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https://www.readbyqxmd.com/read/28109007/retinoic-acid-inducible-gene-i-rig-i-like-receptors-rlrs-in-fish-current-knowledge-and-future-perspectives
#1
REVIEW
Shan Nan Chen, Peng Fei Zou, Pin Nie
Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) are found conservatively present in teleost fish. All three members, RIG-I, MDA5 and LGP2 together with the downstream molecules such as MITA, TRAF3 and TBK1 have been identified in a range of fish species. However, it is a bit unexpected that RIG-I has not been reported in fish of Acanthopterygii, and it would be important to clarify the presence and role of RIG-I gene in a broad range of taxa in Teleostei. RLRs in fish can be induced in vivo and in vitro by viral pathogens as well as synthetic double-stranded RNA (dsRNA), poly(I:C), leading to the production of type I IFNs and the expression of IFN stimulated genes (ISGs)...
January 20, 2017: Immunology
https://www.readbyqxmd.com/read/28108874/surviving-in-isolation-genetic-variation-bottlenecks-and-reproductive-strategies-in-the-canarian-endemic-limonium-macrophyllum-plumbaginaceae
#2
Ares Jiménez, Barbara Weigelt, Arnoldo Santos-Guerra, Juli Caujapé-Castells, José María Fernández-Palacios, Elena Conti
Oceanic archipelagos are typically rich in endemic taxa, because they offer ideal conditions for diversification and speciation in isolation. One of the most remarkable evolutionary radiations on the Canary Islands comprises the 16 species included in Limonium subsection Nobiles, all of which are subject to diverse threats, and legally protected. Since many of them are single-island endemics limited to one or a few populations, there exists a risk that a loss of genetic variation might limit their long-term survival...
January 20, 2017: Genetica
https://www.readbyqxmd.com/read/28108681/re-emergence-of-methicillin-susceptibility-in-a-resistant-lineage-of-staphylococcus-aureus
#3
Alice Ledda, James R Price, Kevin Cole, Martin J Llewelyn, Angela M Kearns, Derrick W Crook, John Paul, Xavier Didelot
OBJECTIVES: MRSA is a leading cause of hospital-associated infection. Acquired resistance is encoded by the mecA gene or its homologue mecC, but little is known about the evolutionary dynamics involved in gain and loss of resistance. The objective of this study was to obtain an expanded understanding of Staphylococcus aureus methicillin resistance microevolution in vivo, by focusing on a single lineage. METHODS: We compared the whole-genome sequences of 231 isolates from a single epidemic lineage [clonal complex 30 (CC30) and spa-type t018] of S...
January 20, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28108601/phylogenomics-using-target-restricted-assembly-resolves-intra-generic-relationships-of-parasitic-lice-phthiraptera-columbicola
#4
Bret M Boyd, Julie M Allen, Nam Nguyen, Andrew D Sweet, Tandy Warnow, Michael D Shapiro, Scott M Villa, Sarah E Bush, Dale H Clayton, Kevin P Johnson
Parasitic "wing lice" (Phthiraptera: Columbicola) and their dove and pigeon hosts are a well-recognized model system for coevolutionary studies at the intersection of micro- and macroevolution. Selection on lice in microevolutionary time occurs as pigeons and doves defend themselves against lice by preening. In turn, behavioral and morphological adaptations of the lice improve their ability to evade host defense. Over macroevolutionary time wing lice tend to cospeciate with their hosts; yet, some species of Columbicola have switched to new host species...
January 19, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28108446/chaincleaner-improves-genome-alignment-specificity-and-sensitivity
#5
Hernando G Suarez, Bjoern E Langer, Pradnya Ladde, Michael Hiller
MOTIVATION: Accurate alignments between entire genomes are crucial for comparative genomics. However, computing sensitive and accurate genome alignments is a challenging problem, complicated by genomic rearrangements. RESULTS: Here we present a fast approach, called chainCleaner, that improves the specificity in genome alignments by accurately detecting and removing local alignments that obscure the evolutionary history of genomic rearrangements. Systematic tests on alignments between the human and other vertebrate genomes show that chainCleaner (i) improves the alignment of numerous orthologous genes, (ii) exposes alignments between exons of orthologous genes that were masked before by alignments to pseudogenes, and (iii) recovers hundreds of kilobases in local alignments that otherwise would fall below a minimum score threshold...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108445/multi-rate-poisson-tree-processes-for-single-locus-species-delimitation-under-maximum-likelihood-and-markov-chain-monte-carlo
#6
P Kapli, S Lutteropp, J Zhang, K Kobert, P Pavlidis, A Stamatakis, T Flouri
MOTIVATION: In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108432/living-on-the-edge-conservation-genetics-of-seven-thermophilous-plant-species-in-a-high-arctic-archipelago
#7
Siri Birkeland, Idunn Elisabeth Borgen Skjetne, Anne Krag Brysting, Reidar Elven, Inger Greve Alsos
Small, isolated, and/or peripheral populations are expected to harbour low levels of genetic variation and may therefore have reduced adaptability to environmental change, including climate warming. In the Arctic, global warming has already caused vegetation change across the region and is acting as a significant stressor on Arctic biodiversity. Many of the rare plants in the Arctic are relicts from early Holocene warm periods, but their ability to benefit from the current warming is dependent on the viability of their populations...
January 20, 2017: AoB Plants
https://www.readbyqxmd.com/read/28108306/bone-remodeling-as-a-spatial-evolutionary-game
#8
Marc D Ryser, Kevin A Murgas
Bone remodeling is a complex process involving cell-cell interactions, biochemical signaling and mechanical stimuli. Early models of the biological aspects of remodeling were non-spatial and focused on the local dynamics at a fixed location in the bone. Several spatial extensions of these models have been proposed, but they generally suffer from two limitations: first, they are not amenable to analysis and are computationally expensive, and second, they neglect the role played by bone-embedded osteocytes. To address these issues, we developed a novel model of spatial remodeling based on the principles of evolutionary game theory...
January 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28108305/efficient-dynamic-programming-algorithm-with-prior-knowledge-for-protein-%C3%AE-strand-alignment
#9
Mostafa Sabzekar, Mahmoud Naghibzadeh, Javad Sadri
One of the main tasks towards the prediction of protein β-sheet structure is to predict the native alignment of β-strands. The alignment of two β-strands defines similar regions that may reflect functional, structural, or evolutionary relationships between them. Therefore, any improvement in β-strands alignment not only reduces the computational search space but also improves β-sheet structure prediction accuracy. To define the alignment scores, previous studies utilized predicted residue-residue contacts (contact maps)...
January 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28108158/evolutionary-plasticity-of-plasma-membrane-interaction-in-drepp-family-proteins
#10
Stanislav Vosolsobě, Jan Petrášek, Kateřina Schwarzerová
The plant-specific DREPP protein family comprises proteins that were shown to regulate the actin and microtubular cytoskeleton in a calcium-dependent manner. Our phylogenetic analysis showed that DREPPs first appeared in ferns and that DREPPs have a rapid and plastic evolutionary history in plants. Arabidopsis DREPP paralogues called AtMDP25/PCaP1 and AtMAP18/PCaP2 are N-myristoylated, which has been reported as a key factor in plasma membrane localization. Here we show that N-myristoylation is neither conserved nor ancestral for the DREPP family...
January 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28107778/parabolic-variation-in-sexual-selection-intensity-across-the-range-of-a%C3%A2-cold-water-pipefish-implications-for-susceptibility-to-climate-change
#11
Nuno Monteiro, Mário Cunha, Lídia Ferreira, Natividade Vieira, Agostinho Antunes, David Lyons, Adam G Jones
While an understanding of evolutionary processes in shifting environments is vital in the context of rapid ecological change, one of the most potent selective forces, sexual selection, remains curiously unexplored. Variation in sexual selection across a species range, especially across a gradient of temperature regimes, has the potential to provide a window into the possible impacts of climate change on the evolution of mating patterns. Here, we investigated some of the links between temperature and indicators of sexual selection, using a cold-water pipefish as model...
January 20, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28107688/sequencing-and-de-novo-assembly-of-visceral-mass-transcriptome-of-the-critically-endangered-land-snail-satsuma-myomphala-annotation-and-ssr-discovery
#12
Se Won Kang, Bharat Bhusan Patnaik, Hee-Ju Hwang, So Young Park, Jong Min Chung, Dae Kwon Song, Hongray Howrelia Patnaik, Jae Bong Lee, Changmu Kim, Soonok Kim, Young-Su Park, Hong Seog Park, Seung-Hwan Park, Yeon Soo Han, Jun Sang Lee, Yong Seok Lee
Satsuma myomphala is critically endangered through loss of natural habitats, predation by natural enemies, and indiscriminate collection. It is a protected species in Korea but lacks genomic resources for an understanding of varied functional processes attributable to evolutionary success under natural habitats. For assessing the genetic information of S. myomphala, we performed for the first time, de novo transcriptome sequencing and functional annotation of expressed sequences using Illumina Next-Generation Sequencing (NGS) platform and bioinformatics analysis...
October 29, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28107432/ongoing-speciation-and-gene-flow-between-taxonomically-challenging-trochulus-species-complex-gastropoda-hygromiidae
#13
Małgorzata Proćków, Tomasz Strzała, Elżbieta Kuźnik-Kowalska, Jarosław Proćków, Paweł Mackiewicz
Geographical isolation, selection and genetic drift can cause the geographical diversification of populations and lead to speciation. Land snail species in the genus Trochulus show overlaps in geographical ranges as well as in morphology, but genetic data do not always support the species-level taxonomy based on morphological characters. Such a group offers an excellent opportunity to explore the processes involved. We have addressed the problem by determining the status of the restricted endemic T. graminicola within the larger context of Trochulus taxonomy...
2017: PloS One
https://www.readbyqxmd.com/read/28107392/upon-accounting-for-the-impact-of-isoenzyme-loss-gene-deletion-costs-anticorrelate-with-their-evolutionary-rates
#14
Christopher Jacobs, Luke Lambourne, Yu Xia, Daniel Segrè
System-level metabolic network models enable the computation of growth and metabolic phenotypes from an organism's genome. In particular, flux balance approaches have been used to estimate the contribution of individual metabolic genes to organismal fitness, offering the opportunity to test whether such contributions carry information about the evolutionary pressure on the corresponding genes. Previous failure to identify the expected negative correlation between such computed gene-loss cost and sequence-derived evolutionary rates in Saccharomyces cerevisiae has been ascribed to a real biological gap between a gene's fitness contribution to an organism "here and now" and the same gene's historical importance as evidenced by its accumulated mutations over millions of years of evolution...
2017: PloS One
https://www.readbyqxmd.com/read/28107060/placing-the-time-of-leaf-emergence-in-an-evolutionary-context
#15
Susanne S Renner
No abstract text is available yet for this article.
February 2017: American Naturalist
https://www.readbyqxmd.com/read/28107055/radiating-despite-a-lack-of-character-ecological-divergence-among-closely-related-morphologically-similar-honeyeaters-aves-meliphagidae-co-occurring-in-arid-australian-environments
#16
Eliot T Miller, Sarah K Wagner, Luke J Harmon, Robert E Ricklefs
Quantifying the relationship between form and function can inform use of morphology as a surrogate for ecology. How the strength of this relationship varies continentally can inform understanding of evolutionary radiations; for example, does the relationship break down when certain lineages invade and diversify in novel habitats? The 75 species of Australian honeyeaters (Meliphagidae) are morphologically and ecologically diverse, with species feeding on nectar, insects, fruit, and other resources. We investigated Meliphagidae ecomorphology and community structure by (1) quantifying the concordance between morphology and ecology (foraging behavior), (2) estimating rates of trait evolution in relation to the packing of ecological space, and (3) comparing phylogenetic and trait community structure across the broad environmental gradients of the continent...
February 2017: American Naturalist
https://www.readbyqxmd.com/read/28107053/diversity-and-coevolutionary-dynamics-in-high-dimensional-phenotype-spaces
#17
Michael Doebeli, Iaroslav Ispolatov
We study macroevolutionary dynamics by extending microevolutionary competition models to long timescales. It has been shown that for a general class of competition models, gradual evolutionary change in continuous phenotypes (evolutionary dynamics) can be nonstationary and even chaotic when the dimension of the phenotype space in which the evolutionary dynamics unfold is high. It has also been shown that evolutionary diversification can occur along nonequilibrium trajectories in phenotype space. We combine these lines of thinking by studying long-term coevolutionary dynamics of emerging lineages in multidimensional phenotype spaces...
February 2017: American Naturalist
https://www.readbyqxmd.com/read/28107052/trait-evolution-in-adaptive-radiations-modeling-and-measuring-interspecific-competition-on-phylogenies
#18
Magnus Clarke, Gavin H Thomas, Robert P Freckleton
The incorporation of ecological processes into models of trait evolution is important for understanding past drivers of evolutionary change. Species interactions have long been thought to be key drivers of trait evolution. However, models for comparative data that account for interactions between species are lacking. One of the challenges is that such models are intractable and difficult to express analytically. Here we present phylogenetic models of trait evolution that include interspecific competition among chosen species...
February 2017: American Naturalist
https://www.readbyqxmd.com/read/28106881/phylogenomics-of-rhodobacteraceae-reveals-evolutionary-adaptation-to-marine-and-non-marine-habitats
#19
Meinhard Simon, Carmen Scheuner, Jan P Meier-Kolthoff, Thorsten Brinkhoff, Irene Wagner-Döbler, Marcus Ulbrich, Hans-Peter Klenk, Dietmar Schomburg, Jörn Petersen, Markus Göker
Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic environments and are often mutualists of eukaryotes. As 'Roseobacter clade', these 'roseobacters' are assumed to be monophyletic, but non-marine Rhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling and its effect on phylogenetic stability, and investigated relationships between marine versus non-marine habitat, evolutionary origin and genomic adaptations...
January 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/28106390/tubulin-binding-and-polymerization-promoting-properties-of-tppp-proteins-are-evolutionarily-conserved
#20
Judit Oláh, Tibor Szénási, Adél Szabó, Kinga Kovács, Péter Lőw, Mauro Stifanic, Ferenc Orosz
Tubulin Polymerization Promoting Proteins (TPPPs) constitute a new eukaryotic protein family. There are three TPPP paralogs in the human genome; denoted as TPPP1, TPPP2 and TPPP3. TPPP1 and TPPP3 are intrinsically unstructured proteins (IUPs) that bind and polymerize tubulin and stabilize microtubules but TPPP2 does not. Vertebrate TPPPs originated from the ancient invertebrate TPPP by two-round whole-genome-duplication thus it was an open question whether the tubulin/microtubule binding function of TPPP1 and TPPP3 is a newly acquired property or it was present in the invertebrate orthologs (generally one TPPP/species)...
January 20, 2017: Biochemistry
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