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https://www.readbyqxmd.com/read/29149300/the-effect-of-non-reversibility-on-inferring-rooted-phylogenies
#1
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/29148397/evolutionary-context-of-non-sorbitol-fermenting-shiga-toxin-producing-escherichia-coli-o55-h7
#2
Kyle Schutz, Lauren A Cowley, Sharif Shaaban, Anne Carroll, Eleanor McNamara, David L Gally, Gauri Godbole, Claire Jenkins, Timothy J Dallman
In July 2014, an outbreak of Shiga toxin-producing Escherichia coli (STEC) O55:H7 in England involved 31 patients, 13 (42%) of whom had hemolytic uremic syndrome. Isolates were sequenced, and the sequences were compared with publicly available sequences of E. coli O55:H7 and O157:H7. A core-genome phylogeny of the evolutionary history of the STEC O55:H7 outbreak strain revealed that the most parsimonious model was a progenitor enteropathogenic O55:H7 sorbitol-fermenting strain, lysogenized by a Shiga toxin (Stx) 2a-encoding phage, followed by loss of the ability to ferment sorbitol because of a non-sense mutation in srlA...
December 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29146262/pathogenic-labyrinthula-associated-with-australian-seagrasses-considerations-for-seagrass-wasting-disease-in-the-southern-hemisphere
#3
Stacey M Trevathan-Tackett, Brooke K Sullivan, Katie Robinson, Osu Lilje, Peter I Macreadie, Frank H Gleason
Marine disease ecology is a growing field of research, particularly for host organisms negatively impacted by a changing climate and anthropogenic activities. A decrease in health and increase in susceptibility to disease has been hypothesised as the mechanism behind wide-spread seagrass die-offs related to wasting disease in the past. However, seagrass wasting disease and the causative pathogen, Labyrinthula, have been vastly understudied in the southern hemisphere. Our aim was to build on the current knowledge of Australian Labyrinthula descriptions and phylogeny, while also providing a first look at wasting disease ecology in Australia...
January 2018: Microbiological Research
https://www.readbyqxmd.com/read/29145809/genome-wide-characterization-and-expression-profiling-of-pdi-family-gene-reveals-function-as-abiotic-and-biotic-stress-tolerance-in-chinese-cabbage-brassica-rapa-ssp-pekinensis
#4
Md Abdul Kayum, Jong-In Park, Ujjal Kumar Nath, Gopal Saha, Manosh Kumar Biswas, Hoy-Taek Kim, Ill-Sup Nou
BACKGROUND: Protein disulfide isomerase (PDI) and PDI-like proteins contain thioredoxin domains that catalyze protein disulfide bond, inhibit aggregation of misfolded proteins, and function in isomerization during protein folding in endoplasmic reticulum and responses during abiotic stresses.Chinese cabbage is widely recognized as an economically important, nutritious vegetable, but its yield is severely hampered by various biotic and abiotic stresses. Because of, it is prime need to identify those genes whose are responsible for biotic and abiotic stress tolerance...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29143714/new-insights-into-mitogenomic-phylogeny-and-copy-number-in-eight-indigenous-sheep-populations-based-on-the-atp-synthase-and-cytochrome-c-oxidase-genes
#5
P Xiao, L L Niu, Q J Zhao, X Y Chen, L J Wang, L Li, H P Zhang, J Z Guo, H Y Xu, T Zhong
The origins and phylogeny of different sheep breeds has been widely studied using polymorphisms within the mitochondrial hypervariable region. However, little is known about the mitochondrial DNA (mtDNA) content and phylogeny based on mtDNA protein-coding genes. In this study, we assessed the phylogeny and copy number of the mtDNA in eight indigenous (population size, n=184) and three introduced (n=66) sheep breeds in China based on five mitochondrial coding genes (COX1, COX2, ATP8, ATP6 and COX3). The mean haplotype and nucleotide diversities were 0...
November 16, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29143653/phylogenetic-study-of-the-endemic-species-oxytropis-almaatensis-fabaceae-based-on-nuclear-ribosomal-dna-its-sequences
#6
Shyryn Almerekova, Nashtay Mukhitdinov, Saule Abugalieva
BACKGROUND: Oxytropis almaatensis Bajt. is a rare, narrow endemic species of the Trans-Ili Alatau mountains in Kazakhstan. Up to now, no studies regarding the taxonomy and variation of key morphological traits of O. almaatensis were undertaken. The purpose of this analysis was to evaluate phenotypic variation of O. almaatensis and assess the position of the species within the genus based on nucleotide sequences of the nuclear ribosomal DNA internal transcribed spacer (ITS) region. RESULTS: Two populations of O...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29143141/prevalence-and-genomic-characteristics-of-canine-kobuvirus-in-southwest-china
#7
Mingxiang Li, Nan Yan, Min Wang, Bin Zhang, Hua Yue, Cheng Tang
To investigate canine kobuvirus (CaKoV) infection in southwest China, 107 fecal samples were collected from dogs with obvious diarrhea in Sichuan and Chongqing regions, China. CaKoV infection was detected in 54 diarrheic samples (50.46%) by RT-PCR targeting a partial fragment (504 bp) of the 3D gene. Comparison of these partial 3D gene sequences from 14 of these CaKoV-positive samples show 95.4%-99.0% nucleotide (nt) identity within this group, and nt identities ranging from 93.1% to 98.2% with previously reported CaKoV 3D gene sequences...
November 15, 2017: Archives of Virology
https://www.readbyqxmd.com/read/29143083/the-polyphyletic-origins-of-primase-helicase-bifunctional-proteins
#8
Ankita Gupta, Supriya Patil, Ramya Vijayakumar, Kiran Kondabagil
We studied the evolutionary relationships of different primase-helicase bifunctional proteins, found mostly in viruses, virophages, plasmids, and organellar genomes, by phylogeny and correlation analysis. Our study suggests independent origins of primase-helicase bifunctional proteins resulting from multiple fusion events between genes encoding primase and helicase domains of different families. The correlation analysis further indicated strong functional dependencies of domains in the bifunctional proteins that are part of smaller genomes and plasmids...
November 15, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29142593/prevailing-clone-st69-of-vibrio-cholerae-o139-in-india-over-10%C3%A2-years
#9
Shalini Anandan, Naveen Kumar Devanga Ragupathi, Dhiviya Prabaa Muthuirulandi Sethuvel, Suji Thangamani, Balaji Veeraraghavan
Vibrio cholerae is responsible for the cause of severe life-threatening infection known as cholera. The study aimed to analyze the genetic make-up of V. cholerae O139 isolates from India and compare its phylogeny with the global strains. The genome data revealed that all isolates were of same sequence type (ST69) which belongs to seventh pandemic clone, with same virulence gene profile and, antimicrobial resistance gene profile except for two isolates. No known CRISPR repeats were identified in any of these isolates...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/29142118/climate-and-foraging-mode-explain-interspecific-variation-in-snake-metabolic-rates
#10
Andréaz Dupoué, François Brischoux, Olivier Lourdais
The energy cost of self-maintenance is a critical facet of life-history strategies. Clarifying the determinant of interspecific variation in metabolic rate (MR) at rest is important to understand and predict ecological patterns such as species distributions or responses to climatic changes. We examined variation of MR in snakes, a group characterized by a remarkable diversity of activity rates and a wide distribution. We collated previously published MR data (n = 491 observations) measured in 90 snake species at different trial temperatures...
November 29, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29142017/modelling-the-effects-of-phylogeny-and-body-size-on-within-host-pathogen-replication-and-immune-response
#11
Soumya Banerjee, Alan S Perelson, Melanie Moses
Understanding how quickly pathogens replicate and how quickly the immune system responds is important for predicting the epidemic spread of emerging pathogens. Host body size, through its correlation with metabolic rates, is theoretically predicted to impact pathogen replication rates and immune system response rates. Here, we use mathematical models of viral time courses from multiple species of birds infected by a generalist pathogen (West Nile Virus; WNV) to test more thoroughly how disease progression and immune response depend on mass and host phylogeny...
November 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29141036/the-disjunct-pattern-of-the-neotropical-harvestman-discocyrtus-dilatatus-gonyleptidae-explained-by-climate-driven-range-shifts-in-the-quaternary-paleodistributional-and-molecular-evidence
#12
Julia Vergara, Luis E Acosta, Raúl E González-Ittig, Luis M Vaschetto, Cristina N Gardenal
The disjunct distribution of the harvestman Discocyrtus dilatatus (Opiliones, Gonyleptidae) is used as a case study to test the hypothesis of a trans-Chaco Pleistocene paleobridge during range expansion stages. This would have temporarily connected humid regions ('Mesopotamia' in northeastern Argentina, and the 'Yungas' in the northwest, NWA) in the subtropical and temperate South American lowlands. The present study combines two independent approaches: paleodistributional reconstruction, using the Species Distribution Modeling method MaxEnt and projection onto Quaternary paleoclimates (6 kya, 21 kya, 130 kya), and phylogeographic analyses based on the cytochrome oxidase subunit I molecular marker...
2017: PloS One
https://www.readbyqxmd.com/read/29140762/the-genus-parasola-phylogeny-and-the-description-of-three-new-species
#13
János G Szarkándi, Geert Schmidt-Stohn, Bálint Dima, Shah Hussain, Sándor Kocsubé, Tamás Papp, Csaba Vágvölgyi, László G Nagy
Parasola represents an enigmatic lineage of veil-less, coprinoid fungi in Psathyrellaceae (Agaricales). The species-level taxonomy of the genus has been in a flux recently, resulting in the elimination of some long-established names and the description of new taxa. Here, we reconstruct the phylogeny of Parasola using two nuc rDNA loci, the internal transcribed spacer region (ITS1-5.8S-ITS2) and 28S and identify several putatively undescribed species, of which three are formally described here (Parasola crataegi, P...
October 9, 2017: Mycologia
https://www.readbyqxmd.com/read/29140552/the-influence-of-phylogeny-social-style-and-sociodemographic-factors-on-macaque-social-network-structure
#14
Krishna N Balasubramaniam, Brianne A Beisner, Carol M Berman, Arianna De Marco, Julie Duboscq, Sabina Koirala, Bonaventura Majolo, Andrew J MacIntosh, Richard McFarland, Sandra Molesti, Hideshi Ogawa, Odile Petit, Gabriele Schino, Sebastian Sosa, Cédric Sueur, Bernard Thierry, Frans B M de Waal, Brenda McCowan
Among nonhuman primates, the evolutionary underpinnings of variation in social structure remain debated, with both ancestral relationships and adaptation to current conditions hypothesized to play determining roles. Here we assess whether interspecific variation in higher-order aspects of female macaque (genus: Macaca) dominance and grooming social structure show phylogenetic signals, that is, greater similarity among more closely-related species. We use a social network approach to describe higher-order characteristics of social structure, based on both direct interactions and secondary pathways that connect group members...
November 15, 2017: American Journal of Primatology
https://www.readbyqxmd.com/read/29140441/the-complete-phylogeny-of-pangolins-scaling-up-resources-for-the-molecular-tracing-of-the-most-trafficked-mammals-on-earth
#15
Philippe Gaubert, Agostinho Antunes, Hao Meng, Lin Miao, Stéphane Peigné, Fabienne Justy, Flobert Njiokou, Sylvain Dufour, Emmanuel Danquah, Jayanthi Alahakoon, Erik Verheyen, William T Stanley, Stephen J O'Brien, Warren E Johnson, Shu-Jin Luo
Pangolins, considered the most-trafficked mammals on Earth, are rapidly heading to extinction. Eight extant species of these African and Asian scale-bodied anteaters are commonly recognized, but their evolutionary relationships remain largely unexplored. Here we present the most comprehensive phylogenetic assessment of pangolins, based on genetic variation of complete mitogenomes and nine nuclear genes. We confirm deep divergence among Asian and African pangolins occurring not later than the Oligocene-Miocene boundary ca...
November 13, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29139236/corrigendum-to-morphology-and-phylogeny-of-three-new-loxophyllum-species-ciliophora-pleurostomatida-from-mangrove-wetlands-of-southern-china-by-wu-et%C3%A2-al
#16
(no author information available yet)
No abstract text is available yet for this article.
November 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/29139234/corrigendum-to-morphology-morphogenesis-and-molecular-phylogeny-of-paraparentocirrus-sibillinensis-n-gen-n-sp-a-stylonychine-oxytrichidae-ciliophora-hypotrichida-without-transverse-cirri-by-kumar-et%C3%A2-al
#17
https://www.readbyqxmd.com/read/29139232/corrigendum-to-the-morphology-of-three-loxophyllum-species-ciliophora-pleurostomatida-from-southern-china-l-lembum-sp-n-l-vesiculosum-sp-n-and-l-perihoplophorum-buddenbrock-1920-with-notes-on-the-molecular-phylogeny-of-loxophyllum-by-wu-et%C3%A2-al
#18
https://www.readbyqxmd.com/read/29139230/corrigendum-to-two-new-brackish-ciliates-amphileptus-spiculatus-sp-n-and-a-bellus-sp-n-from-mangrove-wetlands-in-southern-china-with-notes-on-the-molecular-phylogeny-of-the-family-amphileptidae-protozoa-ciliophora-pleurostomatida-by-wu-et%C3%A2-al
#19
https://www.readbyqxmd.com/read/29139229/corrigendum-to-description-and-phylogeny-of-urostyla-grandis-wiackowskii-subsp-nov-ciliophora-hypotricha-from-an-estuarine-mangrove-in-brazil-by-paiva-et%C3%A2-al
#20
(no author information available yet)
No abstract text is available yet for this article.
November 2017: Journal of Eukaryotic Microbiology
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