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Neutral evolution

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https://www.readbyqxmd.com/read/29679096/protein-evolution-is-potentially-governed-by-protein-stability-directed-evolution-of-an-esterase-from-the-hyperthermophilic-archaeon-sulfolobus-tokodaii
#1
Ryo Kurahashi, Satoshi Sano, Kazufumi Takano
The study of evolution is important to understand biological phenomena. During evolutionary processes, genetic changes confer amino acid substitutions in proteins, resulting in new or improved functions. Unfortunately, most mutations destabilize proteins. Thus, protein stability is a significant factor in evolution; however, its role remains unclear. Here, we simply and directly explored the association between protein activity and stability in random mutant libraries to elucidate the role of protein stability in evolutionary processes...
April 20, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29675137/variation-in-chromosome-number-and-breeding-systems-implications-for-diversification-in-pachycereus-pringlei-cactaceae
#2
Carina Gutiérrez-Flores, José L León-de la Luz, Francisco J García-De León, J Hugo Cota-Sánchez
Polyploidy, the possession of more than two sets of chromosomes, is a major biological process affecting plant evolution and diversification. In the Cactaceae, genome doubling has also been associated with reproductive isolation, changes in breeding systems, colonization ability, and speciation. Pachycereus pringlei (S. Watson, 1885) Britton & Rose, 1909, is a columnar cactus that has long drawn the attention of ecologists, geneticists, and systematists due to its wide distribution range and remarkable assortment of breeding systems in the Mexican Sonoran Desert and the Baja California Peninsula (BCP)...
2018: Comparative Cytogenetics
https://www.readbyqxmd.com/read/29669733/evolution-of-dnaasei-hypersensitive-sites-in-mhc-regulatory-regions-of-primates
#3
Yabin Jin, Rachel M Gittelman, Yueer Lu, Xiaohui Liu, Ming D Li, Fei Ling, Joshua M Akey
It has been challenged to determine the disease-causing variant(s) for most major histocompatibility complex (MHC) associated diseases. However, it is becoming increasingly clear that regulatory variation is pervasive and a fundamentally important mechanism governing phenotypic diversity and disease susceptibility. We leveraged DNase I data from 136 human cells to characterize the regulatory landscape of the MHC region, including 4867 DNase I hypersensitive sites (DHSs). We identified thousands of regulatory elements that have been gained or lost in the human or chimpanzee genomes since their evolutionary divergence...
April 18, 2018: Genetics
https://www.readbyqxmd.com/read/29669130/distinct-patterns-of-selection-in-selenium-dependent-genes-between-land-and-aquatic-vertebrates
#4
Gaurab K Sarangi, Frédéric Romagné, Sergi Castellano
Selenium (Se), a sparse element on earth, is an essential micronutrient in the vertebrate diet and its intake depends on its content in soils and waters worldwide. Selenium is required due to its function in selenoproteins, which contain selenocysteine (Sec), the 21st amino acid in the genetic code, as one of their constituent residues. Selenocysteine is analogous to the amino acid cysteine (Cys), which uses the abounding element sulfur instead. Despite the irregular distribution of Se worldwide, its distinct biochemical properties have made the substitution of Sec for Cys rare in vertebrate proteins...
April 14, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29669008/neutral-theory-is-the-foundation-of-conservation-genetics
#5
Anne D Yoder, Jelmer Poelstra, George P Tiley, Rachel Williams
Kimura's neutral theory of molecular evolution has been essential to virtually every advance in evolutionary genetics, and by extension, is foundational to the field of conservation genetics. Conservation genetics utilizes the key concepts of neutral theory to identify species and populations at risk of losing evolutionary potential by detecting patterns of inbreeding depression and low effective population size. In turn, this information can inform the management of organisms and their habitat providing hope for the long-term preservation of both...
April 16, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29668014/oxytocin-and-arginine-vasopressin-systems-in-the-domestication-process
#6
Bibiana S O Fam, Pamela Paré, Aline B Felkl, Pedro Vargas-Pinilla, Vanessa R Paixão-Côrtes, Lucas Henriques Viscardi, Maria Cátira Bortolini
Domestication is of unquestionable importance to the technological revolution that has given rise to modern human societies. In this study, we analyzed the DNA and protein sequences of six genes of the oxytocin and arginine vasopressin systems (OXT-OXTR; AVP-AVPR1a, AVPR1b and AVPR2) in 40 placental mammals. These systems play an important role in the control of physiology and behavior. According to our analyses, neutrality does not explain the pattern of molecular evolution found in some of these genes. We observed specific sites under positive selection in AVPR1b (ω = 1...
2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29668012/evolution-of-dnmt2-in-drosophilids-evidence-for-positive-and-purifying-selection-and-insights-into-new-protein-pathways-interactions
#7
Gilberto Cavalheiro Vieira, Marícia Fantinel D'Ávila, Rebeca Zanini, Maríndia Deprá, Vera Lúcia da Silva Valente
The DNA methyltransferase 2 (DNMT2) protein is the most conserved member of the DNA methyltransferase family. Nevertheless, its substrate specificity is still controversial and elusive. The genomic role and determinants of DNA methylation are poorly understood in invertebrates, and several mechanisms and associations are suggested. In Drosophila, the only known DNMT gene is Dnmt2. Here we present our findings from a wide search for Dnmt2 homologs in 68 species of Drosophilidae. We investigated its molecular evolution, and in our phylogenetic analyses the main clades of Drosophilidae species were recovered...
2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29665545/characterization-of-isolated-fractions-of-dissolved-organic-matter-derived-from-municipal-solid-waste-compost
#8
Minda Yu, Xiaosong He, Jiaomei Liu, Yuefeng Wang, Beidou Xi, Dan Li, Hui Zhang, Chao Yang
Understanding the heterogeneous evolution characteristics of dissolved organic matter fractions derived from compost is crucial to exploring the composting biodegradation process and the possible applications of compost products. Herein, two-dimensional correlation spectroscopy integrated with reversed-phase high performance liquid chromatography and size exclusion chromatography were utilized to obtain the molecular weight (MW) and polarity evolution characteristics of humic acid (HA), fulvic acid (FA), and the hydrophilic (HyI) fractions during composting...
April 14, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29662494/evolution-of-neutralization-response-in-hiv-1-subtype-c-infected-individuals-exhibiting-broad-cross-clade-neutralization-of-hiv-1-strains
#9
Narayanaiah Cheedarla, Babu Hemalatha, Brahmaiah Anangi, Kannan Muthuramalingam, Murugesan Selvachithiram, Pattabiraman Sathyamurthi, Nandagopal Kailasam, Raghavan Varadarajan, Soumya Swaminathan, Srikanth Prasad Tripathy, S Kalyanaraman Vaniambadi, D Ramanathan Vadakkupattu, Luke Elizabeth Hanna
Strain-specific neutralizing antibodies develop in all human immunodeficiency virus type 1 (HIV-1)-infected individuals. However, only 10-30% of infected individuals produce broadly neutralizing antibodies (bNAbs). Identification and characterization of these bNAbs and understanding their evolution dynamics are critical for obtaining useful clues for the development of an effective HIV vaccine. Very recently, we published a study in which we identified 12 HIV-1 subtype C-infected individuals from India whose plasma showed potent and broad cross-clade neutralization (BCN) ability (1)...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29660712/long-run-operation-of-a-reverse-electrodialysis-system-fed-with-wastewaters
#10
Javier Luque Di Salvo, Alessandro Cosenza, Alessandro Tamburini, Giorgio Micale, Andrea Cipollina
The performance of a Reverse ElectroDialysis (RED) system fed by unconventional wastewater solutions for long operational periods is analysed for the first time. The experimental campaign was divided in a series of five independent long-runs which combined real wastewater solutions with artificial solutions for at least 10 days. The time evolution of electrical variables, gross power output and net power output, considering also pumping losses, was monitored: power density values obtained during the long-runs are comparable to those found in literature with artificial feed solutions of similar salinity...
April 13, 2018: Journal of Environmental Management
https://www.readbyqxmd.com/read/29659993/neutral-theory-and-phenotypic-evolution
#11
Jianzhi Zhang
Although the neutral theory of molecular evolution was proposed to explain DNA and protein sequence evolution, in principle it could also explain phenotypic evolution. Nevertheless, overall, phenotypes should be less likely than genotypes to evolve neutrally. I propose that, when phenotypic traits are stratified according to a hierarchy of biological organization, the fraction of evolutionary changes in phenotype that are adaptive rises with the phenotypic level considered. Consistently, molecular traits are frequently found to evolve neutrally whereas a large, random set of organismal traits were recently reported to vary largely adaptively...
April 5, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29659992/neutral-theory-from-complex-population-history-to-natural-selection-and-socio-cultural-phenomena-in-human-populations
#12
Frédéric Austerlitz, Evelyne Heyer
Here we present a synthetic view on how Kimura's Neutral theory has helped us gaining insight on the different evolutionary forces that shape human evolution. We put this perspective in the frame of recent emerging challenges: the use of whole genome data for reconstructing population histories, natural selection for complex polygenic traits, and integrating cultural processes in human evolution.
April 11, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29659991/consequences-of-asexuality-in-natural-populations-insights-from-stick-insects
#13
Jens Bast, Darren J Parker, Zoé Dumas, Kirsten M Jalvingh, Patrick Tran Van, Kamil S Jaron, Emeric Figuet, Alexander Brandt, Nicolas Galtier, Tanja Schwander
Recombination is a fundamental process with significant impacts on genome evolution. Predicted consequences of the loss of recombination include a reduced effectiveness of selection, changes in the amount of neutral polymorphisms segregating in populations, and an arrest of GC-biased gene conversion. Although these consequences are empirically well documented for non-recombining genome portions, it remains largely unknown if they extend to the whole genome scale in asexual organisms. We identify the consequences of asexuality using de novo transcriptomes of five independently derived, obligately asexual lineages of stick insects and their sexual sister-species...
April 5, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29659981/neutral-variation-in-the-context-of-selection
#14
Brian Charlesworth, Deborah Charlesworth
In its initial formulation by Motoo Kimura, the neutral theory was concerned solely with the level of variability maintained by random genetic drift of selectively neutral mutation, and the rate of molecular evolution caused by the fixation of such mutations. The original theory considered events at a single genetic locus in isolation from the rest of the genome. It did not take long, however, for theoreticians to wonder whether selection at one or more loci might influence neutral variability at linked sites...
April 4, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29658161/parallel-evolutionary-forces-influence-the-evolution-of-male-and-female-songs-in-a-tropical-songbird
#15
Brendan A Graham, Daniel D Heath, Ryan P Walter, Melissa M Mark, Daniel J Mennill
Given the important role that animal vocalizations play in mate attraction and resource defence, acoustic signals are expected to play a significant role in speciation. Most studies, however, have focused on the acoustic traits of male animals living in the temperate zone. In contrast to temperate environments, in the tropics it is commonplace for both sexes to produce complex acoustic signals. Therefore tropical birds offer the opportunity to compare the sexes and provide a more comprehensive understanding of the evolution of animal signals...
April 15, 2018: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29649209/gene-duplicates-cause-hybrid-lethality-between-sympatric-species-of-mimulus
#16
Matthew P Zuellig, Andrea L Sweigart
Hybrid incompatibilities play a critical role in the evolution and maintenance of species. We have discovered a simple genetic incompatibility that causes lethality in hybrids between two closely related species of yellow monkeyflower (Mimulus guttatus and M. nasutus). This hybrid incompatibility, which causes one sixteenth of F2 hybrid seedlings to lack chlorophyll and die shortly after germination, occurs between sympatric populations that are connected by ongoing interspecific gene flow. Using complimentary genetic mapping and gene expression analyses, we show that lethality occurs in hybrids that lack a functional copy of the critical photosynthetic gene pTAC14...
April 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29643236/introduction-of-viral-haemorrhagic-septicaemia-virus-vhsv-to-freshwater-cultured-rainbow-trout-is-followed-by-bursts-of-adaptive-evolution
#17
Anna A Schönherz, Roald Forsberg, Bernt Guldbrandtsen, Albert J Buitenhuis, Katja Einer-Jensen
Viral haemorrhagic septicaemia virus (VHSV), a rhabdovirus infecting teleost fish, has repeatedly crossed the boundary from marine fish species to freshwater cultured rainbow trout. These naturally replicated cross-species transmission events permit the study of general and repeatable evolutionary events occurring in connection with viral emergence into a novel host species.The purpose of this study was to investigate adaptive molecular evolution of the VHSV glycoprotein, one of the key virus proteins involved in viral emergence, following emergence from marine species into freshwater cultured rainbow trout...
April 11, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29623872/origin-evolution-and-loss-of-bacterial-small-rnas
#18
H Auguste Dutcher, Rahul Raghavan
Despite the central role of bacterial noncoding small RNAs (sRNAs) in posttranscriptional regulation, little is understood about their evolution. Here we compile what has been studied to date and trace a life cycle of sRNAs-from their mechanisms of emergence, through processes of change and frequent neofunctionalization, to their loss from bacterial lineages. Because they possess relatively unrestrictive structural requirements, we find that sRNA origins are varied, and include de novo emergence as well as formation from preexisting genetic elements via duplication events and horizontal gene transfer...
April 2018: Microbiology Spectrum
https://www.readbyqxmd.com/read/29619313/nickel-hydr-oxy-oxide-nanoparticles-on-metallic-mos-2-nanosheets-a-synergistic-electrocatalyst-for-hydrogen-evolution-reaction
#19
Xing Zhang, Yongye Liang
Molybdenum disulfide (MoS2 )-based materials have been recently identified as promising electrocatalysts for hydrogen evolution reaction (HER). However, little work has been done to improve the catalytic performance of MoS2 toward HER in alkaline electrolytes, which is more suitable for water splitting in large-scale applications. Here, it is reported that the hybridization of 0D nickel hydr(oxy)oxide nanoparticles with 2D metallic MoS2 nanosheets can significantly enhance the HER activities in alkaline and neutral electrolytes...
February 2018: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
https://www.readbyqxmd.com/read/29617896/an-evaluation-of-function-of-multicopy-non-coding-rnas-in-mammals-using-encode-fantom-data-and-comparative-genomics
#20
Marc P Hoeppner, Elena Denisenko, Paul P Gardner, Sebastian Schmeier, Anthony M Poole
Mammalian diversification has coincided with a rapid proliferation of various types of non-coding RNAs, including members of both snRNAs and snoRNAs. The significance of this expansion however remains obscure. While some ncRNA copy-number expansions have been linked to functionally tractable effects, such events may equally likely be neutral, perhaps as a result of random retrotransposition. Hindering progress in our understanding of such observations is the difficulty in establishing function for the diverse features that have been identified in our own genome...
April 3, 2018: Molecular Biology and Evolution
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