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Evolutionary biology

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https://www.readbyqxmd.com/read/29454308/the-unique-evolutionary-pattern-of-the-hydroxyproline-rich-glycoproteins-superfamily-in-chinese-white-pear-pyrus-bretschneideri
#1
Huijun Jiao, Xing Liu, Shuguang Sun, Peng Wang, Xin Qiao, Jiaming Li, Chao Tang, Juyou Wu, Shaoling Zhang, Shutian Tao
BACKGROUND: The hydroxyproline-rich glycoprotein (HRGP) superfamily, comprising three families (arabinogalactan-proteins, AGPs; extensins, EXTs; proline-rich proteins, PRPs), is a class of proline-rich proteins that exhibit high diversity and are involved in many aspects of plant biology. RESULTS: In this study, 838 HRGPs were identified from Chinese white pear (Pyrus bretschneideri) by searching for biased amino acid composition and conserved motifs. 405 HRGPs were derived from whole genome duplication (WGD) events which is suggested to be the major force of driving HRGPs expansion and the recent WGD event shared by apple and pear generated most duplicated HRGPs in pear...
February 17, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29453332/step-wise-evolution-of-complex-chemical-defenses-in-millipedes-a-phylogenomic-approach
#2
Juanita Rodriguez, Tappey H Jones, Petra Sierwald, Paul E Marek, William A Shear, Michael S Brewer, Kevin M Kocot, Jason E Bond
With fossil representatives from the Silurian capable of respiring atmospheric oxygen, millipedes are among the oldest terrestrial animals, and likely the first to acquire diverse and complex chemical defenses against predators. Exploring the origin of complex adaptive traits is critical for understanding the evolution of Earth's biological complexity, and chemical defense evolution serves as an ideal study system. The classic explanation for the evolution of complexity is by gradual increase from simple to complex, passing through intermediate "stepping stone" states...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29452927/toward-prediction-and-control-of-antibiotic-resistance-evolution
#3
REVIEW
Chikara Furusawa, Takaaki Horinouchi, Tomoya Maeda
The emergence of antibiotic-resistant bacteria is a serious public concern. To deal with this problem, recent advances in technology and the use of laboratory evolution experiments have provided valuable information on the phenotypic and genotypic changes that occur during the evolution of resistance. These studies have demonstrated the existence of evolutionary constraints on the development of drug-resistance, which suggests predictability in its evolution. In this review, we focus on the possibility to predict and control the evolution of antibiotic resistance, based on quantitative analysis of phenotypic and genotypic changes observed in bacterial laboratory evolution...
February 13, 2018: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29452591/ageing-associated-dna-methylation-dynamics-are-a-molecular-readout-of-lifespan-variation-among-mammalian-species
#4
Robert Lowe, Carl Barton, Christopher A Jenkins, Christina Ernst, Oliver Forman, Denise S Fernandez-Twinn, Christoph Bock, Stephen J Rossiter, Chris G Faulkes, Susan E Ozanne, Lutz Walter, Duncan T Odom, Cathryn Mellersh, Vardhman K Rakyan
BACKGROUND: Mammalian species exhibit a wide range of lifespans. To date, a robust and dynamic molecular readout of these lifespan differences has not yet been identified. Recent studies have established the existence of ageing-associated differentially methylated positions (aDMPs) in human and mouse. These are CpG sites at which DNA methylation dynamics show significant correlations with age. We hypothesise that aDMPs are pan-mammalian and are a dynamic molecular readout of lifespan variation among different mammalian species...
February 16, 2018: Genome Biology
https://www.readbyqxmd.com/read/29452155/comparative-developmental-biology-of-the-cardiac-inflow-tract
#5
REVIEW
Rita Carmona, Laura Ariza, Ana Cañete, Ramón Muñoz-Chápuli
The vertebrate heart receives the blood through the cardiac inflow tract. This area has experienced profound changes along the evolution of vertebrates; changes that have a reflection in the cardiac ontogeny. The development of the inflow tract involves dynamic changes due to the progressive addition of tissue derived from the secondary heart field. The inflow tract is the site where oxygenated blood coming from lungs is received separately from the systemic return, where the cardiac pacemaker is established and where the proepicardium develops...
February 13, 2018: Journal of Molecular and Cellular Cardiology
https://www.readbyqxmd.com/read/29449757/why-and-how-the-early-life-environment-affects-development-of-coping-behaviours
#6
REVIEW
M Rohaa Langenhof, Jan Komdeur
Understanding the ways in which individuals cope with threats, respond to challenges, make use of opportunities and mediate the harmful effects of their surroundings is important for predicting their ability to function in a rapidly changing world. Perhaps one of the most essential drivers of coping behaviour of adults is the environment experienced during their early-life development. Although the study of coping, defined as behaviours displayed in response to environmental challenges, has a long and rich research history in biology, recent literature has repeatedly pointed out that the processes through which coping behaviours develop in individuals are still largely unknown...
2018: Behavioral Ecology and Sociobiology
https://www.readbyqxmd.com/read/29447366/parent-of-origin-dependent-gene-expression-in-male-and-female-schistosome-parasites
#7
Julien Kincaid-Smith, Marion A L Picard, Céline Cosseau, Jérôme Boissier, Dany Severac, Christoph Grunau, Eve Toulza
Schistosomes are the causative agents of schistosomiasis, a Neglected Tropical Disease affecting over 230 million people worldwide. Additionally to their major impact on human health, they are also models of choice in evolutionary biology. These parasitic flatworms are unique among the common hermaphroditic trematodes as they have separate sexes. This so-called « evolutionary scandal » displays a female heterogametic genetic sex-determination system (ZZ males and ZW females), as well as a pronounced adult sexual dimorphism...
February 12, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29446800/biology-of-vibrio-cholera-editorial-overview
#8
EDITORIAL
Felipe Cava
In this monographic issue, we have the pleasure to present contributions from six of the leading laboratories at the forefront of Vibrio cholerae genetics, ecology and evolution, together with a brief tribute by Diego Romero to Doctor Jaime Ferrán y Clua, a pioneering Spanish bacteriologist who developed the first vaccine against this pathogen. V. cholerae is a free-living aquatic bacterium that interacts with and infects a variety of organisms. In humans it causes cholera, the deadly diarrhoea that was responsible for millions of deaths during seven pandemics since 1817, and still thousands every year...
September 2017: International Microbiology: the Official Journal of the Spanish Society for Microbiology
https://www.readbyqxmd.com/read/29445617/pathogenic-leptospira-advances-in-understanding-the-molecular-pathogenesis-and-virulence
#9
REVIEW
Ciamak Ghazaei
Leptospirosis is a common zoonotic disease has emerged as a major public health problem, with developing countries bearing disproportionate burdens. Although the diverse range of clinical manifestations of the leptospirosis in humans is widely documented, the mechanisms through which the pathogen causes disease remain undetermined. In addition, leptospirosis is a much-neglected life-threatening disease although it is one of the most important zoonoses occurring in a diverse range of epidemiological distribution...
2018: Open Veterinary Journal
https://www.readbyqxmd.com/read/29445326/structure-function-studies-of-the-%C3%AE-4-subunit-reveal-evolutionary-loss-of-a-glyr-subtype-involved-in-startle-and-escape-responses
#10
Sophie Leacock, Parnayan Syed, Victoria M James, Anna Bode, Koichi Kawakami, Angelo Keramidas, Maximiliano Suster, Joseph W Lynch, Robert J Harvey
Inhibitory glycine receptors (GlyRs) are pentameric ligand-gated anion channels with major roles in startle disease/hyperekplexia (GlyR α1), cortical neuronal migration/autism spectrum disorder (GlyR α2), and inflammatory pain sensitization/rhythmic breathing (GlyR α3). However, the role of the GlyR α4 subunit has remained enigmatic, because the corresponding human gene ( GLRA4 ) is thought to be a pseudogene due to an in-frame stop codon at position 390 within the fourth membrane-spanning domain (M4). Despite this, a recent genetic study has implicated GLRA4 in intellectual disability, behavioral problems and craniofacial anomalies...
2018: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29445020/trade-offs-between-microbial-growth-phases-lead-to-frequency-dependent-and-non-transitive-selection
#11
Michael Manhart, Bharat V Adkar, Eugene I Shakhnovich
Mutations in a microbial population can increase the frequency of a genotype not only by increasing its exponential growth rate, but also by decreasing its lag time or adjusting the yield (resource efficiency). The contribution of multiple life-history traits to selection is a critical question for evolutionary biology as we seek to predict the evolutionary fates of mutations. Here we use a model of microbial growth to show that there are two distinct components of selection corresponding to the growth and lag phases, while the yield modulates their relative importance...
February 14, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29444864/lineage-specific-gene-acquisition-or-loss-is-involved-in-interspecific-hybrid-sterility-in-rice
#12
Yohei Koide, Atsushi Ogino, Takanori Yoshikawa, Yuki Kitashima, Nozomi Saito, Yoshitaka Kanaoka, Kazumitsu Onishi, Yoshihiro Yoshitake, Takuji Tsukiyama, Hiroki Saito, Masayoshi Teraishi, Yoshiyuki Yamagata, Aiko Uemura, Hiroki Takagi, Yoriko Hayashi, Tomoko Abe, Yoshimichi Fukuta, Yutaka Okumoto, Akira Kanazawa
Understanding the genetic basis of reproductive barriers between species has been a central issue in evolutionary biology. The S 1 locus in rice causes hybrid sterility and is a major reproductive barrier between two rice species, Oryza sativa and Oryza glaberrima The O. glaberrima -derived allele (denoted S 1 g ) on the S 1 locus causes preferential abortion of gametes with its allelic alternative (denoted S 1 s ) in S 1 g / S 1 s heterozygotes. Here, we used mutagenesis and screening of fertile hybrid plants to isolate a mutant with an allele, S 1 mut , which does not confer sterility in the S 1 mut / S 1 g and S 1 mut / S 1 s hybrids...
February 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29444327/structural-and-functional-analysis-of-ugt92g6-suggests-evolutionary-link-between-mono-and-disaccharide-glycoside-forming-transferases
#13
Fong-Chin Huang, Ashok Giri, Melina Daniilidis, Guangxin Sun, Katja Härtl, Thomas Hoffmann, Wilfried Schwab
Glycosylation mediated by uridine diphosphate-dependent glycosyltransferase (UGT) is one of the most common reactions for the biosynthesis of small molecule glycosides. As glycosides have various biological roles we characterized UGTs from grapevine (Vitis vinifera). In silico analysis of VvUGTs that were highly expressed in leaves identified UGT92G6 which showed sequence similarity to both, monosaccharide and disaccharide glucoside forming transferases. The recombinant UGT92G6 glucosylated phenolics, among them caffeic acid, carvacrol, eugenol, and raspberry ketone, and also accepted geranyl glucoside and citronellyl glucoside...
February 10, 2018: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29441122/time-consistent-reconciliation-maps-and-forbidden-time-travel
#14
Nikolai Nøjgaard, Manuela Geiß, Daniel Merkle, Peter F Stadler, Nicolas Wieseke, Marc Hellmuth
Background: In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge of the event labels considerably simplifies the problem of reconciling a gene tree T with a species trees S , relative to the reconciliation problem without prior knowledge of the event types. It is well-known that optimal reconciliations in the unlabeled case may violate time-consistency and thus are not biologically feasible...
2018: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/29440637/cytosine-modifications-exhibit-circadian-oscillations-that-are-involved-in-epigenetic-diversity-and-aging
#15
Gabriel Oh, Sasha Ebrahimi, Matthew Carlucci, Aiping Zhang, Akhil Nair, Daniel E Groot, Viviane Labrie, Peixin Jia, Edward S Oh, Richie H Jeremian, Miki Susic, Tenjin C Shrestha, Martin R Ralph, Juozas Gordevičius, Karolis Koncevičius, Art Petronis
Circadian rhythmicity governs a remarkable array of fundamental biological functions and is mediated by cyclical transcriptomic and proteomic activities. Epigenetic factors are also involved in this circadian machinery; however, despite extensive efforts, detection and characterization of circadian cytosine modifications at the nucleotide level have remained elusive. In this study, we report that a large proportion of epigenetically variable cytosines show a circadian pattern in their modification status in mice...
February 13, 2018: Nature Communications
https://www.readbyqxmd.com/read/29440520/assessing-the-relative-impact-of-historical-divergence-and-inter-group-transmission-on-cultural-patterns-a-method-from-evolutionary-ecology
#16
Noreen von Cramon-Taubadel, Stephen J Lycett
In the study of cultural evolution, observed among-group affinity patterns reflect the effects of processes such as mutation (e.g. innovation and copying error), between-group interaction (culture flow), drift and selection. As in biology, cultural affinity patterns are often spatially correlated, making it difficult to distinguish between the opposing geographically mediated forces of divergence and interaction, which cause groups to become more distinct or similar over time, respectively. Analogous difficulties are faced by evolutionary biologists examining the relationship between biological affinity and geography, particularly at lower taxonomic levels where the potential for gene flow between lineages is greatest...
April 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29440318/monitoring-the-5-methoxycarbonylmethyl-2-thiouridine-mcm5s2u-modification-in-eukaryotic-trnas-via-the-gamma-toxin-endonuclease
#17
Jenna M Lentini, Jillian Ramos, Dragony Fu
The post-transcriptional modification of tRNA at the wobble position is a universal process occurring in all domains of life. In eukaryotes, the wobble uridine of particular tRNAs is transformed to the 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification which is critical for proper mRNA decoding and protein translation. However, current methods to detect mcm5s2U are technically challenging and/or require specialized instrumental expertise. Here, we show that gamma-toxin endonuclease from the yeast Kluyveromyces lactis can be used as a probe for assaying mcm5s2U status in the tRNA of diverse eukaryotic organisms ranging from protozoans to mammalian cells...
February 13, 2018: RNA
https://www.readbyqxmd.com/read/29435260/hidden-endemism-deep-polyphyly-and-repeated-dispersal-across-the-isthmus-of-tehuantepec-diversification-of-the-white-collared-seedeater-complex-thraupidae-sporophila-torqueola
#18
Nicholas A Mason, Arturo Olvera-Vital, Irby J Lovette, Adolfo G Navarro-Sigüenza
Phenotypic and genetic variation are present in all species, but lineages differ in how variation is partitioned among populations. Examining phenotypic clustering and genetic structure within a phylogeographic framework can clarify which biological processes have contributed to extant biodiversity in a given lineage. Here, we investigate genetic and phenotypic variation among populations and subspecies within a Neotropical songbird complex, the White-collared Seedeater (Sporophila torqueola) of Central America and Mexico...
February 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29435232/what-factors-shape-genetic-diversity-in-cetaceans
#19
Felicia Vachon, Hal Whitehead, Timothy R Frasier
Understanding what factors drive patterns of genetic diversity is a central aspect of many biological questions, ranging from the inference of historical demography to assessing the evolutionary potential of a species. However, as a larger number of datasets have become available, it is becoming clear that the relationship between the characteristics of a species and its genetic diversity is more complex than previously assumed. This may be particularly true for cetaceans, due to their relatively long lifespans, long generation times, complex social structures, and extensive ranges...
February 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29434337/detection-of-genetic-purging-and-predictive-value-of-purging-parameters-estimated-in-pedigreed-populations
#20
Eugenio López-Cortegano, Diego Bersabé, Jinliang Wang, Aurora García-Dorado
The consequences of inbreeding for fitness are important in evolutionary and conservation biology, but can critically depend on genetic purging. However, estimating purging has proven elusive. Using PURGd software, we assess the performance of the Inbreeding-Purging (IP) model and of ancestral inbreeding (Fa) models to detect purging in simulated pedigreed populations, and to estimate parameters that allow reliably predicting the evolution of fitness under inbreeding. The power to detect purging in a single small population of size N is low for both models during the first few generations of inbreeding (t ≈ N/2), but increases for longer periods of slower inbreeding and is, on average, larger for the IP model...
February 13, 2018: Heredity
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