keyword
MENU ▼
Read by QxMD icon Read
search

"Tree of life"

keyword
https://www.readbyqxmd.com/read/28428864/integrating-biogeography-threat-and-evolutionary-data-to-explore-extinction-crisis-in-the-taxonomic-group-of-cycads
#1
Kowiyou Yessoufou, Barnabas H Daru, Respinah Tafirei, Hosam O Elansary, Isaac Rampedi
Will the ongoing extinction crisis cause a severe loss of evolutionary information accumulated over millions of years on the tree of life? This question has been largely explored, particularly for vertebrates and angiosperms. However, no equivalent effort has been devoted to gymnosperms. Here, we address this question focusing on cycads, the gymnosperm group exhibiting the highest proportion of threatened species in the plant kingdom. We assembled the first complete phylogeny of cycads and assessed how species loss under three scenarios would impact the cycad tree of life...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28410373/parallel-reorganization-of-protein-function-in-the-spindle-checkpoint-pathway-through-evolutionary-paths-in-the-fitness-landscape-that-appear-neutral-in-laboratory-experiments
#2
Alex N Nguyen Ba, Bob Strome, Selma Osman, Elizabeth-Ann Legere, Taraneh Zarin, Alan M Moses
Regulatory networks often increase in complexity during evolution through gene duplication and divergence of component proteins. Two models that explain this increase in complexity are: 1) adaptive changes after gene duplication, such as resolution of adaptive conflicts, and 2) non-adaptive processes such as duplication, degeneration and complementation. Both of these models predict complementary changes in the retained duplicates, but they can be distinguished by direct fitness measurements in organisms with short generation times...
April 14, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28388929/novel-soil-inhabiting-clades-fill-gaps-in-the-fungal-tree-of-life
#3
Leho Tedersoo, Mohammad Bahram, Rasmus Puusepp, R Henrik Nilsson, Timothy Y James
BACKGROUND: Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water. RESULTS: We provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s...
April 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28381628/a-puzzling-homology-a-brittle-star-using-a-putative-cnidarian-type-luciferase-for-bioluminescence
#4
Jérôme Delroisse, Esther Ullrich-Lüter, Stefanie Blaue, Olga Ortega-Martinez, Igor Eeckhaut, Patrick Flammang, Jérôme Mallefet
Bioluminescence relies on the oxidation of a luciferin substrate catalysed by a luciferase enzyme. Luciferins and luciferases are generic terms used to describe a large variety of substrates and enzymes. Whereas luciferins can be shared by phylogenetically distant organisms which feed on organisms producing them, luciferases have been thought to be lineage-specific enzymes. Numerous light emission systems would then have co-emerged independently along the tree of life resulting in a plethora of non-homologous luciferases...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28376330/animal-evolution-last-word-on-sponges-first
#5
D Timothy J Littlewood
A major problem in understanding animal evolution is where early branching phyla, especially sponges and comb jellies (sea gooseberries), sit in the tree of life. A new study seeks to overcome this problem by sampling more species and data cleansing.
April 3, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28369655/why-do-phylogenomic-data-sets-yield-conflicting-trees-data-type-influences-the-avian-tree-of-life-more-than-taxon-sampling
#6
Sushma Reddy, Rebecca T Kimball, Akanksha Pandey, Peter A Hosner, Michael J Braun, Shannon J Hackett, Kin-Lan Han, John Harshman, Christopher J Huddleston, Sarah Kingston, Ben D Marks, Kathleen J Miglia, William S Moore, Frederick H Sheldon, Christopher C Witt, Tamaki Yuri, Edward L Braun
Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic datasets can also result in conflicting estimates of phylogeny. Here we use the early divergences in Neoaves, the largest clade of extant birds, as a 'model system' to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts...
March 27, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28369123/distribution-and-evolution-of-stable-single-%C3%AE-helices-sah-domains-in-myosin-motor-proteins
#7
Dominic Simm, Klas Hatje, Martin Kollmar
Stable single-alpha helices (SAHs) are versatile structural elements in many prokaryotic and eukaryotic proteins acting as semi-flexible linkers and constant force springs. This way SAH-domains function as part of the lever of many different myosins. Canonical myosin levers consist of one or several IQ-motifs to which light chains such as calmodulin bind. SAH-domains provide flexibility in length and stiffness to the myosin levers, and may be particularly suited for myosins working in crowded cellular environments...
2017: PloS One
https://www.readbyqxmd.com/read/28368387/retroelement-guided-protein-diversification-abounds-in-vast-lineages-of-bacteria-and-archaea
#8
Blair G Paul, David Burstein, Cindy J Castelle, Sumit Handa, Diego Arambula, Elizabeth Czornyj, Brian C Thomas, Partho Ghosh, Jeff F Miller, Jillian F Banfield, David L Valentine
Major radiations of enigmatic Bacteria and Archaea with large inventories of uncharacterized proteins are a striking feature of the Tree of Life(1-5). The processes that led to functional diversity in these lineages, which may contribute to a host-dependent lifestyle, are poorly understood. Here, we show that diversity-generating retroelements (DGRs), which guide site-specific protein hypervariability(6-8), are prominent features of genomically reduced organisms from the bacterial candidate phyla radiation (CPR) and as yet uncultivated phyla belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) archaeal superphylum...
April 3, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28361695/silva-rdp-greengenes-ncbi-and-ott-how-do-these-taxonomies-compare
#9
Monika Balvočiūtė, Daniel H Huson
BACKGROUND: A key step in microbiome sequencing analysis is read assignment to taxonomic units. This is often performed using one of four taxonomic classifications, namely SILVA, RDP, Greengenes or NCBI. It is unclear how similar these are and how to compare analysis results that are based on different taxonomies. RESULTS: We provide a method and software for mapping taxonomic entities from one taxonomy onto another. We use it to compare the four taxonomies and the Open Tree of life Taxonomy (OTT)...
March 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28319149/walking-and-talking-the-tree-of-life-why-and-how-to-teach-about-biodiversity
#10
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
#11
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
#12
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
#13
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
#14
Kevin McCluskey, Kyria Boundy-Mills, Greg Dye, Erin Ehmke, Gregg F 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 13, 2017: ELife
https://www.readbyqxmd.com/read/28265520/a-supertree-pipeline-for-summarizing-phylogenetic-and-taxonomic-information-for-millions-of-species
#15
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
#16
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
#17
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
#18
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
#19
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...
March 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28228511/the-opiliones-tree-of-life-shedding-light-on-harvestmen-relationships-through-transcriptomics
#20
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
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"