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https://www.readbyqxmd.com/read/28813039/comparative-assessment-of-ssr-and-snp-markers-for-inferring-the-population-genetic-structure-of-the-common-fungus-armillaria-cepistipes
#1
T Tsykun, C Rellstab, C Dutech, G Sipos, S Prospero
During the last years, simple sequence repeats (SSRs, also known as microsatellites) and single-nucleotide polymorphisms (SNPs) have become the most popular molecular markers for describing neutral genetic variation in populations of a wide range of organisms. However, only a limited number of studies has focused on comparing the performance of these two types of markers for describing the underlying genetic structure of wild populations. Moreover, none of these studies targeted fungi, the group of organisms with one of the most complex reproductive strategies...
August 16, 2017: Heredity
https://www.readbyqxmd.com/read/28812996/reliable-detection-of-herpes-simplex-virus-sequence-variation-by-high-throughput-resequencing
#2
Alison M Morse, Kaitlyn R Calabro, Justin M Fear, David C Bloom, Lauren M McIntyre
High-throughput sequencing (HTS) has resulted in data for a number of herpes simplex virus (HSV) laboratory strains and clinical isolates. The knowledge of these sequences has been critical for investigating viral pathogenicity. However, the assembly of complete herpesviral genomes, including HSV, is complicated due to the existence of large repeat regions and arrays of smaller reiterated sequences that are commonly found in these genomes. In addition, the inherent genetic variation in populations of isolates for viruses and other microorganisms presents an additional challenge to many existing HTS sequence assembly pipelines...
August 16, 2017: Viruses
https://www.readbyqxmd.com/read/28812937/genetic-and-molecular-characterization-of-leaf-rust-resistance-in-two-durum-wheat-landraces
#3
Naeela Qureshi, Harbans Bariana, James A Kolmer, Hanif Miah, Urmil Bansal
Leaf rust, caused by Puccinia triticina, is a constraint to durum wheat (Triticum turgidum subsp. durum) production, and landraces are reported to be an important source of resistance. Two Portuguese landraces (Aus26582 and Aus26579) showed resistance against durum-specific P. triticina races and were crossed with a susceptible landrace (Bansi) to develop recombinant inbred line (RIL) populations. Monogenic segregation for leaf rust resistance was observed among both RIL populations. The underlying locus, temporarily named LrAW2, was mapped to the short arm of chromosome 6B in the Aus26582/Bansi population and five DArTseq markers cosegregated with LrAW2...
August 16, 2017: Phytopathology
https://www.readbyqxmd.com/read/28812736/the-evolution-and-population-diversity-of-human-specific-segmental-duplications
#4
Megan Y Dennis, Lana Harshman, Bradley J Nelson, Osnat Penn, Stuart Cantsilieris, John Huddleston, Francesca Antonacci, Kelsi Penewit, Laura Denman, Archana Raja, Carl Baker, Kenneth Mark, Maika Malig, Nicolette Janke, Claudia Espinoza, Holly A F Stessman, Xander Nuttle, Kendra Hoekzema, Tina A Lindsay-Graves, Richard K Wilson, Evan E Eichler
Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (N = 80 genes from 33 gene families)...
February 17, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812723/the-unconstrained-evolution-of-fast-and-efficient-antibiotic-resistant-bacterial-genomes
#5
Carlos Reding-Roman, Mark Hewlett, Sarah Duxbury, Fabio Gori, Ivana Gudelj, Robert Beardmore
Evolutionary trajectories are constrained by trade-offs when mutations that benefit one life history trait incur fitness costs in other traits. As resistance to tetracycline antibiotics by increased efflux can be associated with an increase in length of the Escherichia coli chromosome of 10% or more, we sought costs of resistance associated with doxycycline. However, it was difficult to identify any because the growth rate (r), carrying capacity (K) and drug efflux rate of E. coli increased during evolutionary experiments where the species was exposed to doxycycline...
January 30, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812720/antagonistic-pleiotropy-and-mutation-accumulation-influence-human-senescence-and-disease
#6
Juan Antonio Rodríguez, Urko M Marigorta, David A Hughes, Nino Spataro, Elena Bosch, Arcadi Navarro
Senescence has long been a public health challenge as well as a fascinating evolutionary problem. There is neither a universally accepted theory for its ultimate causes, nor a consensus about what may be its impact on human health. Here we test the predictions of two evolutionary explanations of senescence-mutation accumulation and antagonistic pleiotropy-which postulate that genetic variants with harmful effects in old ages can be tolerated, or even favoured, by natural selection at early ages. Using data from genome-wide association studies (GWAS), we study the effects of genetic variants associated with diseases appearing at different periods in life, when they are expected to have different impacts on fitness...
January 30, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812709/adaptation-to-deep-sea-chemosynthetic-environments-as-revealed-by-mussel-genomes
#7
Jin Sun, Yu Zhang, Ting Xu, Yang Zhang, Huawei Mu, Yanjie Zhang, Yi Lan, Christopher J Fields, Jerome Ho Lam Hui, Weipeng Zhang, Runsheng Li, Wenyan Nong, Fiona Ka Man Cheung, Jian-Wen Qiu, Pei-Yuan Qian
Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialized macro-benthos such as mussels. But the lack of genome information hinders the understanding of the adaptation of these animals to such inhospitable environments. Here we report the genomes of a deep-sea vent/seep mussel (Bathymodiolus platifrons) and a shallow-water mussel (Modiolus philippinarum). Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago...
April 3, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812657/diminishing-returns-epistasis-decreases-adaptability-along-an-evolutionary-trajectory
#8
Andrea Wünsche, Duy M Dinh, Rebecca S Satterwhite, Carolina Diaz Arenas, Daniel M Stoebel, Tim F Cooper
Populations evolving in constant environments exhibit declining adaptability. Understanding the basis of this pattern could reveal underlying processes determining the repeatability of evolutionary outcomes. In principle, declining adaptability can be due to a decrease in the effect size of beneficial mutations, a decrease in the rate at which they occur, or some combination of both. By evolving Escherichia coli populations started from different steps along a single evolutionary trajectory, we show that declining adaptability is best explained by a decrease in the size of available beneficial mutations...
March 1, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812655/the-placenta-as-a-model-for-understanding-the-origin-and-evolution-of-vertebrate-organs
#9
REVIEW
Oliver W Griffith, Günter P Wagner
How organs originate and evolve is a question fundamental to understanding the evolution of complex multicellular life forms. Vertebrates have a relatively standard body plan with more or less the same conserved set of organs. The placenta is a comparatively more recently evolved organ, derived in many lineages independently. Using placentas as a model, we discuss the genetic basis for organ origins. We show that the evolution of placentas occurs by acquiring new functional attributes to existing tissues, changes in the patterning and development of tissues, and the evolution of novel cell types...
March 23, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812654/transitions-between-phases-of-genomic-differentiation-during-stick-insect-speciation
#10
Rüdiger Riesch, Moritz Muschick, Dorothea Lindtke, Romain Villoutreix, Aaron A Comeault, Timothy E Farkas, Kay Lucek, Elizabeth Hellen, Víctor Soria-Carrasco, Stuart R Dennis, Clarissa F de Carvalho, Rebecca J Safran, Cristina P Sandoval, Jeff Feder, Regine Gries, Bernard J Crespi, Gerhard Gries, Zach Gompert, Patrik Nosil
Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genic speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow...
February 17, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812631/contrasting-effects-of-environment-and-genetics-generate-a-continuum-of-parallel-evolution
#11
Yoel E Stuart, Thor Veen, Jesse N Weber, Dieta Hanson, Mark Ravinet, Brian K Lohman, Cole J Thompson, Tania Tasneem, Andrew Doggett, Rebecca Izen, Newaz Ahmed, Rowan D H Barrett, Andrew P Hendry, Catherine L Peichel, Daniel I Bolnick
Parallel evolution of similar traits by independent populations in similar environments is considered strong evidence for adaptation by natural selection. Often, however, replicate populations in similar environments do not all evolve in the same way, thus deviating from any single, predominant outcome of evolution. This variation might arise from non-adaptive, population-specific effects of genetic drift, gene flow or limited genetic variation. Alternatively, these deviations from parallel evolution might also reflect predictable adaptation to cryptic environmental heterogeneity within discrete habitat categories...
May 22, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812568/gene-expression-plasticity-as-a-mechanism-of-coral-adaptation-to-a-variable-environment
#12
Carly D Kenkel, Mikhail V Matz
Local adaptation is ubiquitous, but the molecular mechanisms that give rise to this ecological phenomenon remain largely unknown. A year-long reciprocal transplant of mustard hill coral (Porites astreoides) between a highly environmentally variable inshore habitat and a more stable offshore habitat demonstrated that populations exhibit phenotypic signatures that are consistent with local adaptation. We characterized the genomic basis of this adaptation in both coral hosts and their intracellular symbionts (Symbiodinium sp...
November 7, 2016: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812561/widespread-maintenance-of-genome-heterozygosity-in-schmidtea%C3%A2-mediterranea
#13
Longhua Guo, Shasha Zhang, Boris Rubinstein, Eric Ross, Alejandro Sánchez Alvarado
Loss of heterozygosity through inbreeding or mitotic errors leads to reductions in progeny survival and fertility. Loss of heterozygosity is particularly exacerbated in geographically isolated populations, which are prone to inbreeding depression and faster rates of extinction. The regenerative capacities of the hermaphroditic biotype of the planarian Schmidtea mediterranea allowed us to perform a systematic genetic test of Mendelian segregation and study the loss of heterozygosity in the Spiralian superclade in general and planarians in particular...
December 5, 2016: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812556/coupling-phenotypic-persistence-to-dna-damage-increases-genetic-diversity-in-severe-stress
#14
Gilad Yaakov, David Lerner, Kajetan Bentele, Joseph Steinberger, Naama Barkai
Mutation rate balances the need to protect genome integrity with the advantage of evolutionary innovations. Microorganisms increase their mutation rate when stressed, perhaps addressing the growing need for evolutionary innovation. Such a strategy, however, is only beneficial under moderate stresses that allow cells to divide and realize their mutagenic potential. In contrast, severe stresses rapidly kill the majority of the population with the exception of a small minority of cells that are in a phenotypically distinct state termed persistence...
January 4, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812540/quantifying-transmission
#15
Mark Woolhouse
Transmissibility is the defining characteristic of infectious diseases. Quantifying transmission matters for understanding infectious disease epidemiology and designing evidence-based disease control programs. Tracing individual transmission events can be achieved by epidemiological investigation coupled with pathogen typing or genome sequencing. Individual infectiousness can be estimated by measuring pathogen loads, but few studies have directly estimated the ability of infected hosts to transmit to uninfected hosts...
July 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28812021/association-analysis-of-arsenic-induced-straighthead-in-rice-oryza-sativa-l-based-on-the-selected-population-with-a-modified-model
#16
Xiaobai Li, Biaolin Hu, Xuhao Pan, Ning Zhang, Dianxing Wu
A rice physiological disorder makes mature panicle keep erect with empty grains termed as "straighthead." Straighthead causes yield losses and is a serious threat to rice production worldwide. Here, a new study of association mapping was conducted to identify QTL involved in straighthead. A subset of 380 accessions was selected from the USDA rice core collection and genotyped with 72 genome-wide SSR markers. An optimal model implemented with principle components (PCs) was used in this association mapping. As a result, five markers were identified to be significantly associated with straighthead...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28811712/association-between-cyp24a1-polymorphisms-and-the-risk-of-colonic-polyps-and-colon-cancer-in-a-chinese-population
#17
Xue-Qi Chen, Jia-Yu Mao, Wen-Bin Li, Jian Li, Hong Yang, Jia-Ming Qian, Jing-Nan Li
AIM: To determine the pathogenesis and potential single nucleotide polymorphisms (SNPs) as screening sites for colonic polyps, colon cancer and ulcerative colitis, and to analyze the possible association between these genetic polymorphisms and the three diseases. METHODS: We evaluated genetic polymorphisms in 144 newly diagnosed colonic polyp patients, 96 colon cancer patients and 44 ulcerative colitis patients. The four SNPs genotyped were rs4809957, rs6068816, rs6091822 and rs8124792...
July 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28811542/identification-replication-and-characterization-of-epigenetic-remodelling-in-the-aging-genome-a-cross-population-analysis
#18
Shuxia Li, Lene Christiansen, Kaare Christensen, Torben A Kruse, Paul Redmond, Riccardo E Marioni, Ian J Deary, Qihua Tan
Aging is a complex biological process regulated by multiple cellular pathways and molecular mechanisms including epigenetics. Using genome-wide DNA methylation data measured in a large collection of Scottish old individuals, we performed discovery association analysis to identify age-methylated CpGs and replicated them in two independent Danish cohorts. The double-replicated CpGs were characterized by distribution over gene regions and location in relation to CpG islands. The replicated CpGs were further characterized by involvement in biological pathways to study their functional implications in aging...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811464/the-origin-of-a-primordial-genome-through-spontaneous-symmetry-breaking
#19
Nobuto Takeuchi, Paulien Hogeweg, Kunihiko Kaneko
The heredity of a cell is provided by a small number of non-catalytic templates-the genome. How did genomes originate? Here, we demonstrate the possibility that genome-like molecules arise from symmetry breaking between complementary strands of self-replicating molecules. Our model assumes a population of protocells, each containing a population of self-replicating catalytic molecules. The protocells evolve towards maximising the catalytic activities of the molecules to increase their growth rates. Conversely, the molecules evolve towards minimising their catalytic activities to increase their intracellular relative fitness...
August 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28811387/selection-constrains-high-rates-of-tandem-repetitive-dna-mutation-in-daphnia-pulex
#20
Jullien M Flynn, Ian Caldas, Melania E Cristescu, Andrew G Clark
A long-standing evolutionary puzzle is that all eukaryotic genomes contain large amounts of tandemly-repeated DNA whose sequence motifs and abundance vary greatly among even closely related species. To elucidate the evolutionary forces governing tandem repeat dynamics, quantification of the rates and patterns of mutations in repeat copy number and tests of its selective neutrality are necessary. Here we used whole-genome sequences of 28 mutation accumulation (MA) lines of Daphnia pulex in addition to six isolates from a non-MA population originating from the same progenitor to both estimate mutation rates of abundances of repeat sequences and evaluate the selective regime acting upon them...
August 15, 2017: Genetics
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