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https://www.readbyqxmd.com/read/28228511/the-opiliones-tree-of-life-shedding-light-on-harvestmen-relationships-through-transcriptomics
#1
Rosa Fernández, Prashant P Sharma, Ana Lúcia Tourinho, Gonzalo Giribet
Opiliones are iconic arachnids with a Palaeozoic origin and a diversity that reflects ancient biogeographic patterns dating back at least to the times of Pangea. Owing to interest in harvestman diversity, evolution and biogeography, their relationships have been thoroughly studied using morphology and PCR-based Sanger approaches to infer their systematic relationships. More recently, two studies utilized transcriptomics-based phylogenomics to explore their basal relationships and diversification, but sampling was limiting for understanding deep evolutionary patterns, as they lacked good taxon representation at the family level...
February 22, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28207761/the-analysis-of-translation-related-gene-set-boosts-debates-around-origin-and-evolution-of-mimiviruses
#2
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/28195309/ploidy-tug-of-war-evolutionary-and-genetic-environments-influence-the-rate-of-ploidy-drive-in-a-human-fungal-pathogen
#3
Aleeza C Gerstein, Heekyung Lim, Judith Berman, Meleah A Hickman
Variation in baseline ploidy is seen throughout the tree of life, yet the factors that determine why one ploidy level is maintained over another remain poorly understood. Experimental evolution studies using asexual fungal microbes with manipulated ploidy levels intriguingly reveals a propensity to return to the historical baseline ploidy, a phenomenon that we term 'ploidy drive'. We evolved haploid, diploid, and polyploid strains of the human fungal pathogen Candida albicans under three different nutrient limitation environments to test whether these conditions, hypothesized to select for low ploidy levels, could counteract ploidy drive...
February 14, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28185947/evolutionary-affinities-of-the-unfathomable-parabrotulidae-molecular-data-indicate-placement-of-parabrotula-within-the-family-bythitidae-ophidiiformes
#4
Matthew A Campbell, Jørgen G Nielsen, Tetsuya Sado, Chuya Shinzato, Miyuki Kanda, Takashi P Satoh, Masaki Miya
Fishes are widely diverse in shape and body size and can quite rapidly undergo these changes. Consequently, some relationships are not clearly resolved with morphological analyses. In the case of fishes of small body size, informative characteristics can be absent due to simplification of body structures. The Parabrotulidae, a small family of diminutive body size consisting of two genera and three species has most recently been classified as either a perciform within the suborder Zoarcoidei or an ophidiiform...
February 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28181008/ccmp-and-cump-across-the-tree-of-life-from-ccmp-and-cump-generators-to-ccmp-and-cump-regulated-cell-functions
#5
Roland Seifert
The cyclic purine nucleotides cAMP and cGMP are well-established second messenger molecules that are generated by distinct nucleotidyl cyclases (NCs) and regulate numerous cell functions via specific effector molecules. In contrast, the existence of the cyclic pyrimidine nucleotides cCMP and cUMP has been controversial for many years. The development of highly specific and sensitive mass spectrometry methods has enabled the unequivocal detection and quantitation of cCMP and cUMP in biological systems. These cNMPs occur broadly in numerous mammalian cell lines and primary cells...
February 9, 2017: Handbook of Experimental Pharmacology
https://www.readbyqxmd.com/read/28131316/genomes-of-multicellular-organisms-have-evolved-to-attract-nucleosomes-to-promoter-regions
#6
Marco Tompitak, Cédric Vaillant, Helmut Schiessel
Sequences that influence nucleosome positioning in promoter regions, and their relation to gene regulation, have been the topic of much research over the last decade. In yeast, significant nucleosome-depleted regions are found, which facilitate transcription. With the arrival of nucleosome positioning maps for the human genome, it was discovered that in our genome, unlike in that of yeast, promoters encode for high nucleosome occupancy. In this work, we look at the genomes of a range of different organisms, to provide a catalog of nucleosome positioning signals in promoters across the tree of life...
February 7, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28118589/evolution-selfing-takes-species-down-stebbins-s-blind%C3%A2-alley
#7
Jeremiah W Busch, Lynda F Delph
Shifts from outcrossing to selfing have occurred thousands of times across the tree of life. By reducing the size of the gene pool, selfing should limit adaptive potential. A refreshing empirical experiment with snails supports this long-standing hypothesis.
January 23, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28111289/ancient-highly-conserved-proteins-from-a-luca-with-complex-cell-biology-provide-evidence-in-support-of-the-nuclear-compartment-commonality-nucom-hypothesis
#8
REVIEW
James T Staley, John A Fuerst
The nuclear compartment commonality (NuCom) hypothesis posits a complex last common ancestor (LUCA) with membranous compartments including a nuclear membrane. Such a LUCA then evolved to produce two nucleated lineages of the tree of life: the Planctomycetes-Verrucomicrobia-Chlamydia superphylum (PVC) within the Bacteria, and the Eukarya. We propose that a group of ancient essential protokaryotic signature proteins (PSPs) originating in LUCA were incorporated into ancestors of PVC Bacteria and Eukarya. Tubulins, ubiquitin system enzymes and sterol-synthesizing enzymes are consistent with early origins of these features shared between the PVC superphylum and Eukarya...
January 19, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28102365/viral-phylogenomics-using-an-alignment-free-method-a-three-step-approach-to-determine-optimal-length-of-k-mer
#9
Qian Zhang, Se-Ran Jun, Michael Leuze, David Ussery, Intawat Nookaew
The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral "tree of life". However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28095611/hypothesis-gene-rich-plastid-genomes-in-red-algae-may-be-an-outcome-of-nuclear-genome-reduction
#10
Huan Qiu, Jun Mo Lee, Hwan Su Yoon, Debashish Bhattacharya
Red algae (Rhodophyta) putatively diverged from the eukaryote tree of life >1.2 billion years ago and are the source of plastids in the ecologically important diatoms, haptophytes, and dinoflagellates. In general, red algae contain the largest plastid gene inventory among all such organelles derived from primary, secondary, or additional rounds of endosymbiosis. In contrast, their nuclear gene inventory is reduced when compared to their putative sister lineage, the Viridiplantae, and other photosynthetic lineages...
January 17, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28086860/nicotiana-attenuata-data-hub-nadh-an-integrative-platform-for-exploring-genomic-transcriptomic-and-metabolomic-data-in-wild-tobacco
#11
Thomas Brockmöller, Zhihao Ling, Dapeng Li, Emmanuel Gaquerel, Ian T Baldwin, Shuqing Xu
BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28065652/the-first-darwinian-phylogenetic-tree-of-plants
#12
Uwe Hoßfeld, Elizabeth Watts, Georgy S Levit
In 1866, the German zoologist Ernst Haeckel (1834-1919) published the first Darwinian trees of life in the history of biology in his book General Morphology of Organisms. We take a specific look at the first phylogenetic trees for the plant kingdom that Haeckel created as part of this two-volume work.
February 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/28057824/the-ecology-and-evolution-of-social-behavior-in-microbes
#13
REVIEW
Corina E Tarnita
Cooperation has been studied extensively across the tree of life, from eusociality in insects to social behavior in humans, but it is only recently that a social dimension has been recognized and extensively explored for microbes. Research into microbial cooperation has accelerated dramatically and microbes have become a favorite system because of their fast evolution, their convenience as lab study systems and the opportunity for molecular investigations. However, the study of microbes also poses significant challenges, such as a lack of knowledge and an inaccessibility of the ecological context (used here to include both the abiotic and the biotic environment) under which the trait deemed cooperative has evolved and is maintained...
January 1, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28054372/what-explains-patterns-of-biodiversity-across-the-tree-of-life-new-research-is-revealing-the-causes-of-the-dramatic-variation-in-species-numbers-across-branches-of-the-tree-of-life
#14
John J Wiens
A major challenge in biology is to explain why some groups have thousands or millions of species whereas others have few. Here, I review the causes of this variation. New studies reveal that higher species numbers in many major groups are explained by higher diversification rates (and traits that accelerate these rates). These traits span most of biology (e.g. genomics, ecology, morphology). Rather than simply testing individual traits, research should now focus on comparing how much variation in diversification rates is explained by different types of traits...
January 5, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28031802/integrating-data-deficient-species-in-analyses-of-evolutionary-history-loss
#15
Simon Veron, Caterina Penone, Philippe Clergeau, Gabriel C Costa, Brunno F Oliveira, Vinícius A São-Pedro, Sandrine Pavoine
There is an increasing interest in measuring loss of phylogenetic diversity and evolutionary distinctiveness which together depict the evolutionary history of conservation interest. Those losses are assessed through the evolutionary relationships between species and species threat status or extinction probabilities. Yet, available information is not always sufficient to quantify the threat status of species that are then classified as data deficient. Data-deficient species are a crucial issue as they cause incomplete assessments of the loss of phylogenetic diversity and evolutionary distinctiveness...
December 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/28025346/the-importance-of-digitized-biocollections-as-a-source-of-trait-data-and-a-new-vertnet-resource
#16
Robert P Guralnick, Paula F Zermoglio, John Wieczorek, Raphael LaFrance, David Bloom, Laura Russell
For vast areas of the globe and large parts of the tree of life, data needed to inform trait diversity is incomplete. Such trait data, when fully assembled, however, form the link between the evolutionary history of organisms, their assembly into communities, and the nature and functioning of ecosystems. Recent efforts to close data gaps have focused on collating trait-by-species databases, which only provide species-level, aggregated value ranges for traits of interest and often lack the direct observations on which those ranges are based...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28005907/lifemap-exploring-the-entire-tree-of-life
#17
Damien M de Vienne
The Tree of Life (ToL) is meant to be a unique representation of the evolutionary relationships between all species on earth. Huge efforts are made to assemble such a large tree, helped by the decrease of sequencing costs and improved methods to reconstruct and combine phylogenies, but no tool exists today to explore the ToL in its entirety in a satisfying manner. By combining methods used in modern cartography, such as OpenStreetMap, with a new way of representing tree-like structures, I created Lifemap, a tool allowing the exploration of a complete representation of the ToL (between 800,000 and 2...
December 2016: PLoS Biology
https://www.readbyqxmd.com/read/28003531/bayes-factors-unmask-highly-variable-information-content-bias-and-extreme-influence-in-phylogenomic-analyses
#18
Jeremy M Brown, Robert C Thomson
As the application of genomic data in phylogenetics has become routine, a number of cases have arisen where alternative datasets strongly support conflicting conclusions. This sensitivity to analytical decisions has prevented firm resolution of some of the most recalcitrant nodes in the tree of life. To better understand the causes and nature of this sensitivity, we analyzed several phylogenomic datasets using an alternative measure of topological support (the Bayes factor) that both demonstrates and averts several limitations of more frequently employed support measures (such as Markov chain Monte Carlo estimates of posterior probabilities)...
December 20, 2016: Systematic Biology
https://www.readbyqxmd.com/read/28003474/phylogenomics-guided-discovery-of-a-novel-conserved-cassette-of-short-linear-motifs-in-bubr1-essential-for-the-spindle-checkpoint
#19
Eelco Tromer, Debora Bade, Berend Snel, Geert J P L Kops
The spindle assembly checkpoint (SAC) maintains genomic integrity by preventing progression of mitotic cell division until all chromosomes are stably attached to spindle microtubules. The SAC critically relies on the paralogues Bub1 and BubR1/Mad3, which integrate kinetochore-spindle attachment status with generation of the anaphase inhibitory complex MCC. We previously reported on the widespread occurrences of independent gene duplications of an ancestral 'MadBub' gene in eukaryotic evolution and the striking parallel subfunctionalization that lead to loss of kinase function in BubR1/Mad3-like paralogues...
December 2016: Open Biology
https://www.readbyqxmd.com/read/28003260/t-bas-tree-based-alignment-selector-toolkit-for-phylogenetic-based-placement-alignment-downloads-and-metadata-visualization-an-example-with-the-pezizomycotina-tree-of-life
#20
Ignazio Carbone, James B White, Jolanta Miadlikowska, A Elizabeth Arnold, Mark A Miller, Frank Kauff, Jana M U'Ren, Georgiana May, François Lutzoni
MOTIVATION: High-quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology and functional biology of diverse groups. We developed the Tree-Based Alignment Selector (T-BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single- and multi-locus alignments for specific clades...
December 21, 2016: Bioinformatics
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