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https://www.readbyqxmd.com/read/29325126/automated-integration-of-trees-and-traits-a-case-study-using-paired-fin-loss-across-teleost-fishes
#1
Laura M Jackson, Pasan C Fernando, Josh S Hanscom, James P Balhoff, Paula M Mabee
Data synthesis required for large-scale macroevolutionary studies is challenging with the current tools available for integration. Using a classic question regarding the frequency of paired fin loss in teleost fishes as a case study, we sought to create automated methods to facilitate the integration of broad-scale trait data with a sizable species-level phylogeny. Similar to the evolutionary pattern previously described for limbs, pelvic and pectoral fin reduction and loss are thought to have occurred independently multiple times in the evolution of fishes...
January 9, 2018: Systematic Biology
https://www.readbyqxmd.com/read/29317511/exploration-of-the-germline-genome-of-the-ciliate-chilodonella-uncinata-through-single-cell-omics-transcriptomics-and-genomics
#2
Xyrus X Maurer-Alcalá, Rob Knight, Laura A Katz
Separate germline and somatic genomes are found in numerous lineages across the eukaryotic tree of life, often separated into distinct tissues (e.g., in plants, animals, and fungi) or distinct nuclei sharing a common cytoplasm (e.g., in ciliates and some foraminifera). In ciliates, germline-limited (i.e., micronuclear-specific) DNA is eliminated during the development of a new somatic (i.e., macronuclear) genome in a process that is tightly linked to large-scale genome rearrangements, such as deletions and reordering of protein-coding sequences...
January 9, 2018: MBio
https://www.readbyqxmd.com/read/29311682/phylogenomics-illuminates-the-backbone-of-the-myriapoda-tree-of-life-and-reconciles-morphological-and-molecular-phylogenies
#3
Rosa Fernández, Gregory D Edgecombe, Gonzalo Giribet
The interrelationships of the four classes of Myriapoda have been an unresolved question in arthropod phylogenetics and an example of conflict between morphology and molecules. Morphology and development provide compelling support for Diplopoda (millipedes) and Pauropoda being closest relatives, and moderate support for Symphyla being more closely related to the diplopod-pauropod group than any of them are to Chilopoda (centipedes). In contrast, several molecular datasets have contradicted the Diplopoda-Pauropoda grouping (named Dignatha), often recovering a Symphyla-Pauropoda group (named Edafopoda)...
January 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29291348/retrieval-of-a-million-high-quality-full-length-microbial-16s-and-18s-rrna-gene-sequences-without-primer-bias
#4
Søren M Karst, Morten S Dueholm, Simon J McIlroy, Rasmus H Kirkegaard, Per H Nielsen, Mads Albertsen
Small subunit ribosomal RNA (SSU rRNA) genes, 16S in bacteria and 18S in eukaryotes, have been the standard phylogenetic markers used to characterize microbial diversity and evolution for decades. However, the reference databases of full-length SSU rRNA gene sequences are skewed to well-studied ecosystems and subject to primer bias and chimerism, which results in an incomplete view of the diversity present in a sample. We combine poly(A)-tailing and reverse transcription of SSU rRNA molecules with synthetic long-read sequencing to generate high-quality, full-length SSU rRNA sequences, without primer bias, at high throughput...
January 1, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29284667/building-the-right-centriole-for-each-cell-type
#5
REVIEW
Jadranka Loncarek, Mónica Bettencourt-Dias
The centriole is a multifunctional structure that organizes centrosomes and cilia and is important for cell signaling, cell cycle progression, polarity, and motility. Defects in centriole number and structure are associated with human diseases including cancer and ciliopathies. Discovery of the centriole dates back to the 19th century. However, recent advances in genetic and biochemical tools, development of high-resolution microscopy, and identification of centriole components have accelerated our understanding of its assembly, function, evolution, and its role in human disease...
December 28, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/29277866/comparative-genome-annotation
#6
Stefanie König, Lars Romoth, Mario Stanke
Newly sequenced genomes are being added to the tree of life at an unprecedented fast pace. Increasingly, such new genomes are phylogenetically close to previously sequenced and annotated genomes. In other cases, whole clades of closely related species or strains ought to be annotated simultaneously. Often, in subsequent studies differences between the closely related species or strains are in the focus of research when the shared gene structures prevail. We here review methods for comparative structural genome annotation...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29277109/collective-narrative-practice-with-unaccompanied-refugee-minors-the-tree-of-life-as-a-response-to-hardship
#7
Suzan Fm Jacobs
During the summer of 2016, in the midst of one of the biggest refugee crises in centuries, the author of this article joined the team from a shelter for unaccompanied refugee minors on Samos, Greece, in an effort to provide young boys seeking asylum in Europe with an opportunity to engage in speaking about the difficulties they have encountered in life. The team used a collective narrative methodology called the "Tree of Life", originally developed by Ncube-Mlilo and Denborough. In addition to traditional psychological treatments, collective narrative practice creates a secure foundation for addressing trauma, suffering, and hardship...
December 1, 2017: Clinical Child Psychology and Psychiatry
https://www.readbyqxmd.com/read/29276725/markerless-gene-editing-in-the-hyperthermophilic-archaeon-thermococcus-kodakarensis
#8
Alexandra M Gehring, Travis J Sanders, Thomas J Santangelo
The advent of single cell genomics and the continued use of metagenomic profiling in diverse environments has exponentially increased the known diversity of life. The recovered and assembled genomes predict physiology, consortium interactions and gene function, but experimental validation of metabolisms and molecular pathways requires more directed approaches. Gene function-and the correlation between phenotype and genotype is most obviously studied with genetics, and it is therefore critical to develop techniques permitting rapid and facile strain construction...
November 20, 2017: Bio-protocol
https://www.readbyqxmd.com/read/29241941/finding-evolutionary-processes-hidden-in-cryptic-species
#9
REVIEW
Torsten H Struck, Jeffrey L Feder, Mika Bendiksby, Siri Birkeland, José Cerca, Vladimir I Gusarov, Sonja Kistenich, Karl-Henrik Larsson, Lee Hsiang Liow, Michael D Nowak, Brita Stedje, Lutz Bachmann, Dimitar Dimitrov
Cryptic species could represent a substantial fraction of biodiversity. However, inconsistent definitions and taxonomic treatment of cryptic species prevent informed estimates of their contribution to biodiversity and impede our understanding of their evolutionary and ecological significance. We propose a conceptual framework that recognizes cryptic species based on their low levels of phenotypic (morphological) disparity relative to their degree of genetic differentiation and divergence times as compared with non-cryptic species...
December 11, 2017: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/29237859/differences-between-hard-and-soft-phylogenetic-data
#10
Robert S Sansom, Matthew A Wills
When building the tree of life, variability of phylogenetic signal is often accounted for by partitioning gene sequences and testing for differences. The same considerations, however, are rarely applied to morphological data, potentially undermining its use in evolutionary contexts. Here, we apply partition heterogeneity tests to 59 animal datasets to demonstrate that significant differences exist between the phylogenetic signal conveyed by 'hard' and 'soft' characters (bones, teeth and shells versus myology, integument etc)...
December 20, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29235498/computational-exploration-of-the-chemical-structure-space-of-possible-reverse-tricarboxylic-acid-cycle-constituents
#11
Markus Meringer, H James Cleaves
The reverse tricarboxylic acid (rTCA) cycle has been explored from various standpoints as an idealized primordial metabolic cycle. Its simplicity and apparent ubiquity in diverse organisms across the tree of life have been used to argue for its antiquity and its optimality. In 2000 it was proposed that chemoinformatics approaches support some of these views. Specifically, defined queries of the Beilstein database showed that the molecules of the rTCA are heavily represented in such compound databases. We explore here the chemical structure "space," e...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29234309/rokubacteria-genomic-giants-among-the-uncultured-bacterial-phyla
#12
Eric D Becraft, Tanja Woyke, Jessica Jarett, Natalia Ivanova, Filipa Godoy-Vitorino, Nicole Poulton, Julia M Brown, Joseph Brown, M C Y Lau, Tullis Onstott, Jonathan A Eisen, Duane Moser, Ramunas Stepanauskas
Recent advances in single-cell genomic and metagenomic techniques have facilitated the discovery of numerous previously unknown, deep branches of the tree of life that lack cultured representatives. Many of these candidate phyla are composed of microorganisms with minimalistic, streamlined genomes lacking some core metabolic pathways, which may contribute to their resistance to growth in pure culture. Here we analyzed single-cell genomes and metagenome bins to show that the "Candidate phylum Rokubacteria," formerly known as SPAM, represents an interesting exception, by having large genomes (6-8 Mbps), high GC content (66-71%), and the potential for a versatile, mixotrophic metabolism...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29234139/author-correction-recovery-of-nearly-8-000-metagenome-assembled-genomes-substantially-expands-the-tree-of-life
#13
Donovan H Parks, Christian Rinke, Maria Chuvochina, Pierre-Alain Chaumeil, Ben J Woodcroft, Paul N Evans, Philip Hugenholtz, Gene W Tyson
In the original version of this Article, the authors stated that the archaeal phylum Parvarchaeota was previously represented by only two single-cell genomes (ARMAN-4_'5-way FS' and ARMAN-5_'5-way FS'). However, these are in fact unpublished, low-quality metagenome-assembled genomes (MAGs) obtained from Richmond Mine, California. In addition, the authors overlooked two higher-quality published Parvarchaeota MAGs from the same habitat, ARMAN-4 (ADCE00000000) and ARMAN-5 (ADHF00000000) (B. J. Baker et al., Proc...
December 12, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29223331/the-nos-like-protein-from-the-microalgae-ostreococcus-tauri-is-a-genuine-and-ultrafast-no-producing-enzyme
#14
Marine Weisslocker-Schaetzel, François André, Nabila Touazi, Noelia Foresi, Mehdi Lembrouk, Pierre Dorlet, Annie Frelet-Barrand, Lorenzo Lamattina, Jérôme Santolini
The exponential increase of genomes' sequencing has revealed the presence of NO-Synthases (NOS) throughout the tree of life, uncovering an extraordinary diversity of genetic structure and biological functions. Although NO has been shown to be a crucial mediator in plant physiology, NOS sequences seem present solely in green algae genomes, with a first identification in the picoplankton species Ostreococcus tauri. There is no rationale so far to account for the presence of NOS in this early-diverging branch of the green lineage and its absence in land plants...
December 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/29198427/towards-the-identification-of-ancestrally-shared-regenerative-mechanisms-across-the-metazoa-a-transcriptomic-case-study-in-the-demosponge-halisarca-caerulea
#15
Nathan J Kenny, Jasper M de Goeij, Didier M de Bakker, Casey G Whalen, Eugene Berezikov, Ana Riesgo
Regeneration is an essential process for all multicellular organisms, allowing them to recover effectively from internal and external injury. This process has been studied extensively in a medical context in vertebrates, with pathways often investigated mechanistically, both to derive increased understanding and as potential drug targets for therapy. Several species from other parts of the metazoan tree of life, including Hydra, planarians and echinoderms, noted for their regenerative capabilities, have previously been targeted for study...
November 29, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29192334/putative-independent-evolutionary-reversals-from-genotypic-to-temperature-dependent-sex-determination-are-associated-with-accelerated-evolution-of-sex-determining-genes-in-turtles
#16
Robert Literman, Alexandria Burrett, Basanta Bista, Nicole Valenzuela
The evolutionary lability of sex-determining mechanisms across the tree of life is well recognized, yet the extent of molecular changes that accompany these repeated transitions remain obscure. Most turtles retain the ancestral temperature-dependent sex determination (TSD) from which multiple transitions to genotypic sex determination (GSD) occurred independently, and two contrasting hypotheses posit the existence or absence of reversals back to TSD. Here we examined the molecular evolution of the coding regions of a set of gene regulators involved in gonadal development in turtles and several other vertebrates...
December 1, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29177474/evaluating-fast-maximum-likelihood-based-phylogenetic-programs-using-empirical-phylogenomic-data-sets
#17
Xiaofan Zhou, Xingxing Shen, Chris Todd Hittinger, Antonis Rokas
The sizes of the data matrices assembled to resolve branches of the tree of life have increased dramatically, motivating the development of programs for fast, yet accurate, inference. For example, several different fast programs have been developed in the very popular maximum likelihood framework, including RAxML/ExaML, PhyML, IQ-TREE, and FastTree. Although these programs are widely used, a systematic evaluation and comparison of their performance using empirical genome-scale data matrices has so far been lacking...
November 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29158032/resolving-taxonomic-turbulence-and-uncovering-cryptic-diversity-in-the-musk-turtles-sternotherus-using-robust-demographic-modeling
#18
Peter A Scott, Travis C Glenn, Leslie J Rissler
Accurate and consistent delimitation of species and their relationships provides a necessary framework for comparative studies, understanding evolutionary relationships, and informing conservation management. Despite the ever-increasing availability of genomic data, evolutionary dynamics can still render some relationships exceedingly difficult to resolve, including underlying speciation events that are rapid, recent, or confounded by post-speciation introgression. Here we present an empirical study of musk turtles (Sternotherus) which illustrates approaches to resolve difficult nodes in the Tree of Life that robust species-tree methods fail to resolve...
November 17, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29153404/fungal-phylogeny-in-the-age-of-genomics-insights-into-phylogenetic-inference-from-genome-scale-datasets
#19
László G Nagy, Gergely Szöllősi
The genomic era has been transformative for many fields, including our understanding of the phylogenetic relationships between organisms. The wide availability of whole-genome sequences practically eliminated data availability as a limiting factor for inferring phylogenetic trees, providing hundreds to thousands of loci for analyses, leading to molecular phylogenetics gradually being replaced by phylogenomics. The new era has also brought new challenges: systematic errors (resulting from, e.g., model violation) can be more pronounced in phylogenomic datasets and can lead to strongly supported incorrect relationships, creating significant incongruence among studies...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153402/phylogenetics-and-phylogenomics-of-rust-fungi
#20
M Catherine Aime, Alistair R McTaggart, Stephen J Mondo, Sébastien Duplessis
Rust fungi (Pucciniales) are the most speciose and the most complex group of plant pathogens. Historically, rust taxonomy was largely influenced by host and phenotypic characters, which are potentially plastic. Molecular systematic studies suggest that the extant diversity of this group was largely shaped by host jumps and subsequent shifts. However, it has been challenging to reconstruct the evolutionary history for the order, especially at deeper (family-level) nodes. Phylogenomics offer a potentially powerful tool to reconstruct the Pucciniales tree of life, although researchers working at this vanguard still face unprecedented challenges working with nonculturable organisms that possess some of the largest and most repetitive genomes now known in kingdom fungi...
2017: Advances in Genetics
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