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"Tree of life"

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https://www.readbyqxmd.com/read/28319149/walking-and-talking-the-tree-of-life-why-and-how-to-teach-about-biodiversity
#1
Cissy J Ballen, Harry W Greene
Taxonomic details of diversity are an essential scaffolding for biology education, yet outdated methods for teaching the tree of life (TOL), as implied by textbook content and usage, are still commonly employed. Here, we show that the traditional approach only vaguely represents evolutionary relationships, fails to denote major events in the history of life, and relies heavily on memorizing near-meaningless taxonomic ranks. Conversely, a clade-based strategy-focused on common ancestry, monophyletic groups, and derived functional traits-is explicitly based on Darwin's "descent with modification," provides students with a rational system for organizing the details of biodiversity, and readily lends itself to active learning techniques...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28298477/central-role-of-the-trehalose-biosynthesis-pathway-in-the-pathogenesis-of-human-fungal-infections-opportunities-and-challenges-for-therapeutic-development
#2
REVIEW
Arsa Thammahong, Srisombat Puttikamonkul, John R Perfect, Richard G Brennan, Robert A Cramer
Invasive fungal infections cause significant morbidity and mortality in part due to a limited antifungal drug arsenal. One therapeutic challenge faced by clinicians is the significant host toxicity associated with antifungal drugs. Another challenge is the fungistatic mechanism of action of some drugs. Consequently, the identification of fungus-specific drug targets essential for fitness in vivo remains a significant goal of medical mycology research. The trehalose biosynthetic pathway is found in a wide variety of organisms, including human-pathogenic fungi, but not in humans...
June 2017: Microbiology and Molecular Biology Reviews: MMBR
https://www.readbyqxmd.com/read/28296007/copper-metallothioneins
#3
REVIEW
Jenifer Calvo, Hunmin Jung, Gabriele Meloni
Metallothioneins (MTs) are a class of low molecular weight and cysteine-rich metal binding proteins present in all the branches of the tree of life. MTs efficiently bind with high affinity several essential and toxic divalent and monovalent transition metals by forming characteristic polynuclear metal-thiolate clusters within their structure. MTs fulfil multiple biological functions related to their metal binding properties, with essential roles in both Zn(II) and Cu(I) homeostasis as well as metal detoxification...
March 13, 2017: IUBMB Life
https://www.readbyqxmd.com/read/28273342/robust-dinoflagellata-phylogeny-inferred-from-public-transcriptome-databases
#4
Dana C Price, Debashish Bhattacharya
Dinoflagellates are dominant members of the plankton and play key roles in ocean ecosystems as primary producers, predators, parasites, coral photobionts, and causative agents of algal blooms that produce toxins harmful to humans and commercial fisheries. These unicellular protists exhibit remarkable trophic and morphological diversity and include species with some of the largest reported nuclear genomes. Despite their high ecological and economic importance, comprehensive genome (or transcriptome) based dinoflagellate trees of life are few in number...
March 8, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28266913/the-challenges-faced-by-living-stock-collections-in-the-usa
#5
Kevin McCluskey, Kyria Boundy-Mills, Greg Dye, Erin Ehmke, Gregg Gunnell, Hippokratis Kiaris, Maxi Polihronakis Richmond, Anne D Yoder, Daniel R Zeigler, Sarah Zehr, Erich Grotewold
Many discoveries in the life sciences have been made using material from living stock collections. These collections provide a uniform and stable supply of living organisms and related materials that enhance the reproducibility of research and minimize the need for repetitive calibration. While collections differ in many ways, they all require expertise in maintaining living organisms and good logistical systems for keeping track of stocks and fulfilling requests for specimens. Here, we review some of the contributions made by living stock collections to research across all branches of the tree of life, and outline the challenges they face...
March 7, 2017: ELife
https://www.readbyqxmd.com/read/28265520/a-supertree-pipeline-for-summarizing-phylogenetic-and-taxonomic-information-for-millions-of-species
#6
Benjamin D Redelings, Mark T Holder
We present a new supertree method that enables rapid estimation of a summary tree on the scale of millions of leaves. This supertree method summarizes a collection of input phylogenies and an input taxonomy. We introduce formal goals and criteria for such a supertree to satisfy in order to transparently and justifiably represent the input trees. In addition to producing a supertree, our method computes annotations that describe which grouping in the input trees support and conflict with each group in the supertree...
2017: PeerJ
https://www.readbyqxmd.com/read/28258659/genome-wide-survey-of-nuclear-protein-coding-markers-for-beetle-phylogenetics-and-their-application-in-resolving-both-deep-and-shallow-level-divergences
#7
Li-Heng Che, Shao-Qian Zhang, Yun Li, Dan Liang, Hong Pang, Adam Ślipiński, Peng Zhang
Beetles (Coleoptera) are the most diverse and species-rich insect group, representing an impressive explosive radiation in the evolutionary history of insects, and their evolutionary relationships are often difficult to resolve. The amount of "traditional markers" (e.g., mitochondrial genes and nuclear rDNAs) for beetle phylogenetics is small and these markers often lack sufficient signals in resolving relationships for such a rapidly radiating lineage. Here, based on the available genome data of beetles and other related insect species, we performed a genome-wide survey to search nuclear protein-coding (NPC) genes suitable for research on beetle phylogenetics...
March 3, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28257556/biological-factors-contributing-to-bark-and-ambrosia-beetle-species-diversification
#8
Jostein Gohli, Lawrence R Kirkendall, Sarah M Smith, Anthony I Cognato, Jiri Hulcr, Bjarte H Jordal
The study of species diversification can identify the processes that shape patterns of species richness across the tree of life. Here we perform comparative analyses of species diversification using a large dataset of bark beetles. Three examined covariates - permanent inbreeding (sibling mating), fungus farming, and major host type - represent a range of factors that may be important for speciation. We studied the association of these covariates with species diversification while controlling for evolutionary lag on adaptation...
March 3, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28254474/new-insights-on-the-sister-lineage-of-percomorph-fishes-with-an-anchored-hybrid-enrichment-dataset
#9
Alex Dornburg, Jeffrey P Townsend, Willa Brooks, Elizabeth Spriggs, Ron I Eytan, Jon A Moore, Peter C Wainwright, Alan Lemmon, Emily Moriarty Lemmon, Thomas J Near
Percomorph fishes represent over 17,100 species, including several model organisms and species of economic importance. Despite continuous advances in the resolution of the percomorph Tree of Life, resolution of the sister lineage to Percomorpha remains inconsistent but restricted to a small number of candidate lineages. Here we use an anchored hybrid enrichment (AHE) dataset of 132 loci with over 99,000 base pairs to identify the sister lineage of percomorph fishes. Initial analyses of this dataset failed to recover a strongly supported sister clade to Percomorpha, however, scrutiny of the AHE dataset revealed a bias towards high GC content at fast-evolving codon partitions (GC bias)...
February 27, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28243688/the-origin-of-life-models-and-data
#10
Kathryn A Lanier, Loren Dean Williams
A general framework for conventional models of the origin of life (OOL) is the specification of a 'privileged function.' A privileged function is an extant biological function that is excised from its biological context, elevated in importance over other functions, and transported back in time to a primitive chemical or geological environment. In RNA or Clay Worlds, the privileged function is replication. In Metabolism-First Worlds, the privileged function is metabolism. In Thermal Vent Worlds, the privileged function is energy harvesting from chemical gradients...
February 27, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28228511/the-opiliones-tree-of-life-shedding-light-on-harvestmen-relationships-through-transcriptomics
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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