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"Evolutionary history"

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https://www.readbyqxmd.com/read/28214944/the-vascular-plants-open-system-of-growth
#1
REVIEW
Alice Basile, Marco Fambrini, Claudio Pugliesi
What is fascinating in plants (true also in sessile animals such as corals and hydroids) is definitely their open and indeterminate growth, as a result of meristematic activity. Plants as well as animals are characterized by a multicellular organization, with which they share a common set of genes inherited from a common eukaryotic ancestor; nevertheless, circa 1.5 billion years of evolutionary history made the two kingdoms very different in their own developmental biology. Flowering plants, also known as angiosperms, arose during the Cretaceous Period (145-65 million years ago), and up to date, they count around 235,000 species, representing the largest and most diverse group within the plant kingdom...
February 18, 2017: Development Genes and Evolution
https://www.readbyqxmd.com/read/28212875/genotyping-by-sequencing-provides-the-first-well-resolved-phylogeny-for-coffee-coffea-and-insights-into-the-evolution-of-caffeine-content-in-its-species-gbs-coffee-phylogeny-and-the-evolution-of-caffeine-content
#2
Perla Hamon, Corrinne E Grover, Aaron P Davis, Jean-Jacques Rakotomalala, Nathalie E Raharimalala, Victor A Albert, Hosahalli L Sreenath, Piet Stoffelen, Sharon E Mitchell, Emmanuel Couturon, Serge Hamon, Alexandre de Kochko, Dominique Crouzillat, Michel Rigoreau, Ucu Sumirat, Sélastique Akaffou, Romain Guyot
A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples...
February 14, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28212607/a-case-of-modular-phenotypic-plasticity-in-the-depth-gradient-for-the-gorgonian-coral-antillogorgia-bipinnata-cnidaria-octocorallia
#3
Iván Calixto-Botía, Juan A Sánchez
BACKGROUND: Phenotypic plasticity, as a phenotypic response induced by the environment, has been proposed as a key factor in the evolutionary history of corals. A significant number of octocoral species show high phenotypic variation, exhibiting a strong overlap in intra- and inter-specific morphologic variation. This is the case of the gorgonian octocoral Antillogorgia bipinnata (Verrill 1864), which shows three polyphyletic morphotypes along a bathymetric gradient. This research tested the phenotypic plasticity of modular traits in A...
February 17, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28210761/the-evolutionary-loss-of-rnai-key-determinants-in-kinetoplastids-as-a-multiple-sporadic-phenomenon
#4
Andrey V Matveyev, João M P Alves, Myrna G Serrano, Vladimir Lee, Ana M Lara, William A Barton, André G Costa-Martins, Stephen M Beverley, Erney P Camargo, Marta M G Teixeira, Gregory A Buck
We screened the genomes of a broad panel of kinetoplastid protists for genes encoding proteins associated with the RNA interference (RNAi) system using probes from the Argonaute (AGO1), Dicer1 (DCL1), and Dicer2 (DCL2) genes of Leishmania brasiliensis and Crithidia fasciculata. We identified homologs for all the three of these genes in the genomes of a subset of these organisms. However, several of these organisms lacked evidence for any of these genes, while others lacked only DCL2. The open reading frames encoding these putative proteins were structurally analyzed in silico...
February 16, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28208529/re-whole-genome-sequencing-of-uropathogenic-escherichia-coli-reveals-long-evolutionary-history-of-diversity-and-virulence
#5
Edward M Schaeffer
No abstract text is available yet for this article.
March 2017: Journal of Urology
https://www.readbyqxmd.com/read/28207761/the-analysis-of-translation-related-gene-set-boosts-debates-around-origin-and-evolution-of-mimiviruses
#6
REVIEW
Jônatas Santos Abrahão, Rodrigo Araújo, Philippe Colson, Bernard La Scola
The giant mimiviruses challenged the well-established concept of viruses, blurring the roots of the tree of life, mainly due to their genetic content. Along with other nucleo-cytoplasmic large DNA viruses, they compose a new proposed order-named Megavirales-whose origin and evolution generate heated debate in the scientific community. The presence of an arsenal of genes not widespread in the virosphere related to important steps of the translational process, including transfer RNAs, aminoacyl-tRNA synthetases, and translation factors for peptide synthesis, constitutes an important element of this debate...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28203571/evolutionary-history-of-multiple-dural-fistula
#7
Braulio Martinez-Burbano, Edgar Patricio Correa Diaz, Carolina Jácome Sánchez
Intracranial dural arteriovenous fistulas (DAVFs) are abnormal communications between arteries and veins or dural venous sinuses, which sit between the sheets of the dura. They represent 10% to 15% of intracranial vascular malformations. Clinical manifestations and prognosis depend on the pattern of venous drainage and location. The clinical presentation of DAVF may be mistaken for vascular or nonvascular brain pathologies. For that reason, within the differential diagnosis come a wide range of conditions, such as secondary headaches, encephalopathies, dementias including those with rapid progression, neurodegenerative diseases, inflammatory processes, or tumors typically at the orbital level or in the cavernous sinus...
October 2016: Journal of Investigative Medicine High Impact Case Reports
https://www.readbyqxmd.com/read/28199447/population-structure-and-genetic-diversity-of-the-giant-anteater-myrmecophaga-tridactyla-myrmecophagidae-pilosa-in-brazil
#8
Camila L Clozato, Flávia R Miranda, Paula Lara-Ruiz, Rosane G Collevatti, Fabrício R Santos
The giant anteater (Myrmecophaga tridactyla, Pilosa, Linnaeus 1758) belongs to the mammalian order Pilosa and presents a large distribution along South America, occupying a great variety of habitats. It is listed in the IUCN Red List of threatened species as Vulnerable. Despite threatened, there is a lack of studies regarding its genetic variability. The aim of this study was to examine the genetic diversity and patterns of genetic structure within remaining populations. We analyzed 77 individuals from seven different populations distributed in four biomes across Brazil: Cerrado, Pantanal, Atlantic Forest and Amazon Forest...
February 13, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28199442/phylogeographic-history-of-south-american-populations-of-the-silky-anteater-cyclopes-didactylus-pilosa-cyclopedidae
#9
Raphael Teodoro Franciscani Coimbra, Flávia Regina Miranda, Camila Clozato Lara, Marco Antônio Alves Schetino, Fabrício Rodrigues Dos Santos
Cyclopes didactylus, commonly called silky anteater, is the smallest and least studied of the anteaters. It is an arboreal species occurring in rainforests, ranging from southern Mexico to Central and South America, with an apparently disjoint distribution between Amazon and Atlantic rainforests in Brazil. Although seven subspecies are recognized, little is known about its geographical variation. Thus, to evaluate the population dynamics and evolutionary history of the South American silky anteater, we analyzed 1542 bp sequences of the mitochondrial control region (CR), COI and Cyt-b genes of 32 individuals...
February 13, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28198372/novel-characteristics-of-the-avian-gyrovirus-2-genome
#10
Shuai Yao, Xiang Gao, Tianbei Tuo, Chunyan Han, Yulong Gao, Xiaole Qi, Yanping Zhang, Changjun Liu, Honglei Gao, Yongqiang Wang, Xiaomei Wang
Avian gyrovirus 2 (AGV2) was the second member of the viral genus Cyclovirus to be discovered. This virus poses a significant potential threat to humans and poultry due to its global dissemination and infectiousness. We used three overlapping polymerase chain reactions (PCRs) to map the whole genome of AGV2. We then modelled the evolutionary history of these novel sequence data in the context of related sequences from GenBank. We analysed the viral protein characteristics of the different phylogenetic groups and explored differences in evolutionary trends between Chinese strains and strains from other countries...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28196465/metabolite-toxicity-determines-the-pace-of-molecular-evolution-within-microbial-populations
#11
Elin E Lilja, David R Johnson
BACKGROUND: The production of toxic metabolites has shaped the spatial and temporal arrangement of metabolic processes within microbial cells. While diverse solutions to mitigate metabolite toxicity have evolved, less is known about how evolution itself is affected by metabolite toxicity. We hypothesized that the pace of molecular evolution should increase as metabolite toxicity increases. At least two mechanisms could cause this. First, metabolite toxicity could increase the mutation rate...
February 14, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28193548/advances-in-understanding-tumour-evolution-through-single-cell-sequencing
#12
Jack Kuipers, Katharina Jahn, Niko Beerenwinkel
The mutational heterogeneity observed within tumours poses additional challenges to the development of effective cancer treatments. A thorough understanding of a tumour's subclonal composition and its mutational history is essential to open up the design of treatments tailored to individual patients. Comparative studies on a large number of tumours permit the identification of mutational patterns which may refine forecasts of cancer progression, response to treatment and metastatic potential. The composition of tumours is shaped by evolutionary processes...
February 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28191634/timing-of-the-evolutionary-history-of-corallinaceae-corallinales-rhodophyta
#13
Anja Rösler, Francisco Perfectti, Viviana Peña, Julio Aguirre, Juan Carlos Braga
The temporal dimension of the most recent Corallinaceae (order Corallinales) phylogeny was presented here, based on first occurrence time estimates from the fossil record. Calibration of the molecular clock of the genetic marker SSU entailed a separation of Corallinales from Hapalidiales in the Albian (Early Cretaceous ~ 105 mya). Neither the calibration nor the fossil record resolved the succession of appearance of the first three emerging subfamilies: Mastophoroideae, Corallinoideae, and Neogoniolithoideae...
February 12, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28190772/sex-differences-a-resultant-of-an-evolutionary-pressure
#14
Sara Della Torre, Adriana Maggi
Spurred by current research policy, we are witnessing a significant growth in the number of studies that observe and describe sexual diversities in human physiology and sex prevalence in a large number of pathologies. Yet we are far from the comprehension of the mechanisms underpinning these differences, which are the result of a long evolutionary history. This Essay is meant to underline female reproductive function as a driver for the positive selection of the specific physiological features that explain male and female differential susceptibility to diseases and metabolic disturbances, in particular...
January 30, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/28190727/the-origin-of-vertebrate-gills
#15
J Andrew Gillis, Olivia R A Tidswell
Pharyngeal gills are a fundamental feature of the vertebrate body plan [1]. However, the evolutionary history of vertebrate gills has been the subject of a long-standing controversy [2-8]. It is thought that gills evolved independently in cyclostomes (jawless vertebrates-lampreys and hagfish) and gnathostomes (jawed vertebrates-cartilaginous and bony fishes), based on their distinct embryonic origins: the gills of cyclostomes derive from endoderm [9-12], while gnathostome gills were classically thought to derive from ectoderm [10, 13]...
February 3, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28188878/towards-a-higher-level-ensifera-phylogeny-inferred-from-mitogenome-sequences
#16
Zhijun Zhou, Ling Zhao, Nian Liu, Huifang Guo, Bei Guan, Juanxia Di, Fuming Shi
Although mitogenomes are useful tools for inferring evolutionary history, only a few representative ones can be used for most Ensifera lineages. Thirty-two ensiferan mitogenomes were determined using ABI Sanger sequencing and standard primer walking of 2-3 overlapping Long-PCR fragments, or Illumina® HiSeq2000 for "shotgun" sequenced long-PCR-amplified mitochondrial or total genomic DNA. Six patterns of gene arrangements, including the novel trnR-trnS(AGN)-trnA-trnN-trnG-nad3 in Lipotactes tripyrga (Lipotactinae), were identified from 59 ensiferan mitogenomes...
February 8, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28187628/an-analytical-review-of-halffter-s-mexican-transition-zone-and-its-relevance-for-evolutionary-biogeography-ecology-and-biogeographical-regionalization
#17
Gonzalo Halffter, Juan J Morrone
The Mexican transition zone (MTZ) is the complex area where the Neotropical and Nearctic biotas overlap, including south-western United States, Mexico and a large part of Central America extending to the Nicaraguan lowlands. In a strict sense, it corresponds to the mountain highlands of Mexico, Guatemala, Honduras, El Salvador and Nicaragua. We review Halffter's theory explaining the biotic evolution of the MTZ, including the description and discussion of the distributional patterns and cenocrons recognized within it...
January 25, 2017: Zootaxa
https://www.readbyqxmd.com/read/28185572/in-the-light-of-deep-coalescence-revisiting-trees-within-networks
#18
Jiafan Zhu, Yun Yu, Luay Nakhleh
BACKGROUND: Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A salient concept underlying a great majority of these developments has been the notion that a network displays a set of trees and those trees can be used to infer, analyze, and study the network. RESULTS: In this paper, we show that in the presence of coalescence effects, the set of displayed trees is not sufficient to capture the network...
November 11, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28185563/exploring-phylogenetic-hypotheses-via-gibbs-sampling-on-evolutionary-networks
#19
Yun Yu, Christopher Jermaine, Luay Nakhleh
BACKGROUND: Phylogenetic networks are leaf-labeled graphs used to model and display complex evolutionary relationships that do not fit a single tree. There are two classes of phylogenetic networks: Data-display networks and evolutionary networks. While data-display networks are very commonly used to explore data, they are not amenable to incorporating probabilistic models of gene and genome evolution. Evolutionary networks, on the other hand, can accommodate such probabilistic models, but they are not commonly used for exploration...
November 11, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28183833/cytogeography-of-the-subalpine-marsh-marigold-polyploid-complex-caltha-leptosepala-s-l-ranunculaceae
#20
Keir M Wefferling, Sílvia Castro, João Loureiro, Mariana Castro, Daniela Tavares, Sara B Hoot
PREMISE OF THE STUDY: Unrecognized variation in ploidy level can lead to an underestimation of species richness and a misleading delineation of geographic range. Caltha leptosepala (Ranunculaceae) comprises a complex of hexaploids (6x), rare nonaploids (9x), and dodecaploids (12x), all with unknown distributions. We delineate the geographic distribution and contact zones of the cytotypes, investigate morphologies of cytotypes and subspecies, and discuss the biogeography and evolutionary history of the polyploid complex...
February 9, 2017: American Journal of Botany
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