Read by QxMD icon Read


R A Leo Elworth, Chabrielle Allen, Travis Benedict, Peter Dulworth, Luay Nakhleh
Summary: The evolutionary histories of individual regions across a genomic alignment - called 'local genealogies' - can differ from each other, due to processes such as recombination. Elucidating and analyzing these local genealogies are important for a large number of inference tasks, including those pertaining to species phylogenies, evolutionary processes, and trait mapping. In this paper, we present a toolkit for automated local phylogenomic analyses, or ALPHA. The purpose of this toolkit is to provide a wide array of functionalities for automated inference of local genealogies as well as analyses based on these local genealogies...
March 19, 2018: Bioinformatics
Stefan P W de Vries, Moses Vurayai, Mark Holmes, Srishti Gupta, Michael Bateman, David Goldfarb, Duncan J Maskell, Maitshwarelo Ignatius Matsheka, Andrew J Grant
Campylobacter spp. are a leading cause of bacterial enteritis worldwide, including countries in Africa, and have been identified by the World Health Organisation (WHO) as one of the high priority antimicrobial resistant pathogens. However, at present there is little knowledge on the prevalence, molecular epidemiology or antimicrobial susceptibility of Campylobacter spp. isolates in Botswana, both in patients and in the zoonotic context. Some data indicate that ~14% of diarrhoeal disease cases in a paediatric setting can be ascribed to Campylobacter spp...
2018: PloS One
Yin Liang, Shuang-Fei Ran, Jayarama Bhat, Kevin D Hyde, Yong Wang, De-Gang Zhao
An undescribed Curvularia sp. was isolated from the leaf spot disease of Barbados Lily ( Hippeastrum striatum (Lam.) Moore). Phylogenetic analyses of combined ITS, 28S, GPD1 and TEF1 sequence data place nine strains of this species in the trifolii -clade, but they clustered together as an independent lineage with strong support. This species was morphologically compared with related species in the trifolii -clade. Based on differences in morphology and phylogeny, it is concluded that this species is a new taxon, introduced as Curvularia microspora sp...
2018: MycoKeys
Weston Testo, Benjamin Øllgaard, Ashley Field, Thaís Almeida, Michael Kessler, David Barrington
The Neotropical clade of the lycophyte genus Phlegmariurus is comprised of an estimated 150 described species and exhibits exceptional morphological and ecological diversity. Because of their simple morphology, frequent convergent evolution, and the recentness of the group's diversification, the delimitation of species and species groups has remained challenging. Here, we present a robustly support phylogeny of Neotropical Phlegmariurus based on six chloroplast markers and ca. 70% of known species, and use ancestral character state reconstruction to investigate morphological evolution in the clade, and define natural species groups...
March 17, 2018: Molecular Phylogenetics and Evolution
Weilin Zeng, Ling Sun, Zheng Xiang, Na Li, Jie Zhang, Yongshu He, Qing Li, Fang Yang, Jingling Song, James Morris, Benjamin M Rosenthal, Le Sun, Huaie Liu, Zhaoqing Yang
While Sarcocystis parasites from the muscles of donkey and horse have been characterized as different species, similarities between the parasites in these host raises questions about this assignment (Levine and Tadros, 1980; Matuschka, 1983; Odening et al., 1995b). To resolve this, we examined the tissue cysts of Sarcocystis collected from donkeys and horses were studied by morphological and molecular methods. Morphological studies performed by light microscopy (LM) revealed that each of two types of cysts were present in samples from each host type...
March 15, 2018: Veterinary Parasitology
Xiaolong Li, Shutian Tao, Shuwei Wei, Meiling Ming, Xiaosan Huang, Shaoling Zhang, Jun Wu
BACKGROUND: In plants, ERF genes participate in a variety of regulatory pathways, such as plant growth and biotic and/or abiotic stress responses. Although the genome of Chinese white pear ('Dangshansuli') has been released, knowledge regarding the ERF family in pear, such as gene functions, evolutionary history and expression patterns, remains limited. RESULTS: In our study, a total of 155 members of ERF families were identified in pear (Pyrus bretschneideri). The Ka and Ks values suggested that whole-genome duplication (WGD) and dispersed duplication have effectively contributed to the expansion of the pear ERF family...
March 20, 2018: BMC Plant Biology
Yarden Shalev, Shannon M Soucy, R Thane Papke, J Peter Gogarten, Jerry Eichler, Uri Gophna
Within the Haloferax genus, both the surface (S)-layer protein, and the glycans that can decorate it, vary between species, which can potentially result in many different surface types, analogous to bacterial serotypes. This variation may mediate phenotypes, such as sensitivity to different viruses and mating preferences. Here, we describe S-layer glycoproteins found in multiple Haloferax strains and perform comparative genomics analyses of major and alternative glycosylation clusters of isolates from two coastal sites...
March 20, 2018: Genes
Erika Viljoen, Damaris A Odeny, Martin P A Coetzee, Dave K Berger, David J G Rees
Amaranthus species are an emerging and promising nutritious traditional vegetable food source. Morphological plasticity and poorly resolved dendrograms have led to the need for well resolved species phylogenies. We hypothesized that whole chloroplast phylogenomics would result in more reliable differentiation between closely related amaranth species. The aims of the study were therefore: to construct a fully assembled, annotated chloroplast genome sequence of Amaranthus tricolor; to characterize Amaranthus accessions phylogenetically by comparing barcoding genes (matK, rbcL, ITS) with whole chloroplast sequencing; and to use whole chloroplast phylogenomics to resolve deeper phylogenetic relationships...
March 19, 2018: Journal of Molecular Evolution
Joaquín Letelier, Elisa de la Calle-Mustienes, Joyce Pieretti, Silvia Naranjo, Ignacio Maeso, Tetsuya Nakamura, Juan Pascual-Anaya, Neil H Shubin, Igor Schneider, Juan Ramón Martinez-Morales, José Luis Gómez-Skarmeta
Despite their evolutionary, developmental and functional importance, the origin of vertebrate paired appendages remains uncertain. In mice, a single enhancer termed ZRS is solely responsible for Shh expression in limbs. Here, zebrafish and mouse transgenic assays trace the functional equivalence of ZRS across the gnathostome phylogeny. CRISPR/Cas9-mediated deletion of the medaka (Oryzias latipes) ZRS and enhancer assays identify the existence of ZRS shadow enhancers in both teleost and human genomes. Deletion of both ZRS and shadow ZRS abolishes shh expression and completely truncates pectoral fin formation...
March 19, 2018: Nature Genetics
Melinda M Pettigrew, Christian P Ahearn, Janneane F Gent, Yong Kong, Mary C Gallo, James B Munro, Adonis D'Mello, Sanjay Sethi, Hervé Tettelin, Timothy F Murphy
Nontypeable Haemophilus influenzae (NTHi) exclusively colonize and infect humans and are critical to the pathogenesis of chronic obstructive pulmonary disease (COPD). In vitro and animal models do not accurately capture the complex environments encountered by NTHi during human infection. We conducted whole-genome sequencing of 269 longitudinally collected cleared and persistent NTHi from a 15-y prospective study of adults with COPD. Genome sequences were used to elucidate the phylogeny of NTHi isolates, identify genomic changes that occur with persistence in the human airways, and evaluate the effect of selective pressure on 12 candidate vaccine antigens...
March 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
Jared A Grummer, Mariana M Morando, Luciano J Avila, Jack W Sites, Adam D Leaché
Rapid evolutionary radiations are difficult to resolve because divergence events are nearly synchronous and gene flow among nascent species can be high, resulting in a phylogenetic "bush". Large datasets composed of sequence loci from across the genome can potentially help resolve some of these difficult phylogenetic problems. A suitable test case is the Liolaemus fitzingerii species group of lizards, which includes twelve species that are broadly distributed in Argentinean Patagonia. The species in the group have had a complex evolutionary history that has led to high morphological variation and unstable taxonomy...
March 16, 2018: Molecular Phylogenetics and Evolution
Panayiota Kotsakiozi, Daniel Jablonski, Çetin Ilgaz, Yusuf Kumlutaş, Aziz Avcı, Shai Meiri, Yuval Itescu, Oleg Kukushkin, Václav Gvoždík, Giovanni Scillitani, Stephen Roussos, David Jandzik, Panagiotis Kasapidis, Petros Lymberakis, Nikos Poulakakis
The Kotschy's Gecko, Mediodactylus kotschyi, is a small gecko native to southeastern Europe and the Eastern Mediterranean. It displays great morphological variation with a large number of morphologically recognized subspecies. However, it has been suggested that it constitutes a species complex of several yet unrecognized species. In this study, we used multilocus sequence data (three mitochondrial and three nuclear gene fragments) to estimate the phylogenetic relationships of 129 populations covering a substantial part of the distribution range of the species...
March 16, 2018: Molecular Phylogenetics and Evolution
Corey Holt, Rachel Foster, Carly L Daniels, Mark van der Giezen, Stephen W Feist, Grant D Stentiford, David Bass
A parasite exhibiting Oomycete-like morphology and pathogenesis was isolated from discoloured eggs of the European lobster (Homarus gammarus) and later found in gill tissues of adults. Group-specific Oomycete primers were designed to amplify the 18S ribosomal small subunit (SSU), which initially identified the organism as the same as the 'Haliphthoros' sp. NJM 0034 strain (AB178865.1) previously isolated from abalone (imported from South Australia to Japan). However, in accordance with other published SSU-based phylogenies, the NJM 0034 isolate did not group with other known Haliphthoros species in our Maximum Likelihood and Bayesian phylogenies...
March 16, 2018: Journal of Invertebrate Pathology
Monica M Lahra, Irene Martin, Walter Demczuk, Amy V Jennison, Ken-Ichi Lee, Shu-Ichi Nakayama, Brigitte Lefebvre, Jean Longtin, Alison Ward, Michael R Mulvey, Teodora Wi, Makoto Ohnishi, David Whiley
Ceftriaxone remains a first-line treatment for patients infected by Neisseria gonorrhoeae in most settings. We investigated the possible spread of a ceftriaxone-resistant FC428 N. gonorrhoeae clone in Japan after recent isolation of similar strains in Denmark (GK124) and Canada (47707). We report 2 instances of the FC428 clone in Australia in heterosexual men traveling from Asia. Our bioinformatic analyses included core single-nucleotide variation phylogeny and in silico molecular typing; phylogenetic analysis showed close genetic relatedness among all 5 isolates...
April 2018: Emerging Infectious Diseases
David Barros-García, Elsa Froufe, Rafael Bañón, Juan Carlos Arronte, Alejandro De Carlos
The Notacanthiformes is an ancient group of deep-sea ray-finned fishes comprising 27 species in two families; Halosauridae and Notacanthidae. Although many studies have tried to reconstruct the phylogenetic relationships among the major clades of Elopomorpha, little is known about the evolutionary history of notacanthiforms. Molecular and morphological data were used to test previous hypotheses regarding the phylogenetic relationships among notacanthiform taxa, and to unravel the origin and evolution of this group...
March 15, 2018: Molecular Phylogenetics and Evolution
Frank Portillo, William R Branch, Werner Conradie, Mark-Oliver Rödel, Johannes Penner, Michael F Barej, Chifundera Kusamba, Wandege M Muninga, Mwenebatu M Aristote, Aaron M Bauer, Jean-François Trape, Zoltán T Nagy, Piero Carlino, Olivier S G Pauwels, Michele Menegon, Marius Burger, Tomáš Mazuch, Kate Jackson, Daniel F Hughes, Mathias Behangana, Eli Greenbaum
Members of the snake subfamily Aparallactinae occur in various habitats throughout sub-Saharan Africa. The monophyly of aparallactine snakes is well established, but relationships within the subfamily are poorly known. We sampled 158 individuals from six of eight aparallactine genera in sub-Saharan Africa. We employed concatenated gene-tree analyses, divergence dating approaches, and ancestral-area reconstructions to infer phylogenies and biogeographic patterns with a multi-locus data set consisting of three mitochondrial (16S, cyt b, and ND4) and two nuclear genes (c-mos and RAG1)...
March 15, 2018: Molecular Phylogenetics and Evolution
Joshua P Egan, Devin D Bloom, Chien-Hsien Kuo, Michael P Hammer, Prasert Tongnunui, Samuel P Iglésias, Marcus Sheaves, Chaiwut Grudpan, Andrew M Simons
Biotic and abiotic forces govern the evolution of trophic niches, which profoundly impact ecological and evolutionary processes and aspects of species biology. Herbivory is a particularly interesting trophic niche because there are theorized trade-offs associated with diets comprised of low quality food that might prevent the evolution of herbivory in certain environments. Herbivory has also been identified as a potential evolutionary "dead-end" that hinders subsequent trophic diversification. For this study we investigated trophic niche evolution in Clupeoidei (anchovies, sardines, herrings, and their relatives) and tested the hypotheses that herbivory is negatively correlated with salinity and latitude using a novel, time-calibrated molecular phylogeny, trophic guilds delimited using diet data and cluster analysis, and standard and phylogenetically-informed statistical methods...
March 15, 2018: Molecular Phylogenetics and Evolution
Cecilia C Cundon, Alejandro Ameal, Elsa Maubecín, Adriana Bentancor
The pangenome of Escherichia coli is composed of a conserved core and variable genomic regions. The constant genetic component allows to determine the phylogeny of the microorganism, while genetic variability promoted the emergence of intestinal pathogenic strains and extraintestinal strains. In this study we characterized 85 extraintestinal pathogenic isolates genetically isolated from canines and felines. We used the Clermont scheme that includes intestinal (A and B1) and extraintestinal (B2 and D) phylogroups, virulence markers (pap1-2, pap3-4, sfa, afa, hlyA, aer and cnf) and hybrid pathogens...
March 15, 2018: Revista Argentina de Microbiología
Niloofar Vaghefi, Julie R Kikkert, Frank S Hay, Gavriela D Carver, Lori B Koenick, Melvin D Bolton, Linda E Hanson, Gary A Secor, Sarah J Pethybridge
The taxonomy and evolutionary species boundaries in a global collection of Cercospora isolates from Beta vulgaris was investigated based on sequences of six loci. Species boundaries were assessed using concatenated multi-locus phylogenies, Generalized Mixed Yule Coalescent (GMYC), Poisson Tree Processes (PTP), and Bayes factor delimitation (BFD) framework. Cercospora beticola was confirmed as the primary cause of Cercospora leaf spot (CLS) on B. vulgaris. Cercospora apii, C. cf. flagellaris, Cercospora sp...
April 2018: Fungal Biology
Tuo Yang, Li-Min Lu, Wei Wang, Jian-Hua Li, Steven R Manchester, Jun Wen, Zhi-Duan Chen
Sabiaceae comprises three genera and ca. 80 species with an amphi-Pacific tropical disjunct distribution. It has been unclear whether the family is monophyletic, where the family belongs within the angiosperm phylogeny, and when and how is present-day disjunct distribution originated. To address these questions, we conducted a phylogenetic analysis of Sabiaceae with comprehensive sampling of the family and basal eudicots using six chloroplast DNA loci (atpB, rbcL, matK, ndhF, atpB-rbcL and trnL-trnF). Our results support the monophyly of Sabiaceae s...
March 13, 2018: Molecular Phylogenetics and Evolution
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"