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Phylogenetics

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https://www.readbyqxmd.com/read/29150984/how-the-environment-shapes-animal-signals-a-test-of-the-acoustic-adaptation-hypothesis-in-frogs
#1
Sandra Goutte, Alain Dubois, Samuel D Howard, Rafael Márquez, Jodi J L Rowley, J Maximilian Dehling, Philippe Grandcolas, Rongchuan Xiong, Frédéric Legendre
Long distance acoustic signals are widely used in animal communication systems and, in many cases, essential for reproduction. The Acoustic Adaptation Hypothesis (AAH) implies that acoustic signals should be selected for further transmission and better content integrity under the acoustic constraints of the habitat in which they are produced. In the present study, we test predictions derived from the AAH in frogs. Specifically, we focus on the difference between torrent frogs and frogs calling in less noisy habitats...
November 18, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29150913/molecular-epidemiology-of-goat-pox-viruses
#2
P Roy, S Jaisree, S Balakrishnan, K Senthilkumar, R Mahaprabhu, A Mishra, B Maity, T K Ghosh, A P Karmakar
Goat pox disease outbreaks were observed in different places affecting Black Bengal Goats in West Bengal (WB) and Tellicherry, Vembur and non-descriptive breeds in Tamil Nadu (TN) causing severe lesions and mortality up to 30%. Clinical specimens from all the outbreaks were screened by polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) and confirmed the diseases as Goat Pox. Virus isolation in Vero cell line was done with randomly selected ten samples, cytopathic effects (CPE) characterized by syncytia and intracytoplasmic inclusion bodies were observed after several blind passages...
November 18, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29150903/phylogenetic-and-genetic-variation-analyses-of-porcine-circovirus-type-2-isolated-from-china
#3
S Yang, S Yin, Y Shang, B Liu, L Yuan, M U Zafar Khan, X Liu, J Cai
Porcine circovirus type 2 (PCV2) is a causative agent of PCV2-associated disease, which is a growing problem in the swine industry worldwide. High nucleotide substitution occurs in the capsid (Cap) gene of PCV2, which allows the continuous evolution and the emergence of novel PCV2 strains. In this study, we sequenced 24 Chinese PCV2 strains collected from healthy and diseased pigs between 2013 and 2015. Analyses of the genome, Cap and phylogeny classified the 24 Chinese PCV2 strains as PCV-2a (four of 24), PCV-2b (five of 24) and PCV-2d (15 of 24)...
November 17, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29150825/correction-to-phylogenetic-insight-into-zika-and-emerging-viruses-for-a-perspective-on-potential-hosts
#4
Diana S Weber, Karen A Alroy, Samuel M Scheiner
The article Phylogenetic Insight into Zika and Emerging Viruses for a Perspective on Potential Hosts, written by Diana S. Weber, Karen A. Alroy, and Samuel M. Scheiner, was originally published Online First without open access.
November 17, 2017: EcoHealth
https://www.readbyqxmd.com/read/29150772/norovirus-gii-17-associated-with-a-foodborne-acute-gastroenteritis-outbreak-in-brazil-2016
#5
Juliana da Silva Ribeiro de Andrade, Tulio Machado Fumian, José Paulo Gagliardi Leite, Matheus Ribeiro de Assis, Alexandre Madi Fialho, Sergio Mouta, Cristiane Mendes Pereira Santiago, Marize Pereira Miagostovich
Foodborne transmission gastroenteritis (AGE) outbreak occurred during a celebration lunch in July, 2016, Brazil. All stool samples tested were positive for noroviruses (NoV) and phylogenetic analysis revealed that strains were genetically close to GII.17 Kawasaki_2014. These findings indicated circulation of NoV GII.17 Kawasaki_2014 in the Brazilian population, associated with AGE outbreak.
November 17, 2017: Food and Environmental Virology
https://www.readbyqxmd.com/read/29150717/genetic-diversity-and-phylogenetic-study-of-the-chinese-gelao-ethnic-minority-via-23-y-str-loci
#6
Pengyu Chen, Yanyan Han, Guanglin He, Haibo Luo, Tianzhen Gao, Feng Song, Dengfu Wan, Jian Yu, Yiping Hou
Haplotype diversity for 23 Y chromosomal short tandem repeat (Y-STR) loci included in the PowerPlex(®) Y23 System was analyzed in the Chinese Gelao minority group of 234 unrelated males living in Daozhen Gelao-Miao Autonomous County in Guizhou Province, southwest China. A total of 216 different haplotypes were detected, of which 199 haplotypes were unique. The overall haplotype diversity (HD) and discrimination capacity (DC) were 0.9996 and 0.9231, respectively. The gene diversity (GD) ranged from 0.4159 (DYS438) to 0...
November 17, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29150716/slow-life-histories-in-lizards-living-in-the-highlands-of-the-andes-mountains
#7
Jorgelina M Boretto, Facundo Cabezas-Cartes, Nora R Ibargüengoytía
In the highlands of the Andes, lizards must balance precisely the allocation of energy for growth and reproduction to ensure their survival. We studied the individuals' age, growth rates, age at sexual maturity, and maximum life span of the viviparous lizard Phymaturus antofagastensis, endemic of cold and harsh environments at high altitudes in the Andes Mountains of Catamarca province, Argentina. We also estimated key life history parameters like reproductive effort, lifetime reproductive effort, net reproductive rate, and relative reproductive time in P...
November 17, 2017: Journal of Comparative Physiology. B, Biochemical, Systemic, and Environmental Physiology
https://www.readbyqxmd.com/read/29150699/three-new-species-of-gyrodactylus-von-nordmann-1832-described-from-goodea-atripinnis-pisces-goodeidae-an-endemic-freshwater-fish-from-the-central-highlands-of-mexico
#8
Adriana García-Vásquez, Ismael Guzmán-Valdivieso, Ulises Razo-Mendivil, Miguel Rubio-Godoy
Goodea atripinnis Jordan, 1880 has a broad range of habitats and is the most widespread species of the endemic goodeid fishes, which inhabit the central highlands of Mexico. This species is known to be host to a high diversity of helminth parasites from which only three belong to the genus Gyrodactylus von Nordmann, 1832: G. lamothei Mendoza-Palmero, Sereno-Uribe et Salgado-Maldonado, 2009, G. mexicanus Mendoza-Palmero, Sereno-Uribe et Salgado-Maldonado, 2009, and G. tomahuac Rubio-Godoy, Razo-Mendivil, García-Vásquez, Freeman, Shinn et Paladini, 2016...
November 17, 2017: Parasitology Research
https://www.readbyqxmd.com/read/29150669/genome-wide-survey-indicates-diverse-physiological-roles-of-the-turnip-brassica-rapa-var-rapa-calcium-dependent-protein-kinase-genes
#9
Qiuli Wang, Xin Yin, Qian Chen, Nan Xiang, Xudong Sun, Yunqiang Yang, Yongping Yang
Calcium-dependent protein kinases (CDPKs) as crucial sensors of calcium concentration changes play important roles in responding to abiotic and biotic stresses. In this study, 55 BrrCDPK genes, which were phylogenetically clustered into four subfamilies, were identified. Chromosome locations indicated that the CDPK family in turnip expanded by segmental duplication and genome rearrangement. Moreover, gene expression profiles showed that different BrrCDPKs were expressed in specific tissues or stages. Transcript levels of BrrCDPKs indicated that they were involved in abiotic and biotic stresses and that paralogs exhibited functional divergence...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150508/community-composition-and-ultrastructure-of-a-nitrate-dependent-anaerobic-methane-oxidizing-enrichment-culture
#10
Lavinia Gambelli, Simon Guerrero-Cruz, Rob J Mesman, Geert Cremers, Mike S M Jetten, Huub J M Op den Camp, Boran Kartal, Claudia Lueke, Laura van Niftrik
Methane is a very potent greenhouse gas and can be oxidized aerobically or anaerobically through microbial-mediated processes, thus decreasing methane emissions to the atmosphere. Using a complementary array of methods including phylogenetic analysis, physiological experiments, and light and electron microscopy techniques (including electron tomography), we investigated the community composition and ultrastructure of a continuous bioreactor enrichment culture, in which anaerobic methane oxidation (AOM) was coupled to nitrate reduction...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29150506/the-swinholide-biosynthetic-gene-cluster-from-a-terrestrial-cyanobacterium-nostoc-sp-uhcc-0450
#11
Anu Humisto, Jouni Jokela, Liwei Liu, Matti Wahlsten, Hao Wang, Perttu Permi, João Paulo Machado, Agostinho Antunes, David P Fewer, Kaarina Sivonen
Swinholides are 42-carbon ring polyketides with a twofold axis of symmetry. They are potent cytotoxins that disrupt the actin cytoskeleton. Swinholides were discovered from the marine sponge Theonella sp. and were long-suspected to be produced by symbiotic bacteria. Misakinolide, a structural variant of swinholide, was recently demonstrated to be the product of the symbiotic heterotrophic proteobacterium. Here we report the production of swinholide A by an axenic strain of the terrestrial cyanobacterium Nostoc sp...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29150450/aerobic-power-and-flight-capacity-in-birds-a-phylogenetic-test-of-the-heart-size-hypothesis
#12
Roberto F Nespolo, César González-Lagos, Jaiber J Solano-Iguaran, Magnus Elfwing, Alvaro Garitano-Zavala, Santiago Mañosa, Juan Carlos Alonso, Jordi Altimiras
Flight capacity is one of the most important innovations in animal evolution; it only evolved in insects, birds, mammals and the extinct pterodactyls. Given that powered flight represents a demanding aerobic activity, an efficient cardiovascular system is essential for the continuous delivery of oxygen to the pectoral muscles during flight. It is well known that the limiting step in the circulation is stroke volume (the volume of blood pumped from the ventricle to the body during each beat), which is determined by the size of the ventricle...
November 17, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/29150355/contribution-of-nitric-oxide-synthase-from-coagulase-negative-staphylococci-to-the-development-of-red-myoglobin-derivatives
#13
Geoffrey Ras, Xavier Bailly, Jean-Paul Chacornac, Véronique Zuliani, Patrick Derkx, Tim M Seibert, Régine Talon, Sabine Leroy
As part of the microbial community of meat or as starter cultures, coagulase-negative staphylococci (CNS) serve several essential technological purposes in meat products, such as color development through the reduction of nitrate to nitrite. As the safety of nitrite as an additive has been questioned, we explored the potential of CNS to develop red myoglobin derivatives such as oxymyoglobin and nitrosomyoglobin. Nitrosoheme was extracted to evaluate NO production. This production could be due to a nitric oxide synthase (NOS) activity...
November 13, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29150186/articular-scaling-and-body-mass-estimation-in-platyrrhines-and-catarrhines-modern-variation-and-application-to-fossil-anthropoids
#14
Jonathan M G Perry, Siobhán B Cooke, Jacqueline A Runestad Connour, M Loring Burgess, Christopher B Ruff
Body mass is an important component of any paleobiological reconstruction. Reliable skeletal dimensions for making estimates are desirable but extant primate reference samples with known body masses are rare. We estimated body mass in a sample of extinct platyrrhines and Fayum anthropoids based on four measurements of the articular surfaces of the humerus and femur. Estimates were based on a large extant reference sample of wild-collected individuals with associated body masses, including previously published and new data from extant platyrrhines, cercopithecoids, and hominoids...
November 14, 2017: Journal of Human Evolution
https://www.readbyqxmd.com/read/29150081/turning-over-a-new-leaf-bacteriocins-going-green
#15
Maarten G K Ghequire, René De Mot
Bacteriocins are potent antibacterial proteins that selectively kill phylogenetic relatives of the producer. Their polymorphic nature, most prominent in γ-Proteobacteria, offers potential for the design of customized bacteriocin cocktails targeting Gram-negative pathogens. As an alternative to recombinant production in bacteria, they are eligible for large-scale production in plants.
November 14, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/29149857/putative-progressive-and-abortive-feline-leukemia-virus-infection-outcomes-in-captive-jaguarundis-puma-yagouaroundi
#16
Claudia Filoni, A Katrin Helfer-Hungerbuehler, José Luiz Catão-Dias, Mara Cristina Marques, Luciana Neves Torres, Manfred Reinacher, Regina Hofmann-Lehmann
BACKGROUND: Feline leukemia virus (FeLV) is an exogenous gammaretrovirus of domestic cats (Felis catus) and some wild felids. The outcomes of FeLV infection in domestic cats vary according to host susceptibility, virus strain, and infectious challenge dose. Jaguarundis (Puma yagouaroundi) are small wild felids from South and Central America. We previously reported on FeLV infections in jaguarundis. We hypothesized here that the outcomes of FeLV infection in P. yagouaroundi mimic those observed in domestic cats...
November 17, 2017: Virology Journal
https://www.readbyqxmd.com/read/29149421/kribbella-podocarpi-sp-nov-isolated-from-the-leaves-of-a-yellowwood-tree-podocarpus-latifolius
#17
Sarah M Curtis, Iulia Norton, Gareth J Everest, Paul R Meyers
An endophytic actinobacterial strain was isolated from a yellowwood tree growing on the slope of Devil's Peak, Cape Town, South Africa. Analysis of the 16S rRNA gene showed that the strain belongs to the genus Kribbella. Phylogenetic analyses using the 16S rRNA gene and multilocus sequence analysis using the concatenated gene sequences of the gyrB, rpoB, relA, recA and atpD genes showed that strain YPL1(T) is closely related to the type strains of Kribbella karoonensis and Kribbella shirazensis. DDH experiments showed that strain YPL1(T) is a distinct genomic species from its close phylogenetic relative, K...
November 17, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29149300/the-effect-of-non-reversibility-on-inferring-rooted-phylogenies
#18
Svetlana Cherlin, Sarah E Heaps, Tom M W Nye, Richard J Boys, Tom A Williams, T Martin Embley
Most phylogenetic models assume that the evolutionary process is stationary and reversible. In addition to being biologically improbable, these assumptions also impair inference by generating models under which the likelihood does not depend on the position of the root. Consequently, the root of the tree cannot be inferred as part of the analysis. Yet identifying the root position is a key component of phylogenetic inference because it provides a point of reference for polarising ancestor/descendant relationships and therefore interpreting the tree...
November 15, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29149287/genomic-and-epigenomic-immunity-in-common-bean-the-unusual-features-of-nb-lrr-gene-family
#19
Manon M S Richard, Ariane Gratias, Vincent Thareau, Kyung Do Kim, Sandrine Balzergue, Johann Joets, Scott A Jackson, Valérie Geffroy
In plants, a key class of genes comprising most of disease resistance (R) genes encodes Nucleotide-binding leucine-rich repeat (NL) proteins. Access to common bean (Phaseolus vulgaris) genome sequence provides unparalleled insight into the organization and evolution of this large gene family (∼400 NL) in this important crop. As observed in other plant species, most common bean NL are organized in cluster of genes. However, a particularity of common bean is that these clusters are often located in subtelomeric regions close to terminal knobs containing the satellite DNA khipu...
November 15, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29149270/aniseed-2017-extending-the-integrated-ascidian-database-to-the-exploration-and-evolutionary-comparison-of-genome-scale-datasets
#20
Matija Brozovic, Christelle Dantec, Justine Dardaillon, Delphine Dauga, Emmanuel Faure, Mathieu Gineste, Alexandra Louis, Magali Naville, Kazuhiro R Nitta, Jacques Piette, Wendy Reeves, Céline Scornavacca, Paul Simion, Renaud Vincentelli, Maelle Bellec, Sameh Ben Aicha, Marie Fagotto, Marion Guéroult-Bellone, Maximilian Haeussler, Edwin Jacox, Elijah K Lowe, Mickael Mendez, Alexis Roberge, Alberto Stolfi, Rui Yokomori, C Titus Brown, Christian Cambillau, Lionel Christiaen, Frédéric Delsuc, Emmanuel Douzery, Rémi Dumollard, Takehiro Kusakabe, Kenta Nakai, Hiroki Nishida, Yutaka Satou, Billie Swalla, Michael Veeman, Jean-Nicolas Volff, Patrick Lemaire
ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes...
November 15, 2017: Nucleic Acids Research
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