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"Evolutionary mechanisms"

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https://www.readbyqxmd.com/read/28430395/flower-colour-polymorphism%C3%A2-in-the-mediterranean-basin-occurrence-maintenance-and-implications-for-speciation
#1
REVIEW
E Narbona, H Wang, P L Ortiz, M Arista, E Imbert
Flower colour polymorphism (FCP) is the occurrence of at least two discrete flower colour variants in the same population. Despite a vast body of research concerning the maintenance and evolutionary consequences of FCP, only recently has the spatial variation in morph frequencies among populations been explored. Here we have summarized the biochemical and genetic basis of FCP, the factors that have been proposed to explain their maintenance, and the importance of FCP and its geographic variation in the speciation process...
April 21, 2017: Plant Biology
https://www.readbyqxmd.com/read/28414273/oriented-clonal-cell-dynamics-enables-accurate-growth-and-shaping-of-vertebrate-cartilage
#2
Marketa Kaucka, Tomas Zikmund, Marketa Tesarova, Daniel Gyllborg, Andreas Hellander, Josef Jaros, Jozef Kaiser, Julian Petersen, Bara Szarowska, Phillip T Newton, Vyacheslav Dyachuk, Lei Li, Hong Qian, Anne-Sofie Johansson, Yuji Mishina, Josh Currie, Elly M Tanaka, Alek Erickson, Andrew Dudley, Hjalmar Brismar, Paul Southam, Enrico Coen, Min Chen, Lee S Weinstein, Ales Hampl, Ernest Arenas, Andrei S Chagin, Kaj Fried, Igor Adameyko
Cartilaginous structures are at the core of embryo growth and shaping before the bone forms. Here we report a novel principle of vertebrate cartilage growth that is based on introducing transversally-oriented clones into pre-existing cartilage. This mechanism of growth uncouples the lateral expansion of curved cartilaginous sheets from the control of cartilage thickness, a process which might be the evolutionary mechanism underlying adaptations of facial shape. In rod-shaped cartilage structures (Meckel, ribs and skeletal elements in developing limbs), the transverse integration of clonal columns determines the well-defined diameter and resulting rod-like morphology...
April 17, 2017: ELife
https://www.readbyqxmd.com/read/28401928/molecular-evolutionary-mechanisms-driving-functional-diversification-of-%C3%AE-glucosidase-in-lepidoptera
#3
Xiaotong Li, Liangen Shi, Yanyan Zhou, Hongqing Xie, Xiangping Dai, Rongqiao Li, Yuyin Chen, Huabing Wang
The digestive tract of lepidopteran insects is unique given its highly alkaline pH. The adaptive plasticity of digestive enzymes in this environment is crucial to the highly-efficient nutritional absorption in Lepidoptera. However, little is known about the molecular adaptation of digestive enzymes to this environment. Here, we show that lepidopteran α-glucosidase, a pivotal digestive enzyme, diverged into sucrose hydrolase (SUH) and other maltase subfamilies. SUH, which is specific for sucrose, was only detected in Lepidoptera...
April 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28394908/natural-non-homologous-recombination-led-to-the-emergence-of-a-duplicated-v3-ns5a-region-in-hcv-1b-strains-associated-with-hepatocellular-carcinoma
#4
Hélène Le Guillou-Guillemette, Adeline Pivert, Elise Bouthry, Cécile Henquell, Odile Petsaris, Alexandra Ducancelle, Pascal Veillon, Sophie Vallet, Sophie Alain, Vincent Thibault, Florence Abravanel, Arielle A Rosenberg, Elisabeth André-Garnier, Jean-Baptiste Bour, Yazid Baazia, Pascale Trimoulet, Patrice André, Catherine Gaudy-Graffin, Dominique Bettinger, Sylvie Larrat, Anne Signori-Schmuck, Hénia Saoudin, Bruno Pozzetto, Gisèle Lagathu, Sophie Minjolle-Cha, Françoise Stoll-Keller, Jean-Michel Pawlotsky, Jacques Izopet, Christopher Payan, Françoise Lunel-Fabiani, Christophe Lemaire
BACKGROUND: The emergence of new strains in RNA viruses is mainly due to mutations or intra and inter-genotype homologous recombination. Non-homologous recombinations may be deleterious and are rarely detected. In previous studies, we identified HCV-1b strains bearing two tandemly repeated V3 regions in the NS5A gene without ORF disruption. This polymorphism may be associated with an unfavorable course of liver disease and possibly involved in liver carcinogenesis. Here we aimed at characterizing the origin of these mutant strains and identifying the evolutionary mechanism on which the V3 duplication relies...
2017: PloS One
https://www.readbyqxmd.com/read/28391923/evolutionary-processes-and-sources-of-high-nitrate-haze-episodes-over-beijing-spring
#5
Ting Yang, Yele Sun, Wei Zhang, Zifa Wang, Xingang Liu, Pingqing Fu, Xiquan Wang
Rare and consecutive high-nitrate haze pollution episodes were observed in Beijing in spring 2012. We present detailed characterization of the sources and evolutionary mechanisms of this haze pollution, and focus on an episode that occurred between 15 and 26 April. Submicron aerosol species were found to be substantially elevated during haze episodes, and nitrates showed the largest increase and occupation (average: 32.2%) in non-refractory submicron particles (NR-PM1), which did not occur in other seasons as previously reported...
April 2017: Journal of Environmental Sciences (China)
https://www.readbyqxmd.com/read/28389535/experimental-evaluation-of-host-adaptation-of-lactobacillus-reuteri-to-different-vertebrate-species
#6
Rebbeca M Duar, Steven A Frese, Xiaoxi B Lin, Samodha C Fernando, Thomas E Burkey, Guergana Tasseva, Daniel A Peterson, Jochen Blom, Cory Q Wenzel, Christine M Szymanski, Jens Walter
The species Lactobacillus reuteri has diversified into host-specific lineages implying a long term association with different vertebrates. Strains from rodent lineages show specific adaptations to mice, but the processes underlying the evolution of L. reuteri in other hosts remain unknown. We administered three standardized inocula composed of strains from different host-confined lineages to mice, pigs, chickens and humans. The ecological performance of each strain in the gastrointestinal tract of each host was determined by typing random colonies recovered from fecal samples collected over five consecutive days post-administration...
April 7, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28387730/mimilook-a-phylogenetic-workflow-for-detection-of-gene-acquisition-in-major-orthologous-groups-of-megavirales
#7
Sourabh Jain, Arup Panda, Philippe Colson, Didier Raoult, Pierre Pontarotti
With the inclusion of new members, understanding about evolutionary mechanisms and processes by which members of the proposed order, Megavirales, have evolved has become a key area of interest. The central role of gene acquisition has been shown in previous studies. However, the major drawback in gene acquisition studies is the focus on few MV families or putative families with large variation in their genetic structure. Thus, here we have tried to develop a methodology by which we can detect horizontal gene transfers (HGTs), taking into consideration orthologous groups of distantly related Megavirale families...
April 7, 2017: Viruses
https://www.readbyqxmd.com/read/28369658/tracking-the-evolution-of-3d-gene-organization-demonstrates-its-connection-to-phenotypic-divergence
#8
Alon Diament, Tamir Tuller
It has recently been shown that the organization of genes in eukaryotic genomes, and specifically in 3D, is strongly related to gene expression and function and partially conserved between organisms. However, previous studies of 3D genomic organization analyzed each organism independently from others. Here, we propose an approach for unified inter-organismal analysis of gene organization based on a network representation of Hi-C data. We define and detect four classes of spatially co-evolving orthologous modules (SCOMs), i...
March 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28335389/characteristics%C3%A2-and%C3%A2-lethality%C3%A2-of%C3%A2-a%C3%A2-novel%C3%A2-recombinant%C3%A2-dermonecrotic%C3%A2-venom%C3%A2-phospholipase%C3%A2-d%C3%A2-from%C3%A2-hemiscorpius%C3%A2-lepturus
#9
Elham Torabi, Mahdi Behdani, Mohammad Hosseininejad Chafi, Reza Moazzami, Jean-Marc Sabatier, Vahid Khalaj, Delavar Shahbazzadeh, Kamran Pooshang Bagheri
Hemoscorpius lepturus is the most medically important scorpion in Iran. The clinical signs of H. lepturus envenomation are remarkably similar to those reported for brown spiders, including dermonecrosis, hematuria, renal failure and even death. The lethality and toxicity of brown spiders' venom have been attributed to its phospholipase D activity. This study aims to identify a phospholipase D with possible lethality and dermonecrotic activity in H. lepturus venom. In this study, a cDNA library of the venom glands was generated by Illumina RNA sequencing...
March 13, 2017: Toxins
https://www.readbyqxmd.com/read/28332079/gorilla-mhc-class-i-gene-and-sequence-variation-in-a-comparative-context
#10
Jörg B Hans, Richard A Bergl, Linda Vigilant
Comparisons of MHC gene content and diversity among closely related species can provide insights into the evolutionary mechanisms shaping immune system variation. After chimpanzees and bonobos, gorillas are humans' closest living relatives; but in contrast, relatively little is known about the structure and variation of gorilla MHC class I genes (Gogo). Here, we combined long-range amplifications and long-read sequencing technology to analyze full-length MHC class I genes in 35 gorillas. We obtained 50 full-length genomic sequences corresponding to 15 Gogo-A alleles, 4 Gogo-Oko alleles, 21 Gogo-B alleles, and 10 Gogo-C alleles including 19 novel coding region sequences...
March 22, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28292260/ruminant-specific-multiple-duplication-events-of-prdm9-before-speciation
#11
Abinash Padhi, Botong Shen, Jicai Jiang, Yang Zhou, George E Liu, Li Ma
BACKGROUND: Understanding the genetic and evolutionary mechanisms of speciation genes in sexually reproducing organisms would provide important insights into mammalian reproduction and fitness. PRDM9, a widely known speciation gene, has recently gained attention for its important role in meiotic recombination and hybrid incompatibility. Despite the fact that PRDM9 is a key regulator of recombination and plays a dominant role in hybrid incompatibility, little is known about the underlying genetic and evolutionary mechanisms that generated multiple copies of PRDM9 in many metazoan lineages...
March 14, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28289885/generation-of-stable-nulliplex-autopolyploid-lines-of-arabidopsis-thaliana-using-crispr-cas9-genome-editing
#12
Peter Ryder, Marcus McHale, Antoine Fort, Charles Spillane
RNA-guided endonuclease-mediated targeted mutagenesis using the clustered regularly interspersed short palindromic repeats (CRISPR)/Cas9 system has been successful at targeting specific loci for modification in plants. While polyploidy is an evolutionary mechanism enabling plant adaptation, the analysis of gene function in polyploid plants has been limited due to challenges associated with generating polyploid knockout mutants for all gene copies in polyploid plant lines. This study investigated whether CRISPR/Cas9 mediated targeted mutagenesis can generate nulliplex tetraploid mutant lines in Arabidopsis thaliana, while also comparing the relative efficiency of targeted mutagenesis in tetraploid (4x) versus diploid (2x) backgrounds...
March 13, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28289732/adaptation-of-escherichia-coli-to-long-term-serial-passage-in-complex-medium-evidence-of-parallel-evolution
#13
Karin E Kram, Christopher Geiger, Wazim Mohammed Ismail, Heewook Lee, Haixu Tang, Patricia L Foster, Steven E Finkel
Experimental evolution of bacterial populations in the laboratory has led to identification of several themes, including parallel evolution of populations adapting to carbon starvation, heat stress, and pH stress. However, most of these experiments study growth in defined and/or constant environments. We hypothesized that while there would likely continue to be parallelism in more complex and changing environments, there would also be more variation in what types of mutations would benefit the cells. In order to test our hypothesis, we serially passaged Escherichia coli in a complex medium (Luria-Bertani broth) throughout the five phases of bacterial growth...
March 2017: MSystems
https://www.readbyqxmd.com/read/28289251/the-evolution-of-transmission-mode
#14
REVIEW
Janis Antonovics, Anthony J Wilson, Mark R Forbes, Heidi C Hauffe, Eva R Kallio, Helen C Leggett, Ben Longdon, Beth Okamura, Steven M Sait, Joanne P Webster
This article reviews research on the evolutionary mechanisms leading to different transmission modes. Such modes are often under genetic control of the host or the pathogen, and often in conflict with each other via trade-offs. Transmission modes may vary among pathogen strains and among host populations. Evolutionary changes in transmission mode have been inferred through experimental and phylogenetic studies, including changes in transmission associated with host shifts and with evolution of the unusually complex life cycles of many parasites...
May 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28270817/regulation-of-apetala2-ethylene-response-factors-in-plants
#15
REVIEW
Ujjal J Phukan, Gajendra S Jeena, Vineeta Tripathi, Rakesh K Shukla
Multiple environmental stresses affect growth and development of plants. Plants try to adapt under these unfavorable condition through various evolutionary mechanisms like physiological and biochemical alterations connecting various network of regulatory processes. Transcription factors (TFs) like APETALA2/ETHYLENE RESPONSE FACTORS (AP2/ERFs) are an integral component of these signaling cascades because they regulate expression of a wide variety of down stream target genes related to stress response and development through different mechanism...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28259118/evolution-of-aging-theories-why-modern-programmed-aging-concepts-are-transforming-medical-research
#16
Theodore C Goldsmith
Programmed aging refers to the idea that senescence in humans and other organisms is purposely caused by evolved biological mechanisms to obtain an evolutionary advantage. Until recently, programmed aging was considered theoretically impossible because of the mechanics of the evolution process, and medical research was based on the idea that aging was not programmed. Theorists struggled for more than a century in efforts to develop non-programmed theories that fit observations, without obtaining a consensus supporting any non-programmed theory...
December 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28254477/symbiosis-in-eukaryotic-evolution
#17
Purificación López-García, Laura Eme, David Moreira
Fifty years ago, Lynn Margulis, inspiring in early twentieth-century ideas that put forward a symbiotic origin for some eukaryotic organelles, proposed a unified theory for the origin of the eukaryotic cell based on symbiosis as evolutionary mechanism. Margulis was profoundly aware of the importance of symbiosis in the natural microbial world and anticipated the evolutionary significance that integrated cooperative interactions might have as mechanism to increase cellular complexity. Today, we have started fully appreciating the vast extent of microbial diversity and the importance of syntrophic metabolic cooperation in natural ecosystems, especially in sediments and microbial mats...
February 28, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28250810/managing-cryptic-biodiversity-fine-scale-intralacustrine-speciation-along-a-benthic-gradient-in-alpine-whitefish-coregonus-spp
#18
Alan G Hudson, Baenz Lundsgaard-Hansen, Kay Lucek, Pascal Vonlanthen, Ole Seehausen
Whitefish (Coregonus spp.) are an important catch for many freshwater fisheries, particularly in Switzerland. In support of this, supplemental stocking of whitefish species is carried out, despite lacking complete knowledge of the extent, distribution and origin of whitefish diversity in these lakes, potentially threatening local endemics via artificial gene flow. Here, we investigate phenotypic and genetic differentiation among coexisting whitefish species spawning along a depth gradient in a subalpine Swiss lake to better delineate intralacustrine whitefish biodiversity...
March 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28225773/whole-genome-duplication-and-molecular-evolution-in-cornus-l-cornaceae-insights-from-transcriptome-sequences
#19
Yan Yu, Qiuyun Xiang, Paul S Manos, Douglas E Soltis, Pamela S Soltis, Bao-Hua Song, Shifeng Cheng, Xin Liu, Gane Wong
The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework...
2017: PloS One
https://www.readbyqxmd.com/read/28222092/the-genetic-basis-of-resistance-and-matching-allele-interactions-of-a-host-parasite-system-the-daphnia-magna-pasteuria-ramosa-model
#20
Gilberto Bento, Jarkko Routtu, Peter D Fields, Yann Bourgeois, Louis Du Pasquier, Dieter Ebert
Negative frequency-dependent selection (NFDS) is an evolutionary mechanism suggested to govern host-parasite coevolution and the maintenance of genetic diversity at host resistance loci, such as the vertebrate MHC and R-genes in plants. Matching-allele interactions of hosts and parasites that prevent the emergence of host and parasite genotypes that are universally resistant and infective are a genetic mechanism predicted to underpin NFDS. The underlying genetics of matching-allele interactions are unknown even in host-parasite systems with empirical support for coevolution by NFDS, as is the case for the planktonic crustacean Daphnia magna and the bacterial pathogen Pasteuria ramosa...
February 2017: PLoS Genetics
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