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https://www.readbyqxmd.com/read/28453679/biopaxviz-a-cytoscape-application-for-the-visual-exploration-of-metabolic-pathway-evolution
#1
Fotis E Psomopoulos, Dimitrios M Vitsios, Shakuntala Baichoo, Christos A Ouzounis
Summary: BioPAXViz is a Cytoscape (version 3) application, providing a comprehensive framework for metabolic pathway visualization. Beyond the basic parsing, viewing and browsing roles, the main novel function that BioPAXViz provides is a visual comparative analysis of metabolic pathway topologies across pre-computed pathway phylogenomic profiles given a species phylogeny. Furthermore, BioPAXViz supports the display of hierarchical trees that allow efficient navigation through sets of variants of a single reference pathway...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453644/traitrateprop-a-web-server-for-the-detection-of-trait-dependent-evolutionary-rate-shifts-in-sequence-sites
#2
Eli Levy Karin, Haim Ashkenazy, Susann Wicke, Tal Pupko, Itay Mayrose
Understanding species adaptation at the molecular level has been a central goal of evolutionary biology and genomics research. This important task becomes increasingly relevant with the constant rise in both genotypic and phenotypic data availabilities. The TraitRateProp web server offers a unique perspective into this task by allowing the detection of associations between sequence evolution rate and whole-organism phenotypes. By analyzing sequences and phenotypes of extant species in the context of their phylogeny, it identifies sequence sites in a gene/protein whose evolutionary rate is associated with shifts in the phenotype...
April 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28453569/molecular-exploration-of-hidden-diversity-in-the-indo-west-pacific-sciaenid-clade
#3
Pei-Chun Lo, Shu-Hui Liu, Siti Azizah Mohd Nor, Wei-Jen Chen
The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa...
2017: PloS One
https://www.readbyqxmd.com/read/28449025/reltime-rates-collapses-to-a-strict-clock-when-estimating-the-timeline-of-animal-diversification
#4
Jesus Lozano-Fernandez, Mario Dos Reis, Philip C J Donoghue, Davide Pisani
Establishing an accurate timescale for the history of life is crucial to understand evolutionary processes. To this scope, relaxed molecular clock models implemented in a Bayesian MCMC framework are generally used. However, these methods are time consuming. RelTime, a non-Bayesian method implementing a fast, ad hoc, algorithm for relative dating, was developed to overcome the computational inefficiencies of Bayesian software. RelTime was recently used to investigate the origin of animals, and found results consistent with outdated studies from the 1980es and 1990es that recovered metazoans to have a Mesoproterozoic origin (originating approximately 1...
April 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28446692/linking-species-habitat-and-past-palaeoclimatic-events-to-evolution-of-the-teleost-innate-immune-system
#5
Monica Hongrø Solbakken, Kjetil Lysne Voje, Kjetill Sigurd Jakobsen, Sissel Jentoft
Host-intrinsic factors as well as environmental changes are known to be strong evolutionary drivers defining the genetic foundation of immunity. Using a novel set of teleost genomes and a time-calibrated phylogeny, we here investigate the family of Toll-like receptor (TLR) genes and address the underlying evolutionary processes shaping the diversity of the first-line defence. Our findings reveal remarkable flexibility within the evolutionary design of teleost innate immunity characterized by prominent TLR gene losses and expansions...
April 26, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28446617/is-embryonic-hypothermia-tolerance-common-in-birds
#6
Jin-Ming Zhao, Zhi-Ming Han, Yue-Hua Sun
Avian incubation temperatures oscillate within narrow limits to ensure proper embryonic development. However, field observations and experimental studies have found that some species can tolerate very low incubation temperatures, either regularly or occasionally. We artificially incubated eggs from five domestic species, which represent a range of egg sizes, to examine whether a diversity of avian species could exhibit an unusual hypothermia tolerance, as observed in the field. We found that eggs of the chicken (Gallus gallus domesticus), pigeon (Columba livia domestica), Japanese quail (Coturnix japonica) and budgerigar (Melopsittacus undulatus) survived the incubation period and hatched after experiencing 10°C hypothermia for 6 h each day...
April 2017: Biology Letters
https://www.readbyqxmd.com/read/28445658/a-time-and-a-place-for-everything-phylogenetic-history-and-geography-as-joint-predictors-of-oak-plastome-phylogeny
#7
Kasey Khanh Pham, Andrew L Hipp, Paul S Manos, Richard C Cronn
Due to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation generally cause topology to reflect geographic structure, while deeper branches reflect lineage divergence. In this study, we quantify the simple and partial effects of geographic proximity and nucleome-inferred phylogenetic history on oak plastome phylogeny at different evolutionary scales...
April 26, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28444795/systematics-and-molecular-phylogeny-of-the-ciliate-genus-pseudokeronopsis-ciliophora-hypotrichia
#8
Ju Li, Zifeng Zhan, Kuidong Xu
A still challenging study on ciliate systematics is to clarify the taxonomic and phylogenetic confusions of the fascinating pigmented Pseudokeronopsis species because of their high inter-specific similarities. We evaluated the identities and internal relationships within Pseudokeronopsis based on morphological descriptions in combination with the 18S and ITS-5.8S rDNA genetic distances, ITS2 secondary structures and phylogenetic analyses. Results showed that (1) Pseudokeronopsis pararubra, a species ever synonymized as Pseudokeronopsis carnea, is a valid species; (2) most Chinese populations identified as Pseudokeronopsis rubra represent a new species namely Pseudokeronopsis songi sp...
April 26, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/28444560/y-chromosomal-sequences-of-diverse-indian-populations-and-the-ancestry-of-the-andamanese
#9
Mayukh Mondal, Anders Bergström, Yali Xue, Francesc Calafell, Hafid Laayouni, Ferran Casals, Partha P Majumder, Chris Tyler-Smith, Jaume Bertranpetit
We present 42 new Y-chromosomal sequences from diverse Indian tribal and non-tribal populations, including the Jarawa and Onge from the Andaman Islands, which are analysed within a calibrated Y-chromosomal phylogeny incorporating South Asian (in total 305 individuals) and worldwide (in total 1286 individuals) data from the 1000 Genomes Project. In contrast to the more ancient ancestry in the South than in the North that has been claimed, we detected very similar coalescence times within Northern and Southern non-tribal Indian populations...
April 25, 2017: Human Genetics
https://www.readbyqxmd.com/read/28444386/coevolution-with-pollinating-resin-midges-led-to-resin-filled-nurseries-in-the-androecia-gynoecia-and-tepals-of-kadsura-schisandraceae
#10
Shi-Xiao Luo, Ting-Ting Liu, Fei Cui, Zi-Yin Yang, Xiao-Ying Hu, Susanne S Renner
Background and Aims: Resin is a defence against herbivores and a floral reward in a few African and South American species whose bee pollinators collect it for nest construction. Here we describe a new role for floral resin from the Asian genus Kadsura (Schisandraceae). Kadsura tepals tightly cover a globe formed by carpels (in females) or near-fused stamens with fleshy connectives (in male flowers of most, but not all species). Methods: We carried out field observations at four sites in China and used pollinator behavioural assays, chemical analyses and time-calibrated insect and plant phylogenies to investigate the specificity of the interactions and their relationship to floral structure...
April 21, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28444200/the-mediterranean-the-cradle-of-anthoxanthum-poaceae-diploid-diversity
#11
Zuzana Chumová, Eliška Záveská, Terezie Mandáková, Karol Krak, Pavel Trávnícek
Background and Aims: Knowledge of diploid phylogeny and ecogeography provide a foundation for understanding plant evolutionary history, diversification patterns and taxonomy. The genus Anthoxanthum (vernal grasses, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and poorly resolved evolutionary relationships. The aims of the study were to reveal: (1) evolutionary lineages of the diploid taxa and their genetic differentiation; (2) the past distribution of the rediscovered 'Mediterranean diploid'; and (3) possible migration routes of diploids in the Mediterranean...
April 21, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28443072/distribution-of-integrons-and-phylogenetic-groups-among-enteropathogenic-escherichia-coli-isolates-from-children-5-years-of-age-in-delhi-india
#12
Taru Singh, Shukla Das, V G Ramachandran, Sayim Wani, Dheeraj Shah, Khan A Maroof, Aditi Sharma
Integrons by means of horizontal gene transfer carry multidrug resistance genes (MDR) among bacteria, including E. coli. The aim of this study was to determine the antibiotic resistance profiles and the genes associated with them, to gain insights in the distribution of phylogroups, prevalence, and characterization of class 1, 2 and 3 integrons among Enteropathogenic E. coli (EPEC) isolates, from children upto 5 years of age from Delhi and National Capital Region (NCR), India. A total of 120 E. coli isolates, including 80 from diarrheagenic E...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28442769/improved-phylogenetic-resolution-for-y-chromosome-haplogroup-o2a1c-002611
#13
Xiaotian Yao, Senwei Tang, Beilei Bian, Xiaoli Wu, Gang Chen, Chuan-Chao Wang
Y-chromosome Haplogroup O2a1c-002611 is one of the dominant lineages of East Asians and Southeast Asians. However, its internal phylogeny remains insufficiently investigated. In this study, we genotyped 89 new highly informative single nucleotide polymorphisms (SNPs) in 305 individuals with Haplogroup O2a1c-002611 identified from 2139 Han Chinese males. Two major branches were identified, O2a1c1-F18 and O2a1c2-L133.2 and the first was further divided into two main subclades, O2a1c1a-F11 and O2a1c1b-F449, accounting for 11...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28442729/the-mapkkk-and-mapkk-gene-families-in-banana-identification-phylogeny-and-expression-during-development-ripening-and-abiotic-stress
#14
Lianzhe Wang, Wei Hu, Weiwei Tie, Zehong Ding, Xupo Ding, Yang Liu, Yan Yan, Chunlai Wu, Ming Peng, Biyu Xu, Zhiqiang Jin
The mitogen-activated protein kinase (MAPK) cascade, which is a major signal transduction pathway widely distributed in eukaryotes, has an important function in plant development and stress responses. However, less information is known regarding the MAPKKK and MAPKK gene families in the important fruit crop banana. In this study, 10 MAPKK and 77 MAPKKK genes were identified in the banana genome, and were classified into 4 and 3 subfamilies respectively based on phylogenetic analysis. Majority of MAPKKK and MAPKK genes in the same subfamily shared similar gene structures and conserved motifs...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28441395/molecular-phylogeny-of-oncaeidae-copepoda-using-nuclear-ribosomal-internal-transcribed-spacer-its-rdna
#15
Iole Di Capua, Fulvio Maffucci, Raimondo Pannone, Maria Grazia Mazzocchi, Elio Biffali, Alberto Amato
Copepods belonging to the Oncaeidae family are commonly and abundantly found in marine zooplankton. In the Mediterranean Sea, forty-seven oncaeid species occur, of which eleven in the Gulf of Naples. In this Gulf, several Oncaea species were morphologically analysed and described at the end of the XIX century by W. Giesbrecht. In the same area, oncaeids are being investigated over seasonal and inter-annual scales at the long-term coastal station LTER-MC. In the present work, we identified six oncaeid species using the nuclear ribosomal internal transcribed spacers (ITS rDNA) and the mitochondrial cytochrome c oxidase subunit I (mtCOI)...
2017: PloS One
https://www.readbyqxmd.com/read/28440791/a-curated-database-of-cyanobacterial-strains-relevant-for-modern-taxonomy-and-phylogenetic-studies
#16
Vitor Ramos, João Morais, Vitor M Vasconcelos
The dataset herein described lays the groundwork for an online database of relevant cyanobacterial strains, named CyanoType (http://lege.ciimar.up.pt/cyanotype). It is a database that includes categorized cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes, with associated information obtained by means of a literature-based curation. The dataset lists 371 strains and represents the first version of the database (CyanoType v.1). Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to three different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies (including this), and important bibliographic references...
April 25, 2017: Scientific Data
https://www.readbyqxmd.com/read/28439758/molecular-phylogeny-of-21-tropical-bamboo-species-reconstructed-by-integrating-non-coding-internal-transcribed-spacer-its1-and-2-sequences-and-their-consensus-secondary-structure
#17
Jayadri Sekhar Ghosh, Samik Bhattacharya, Amita Pal
The unavailability of the reproductive structure and unpredictability of vegetative characters for the identification and phylogenetic study of bamboo prompted the application of molecular techniques for greater resolution and consensus. We first employed internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) sequences to construct the phylogenetic tree of 21 tropical bamboo species. While the sequence alone could grossly reconstruct the traditional phylogeny amongst the 21-tropical species studied, some anomalies were encountered that prompted a further refinement of the phylogenetic analyses...
April 24, 2017: Genetica
https://www.readbyqxmd.com/read/28439466/arrival-and-diversification-of-mabuyine-skinks-squamata-scincidae-in-the-neotropics-based-on-a-fossil-calibrated-timetree
#18
Anieli Guirro Pereira, Carlos G Schrago
BACKGROUND: The evolution of South American Mabuyinae skinks holds significant biogeographic interest because its sister lineage is distributed across the African continent and adjacent islands. Moreover, at least one insular species, Trachylepis atlantica, has independently reached the New World through transoceanic dispersal. To clarify the evolutionary history of both Neotropical lineages, this study aimed to infer an updated timescale using the largest species and gene sampling dataset ever assembled for this group...
2017: PeerJ
https://www.readbyqxmd.com/read/28439127/diversity-and-evolution-of-sex-determination-systems-in-terrestrial-isopods
#19
Thomas Becking, Isabelle Giraud, Maryline Raimond, Bouziane Moumen, Christopher Chandler, Richard Cordaux, Clément Gilbert
Sex determination systems are highly variable in many taxa, sometimes even between closely related species. Yet the number and direction of transitions between these systems have seldom been characterized, and the underlying mechanisms are still poorly understood. Here we generated transcriptomes for 19 species of terrestrial isopod crustaceans, many of which are infected by Wolbachia bacterial endosymbionts. Using 88 single-copy orthologous genes, we reconstructed a fully resolved and dated phylogeny of terrestrial isopods...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28438702/global-phylogeny-and-biogeography-of-the-fern-genus-ctenitis-dryopteridaceae-with-a-focus-on-the-indian-ocean-region
#20
Sabine Hennequin, Germinal Rouhan, Alexandre Salino, Yi-Fan Duan, Marie-Capucine Lepeigneux, Marguerite Guillou, Steve Ansell, Thaís Elias Almeida, Li-Bing Zhang, Harald Schneider
The diverse and pantropical genus Ctenitis, in the Dryopteridaceae, has been largely ignored in phylogenetic studies until now. In this study, we fill in this gap by reconstructing the first comprehensive phylogeny of the genus including 53 species currently recognized in the genus Ctenitis, among which seven species formerly were assigned to the genus Pseudotectaria and one to Heterogonium. Special emphasis was given to the sampling of species occurring in the African-Indian Ocean region. The presented results include reconstruction of a biogeographic scenario based on estimated divergence times and ancestral area reconstruction...
April 21, 2017: Molecular Phylogenetics and Evolution
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