keyword
MENU ▼
Read by QxMD icon Read
search

"Tree of life"

keyword
https://www.readbyqxmd.com/read/28733590/hypersaline-sapropels-act-as-hotspots-for-microbial-dark-matter
#1
Adrian-Ştefan Andrei, Andreea Baricz, Michael Scott Robeson, Manuela Raluca Păuşan, Tudor Tămaş, Cecilia Chiriac, Edina Szekeres, Lucian Barbu-Tudoran, Erika Andrea Levei, Cristian Coman, Mircea Podar, Horia Leonard Banciu
Present-day terrestrial analogue sites are crucial ground truth proxies for studying life in geochemical conditions close to those assumed to be present on early Earth or inferred to exist on other celestial bodies (e.g. Mars, Europa). Although hypersaline sapropels are border-of-life habitats with moderate occurrence, their microbiological and physicochemical characterization lags behind. Here, we study the diversity of life under low water activity by describing the prokaryotic communities from two disparate hypersaline sapropels (Transylvanian Basin, Romania) in relation to geochemical milieu and pore water chemistry, while inferring their role in carbon cycling by matching taxa to known taxon-specific biogeochemical functions...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28731792/the-evolution-of-energetic-scaling-across-the-vertebrate-tree-of-life
#2
Josef C Uyeda, Matthew W Pennell, Eliot T Miller, Rafael Maia, Craig R McClain
Metabolism is the link between ecology and physiology-it dictates the flow of energy through individuals and across trophic levels. Much of the predictive power of metabolic theories of ecology derives from the scaling relationship between organismal size and metabolic rate. There is growing evidence that this scaling relationship is not universal, but we have little knowledge of how it has evolved over macroevolutionary time. Here we develop a novel phylogenetic comparative method to investigate how often and in which clades the macroevolutionary dynamics of the metabolic scaling have changed...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28723902/seed-size-and-its-rate-of-evolution-correlate-with-species-diversification-across-angiosperms
#3
Javier Igea, Eleanor F Miller, Alexander S T Papadopulos, Andrew J Tanentzap
Species diversity varies greatly across the different taxonomic groups that comprise the Tree of Life (ToL). This imbalance is particularly conspicuous within angiosperms, but is largely unexplained. Seed mass is one trait that may help clarify why some lineages diversify more than others because it confers adaptation to different environments, which can subsequently influence speciation and extinction. The rate at which seed mass changes across the angiosperm phylogeny may also be linked to diversification by increasing reproductive isolation and allowing access to novel ecological niches...
July 19, 2017: PLoS Biology
https://www.readbyqxmd.com/read/28721186/factors-driving-the-global-decline-of-cycad-diversity
#4
Ledile T Mankga, Kowiyou Yessoufou
Mounting evidence indicates that we are witnessing the sixth mass extinction period. Given the important goods and services biodiversity delivers to humans, there is a need for a continued commitment to investigate what pre-disposes some taxa to greater risk of extinction. Here, we investigate this question using a phylogenetic comparative method and fitting a cumulative link mixed effect model on biological, ecological and evolutionary data of cycads, the most threatened lineage in the plant kingdom. We identified nine groups of threats to cycads, with habitat loss, over-collection, fire and reproduction failure being the most prominent, but only four of these threats (habitat loss, over-collection, medicinal uses and reproduction failure) clustered on the cycad tree of life...
July 2017: AoB Plants
https://www.readbyqxmd.com/read/28720649/the-greatest-kinetochore-show-on-earth
#5
Gerben Vader, Andrea Musacchio
Coordinated chromosome duplication and segregation is key to the existence of every organism on our planet. In eukaryotes, sophisticated protein assemblies called kinetochores are universally required for chromosome segregation, but their protein composition can diverge across the eukaryotic tree of life. In this issue of EMBO Reports, van Hooff et al [1] shed light on kinetochore evolution with a comprehensive study of kinetochore composition across 90 phylogenetically diverse eukaryotes. They show that certain kinetochore complexes have taken distinct evolutionary paths to arrive at a strikingly broad compositional array in present-day eukaryotes, providing exciting new insights into the origins, function, and flexibility of eukaryotic kinetochores...
July 18, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28716385/protein-lipograms
#6
Jason Laurie, Amit K Chattopadhyay, Darren R Flower
Linguistic analysis of protein sequences is an underexploited technique. Here, we capitalize on the concept of the lipogram to characterize sequences at the proteome levels. A lipogram is a literary composition which omits one or more letters. A protein lipogram likewise omits one or more types of amino acid. In this article, we establish a usable terminology for the decomposition of a sequence collection in terms of the lipogram. Next, we characterize Uniref50 using a lipogram decomposition. At the global level, protein lipograms exhibit power-law properties...
July 15, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28705195/peto-s-paradox-how-has-evolution-solved-the-problem-of-cancer-prevention
#7
Marc Tollis, Amy M Boddy, Carlo C Maley
The risk of developing cancer should theoretically increase with both the number of cells and the lifespan of an organism. However, gigantic animals do not get more cancer than humans, suggesting that super-human cancer suppression has evolved numerous times across the tree of life. This is the essence and promise of Peto's Paradox. We discuss what is known about Peto's Paradox and provide hints of what is yet to be discovered.
July 13, 2017: BMC Biology
https://www.readbyqxmd.com/read/28690608/phylogenetic-tracings-of-proteome-size-support-the-gradual-accretion-of-protein-structural-domains-and-the-early-origin-of-viruses-from-primordial-cells
#8
Arshan Nasir, Kyung Mo Kim, Gustavo Caetano-Anollés
Untangling the origin and evolution of viruses remains a challenging proposition. We recently studied the global distribution of protein domain structures in thousands of completely sequenced viral and cellular proteomes with comparative genomics, phylogenomics, and multidimensional scaling methods. A tree of life describing the evolution of proteomes revealed viruses emerging from the base of the tree as a fourth supergroup of life. A tree of domains indicated an early origin of modern viral lineages from ancient cells that co-existed with the cellular ancestors...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28690188/aging-across-the-tree-of-life-the-importance-of-a-comparative-perspective-for-the-use-of-animal-models-in-aging
#9
REVIEW
Alan A Cohen
Use of model organisms in aging research is problematic because our ability to extrapolate across the tree of life is not clear. On one hand, there are conserved pathways that regulate lifespan in organisms including yeast, nematodes, fruit flies, and mice. On the other, many intermediate taxa across the tree of life appear not to age at all, and there is substantial variation in aging mechanisms and patterns, sometimes even between closely related species. There are good evolutionary and mechanistic reasons to expect this complexity, but it means that model organisms must be used with caution and that results must always be interpreted through a broader comparative framework...
July 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28683774/phylogenetic-classification-of-bony-fishes
#10
Ricardo Betancur-R, Edward O Wiley, Gloria Arratia, Arturo Acero, Nicolas Bailly, Masaki Miya, Guillaume Lecointre, Guillermo Ortí
BACKGROUND: Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings...
July 6, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28679730/constraining-the-timing-of-whole-genome-duplication-in-plant-evolutionary-history
#11
James W Clark, Philip C J Donoghue
Whole genome duplication (WGD) has occurred in many lineages within the tree of life and is invariably invoked as causal to evolutionary innovation, increased diversity, and extinction resistance. Testing such hypotheses is problematic, not least since the timing of WGD events has proven hard to constrain. Here we show that WGD events can be dated through molecular clock analysis of concatenated gene families, calibrated using fossil evidence for the ages of species divergences that bracket WGD events. We apply this approach to dating the two major genome duplication events shared by all seed plants (ζ) and flowering plants (ɛ), estimating the seed plant WGD event at 399-381 Ma, and the angiosperm WGD event at 319-297 Ma...
July 12, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28675159/the-evolution-of-host-symbiont-dependence
#12
Roberta M Fisher, Lee M Henry, Charlie K Cornwallis, E Toby Kiers, Stuart A West
Organisms across the tree of life form symbiotic partnerships with microbes for metabolism, protection and resources. While some hosts evolve extreme dependence on their symbionts, others maintain facultative associations. Explaining this variation is fundamental to understanding when symbiosis can lead to new higher-level individuals, such as during the evolution of the eukaryotic cell. Here we perform phylogenetic comparative analyses on 106 unique host-bacterial symbioses to test for correlations between symbiont function, transmission mode, genome size and host dependence...
July 4, 2017: Nature Communications
https://www.readbyqxmd.com/read/28643626/what-defines-the-kingdom-fungi
#13
Thomas A Richards, Guy Leonard, Jeremy G Wideman
The application of environmental DNA techniques and increased genome sequencing of microbial diversity, combined with detailed study of cellular characters, has consistently led to the reexamination of our understanding of the tree of life. This has challenged many of the definitions of taxonomic groups, especially higher taxonomic ranks such as eukaryotic kingdoms. The Fungi is an example of a kingdom which, together with the features that define it and the taxa that are grouped within it, has been in a continual state of flux...
June 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28620233/dating-early-animal-evolution-using-phylogenomic-data
#14
Martin Dohrmann, Gert Wörheide
Information about the geological timeframe during which animals radiated into their major subclades is crucial to understanding early animal ecology and evolution. Unfortunately, the pre-Cambrian fossil record is sparse and its interpretation controversial. Relaxed molecular-clock methods provide an alternative means of estimating the timing of cladogenesis deep in the metazoan tree of life. So far, thorough molecular clock studies focusing specifically on Metazoa as a whole have been based on relatively small datasets or incomplete representation of the main non-bilaterian lineages (such as sponges and ctenophores), which are fundamental for understanding early metazoan evolution...
June 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28610890/the-algal-revolution
#15
REVIEW
Juliet Brodie, Cheong Xin Chan, Olivier De Clerck, J Mark Cock, Susana M Coelho, Claire Gachon, Arthur R Grossman, Thomas Mock, John A Raven, Alison G Smith, Hwan Su Yoon, Debashish Bhattacharya
Algae are (mostly) photosynthetic eukaryotes that occupy multiple branches of the tree of life, and are vital for planet function and health. In this review, we highlight a transformative period in studies of the evolution and functioning of this extraordinary group of organisms and their potential for novel applications, wrought by high-throughput 'omic' and reverse genetic methods. We cover the origin and diversification of algal groups, explore advances in understanding the link between phenotype and genotype, consider algal sex determination, and review progress in understanding the roots of algal multicellularity...
June 10, 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/28604769/lokiarchaea-are-close-relatives-of-euryarchaeota-not-bridging-the-gap-between-prokaryotes-and-eukaryotes
#16
Violette Da Cunha, Morgan Gaia, Daniele Gadelle, Arshan Nasir, Patrick Forterre
The eocyte hypothesis, in which Eukarya emerged from within Archaea, has been boosted by the description of a new candidate archaeal phylum, "Lokiarchaeota", from metagenomic data. Eukarya branch within Lokiarchaeota in a tree reconstructed from the concatenation of 36 universal proteins. However, individual phylogenies revealed that lokiarchaeal proteins sequences have different evolutionary histories. The individual markers phylogenies revealed at least two subsets of proteins, either supporting the Woese or the Eocyte tree of life...
June 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28604660/1-003-reference-genomes-of-bacterial-and-archaeal-isolates-expand-coverage-of-the-tree-of-life
#17
Supratim Mukherjee, Rekha Seshadri, Neha J Varghese, Emiley A Eloe-Fadrosh, Jan P Meier-Kolthoff, Markus Göker, R Cameron Coates, Michalis Hadjithomas, Georgios A Pavlopoulos, David Paez-Espino, Yasuo Yoshikuni, Axel Visel, William B Whitman, George M Garrity, Jonathan A Eisen, Philip Hugenholtz, Amrita Pati, Natalia N Ivanova, Tanja Woyke, Hans-Peter Klenk, Nikos C Kyrpides
We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation...
July 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28602657/fatty-acid-availability-sets-cell-envelope-capacity-and-dictates-microbial-cell-size
#18
Stephen Vadia, Jessica L Tse, Rafael Lucena, Zhizhou Yang, Douglas R Kellogg, Jue D Wang, Petra Anne Levin
Nutrients-and by extension biosynthetic capacity-positively impact cell size in organisms throughout the tree of life. In bacteria, cell size is reduced 3-fold in response to nutrient starvation or accumulation of the alarmone ppGpp, a global inhibitor of biosynthesis. However, whether biosynthetic capacity as a whole determines cell size or whether particular anabolic pathways are more important than others remains an open question. Here we identify fatty acid synthesis as the primary biosynthetic determinant of Escherichia coli size and present evidence supporting a similar role for fatty acids as a positive determinant of size in the Gram-positive bacterium Bacillus subtilis and the single-celled eukaryote Saccharomyces cerevisiae...
June 19, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28602622/homoeologous-chromosome-pairing-across-the-eukaryote-phylogeny
#19
REVIEW
Amanda L Grusz, Erin M Sigel, Colby Witherup
During the past quarter century, molecular phylogenetic inferences have significantly resolved evolutionary relationships spanning the eukaryotic tree of life. With improved phylogenies in hand, the focus of systematics will continue to expand from estimating species relationships toward examining the evolution of specific, fundamental traits across the eukaryotic tree. Undoubtedly, this will expose knowledge gaps in the evolution of key traits, particularly with respect to non-model lineages. Here, we examine one such trait across eukaryotes-the regulation of homologous chromosome pairing during meiosis-as an illustrative example...
June 8, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28595363/more-on-the-best-evolutionary-rate-for-phylogenetic-analysis
#20
Seraina Klopfstein, Tim Massingham, Nick Goldman
The accumulation of genome-scale molecular datasets for non-model taxa brings us ever closer to resolving the tree of life of all living organisms. However, despite the depth of data available, a number of studies that each used thousands of genes have reported conflicting results. The focus of phylogenomic projects must thus shift to more careful experimental design. Even though we still have a limited understanding of what are the best predictors of the phylogenetic informativeness of a gene, there is wide agreement that one key factor is its evolutionary rate; but there is no consensus as to whether the rates derived as optimal in various analytical, empirical, and simulation approaches have any general applicability...
June 8, 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"