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Genetic evolution

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https://www.readbyqxmd.com/read/28647304/phylogenies-of-symbiotic-genes-of-bradyrhizobium-symbionts-of-legumes-of-economic-and-environmental-importance-in-brazil-support-the-definition-of-the-new-symbiovars-pachyrhizi-and-sojae
#1
Jakeline Renata Marçon Delamuta, Pâmela Menna, Renan Augusto Ribeiro, Mariangela Hungria
Bradyrhizobium comprises most tropical symbiotic nitrogen-fixing strains, but the correlation between symbiotic and core genes with host specificity is still unclear. In this study, the phylogenies of the nodY/K and nifH genes of 45 Bradyrhizobium strains isolated from legumes of economic and environmental importance in Brazil (Arachis hypogaea, Acacia auriculiformis, Glycine max, Lespedeza striata, Lupinus albus, Stylosanthes sp. and Vigna unguiculata) were compared to 16S rRNA gene phylogeny and genetic diversity by rep-PCR...
June 7, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28646875/genome-analysis-of-diploscapter-coronatus-insights-into-molecular-peculiarities-of-a-nematode-with-parthenogenetic-reproduction
#2
Hideaki Hiraki, Hiroshi Kagoshima, Christopher Kraus, Philipp H Schiffer, Yumiko Ueta, Michael Kroiher, Einhard Schierenberg, Yuji Kohara
BACKGROUND: Sexual reproduction involving the fusion of egg and sperm is prevailing among eukaryotes. In contrast, the nematode Diploscapter coronatus, a close relative of the model Caenorhabditis elegans, reproduces parthenogenetically. Neither males nor sperm have been observed and some steps of meiosis are apparently skipped in this species. To uncover the genomic changes associated with the evolution of parthenogenesis in this nematode, we carried out a genome analysis. RESULTS: We obtained a 170 Mbp draft genome in only 511 scaffolds with a N50 length of 1 Mbp...
June 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28646625/fluctuating-effects-of-genetic-and-plastic-changes-in-body-mass-on-population-dynamics-in-a-large-herbivore
#3
Gabriel Pigeon, Thomas H G Ezard, Marco Festa-Bianchet, David W Coltman, Fanie Pelletier
Recent studies suggest that evolutionary changes can occur on a contemporary time scale. Hence, evolution can influence ecology and vice-versa. To understand the importance of eco-evolutionary dynamics in population dynamics, we must quantify the relative contribution of ecological and evolutionary changes to population growth and other ecological processes. To date, however, most eco-evolutionary dynamics studies have not partitioned the relative contribution of plastic and evolutionary changes in traits on population, community and ecosystem processes...
June 24, 2017: Ecology
https://www.readbyqxmd.com/read/28646506/three-lessons-for-genetic-toxicology-from-baseball-analytics
#4
EDITORIAL
Stephen D Dertinger
In many respects the evolution of baseball statistics mirrors advances made in the field of genetic toxicology. From its inception, baseball and statistics have been inextricably linked. Generations of players and fans have used a number of relatively simple measurements to describe team and individual player's current performance, as well as for historical record-keeping purposes. Over the years, baseball analytics has progressed in several important ways. Early advances were based on deriving more meaningful metrics from simpler forerunners...
June 24, 2017: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/28646326/transposable-elements-mediate-adaptive-debilitation-of-flagella-in-experimental-escherichia-coli-populations
#5
Gordon R Plague, Krystal S Boodram, Kevin M Dougherty, Sandar Bregg, Daniel P Gilbert, Hira Bakshi, Daniel Costa
Although insertion sequence (IS) elements are generally considered genomic parasites, they can mediate adaptive genetic changes in bacterial genomes. We discovered that among 12 laboratory-evolved Escherichia coli populations, three had experienced at least six different IS1-mediated deletions of flagellar genes. These deletions all involved the master flagellar regulator flhDC, and as such completely incapacitate motility. Two lines of evidence strongly suggest that these deletions were adaptive in our evolution experiment: (1) parallel evolution in three independent populations is highly unlikely just by chance, and (2) one of these deletion mutations swept to fixation within ~1000 generations, which is over two million times faster than expected if this deletion was instead selectively neutral and thus evolving by genetic drift...
June 23, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28646074/divergence-of-the-floral-a-function-between-an-asterid-and-a-rosid-species
#6
Patrice Morel, Klaas Heijmans, Frederique Rozier, Jan Zethof, Sophy Chamot, Suzanne Rodrigues Bento, Aurelie Vialette-Guiraud, Pierre Chambrier, Trehin Christophe, Michiel Vandenbussche
The ABC model is widely used as a genetic framework for understanding floral development and evolution. In this model, the A-function is required for the development of sepals and petals and to antagonize the C-function in the outer floral whorls. In the rosid species Arabidopsis thaliana, the AP2-type AP2 transcription factor represents a major A-function protein, but how the A-function is encoded in other species is not well understood. Here we show that in the asterid species petunia (Petunia hybrida), AP2B/BLIND ENHANCER (BEN) confines the C-function to the inner petunia floral whorls, in parallel with the microRNA BLIND...
June 23, 2017: Plant Cell
https://www.readbyqxmd.com/read/28645870/impact-on-environment-ecosystem-diversity-and-health-from-culturing-and-using-gmos-as-feed-and-food
#7
REVIEW
Aristidis M Tsatsakis, Muhammad Amjad Nawaz, Victor A Tutelyan, Kirill S Golokhvast, Olga-Ioanna Kalantzi, Duck Hwa Chung, Sung Jo Kang, Michael D Coleman, Nadia Tyshko, Seung Hwan Yang, Gyuhwa Chung
Modern agriculture provides the potential for sustainable feeding of the world's increasing population. Up to the present moment, genetically modified (GM) products have enabled increased yields and reduced pesticide usage. Nevertheless, GM products are controversial amongst policy makers, scientists and the consumers, regarding their possible environmental, ecological, and health risks. Scientific-and-political debates can even influence legislation and prospective risk assessment procedure. Currently, the scientifically-assessed direct hazardous impacts of GM food and feed on fauna and flora are conflicting; indeed, a review of literature available data provides some evidence of GM environmental and health risks...
June 20, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28645766/phylogenomic-analysis-supports-multiple-instances-of-polyphyly-in-the-oomycete-peronosporalean-lineage
#8
Marina S Ascunce, Jose C Huguet-Tapia, Almudena Ortiz-Urquiza, Nemat O Keyhani, Edward L Braun, Erica M Goss
The study of biological diversification of oomycetes has been a difficult task for more than a century. Pioneer researchers used morphological characters to describe this heterogeneous group, and physiological and genetic tools expanded knowledge of these microorganisms. However, research on oomycete diversification is limited by conflicting phylogenies. Using whole genomic data from 17 oomycete taxa, we obtained a dataset of 277 core orthologous genes shared among these genomes. Analyses of this dataset resulted in highly congruent and strongly supported estimates of oomycete phylogeny when we used concatenated maximum likelihood and coalescent-based methods; the one important exception was the position of Albugo...
June 20, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28645748/developmental-and-genetic-mechanisms-of-neural-circuit-evolution
#9
REVIEW
Maria Antonietta Tosches
No matter how a nervous system is genetically built, natural selection acts on the functional outcome of its activity. To understand how nervous systems evolve, it is essential to analyze how their functional units - the neural circuits - change and adapt over time. Different developmental and genetic mechanisms participate to the structural evolution of neural circuits. These mechanisms involve regulatory changes at the level of different gene sets. Functional constraints on neural circuit evolution suggest that these mechanisms are not employed randomly, and that the evolution of neuroanatomy might be biased...
June 20, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28645318/detecting-consistent-patterns-of-directional-adaptation-using-differential-selection-codon-models
#10
Sahar Parto, Nicolas Lartillot
BACKGROUND: Phylogenetic codon models are often used to characterize the selective regimes acting on protein-coding sequences. Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by modeling the amino acid fitness landscape along the sequence. However, thus far, most of these models have assumed that the fitness landscape is constant over time. Fluctuations of the fitness landscape may often be random or depend on complex and unknown factors...
June 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28645249/comparative-transcriptomic-analysis-of-the-evolution-and-development-of-flower-size-in-saltugilia-polemoniaceae
#11
Jacob B Landis, Douglas E Soltis, Pamela S Soltis
BACKGROUND: Flower size varies dramatically across angiosperms, representing innovations over the course of >130 million years of evolution and contributing substantially to relationships with pollinators. However, the genetic underpinning of flower size is not well understood. Saltugilia (Polemoniaceae) provides an excellent non-model system for extending the genetic study of flower size to interspecific differences that coincide with variation in pollinators. RESULTS: Using targeted gene capture methods, we infer phylogenetic relationships among all members of Saltugilia to provide a framework for investigating the genetic control of flower size differences via RNA-Seq de novo assembly...
June 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28644542/the-conservation-significance-of-natural-hybridisation-in-mediterranean-plants-from-a-case-study-on-cyclamen-primulaceae-to-a-general-perspective
#12
John D Thompson, Perrine Gauthier, Guillaume Papuga, Virginie Pons, Max Debussche, Emmanuele Farris
Hybridisation plays a prominent role in plant evolution due to its influence on genetic diversity, fitness and adaptive potential We identify a case of on-going hybrid evolution of floral phenotypes in disjunct populations of Cyclamen balearicum and C. repandum subsp. repandum on Corsica and Sardinia. Hybrid populations on the two islands contain similar patterns of variation in flower colour and size but are probably at different stages in the evolutionary process of hybridisation and differences in the frequency of floral types and flower size suggest hybrid vigour that may contribute to the dynamics and maintenance of hybrid forms...
June 23, 2017: Plant Biology
https://www.readbyqxmd.com/read/28643786/a-unified-model-of-hymenopteran-preadaptations-that-trigger-the-evolutionary-transition-to-eusociality
#13
Andrés E Quiñones, Ido Pen
Explaining the origin of eusociality, with strict division of labour between workers and reproductives, remains one of evolutionary biology's greatest challenges. Specific combinations of genetic, behavioural and demographic traits in Hymenoptera are thought to explain their relatively high frequency of eusociality, but quantitative models integrating such preadaptations are lacking. Here we use mathematical models to show that the joint evolution of helping behaviour and maternal sex ratio adjustment can synergistically trigger both a behavioural change from solitary to eusocial breeding, and a demographic change from a life cycle with two reproductive broods to a life cycle in which an unmated cohort of female workers precedes a final generation of dispersing reproductives...
June 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28643131/strong-comma-free-codes-in-genetic-information
#14
Elena Fimmel, Christian J Michel, Lutz Strüngmann
Comma-free codes constitute a class of circular codes, which has been widely studied, in particular by Golomb et al. (Biologiske Meddelelser, Kongelige Danske Videnskabernes Selskab 23:1-34, 1958a, Can J Math 10:202-209, 1958b), Michel et al. (Comput Math Appl 55:989-996, 2008a, Theor Comput Sci 401:17-26, 2008b, Inf Comput 212:55-63, 2012), Michel and Pirillo (Int J Comb 2011:659567, 2011), and Fimmel and Strüngmann (J Theor Biol 389:206-213, 2016). Based on a recent approach using graph theory to study circular codes Fimmel et al...
June 22, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28642778/characterization-of-salt-induced-epigenetic-segregation-by-genome-wide-loss-of-heterozygosity-and-its-association-with-salt-tolerance-in-rice-oryza-sativa-l
#15
Min Li, Wen-Sheng Wang, Yun-Long Pang, Jessica R Domingo, Jauhar Ali, Jian-Long Xu, Bin-Ying Fu, Elec B Venus, Zhi-Kang Li
In a breeding effort to develop salt tolerant (ST) rice varieties by designed QTL pyramiding, large numbers of progenies derived from four crosses between salt- or drought- tolerant BC2F5 IR64 introgression lines, were subjected to severe salt stress, resulting in 422 ST plants. The progeny testing of the selected F3 lines under more severe salt stress resulted in identification of 16 promising homozygous lines with high levels of ST. Genetic characterization of the 422 ST F3 progeny and 318 random F2 plants from the same four crosses using 105 segregating SSR markers lead to three interesting discoveries: (1) salt stress can induce genome-wide epigenetic segregation (ES) characterized by complete loss of heterozygosity (LOH) and nearly complete loss of an allele (LOA) in the F3 progenies of four rice populations in a single generation; (2) ∼25% of the stress-induced ES loci were transgenerational and inherited from their salt- and drought- selected parents; and (3) the salt-induced LOH and LOA loci (regions) appeared to contain genes/alleles associated with ST and/or drought tolerance...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28642158/genetic-diversity-of-environmental-vibrio-cholerae-o1-strains-isolated-in-northern-vietnam
#16
Taichiro Takemura, Kazunori Murase, Fumito Maruyama, Tran Thi Luong, Atsushi Ota, Ichiro Nakagawa, Nguyen Dong Tu, Ngo Tu Cuong, Nguyen Thi Hang, Asako Tokizawa, Masatomo Morita, Makoto Ohnishi, Nguyen Binh Minh, Tetsu Yamashiro
Cholera epidemics have been recorded periodically in Vietnam during the seventh cholera pandemic. Since cholera is a water-borne disease, systematic monitoring of environmental waters for Vibrio cholerae presence is important for predicting and preventing cholera epidemics. We conducted monitoring, isolation, and genetic characterization of V. cholerae strains in Nam Dinh province of Northern Vietnam from Jul 2013 to Feb 2015. In this study, four V. cholerae O1 strains were detected and isolated from 110 analyzed water samples (3...
June 19, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28641396/geneticization-in-mim-omim%C3%A2-exploring-historic-and-epistemic-drivers-of-contemporary-understandings-of-genetic-disease
#17
Rachel A Ankeny
Prior to the genomic sequencing era, the bible for those working in clinical genetics was McKusick's Mendelian Inheritance in Man (MIM), which appeared in multiple editions between the 1960s and the late 1990s. This catalogue was organized according to general patterns of inheritance and focused on phenotypes. Beginning in the mid-1980s, it was replaced by Online Mendelian Inheritance in Man (OMIM®), a continuously updated catalogue documenting molecular relationships between genetic variation and phenotypic expression...
June 21, 2017: Journal of Medicine and Philosophy
https://www.readbyqxmd.com/read/28640838/next-generation-sequencing-of-the-clonal-igh-rearrangement-detects-ongoing-mutations-and-interfollicular-trafficking-in-in-situ-follicular-neoplasia
#18
Perikles Kosmidis, Irina Bonzheim, Claudia Dufke, Sema Colak, Thomas Hentrich, Christopher Schroeder, Peter Bauer, Patrick Adam, Falko Fend
Follicular lymphoma (FL) is characterized genetically by a significant intraclonal diversity of rearranged immunoglobulin heavy chain (IGH) genes and a substantial cell migration activity (follicular trafficking). Recently, in situ follicular neoplasia (ISFN), characterized by accumulations of immunohistochemically strongly BCL2-positive, t(14;18)+ clonal B cells confined to germinal centers in reactive lymph nodes, has been identified as a precursor lesion of FL with low risk of progression to manifest FL...
2017: PloS One
https://www.readbyqxmd.com/read/28640400/little-evidence-for-intralocus-sexual-conflict-over-the-optimal-intake-of-nutrients-for-lifespan-and-reproduction-in-the-black-field-cricket-teleogryllus-commodus
#19
James Rapkin, Ruth C Archer, Charles E Grant, Kim Jensen, Clarissa M House, Alastair J Wilson, John Hunt
There is often large divergence in the effects of key nutrients on lifespan and reproduction in the sexes, yet nutrient intake is regulated in the same way in males and females given dietary choice. This suggests that the sexes are constrained from feeding to their sex-specific nutritional optima for these traits. Here we examine the potential for intralocus sexual conflict (IASC) over optimal protein and carbohydrate intake for lifespan and reproduction to constrain the evolution of sex-specific nutrient regulation in the field cricket, Teleogryllus commodus...
June 22, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28640150/evaluation-of-research-topic-evolution-in-psychiatry-using-co-word-analysis
#20
Ying Wu, Xing Jin, Yunzhen Xue
With the rapid increase in the incidence of mental disorders and mental issues, psychiatry has become one of the fastest growing clinical medical disciplines. Development priorities and research foci in this field have evolved over different periods.All the articles in 10 psychiatric journals with the highest impact factors were selected from the Science Citation Index (SCI) in Web of Science from 2001 to 2015. The information visualization software Sci was used to conduct co-word and clustering analyses on these articles...
June 2017: Medicine (Baltimore)
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