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"Evolutionary mechanisms"

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https://www.readbyqxmd.com/read/28634295/population-genomic-inference-of-the-strength-and-timing-of-selection-against-gene-flow
#1
Simon Aeschbacher, Jessica P Selby, John H Willis, Graham Coop
The interplay of divergent selection and gene flow is key to understanding how populations adapt to local environments and how new species form. Here, we use DNA polymorphism data and genome-wide variation in recombination rate to jointly infer the strength and timing of selection, as well as the baseline level of gene flow under various demographic scenarios. We model how divergent selection leads to a genome-wide negative correlation between recombination rate and genetic differentiation among populations...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28630745/correlation-between-hox-code-and-vertebral-morphology-in-the-mouse-towards-a-universal-model-for-synapsida
#2
Christine Böhmer
BACKGROUND: The importance of the cervical vertebrae as part of the skull-neck system in facilitating the success and diversity of tetrapods is clear. The reconstruction of its evolution, however, is problematic because of the variation in the number of vertebrae, making it difficult to identify homologous elements. Quantification of the morphological differentiation in the neck of diverse archosaurs established homologous units of vertebrae (i.e. modules) resulting from Hox gene expression patterns within the cervical vertebral column...
2017: Zoological Letters
https://www.readbyqxmd.com/read/28611746/adaptations-to-high-salt-in-a-halophilic-protist-differential-expression-and-gene-acquisitions-through-duplications-and-gene-transfers
#3
Tommy Harding, Andrew J Roger, Alastair G B Simpson
The capacity of halophiles to thrive in extreme hypersaline habitats derives partly from the tight regulation of ion homeostasis, the salt-dependent adjustment of plasma membrane fluidity, and the increased capability to manage oxidative stress. Halophilic bacteria, and archaea have been intensively studied, and substantial research has been conducted on halophilic fungi, and the green alga Dunaliella. By contrast, there have been very few investigations of halophiles that are phagotrophic protists, i.e., protozoa...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28592544/time-sampled-population-sequencing-reveals-the-interplay-of-selection-and-genetic-drift-in-experimental-evolution-of-potato-virus-y
#4
Denis Kutnjak, Santiago F Elena, Maja Ravnikar
RNA viruses are one of the fastest evolving biological entities. Within their hosts, they exist as genetically diverse populations (i.e., viral mutant swarms), which are sculpted by different evolutionary mechanisms, such as mutation, natural selection and genetic drift, and also the interactions between genetic variants within the mutant swarms. To elucidate the mechanisms that modulate the population diversity of an important plant pathogenic virus, we performed evolution experiments with Potato virus Y (PVY) in potato genotypes that differ in their defense response against the virus...
June 7, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28591676/evolution-of-commensal-bacteria-in-the-intestinal-tract-of-mice
#5
REVIEW
Ana Sousa, Nelson Frazão, Ricardo S Ramiro, Isabel Gordo
Hundreds of different bacterial species inhabit our intestines and contribute to our health status, with significant loss of species diversity typically observed in disease conditions. Within each microbial species a great deal of diversity is hidden and such intra-specific variation is also key to the proper homeostasis between the host and its microbial inhabitants. Indeed, it is at this level that new mechanisms of antibiotic resistance emerge and pathogenic characteristics evolve. Yet, our knowledge on intra-species variation in the gut is still limited and an understanding of the evolutionary mechanisms acting on it is extremely reduced...
June 4, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28578268/carbon-emission-allowance-allocation-with-a-mixed-mechanism-in-air-passenger-transport
#6
Rui Qiu, Jiuping Xu, Ziqiang Zeng
Air passenger transport carbon emissions have become a great challenge for both governments and airlines because of rapid developments in the aviation industry in recent decades. In this paper, a mixed mechanism composed of a cap-and-trade mechanism and a carbon tax mechanism is developed to assist governments in allocating carbon emission allowances to airlines operating on the routes. Combined this mixed mechanism with an equilibrium strategy, a bi-level multi-objective model is proposed for an air passenger transport carbon emission allowance allocation problem, in which a government is considered as a leader and the airlines as the followers...
June 1, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28576775/cold-fusion-massive-karyotype-evolution-in-the-antarctic-bullhead-notothen-notothenia-coriiceps
#7
Angel Amores, Catherine A Wilson, Corey A H Allard, H William Detrich, John H Postlethwait
Half of all vertebrate species share a series of chromosome fusions that preceded the teleost genome duplication, but we don't understand the causative evolutionary mechanisms. The "Robertsonian-translocation hypothesis" suggests a regular fusion of each ancestral acro- or telocentric chromosome to just one other by centromere fusions, thus halving the karyotype. An alternative "genome-stirring hypothesis" posits haphazard and repeated fusions, inversions, and reciprocal and non-reciprocal translocations. To study large-scale karyotype reduction, we investigated the decrease of chromosome numbers in Antarctic notothenioid fish...
June 2, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28559354/rna-seq-reveals-conservation-of-function-among-the-yolk-sacs-of-human-mouse-and-chicken
#8
Tereza Cindrova-Davies, Eric Jauniaux, Michael G Elliot, Sungsam Gong, Graham J Burton, D Stephen Charnock-Jones
The yolk sac is phylogenetically the oldest of the extraembryonic membranes. The human embryo retains a yolk sac, which goes through primary and secondary phases of development, but its importance is controversial. Although it is known to synthesize proteins, its transport functions are widely considered vestigial. Here, we report RNA-sequencing (RNA-seq) data for the human and murine yolk sacs and compare those data with data for the chicken. We also relate the human RNA-seq data to proteomic data for the coelomic fluid bathing the yolk sac...
May 30, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28554837/identification-polymorphism-and-expression-of-mhc-class-i%C3%AE-in-golden-pompano-trachinotus-ovatus
#9
Zhenjie Cao, Mingwang He, Xiaojuan Chen, Shifeng Wang, Yan Cai, Zhenyu Xie, Yun Sun, Yongcan Zhou
The classical major histocompatibility complex class I (MHC I) plays a vital role in the immune system. In this study, we cloned and identified golden pompano (Trachinotus ovatus) MHC Iα (Trov-MHC Iα), which encodes 351 amino acid residues including a leader peptide, α1, α2, α3 domain, a transmembrane region and a cytoplasmic domain. Twenty six different sequences, which encoded various numbers of amino acid residues ranging from 348 to 354, were obtained from 12 individuals. Highly genetic polymorphism was found in the Trov-MHC Iα, especially in the α1 and α2 domains...
May 26, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28533897/introduction-to-the-special-issue-tree-invasions-towards-a-better-understanding-of-their-complex-evolutionary-dynamics
#10
Heidi Hirsch, David M Richardson, Johannes J Le Roux
Many invasive plants show evidence of trait-based evolutionary change, but these remain largely unexplored for invasive trees. The increasing number of invasive trees and their tremendous impacts worldwide, however, illustrates the urgent need to bridge this knowledge gap to apply efficient management. Consequently, an interdisciplinary workshop, held in 2015 at Stellenbosch University in Stellenbosch, South Africa, brought together international researchers to discuss our understanding of evolutionary dynamics in invasive trees...
May 2017: AoB Plants
https://www.readbyqxmd.com/read/28532797/genetic-basis-for-loss-of-immuno-reactive-o-chain-in-salmonella-enterica-serovar-enteritidis-veterinary-isolates
#11
Istvan Szabo, Marianne Grafe, Nicole Kemper, Ernst Junker, Burkhard Malorny
Fifty-two rough Salmonella enterica serovar Enteritidis (S. Enteritidis) isolates from broilers and the environment were characterized for their serological and genotypic properties. Under routine diagnostic serotyping methods such isolates lack the immuno-reactivity of the O-chain of the lipopolysaccharide (LPS), and are referred to as non-typeable. Using a modified slide agglutination method, the isolates could be differentiated into three different serological variants. Twenty-six isolates (50%) were defined as semi-rough, nineteen isolates (37%) as deep-rough, four isolates (8%) as rough and three isolates could not be assigned...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28521939/developmental-and-evolutionary-mechanisms-shaping-butterfly-eyespots
#12
REVIEW
Patrícia Beldade, Carolina M Peralta
Butterfly eyespots are visually compelling models to study the reciprocal interactions between evolutionary and developmental processes that shape phenotypic variation. They are evolutionarily diversified, ecologically relevant, and developmentally tractable, and have made key contributions to linking genotype, development, phenotype and fitness. Advances in the availability of analytical tools (e.g. gene editing and visualization techniques) and resources (e.g. genomic and transcriptomic data) are boosting the detailed dissection of the mechanisms underlying eyespot development and evolution...
February 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28514442/architecture-of-the-human-interactome-defines-protein-communities-and-disease-networks
#13
Edward L Huttlin, Raphael J Bruckner, Joao A Paulo, Joe R Cannon, Lily Ting, Kurt Baltier, Greg Colby, Fana Gebreab, Melanie P Gygi, Hannah Parzen, John Szpyt, Stanley Tam, Gabriela Zarraga, Laura Pontano-Vaites, Sharan Swarup, Anne E White, Devin K Schweppe, Ramin Rad, Brian K Erickson, Robert A Obar, K G Guruharsha, Kejie Li, Spyros Artavanis-Tsakonas, Steven P Gygi, J Wade Harper
The physiology of a cell can be viewed as the product of thousands of proteins acting in concert to shape the cellular response. Coordination is achieved in part through networks of protein-protein interactions that assemble functionally related proteins into complexes, organelles, and signal transduction pathways. Understanding the architecture of the human proteome has the potential to inform cellular, structural, and evolutionary mechanisms and is critical to elucidating how genome variation contributes to disease...
May 25, 2017: Nature
https://www.readbyqxmd.com/read/28510588/evolutionary-restoration-of-fertility-in-an-interspecies-hybrid-yeast-by-whole-genome-duplication-after-a-failed-mating-type-switch
#14
Raúl A Ortiz-Merino, Nurzhan Kuanyshev, Stephanie Braun-Galleani, Kevin P Byrne, Danilo Porro, Paola Branduardi, Kenneth H Wolfe
Many interspecies hybrids have been discovered in yeasts, but most of these hybrids are asexual and can replicate only mitotically. Whole-genome duplication has been proposed as a mechanism by which interspecies hybrids can regain fertility, restoring their ability to perform meiosis and sporulate. Here, we show that this process occurred naturally during the evolution of Zygosaccharomyces parabailii, an interspecies hybrid that was formed by mating between 2 parents that differed by 7% in genome sequence and by many interchromosomal rearrangements...
May 2017: PLoS Biology
https://www.readbyqxmd.com/read/28507050/tumor-dormancy-and-relapse-from-a-natural-byproduct-of-evolution-to-a-disease-state
#15
REVIEW
Masoud H Manjili
Species evolve by mutations and epigenetic changes acting on individuals in a population; tumors evolve by similar mechanisms at a cellular level in a tissue. This article reviews growing evidence about tumor dormancy and suggests that (i) cellular malignancy is a natural byproduct of evolutionary mechanisms, such as gene mutations and epigenetic modifications, which is manifested in the form of tumor dormancy in healthy individuals as well as in cancer survivors; (ii) cancer metastasis could be an early dissemination event that could occur during malignant dormancy even before primary cancer is clinically detectable; and (iii) chronic inflammation is a key factor in awakening dormant malignant cells at the primary site, leading to primary cancer development, and at distant sites, leading to advanced stage diseases...
May 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28503179/molecular-and-evolutionary-mechanisms-of-cuticular-wax-for-plant-drought-tolerance
#16
REVIEW
Dawei Xue, Xiaoqin Zhang, Xueli Lu, Guang Chen, Zhong-Hua Chen
Cuticular wax, the first protective layer of above ground tissues of many plant species, is a key evolutionary innovation in plants. Cuticular wax safeguards the evolution from certain green algae to flowering plants and the diversification of plant taxa during the eras of dry and adverse terrestrial living conditions and global climate changes. Cuticular wax plays significant roles in plant abiotic and biotic stress tolerance and has been implicated in defense mechanisms against excessive ultraviolet radiation, high temperature, bacterial and fungal pathogens, insects, high salinity, and low temperature...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28493321/local-genes-for-local-bacteria-evidence-of-allopatry-in-the-genomes-of-transatlantic-campylobacter-populations
#17
Ben Pascoe, Guillaume Méric, Koji Yahara, Helen Wimalarathna, Susan Murray, Matthew D Hitchings, Emma L Sproston, Catherine D Carrillo, Eduardo N Taboada, Kerry K Cooper, Steven Huynh, Alison J Cody, Keith A Jolley, Martin C J Maiden, Noel D McCarthy, Xavier Didelot, Craig T Parker, Samuel K Sheppard
The genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distance and genetic distance, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance with past human migration, whereas in Mycobacterium tuberculosis it is the lack of recombination that causes allopatric clusters. In Campylobacter, analyses of genomic data and molecular typing have been successful in determining the reservoir host species, but not geographical origin...
May 10, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28484234/inferring-the-evolutionary-mechanism-of-the-chloroplast-genome-size-by-comparing-whole-chloroplast-genome-sequences-in-seed-plants
#18
Zheng Xiao-Ming, Wang Junrui, Feng Li, Liu Sha, Pang Hongbo, Qi Lan, Li Jing, Sun Yan, Qiao Weihua, Zhang Lifang, Cheng Yunlian, Yang Qingwen
The chloroplast genome originated from photosynthetic organisms and has retained the core genes that mainly encode components of photosynthesis. However, the causes of variations in chloroplast genome size in seed plants have only been thoroughly analyzed within small subsets of spermatophytes. In this study, we conducted the first comparative analysis on a large scale to examine the relationship between sequence characteristics and genome size in 272 seed plants based on cross-species and phylogenetic signal analysis...
May 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28475810/draft-genome-sequence-of-the-tibetan-medicinal-herb-rhodiola-crenulata
#19
Yuanyuan Fu, Liangwei Li, Shijie Hao, Rui Guan, Guangyi Fan, Chengcheng Shi, Haibo Wan, Wenbin Chen, He Zhang, Guocheng Liu, Jihua Wang, Lulin Ma, Jianling You, Xuemei Ni, Zhen Yue, Xun Xu, Xiao Sun, Xin Liu, Simon Ming-Yuen Lee
Background: Rhodiola crenulata , a well-known medicinal Tibetan herb, is mainly grown in high-altitude regions of Tibet, Yunnan and Sichuan provinces in China. In the past few years increasing numbers of studies have been published on the potential pharmacological activities of R. crenulata , strengthening our understanding into its putitive active ingredient composition, pharmacological activity and mechanism of action. These findings also provide strong evidence supporting the important medicinal and economical value of R...
May 5, 2017: GigaScience
https://www.readbyqxmd.com/read/28472922/phenotypic-disparity-in-iberian-short-horned-grasshoppers-acrididae-the-role-of-ecology-and-phylogeny
#20
Vicente García-Navas, Víctor Noguerales, Pedro J Cordero, Joaquín Ortego
BACKGROUND: The combination of model-based comparative techniques, disparity analyses and ecomorphological correlations constitutes a powerful method to gain insight into the evolutionary mechanisms that shape morphological variation and speciation processes. In this study, we used a time-calibrated phylogeny of 70 Iberian species of short-horned grasshoppers (Acrididae) to test for patterns of morphological disparity in relation to their ecology and phylogenetic history. Specifically, we examined the role of substrate type and level of ecological specialization in driving different aspects of morphological evolution (locomotory traits, chemosensitive organs and cranial morphology) in this recent radiation...
May 4, 2017: BMC Evolutionary Biology
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