVIEW
Bruce A McDonald, Eva H Stukenbrock
Agricultural ecosystems are composed of genetically depauperate populations of crop plants grown at a high density and over large spatial scales, with the regional composition of crop species changing little from year to year. These environments are highly conducive for the emergence and dissemination of pathogens. The uniform host populations facilitate the specialization of pathogens to particular crop cultivars and allow the build-up of large population sizes. Population genetic and genomic studies have shed light on the evolutionary mechanisms underlying speciation processes, adaptive evolution and long-distance dispersal of highly damaging pathogens in agro-ecosystems...
December 5, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28077774/tropical-ancient-dna-reveals-relationships-of-the-extinct-bahamian-giant-tortoise-chelonoidis-alburyorum
#15
Christian Kehlmaier, Axel Barlow, Alexander K Hastings, Melita Vamberger, Johanna L A Paijmans, David W Steadman, Nancy A Albury, Richard Franz, Michael Hofreiter, Uwe Fritz
Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas (Chelonoidis alburyorum) using an approximately 1 000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island...
January 11, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28077633/surveillance-of-bat-coronaviruses-in-kenya-identifies-relatives-of-human-coronaviruses-nl63-and-229e-and-their-recombination-history
#16
Ying Tao, Mang Shi, Christina Chommanard, Krista Queen, Jing Zhang, Wanda Markotter, Ivan V Kuzmin, Edward C Holmes, Suxiang Tong
: Bats harbor a large diversity of coronaviruses (CoVs), several of which are related to zoonotic pathogens that cause severe disease in humans. Our screening of bat samples collected in Kenya during 2007-2010 not only detected RNA from several novel CoVs but, more significantly, identified sequences that were closely related to human CoVs NL63 and 229E, suggesting that these two human viruses originate from bats. We also demonstrated that human CoV NL63 is a recombinant between NL63-like viruses circulating in Triaenops bats and 229E-like viruses circulating in Hipposideros bats, with the break-point located near 5' and 3' end of the spike (S) protein gene...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28069633/population-level-genetic-variation-and-climate-change-in-a-biodiversity-hotspot
#17
REVIEW
Kristina A Schierenbeck
INTRODUCTION: Estimated future climate scenarios can be used to predict where hotspots of endemism may occur over the next century, but life history, ecological and genetic traits will be important in informing the varying responses within myriad taxa. Essential to predicting the consequences of climate change to individual species will be an understanding of the factors that drive genetic structure within and among populations. Here, I review the factors that influence the genetic structure of plant species in California, but are applicable elsewhere; existing levels of genetic variation, life history and ecological characteristics will affect the ability of an individual taxon to persist in the presence of anthropogenic change...
January 9, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28067622/a-homozygous-fitm2-mutation-causes-a-deafness-dystonia-syndrome-with-motor-regression-and-signs-of-ichthyosis-and-sensory-neuropathy
#18
Celia Zazo Seco, Anna Castells-Nobau, Seol-Hee Joo, Margit Schraders, Jia Nee Foo, Monique van der Voet, S Sendhil Velan, Bonnie Nijhof, Jaap Oostrik, Erik de Vrieze, Radoslaw Katana, Atika Mansoor, Martijn Huynen, Radek Szklarczyk, Martin Oti, Lisbeth Tranebjærg, Erwin van Wijk, Jolanda M Scheffer-de Gooyert, Saadat Siddique, Jonathan Baets, Peter de Jonghe, Syed Ali Raza Kazmi, Suresh Anand Sadananthan, Bart P van de Warrenburg, Chiea Chuen Khor, Martin C Göpfert, Raheel Qamar, Annette Schenck, Hannie Kremer, Saima Siddiqi
A consanguineous family from Pakistan was ascertained with a novel deafness-dystonia syndrome with motor regression, ichthyosis-like features and signs of sensory neuropathy. By applying a combined strategy of linkage analysis and whole-exome sequencing in the presented family, a homozygous nonsense mutation, c.4G>T (p.Glu2*), in FITM2 was identified. FITM2 and its paralog FITM1 constitute an evolutionary conserved protein family involved in partitioning of triglycerides into cellular lipid droplets. Despite the role of FITM2 in neutral lipid storage and metabolism, no indications for lipodystrophy were observed in the affected individuals...
December 15, 2016: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28062191/tracking-hcv-protease-population-diversity-during-transmission-and-susceptibility-of-founder-populations-to-antiviral-therapy
#19
Tanvi Khera, Daniel Todt, Koen Vercauteren, C Patrick McClure, Lieven Verhoye, Ali Farhoudi, Sabin Bhuju, Robert Geffers, Thomas F Baumert, Eike Steinmann, Philip Meuleman, Thomas Pietschmann, Richard J P Brown
Due to the highly restricted species-tropism of Hepatitis C virus (HCV) a limited number of animal models exist for pre-clinical evaluation of vaccines and antiviral compounds. The human-liver chimeric mouse model allows heterologous challenge with clinically relevant strains derived from patients. However, to date, the transmission and longitudinal evolution of founder viral populations in this model have not been characterized in-depth using state-of-the-art sequencing technologies. Focusing on NS3 protease encoding region of the viral genome, mutant spectra in a donor inoculum and individual recipient mice were determined via Illumina sequencing and compared, to determine the effects of transmission on founder viral population complexity...
January 3, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28057304/drosophila-as-a-model-for-human-diseases-focus-on-innate-immunity-in-barrier-epithelia
#20
P Bergman, S Seyedoleslami Esfahani, Y Engström
Epithelial immunity protects the host from harmful microbial invaders but also controls the beneficial microbiota on epithelial surfaces. When this delicate balance between pathogen and symbiont is disturbed, clinical disease often occurs, such as in inflammatory bowel disease, cystic fibrosis, or atopic dermatitis, which all can be in part linked to impairment of barrier epithelia. Many innate immune receptors, signaling pathways, and effector molecules are evolutionarily conserved between human and Drosophila...
2017: Current Topics in Developmental Biology
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