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"Natural selection"

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https://www.readbyqxmd.com/read/28631230/sequence-analysis-of-chromosome-1-revealed-different-selection-patterns-between-chinese-wild-mice-and-laboratory-strains
#1
Fuyi Xu, Shixian Hu, Tianzhu Chao, Maochun Wang, Kai Li, Yuxun Zhou, Hongyan Xu, Junhua Xiao
Both natural and artificial selection play a critical role in animals' adaptation to the environment. Detection of the signature of selection in genomic regions can provide insights for understanding the function of specific phenotypes. It is generally assumed that laboratory mice may experience intense artificial selection while wild mice more natural selection. However, the differences of selection signature in the mouse genome and underlying genes between wild and laboratory mice remain unclear. In this study, we used two mouse populations: chromosome 1 (Chr 1) substitution lines (C1SLs) derived from Chinese wild mice and mouse genome project (MGP) sequenced inbred strains and two selection detection statistics: Fst and Tajima's D to identify the signature of selection footprint on Chr 1...
June 19, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28630336/the-red-queen-and-king-in-finite-populations
#2
Carl Veller, Laura K Hayward, Christian Hilbe, Martin A Nowak
In antagonistic symbioses, such as host-parasite interactions, one population's success is the other's loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the "Red Queen effect"), but disfavored in certain mutualistic symbioses (the "Red King effect")...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28630113/complex-coding-and-regulatory-polymorphisms-in-a-restriction-factor-determine-the-susceptibility-of-drosophila-to-viral-infection
#3
Chuan Cao, Rodrigo Cogni, Vincent Barbier, Francis M Jiggins
It is common to find that major-effect genes are an important cause of variation in susceptibility to infection. Here we have characterised natural variation in a gene called pastrel that explains over half of the genetic variance in susceptibility to the virus DCV in populations of Drosophila melanogaster We found extensive allelic heterogeneity, with a sample of seven alleles of pastrel from around the world conferring four phenotypically distinct levels of resistance. By modifying candidate SNPs in transgenic flies, we show that the largest effect is caused by an amino acid polymorphism that arose when an ancestral threonine was mutated to alanine, greatly increasing resistance to DCV...
June 19, 2017: Genetics
https://www.readbyqxmd.com/read/28630001/host-influence-in-the-genomic-composition-of-flaviviruses-a-multivariate-approach
#4
Diego Simón, Alvaro Fajardo, Martín Sóñora, Adriana Delfraro, Héctor Musto
Flaviviruses present substantial differences in their host range and transmissibility. We studied the evolution of base composition, dinucleotide biases, codon usage and amino acid frequencies in the genus Flavivirus within a phylogenetic framework by principal components analysis. There is a mutual interplay between the evolutionary history of flaviviruses and their respective vectors and/or hosts. Hosts associated to distinct phylogenetic groups may be driving flaviviruses at different pace and through various sequence landscapes, as can be seen for viruses associated with Aedes or Culex spp...
June 16, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28627970/genome-wide-codon-usage-profiling-of-ocular-infective-chlamydia-trachomatis-serovars-and-drug-target-identification
#5
Anupriya Sadhasivam, Umashankar Vetrivel
Chlamydia trachomatis (C.t) is a gram-negative obligate intracellular bacteria and is a major causative of infectious blindness and sexually transmitted diseases. Among the varied serovars of this organism, A, B & C are reported as prominent ocular pathogens. Genomic studies of these strains shall aid in deciphering potential drug targets and genomic influence on pathogenesis. Hence, in this study we performed deep statistical profiling of codon usage in these serovars. The overall base composition analysis reveals that these serovars are over biased to AU than GC...
June 19, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28625542/analysis-of-the-codon-usage-of-the-orf2-gene-of-feline-calicivirus
#6
Minghui Zang, Wanting He, Fanshu Du, Gongjian Wu, Bohao Wu, Zhenlei Zhou
Feline calicivirus (FCV) is a highly prevalent pathogen of the domestic cat that causes acute infections of the oral and upper respiratory tract. The E region of the ORF2 protein is responsible for the induction of virus-neutralizing antibodies, thus it is important to understand the codon usage of this gene. Here, analysed 90 coding sequences of ORF2 and show that it undergoes a low codon usage bias. In addition, although mutational bias is one of the factors shaping the codon usage bias of this gene, natural selection plays a more significant role...
June 15, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28623896/with-a-little-help-from-my-friends-cooperation-can-accelerate-the-rate-of-adaptive-valley-crossing
#7
Uri Obolski, Ohad Lewin-Epstein, Eran Even-Tov, Yoav Ram, Lilach Hadany
BACKGROUND: Natural selection favors changes that lead to genotypes possessing high fitness. A conflict arises when several mutations are required for adaptation, but each mutation is separately deleterious. The process of a population evolving from a genotype encoding for a local fitness maximum to a higher fitness genotype is termed an adaptive peak shift. RESULTS: Here we suggest cooperative behavior as a factor that can facilitate adaptive peak shifts. We model cooperation in a public goods scenario, wherein each individual contributes resources that are later equally redistributed among all cooperating individuals...
June 17, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28618009/evidence-of-an-evolutionary-hourglass-pattern-in-herbivory-induced-transcriptomic-responses
#8
Matthew Durrant, Justin Boyer, Wenwu Zhou, Ian T Baldwin, Shuqing Xu
Herbivory-induced defenses are specific and activated in plants when elicitors, frequently found in the herbivores' oral secretions, are introduced into wounds during attack. While complex signaling cascades are known to be involved, it remains largely unclear how natural selection has shaped the evolution of these induced defenses. We analyzed herbivory-induced transcriptomic responses in wild tobacco, Nicotiana attenuata, using a phylotranscriptomic approach that measures the origin and sequence divergence of herbivory-induced genes...
June 15, 2017: New Phytologist
https://www.readbyqxmd.com/read/28617637/how-parallel-is-parallel-evolution-a-comparative-analysis-in-fishes
#9
Krista B Oke, Gregor Rolshausen, Caroline LeBlond, Andrew P Hendry
Evidence of phenotypic parallelism is often used to infer the deterministic role played by natural selection. However, variation in the extent or direction of divergence is often evident among independent evolutionary replicates, raising the following question: just how parallel, overall, is parallel evolution? We answer this question through a comparative analysis of studies of fishes, a taxon where parallel evolution has been much discussed. We first ask how much of the among-population variance in phenotypic traits can be explained by different "environment" types, such as high predation versus low predation or benthic versus limnetic...
July 2017: American Naturalist
https://www.readbyqxmd.com/read/28616168/does-selection-on-horn-length-of-males-and-females-differ-in-protected-and-hunted-populations-of-a-weakly-dimorphic-ungulate
#10
Luca Corlatti, Ilse Storch, Flurin Filli, Pia Anderwald
Weaponry in ungulates may be costly to grow and maintain, and different selective pressures in males and females may lead to sex-biased natural survival. Sexual differences in the relationship between weapon growth and survival may increase under anthropogenic selection through culling, for example because of trophy hunting. Selection on weaponry growth under different scenarios has been largely investigated in males of highly dimorphic ungulates, for which survival costs (either natural or hunting related) are thought to be greatest...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28615130/different-breeds-different-blood-cytometric-analysis-of-whole-blood-cellular-composition-in-chicken-breeds
#11
Barbora Bílková, Zuzana Bainová, Jozef Janda, Lukáš Zita, Michal Vinkler
While haematological variation is well known in birds, variation in avian breeds (distinct morphotypes of the same species) remains unexplored. Poultry breeds, in particular, may show interesting evolutionary patterns and economically-relevant physiological differences. We performed a comparative examination of blood cellular composition in five chicken (Gallus gallus domesticus) breeds: Araucana, Booted bantam, Czech, Minorca and Rosecomb bantam. In standard-environment-reared hens whole-blood flow cytometry revealed remarkable differences in most erythrocyte- and leukocyte-related parameters...
June 2017: Veterinary Immunology and Immunopathology
https://www.readbyqxmd.com/read/28612961/genome-wide-analysis-of-allele-frequency-change-in-sunflower-crop-wild-hybrid-populations-evolving-under-natural-conditions
#12
Jonathan Corbi, Eric J Baack, Jennifer M Dechaine, Gerald Seiler, John M Burke
Crop-wild hybridization occurs in numerous plant species, and could alter the genetic structure and evolutionary dynamics of wild populations. Studying crop-derived alleles in wild populations is also relevant to assessing/mitigating the risks associated with transgene escape. To date, crop-wild hybridization has generally been examined via short-term studies, typically within a single generation, focusing on few traits or genetic markers. Little is known about patterns of selection on crop-derived alleles over multiple generations, particularly at a genome-wide scale...
June 14, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28611072/decoupled-leaf-and-root-carbon-economics-is-a-key-component-in-the-ecological-diversity-and-evolutionary-divergence-of-deciduous-and-evergreen-lineages-of-genus-rhododendron
#13
Juliana S Medeiros, Jean H Burns, Jaynell Nicholson, Louisa Rogers, Oscar Valverde-Barrantes
PREMISE: We explored trait-trait and trait-climate relationships for 27 Rhododendron species while accounting for phylogenetic relationships and within-species variation to investigate whether leaf and root traits are coordinated across environments and over evolutionary time, as part of a whole-plant economics spectrum. METHODS: We examined specific leaf area (SLA) and four root traits: specific root length (SRL), specific root tip abundance (SRTA), first order diameter, and link average length, for plants growing in a cold, seasonal climate (Kirtland, Ohio) and a warmer, less seasonal climate (Federal Way, Washington) in the United States...
June 13, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28606821/analysis-of-synonymous-codon-usage-in-zika-virus
#14
Snawar Hussain, Sahibzada Tasleem Rasool
Zika virus is a zoonotic pathogen, which have made frequent incursion into the human population in Africa and South East Asia over the course of several decades but never reached to the pandemic proportions until the most recent outbreak. Viruses are solely dependent on host synthetic machinery for their replication cycle; therefore, replication and persistence in a host species of different genetic background requires certain degree of adaptation. These adaptations are necessary to avoid detection from host immune surveillance and maximize the utilization of available resources for efficient viral replication...
June 9, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28601632/intraspecific-gestural-laterality-in-chimpanzees-and-gorillas-and-the-impact-of-social-propensities
#15
Jacques Prieur, Simone Pika, Stéphanie Barbu, Catherine Blois-Heulin
A relevant approach to address the mechanisms underlying the emergence of the right-handedness/left-hemisphere language specialization of humans is to investigate both proximal and distal causes of language lateralization through the study of non-human primates' gestural laterality. We carried out the first systematic, quantitative comparison of within-subjects' and between-species' laterality by focusing on the laterality of intraspecific gestures of chimpanzees (Pan troglodytes) and gorillas (Gorilla gorilla) living in six different captive groups...
June 7, 2017: Brain Research
https://www.readbyqxmd.com/read/28598644/proof-of-concept-for-an-ultrasensitive-technique-to-detect-and-localize-sources-of-elastic-nonlinearity-using-phononic-crystals
#16
M Miniaci, A S Gliozzi, B Morvan, A Krushynska, F Bosia, M Scalerandi, N M Pugno
The appearance of nonlinear effects in elastic wave propagation is one of the most reliable and sensitive indicators of the onset of material damage. However, these effects are usually very small and can be detected only using cumbersome digital signal processing techniques. Here, we propose and experimentally validate an alternative approach, using the filtering and focusing properties of phononic crystals to naturally select and reflect the higher harmonics generated by nonlinear effects, enabling the realization of time-reversal procedures for nonlinear elastic source detection...
May 26, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28597968/genetic-epidemiology-of-familial-mediterranean-fever-through-integrative-analysis-of-whole-genome-and-exome-sequences-from-middle-east-and-north-africa
#17
Remya Koshy, Ambily Sivadas, Vinod Scaria
Familial Mediterranean fever (FMF), an autosomal recessive and rare autoinflammatory disease is caused by genetic mutations in the MEFV gene and is highly prevalent in the Mediterranean basin. Though the carrier frequency of specific disease variants in the MEFV gene has been reported from isolated studies, a comprehensive view of variants in the Mediterranean region has not been possible due to paucity of data. The recent availability of whole-genome and whole-exome datasets prompted us to study the genetic epidemiology of MEFV variants in the region...
June 9, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28592948/occurrence-and-evolutionary-analysis-of-coat-protein-gene-sequences-of-iranian-isolates-of-sugarcane-mosaic-virus
#18
Zohreh Moradi, Ehsan Nazifi, Mohsen Mehrvar
Sugarcane mosaic virus (SCMV) is one of the most damaging viruses infecting sugarcane, maize and some other graminaceous species around the world. To investigate the genetic diversity of SCMV in Iran, the coat protein (CP) gene sequences of 23 SCMV isolates from different hosts were determined. The nucleotide sequence identity among Iranian isolates was more than 96%. They shared nucleotide identities of 75.5-99.9% with those of other SCMV isolates available in GenBank, the highest with the Egyptian isolate EGY7-1 (97...
June 2017: Plant Pathology Journal
https://www.readbyqxmd.com/read/28592669/what-shapes-the-continuum-of-reproductive-isolation-lessons-from-heliconius-butterflies
#19
C Mérot, C Salazar, R M Merrill, C D Jiggins, M Joron
The process by which species evolve can be illuminated by investigating barriers that limit gene flow between taxa. Recent radiations, such as Heliconius butterflies, offer the opportunity to compare isolation between pairs of taxa at different stages of ecological, geographical, and phylogenetic divergence. Here, we report a comparative analysis of existing and novel data in order to quantify the strength and direction of isolating barriers within a well-studied clade of Heliconius Our results highlight that increased divergence is associated with the accumulation of stronger and more numerous barriers to gene flow...
June 14, 2017: Proceedings. Biological Sciences
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
#20
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
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