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"Evolutionary mechanisms"

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https://www.readbyqxmd.com/read/28292260/ruminant-specific-multiple-duplication-events-of-prdm9-before-speciation
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28219972/venomics-integrative-venom-proteomics-and-beyond
#11
REVIEW
Juan J Calvete
Venoms are integrated phenotypes that evolved independently in, and are used for predatory and defensive purposes by, a wide phylogenetic range of organisms. The same principles that contribute to the evolutionary success of venoms, contribute to making the study of venoms of great interest in such diverse fields as evolutionary ecology and biotechnology. Evolution is profoundly contingent, and nature also reinvents itself continuosly. Changes in a complex phenotypic trait, such as venom, reflect the influences of prior evolutionary history, chance events, and selection...
February 20, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28212437/the-nature-of-allometry-in-an-exaggerated-trait-the-postocular-flange-in-platyneuromus-weele-insecta-megaloptera
#12
Andrés Ramírez-Ponce, Gabriela Garfias-Lozano, Atilano Contreras-Ramos
The origin and function of exaggerated traits exhibited by a great number of species with sexual dimorphism remain largely unexplored. The usual model considered as the evolutionary mechanism for the development of these structures is sexual selection. The nature of growth of the postocular flange (POF) in three species of the dobsonfly genus Platyneuromus (Megaloptera, Corydalidae, Corydalinae) is analyzed to explore sexual size dimorphism and allometric scaling. Results involve positive allometry of POF in males of two species, and negative allometry in males of one species, in general with a female-biased sexual dimorphism...
2017: PloS One
https://www.readbyqxmd.com/read/28205599/network-growth-models-a-behavioural-basis-for-attachment-proportional-to-fitness
#13
Michael Bell, Supun Perera, Mahendrarajah Piraveenan, Michiel Bliemer, Tanya Latty, Chris Reid
Several growth models have been proposed in the literature for scale-free complex networks, with a range of fitness-based attachment models gaining prominence recently. However, the processes by which such fitness-based attachment behaviour can arise are less well understood, making it difficult to compare the relative merits of such models. This paper analyses an evolutionary mechanism that would give rise to a fitness-based attachment process. In particular, it is proven by analytical and numerical methods that in homogeneous networks, the minimisation of maximum exposure to node unfitness leads to attachment probabilities that are proportional to node fitness...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28185554/evolution-of-transcriptional-networks-in-yeast-alternative-teams-of-transcriptional-factors-for-different-species
#14
Adriana Muñoz, Daniella Santos Muñoz, Aleksey Zimin, James A Yorke
BACKGROUND: The diversity in eukaryotic life reflects a diversity in regulatory pathways. Nocedal and Johnson argue that the rewiring of gene regulatory networks is a major force for the diversity of life, that changes in regulation can create new species. RESULTS: We have created a method (based on our new "ping-pong algorithm) for detecting more complicated rewirings, where several transcription factors can substitute for one or more transcription factors in the regulation of a family of co-regulated genes...
November 11, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28185400/microdiversity-shapes-the-traits-niche-space-and-biogeography-of-microbial-taxa
#15
REVIEW
Alyse A Larkin, Adam C Martiny
With rapidly improving sequencing technologies, scientists have recently gained the ability to examine diverse microbial communities at high genomic resolution, revealing that both free-living and host-associated microbes partition their environment at fine phylogenetic scales. This 'microdiversity,' or closely related (> 97% similar 16S rRNA gene) but ecologically and physiologically distinct sub-taxonomic groups, appears to be an intrinsic property of microorganisms. However, the functional implications of microdiversity as well as its effects on microbial biogeography are poorly understood...
February 10, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28181048/evolutionary-mechanism-and-biological-functions-of-8-mers-containing-cg-dinucleotide-in-yeast
#16
Yan Zheng, Hong Li, Yue Wang, Hu Meng, Qiang Zhang, Xiaoqing Zhao
The rules of k-mer non-random usage and the biological functions are worthy of special attention. Firstly, the article studied human 8-mer spectra and found that only the spectra of cytosine-guanine (CG) dinucleotide classification formed independent unimodal distributions when the 8-mers were classified into three subsets under 16 dinucleotide classifications. Secondly, the distribution rules were reproduced by other seven species including yeast, which showed that the evolution phenomenon had species universality...
February 9, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28173627/genetic-architecture-and-balancing-selection-the-life-and-death-of-differentiated-variants
#17
Violaine Llaurens, Annabel Whibley, Mathieu Joron
Balancing selection describes any form of natural selection which results in the persistence of multiple variants of a trait at intermediate frequencies within populations. By offering up a snapshot of multiple co-occurring functional variants and their interactions, systems under balancing selection can reveal the evolutionary mechanisms favouring the emergence and persistence of adaptive variation in natural populations. We here focus on the mechanisms by which several functional variants for a given trait can arise, a process typically requiring multiple epistatic mutations...
February 7, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28165020/a-potent-synthetic-inorganic-antibiotic-with-activity-against-drug-resistant-pathogens
#18
Shelby Hubick, Arumugam Jayaraman, Alexander McKeen, Shelby Reid, Jane Alcorn, John Stavrinides, Brian T Sterenberg
The acronymously named "ESKAPE" pathogens represent a group of bacteria that continue to pose a serious threat to human health, not only due to their propensity for repeated emergence, but also due to their ability to "eskape" antibiotic treatment. The evolution of multi-drug resistance in these pathogens alone has greatly outpaced the development of new therapeutics, necessitating an alternative strategy for antibiotic development that considers the evolutionary mechanisms driving antibiotic resistance. In this study, we synthesize a novel inorganic antibiotic, phosphopyricin, which has antibiotic activity against the Gram-positive methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VRE)...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28161510/the-material-record-and-the-antiquity-of-language
#19
REVIEW
Ian Tattersall
One view of language origins sees it as ancient and selection-driven; the other as recent and emergent. Such disagreement occurs because language is ephemeral, detectable only by indirect proxies. Because internalized language and symbolic thought are tightly linked, the best archaeological proxies for language are symbolic objects. Nothing indicates convincingly that any hominid behaved symbolically prior to Homo sapiens, which originated 200 kyr ago but started behaving symbolically only 100 kyr later. Most probably the necessary neural underpinnings arose exaptively in the extensive developmental reorganization that gave rise to anatomically distinctive Homo sapiens, and were recruited subsequently via a necessarily behavioral stimulus...
February 1, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28160497/unusual-evolutionary-mechanisms-to-escape-effector-triggered-immunity-in-the-fungal-phytopathogen-leptosphaeria-maculans
#20
C Plissonneau, F Blaise, B Ollivier, M Leflon, J Carpezat, T Rouxel, M-H Balesdent
Leptosphaeria maculans is the fungus responsible for the stem canker disease of oilseed rape (Brassica napus). AvrLm3 and AvrLm4-7, two avirulence effector genes of L. maculans, are involved in an unusual relationship: AvrLm4-7 suppresses the Rlm3-mediated resistance. Here, we assessed AvrLm3 polymorphism in a collection of 235 L. maculans isolates. No field isolates exhibited deletion or inactivating mutations in AvrLm3, as observed for other L. maculans avirulence genes. Eleven isoforms of the AvrLm3 protein were found...
February 4, 2017: Molecular Ecology
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