keyword
MENU ▼
Read by QxMD icon Read
search

"Tree of life"

keyword
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/29142065/maintaining-centrosomes-and-cilia
#2
REVIEW
Sascha Werner, Ana Pimenta-Marques, Mónica Bettencourt-Dias
Centrosomes and cilia are present in organisms from all branches of the eukaryotic tree of life. These structures are composed of microtubules and various other proteins, and are required for a plethora of cell processes such as structuring the cytoskeleton, sensing the environment, and motility. Deregulation of centrosome and cilium components leads to a wide range of diseases, some of which are incompatible with life. Centrosomes and cilia are thought to be very stable and can persist over long periods of time...
November 15, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/29141685/correction-to-towards-a-balanced-view-of-the-bacterial-tree-of-life
#3
Frederik Schulz, Emiley A Eloe-Fadrosh, Robert M Bowers, Jessica Jarett, Torben Nielsen, Natalia N Ivanova, Nikos C Kyrpides, Tanja Woyke
Following publication of the original article [1], the authors pointed out that the figure shown as figure S1 is actually figure S2 and vice versa. Figure S1 should show the barcharts, and figure S2 should shows the heatmaps. Figures captions are in the correct order. 1) "...SILVA-only OTUs (37,066 97% OTUs and 1266 85% clusters) (Additional file 3: Figure S2 )..." - > ...SILVA-only OTUs (37,066 97% OTUs and 1266 85% clusters) (Additional file 3: Figure S1 )..." 2) "...in groundwater and soil (Fig. 2, Additional file 2: Figure S1 )...
November 15, 2017: Microbiome
https://www.readbyqxmd.com/read/29138003/serine-threonine-protein-kinases-from-bacteria-archaea-and-eukarya-share-a-common-evolutionary-origin-deeply-rooted-in-the-tree-of-life
#4
Ivan Andreas Stancik, Martin Sebastijan Šestak, Boyang Ji, Marina Axelson-Fisk, Damjan Franjevic, Carsten Jers, Tomislav Domazet-Lošo, Ivan Mijakovic
The main family of serine/threonine/tyrosine protein kinases present in eukarya was defined and described by Hanks et al. in 1988. It was initially believed that these kinases do not exist in bacteria, but extensive genome sequencing revealed their existence in many bacteria. For historical reasons, the term "eukaryotic-type kinases" propagated in the literature to describe bacterial members of this protein family. Here, we argue that this term should be abandoned as a misnomer, and we provide several lines of evidence to support this claim...
November 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29123225/archaea-and-the-origin-of-eukaryotes
#5
REVIEW
Laura Eme, Anja Spang, Jonathan Lombard, Courtney W Stairs, Thijs J G Ettema
Woese and Fox's 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features...
November 10, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/29118135/mass-extinction-in-tetraodontiform-fishes-linked-to-the-palaeocene-eocene-thermal-maximum
#6
Dahiana Arcila, James C Tyler
Integrative evolutionary analyses based upon fossil and extant species provide a powerful approach for understanding past diversification events and for assessing the tempo of evolution across the Tree of Life. Herein, we demonstrate the importance of integrating fossil and extant species for inferring patterns of lineage diversification that would otherwise be masked in analyses that examine only one source of evidence. We infer the phylogeny and macroevolutionary history of the Tetraodontiformes (triggerfishes, pufferfishes and allies), a group with one of the most extensive fossil records among fishes...
November 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29112874/the-origin-and-diversification-of-mitochondria
#7
REVIEW
Andrew J Roger, Sergio A Muñoz-Gómez, Ryoma Kamikawa
Mitochondria are best known for their role in the generation of ATP by aerobic respiration. Yet, research in the past half century has shown that they perform a much larger suite of functions and that these functions can vary substantially among diverse eukaryotic lineages. Despite this diversity, all mitochondria derive from a common ancestral organelle that originated from the integration of an endosymbiotic alphaproteobacterium into a host cell related to Asgard Archaea. The transition from endosymbiotic bacterium to permanent organelle entailed a massive number of evolutionary changes including the origins of hundreds of new genes and a protein import system, insertion of membrane transporters, integration of metabolism and reproduction, genome reduction, endosymbiotic gene transfer, lateral gene transfer and the retargeting of proteins...
November 6, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29099307/what-makes-ribosomes-tick
#8
Sarah Catherine Mills, Ramya Enganti, Albrecht G von Arnim
In most organisms gene expression over the course of the day is under the control of the circadian clock. The canonical clock operates as a gene expression circuit that is controlled at the level of transcription, and transcriptional control is also a major clock output. However, rhythmic transcription cannot explain all the observed rhythms in protein accumulation. Although it is clear that rhythmic gene expression also involves RNA processing and protein turnover, until two years ago little was known in any eukaryote about diel dynamics of mRNA translation into protein...
November 3, 2017: RNA Biology
https://www.readbyqxmd.com/read/29091997/efficient-comparative-phylogenetics-on-large-trees
#9
Stilianos Louca, Michael Doebeli
Motivation: Biodiversity databases now comprise hundreds of thousands of sequences and trait records. For example, the Open Tree of Life includes over 1,491,000 metazoan and over 300,000 bacterial taxa. These data provide unique opportunities for analysis of phylogenetic trait distribution and reconstruction of ancestral biodiversity. However, existing tools for comparative phylogenetics scale poorly to such large trees, to the point of being almost unusable. Results: Here we present a new R package, named "castor", for comparative phylogenetics on large trees spanning millions of tips...
October 30, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29077895/pinniped-diphyly-and-bat-triphyly-more-homology-errors-drive-conflicts-in-the-mammalian-tree
#10
Mark S Springer, John Gatesy
Homology is perhaps the most central concept of phylogenetic biology. At difficult to resolve polytomies that are deep in the Tree of Life, a few homology errors in phylogenomic data can drive spurious phylogenetic results. Feijoo and Parada (2017) assembled three phylogenomic data sets for mammals and reported methodological discrepancies and unexpected results that contradict the monophyly of well-established clades in Pinnipedia and Yangochiroptera. Examination of Feijoo and Parada's (2017) data sets reveals extensive homology errors (paralogous sequences, alignments of different exons to each other) and cross-contamination of sequences from different species...
October 25, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29074461/comprehensive-phylogeny-of-acariform-mites-acariformes-provides-insights-on-the-origin-of-the-four-legged-mites-eriophyoidea-a-long-branch
#11
Pavel B Klimov, Barry M OConnor, Philipp E Chetverikov, Samuel J Bolton, Amir R Pepato, Abdolazim L Mortazavi, Andrey V Tolstikov, Gary R Bauchan, Ronald Ochoa
Eriophyoid, or four-legged mites, represent a large and ancient radiation of exclusively phytophagous organisms known from the Triassic (230 Mya). Hypothesizing phylogenetic relatedness of Eriophyoidea among mites is a major challenge due to the absence of unambiguous morphological synapomorphies, resulting in ten published hypotheses placing eriophyoids in various places in the acariform tree of life. Here we test the evolutionary relationships of eriophyoids using six genes and a representative taxonomic sampling of acariform mites...
October 23, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29070718/phylogenetically-informed-spatial-planning-is-required-to-conserve-the-mammalian-tree-of-life
#12
Dan F Rosauer, Laura J Pollock, Simon Linke, Walter Jetz
In the face of the current extinction crisis and severely limited conservation resources, safeguarding the tree of life is increasingly recognized as a high priority. We conducted a first systematic global assessment of the conservation of phylogenetic diversity (PD) that uses realistic area targets and highlights the key areas for conservation of the mammalian tree of life. Our approach offers a substantially more effective conservation solution than one focused on species. In many locations, priorities for PD differ substantially from those of a species-based approach that ignores evolutionary relationships...
October 25, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29061890/phylogenetic-tests-for-evolutionary-innovation-the-problematic-link-between-key-innovations-and-exceptional-diversification
#13
REVIEW
Daniel L Rabosky
Evolutionary innovation contributes to the spectacular diversity of species and phenotypes across the tree of life. 'Key innovations' are widely operationalized within evolutionary biology as traits that facilitate increased diversification rates, such that lineages bearing the traits ultimately contain more species than closely related lineages lacking the focal trait. In this article, I briefly review the inference, analysis and interpretation of evolutionary innovation on phylogenetic trees. I argue that differential rates of lineage diversification should not be used as the basis for key innovation tests, despite the statistical tractability of such approaches...
December 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29048547/perspectives-on-integrating-genetic-and-physical-explanations-of-evolution-and-development-an-introduction-to-the-symposium
#14
Alan C Love, Thomas A Stewart, Gunter P Wagner, Stuart A Newman
In the 20th century, genetic explanatory approaches became dominant in both developmental and evolutionary biological research. By contrast, physical approaches, which appeal to properties such as mechanical forces, were largely relegated to the margins, despite important advances in modeling. Recently, there have been renewed attempts to find balanced viewpoints that integrate both biological physics and molecular genetics into explanations of developmental and evolutionary phenomena. Here we introduce the 2017 SICB symposium "Physical and Genetic Mechanisms for Evolutionary Novelty" that was dedicated to exploring empirical cases where both biological physics and developmental genetic considerations are crucial...
October 17, 2017: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/29048529/the-rhizome-of-lokiarchaeota-illustrates-the-mosaicity-of-archaeal-genomes
#15
Anthony Levasseur, Vicky Merhej, Emeline Baptiste, Vikas Sharma, Pierre Pontarotti, Didier Raoult
Genome remodeling and exchange of sequences are widespread in the prokaryotic world and mosaic genomes challenge the classification of prokaryotes, which cannot be properly achieved in terms of a single gene or group of genes. Here, we studied individually the gene collection of the archaic microorganism Lokiarchaeum sp., suggested as an archaeal host close to the emergence of the eukaryotes. The network or rhizome of all Lokiarchaeum sp. genes revealed that the genomic repertoire is mainly composed of genes from archaeal (∼36%) and bacterial origin (∼28%), distantly followed by components of eukaryotic origin (∼2%)...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29042516/across-the-tree-of-life-radiation-resistance-is-governed-by-antioxidant-mn-2-gauged-by-paramagnetic-resonance
#16
Ajay Sharma, Elena K Gaidamakova, Olga Grichenko, Vera Y Matrosova, Veronika Hoeke, Polina Klimenkova, Isabel H Conze, Robert P Volpe, Rok Tkavc, Cene Gostinčar, Nina Gunde-Cimerman, Jocelyne DiRuggiero, Igor Shuryak, Andrew Ozarowski, Brian M Hoffman, Michael J Daly
Despite concerted functional genomic efforts to understand the complex phenotype of ionizing radiation (IR) resistance, a genome sequence cannot predict whether a cell is IR-resistant or not. Instead, we report that absorption-display electron paramagnetic resonance (EPR) spectroscopy of nonirradiated cells is highly diagnostic of IR survival and repair efficiency of DNA double-strand breaks (DSBs) caused by exposure to gamma radiation across archaea, bacteria, and eukaryotes, including fungi and human cells...
October 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29041958/towards-a-balanced-view-of-the-bacterial-tree-of-life
#17
Frederik Schulz, Emiley A Eloe-Fadrosh, Robert M Bowers, Jessica Jarett, Torben Nielsen, Natalia N Ivanova, Nikos C Kyrpides, Tanja Woyke
The bacterial tree of life has recently undergone significant expansion, chiefly from candidate phyla retrieved through genome-resolved metagenomics. Bypassing the need for genome availability, we present a snapshot of bacterial phylogenetic diversity based on the recovery of high-quality SSU rRNA gene sequences extracted from nearly 7000 metagenomes and all available reference genomes. We illuminate taxonomic richness within established bacterial phyla together with environmental distribution patterns, providing a revised framework for future phylogeny-driven sequencing efforts...
October 17, 2017: Microbiome
https://www.readbyqxmd.com/read/29040399/toward-completion-of-the-earth-s-proteome-an-update-a-decade-later
#18
Pablo Mier, Miguel A Andrade-Navarro
Protein databases are steadily growing driven by the spread of new more efficient sequencing techniques. This growth is dominated by an increase in redundancy (homologous proteins with various degrees of sequence similarity) and by the incapability to process and curate sequence entries as fast as they are created. To understand these trends and aid bioinformatic resources that might be compromised by the increasing size of the protein sequence databases, we have created a less-redundant protein data set. In parallel, we analyzed the evolution of protein sequence databases in terms of size and redundancy...
October 12, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29030445/microhomology-mediated-high-throughput-gene-inactivation-strategy-for-hyperthermophilic-crenarchaeon-sulfolobus-islandicus
#19
Changyi Zhang, Rachel J Whitaker
Sulfolobus islandicus is rapidly emerging as a model system for studying the biology and evolution within the TACK lineage of the Archaeal domain. As the tree of life grows, identifying the cellular function of genes within this lineage will have significant impacts on our understanding of the evolution of Last Archaeal Eukaryote Common Ancestor (LEACA) and the differentiation of Archaea from Eukaryotes during the evolution of the modernday cell. To progress our understanding of this key Archaeal organism, we report a novel high-throughput method for targeted gene inactivation in S...
October 13, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29029231/analysis-of-phylogenomic-tree-space-resolves-relationships-among-marsupial-families
#20
David A Duchêne, Jason G Bragg, Sebastián Duchêne, Linda E Neaves, Sally Potter, Craig Moritz, Rebecca N Johnson, Simon Y W Ho, Mark D B Eldridge
A fundamental challenge in resolving evolutionary relationships across the Tree of Life is to account for heterogeneity in the evolutionary signal across loci. Studies of marsupial mammals have demonstrated that this heterogeneity can be substantial, leaving considerable uncertainty in the evolutionary timescale and relationships within the group. Using simulations and a new phylogenomic data set comprising nucleotide sequences of 1550 loci from 18 of the 22 extant marsupial families, we demonstrate the power of a method for identifying clusters of loci that support different phylogenetic trees...
September 22, 2017: Systematic Biology
keyword
keyword
71204
1
2
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"