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https://www.readbyqxmd.com/read/28643626/what-defines-the-kingdom-fungi
#1
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
#2
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
#3
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
#4
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 12, 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
#5
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...
June 12, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28602657/fatty-acid-availability-sets-cell-envelope-capacity-and-dictates-microbial-cell-size
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/28591840/novel-approaches-in-function-driven-single-cell-genomics
#9
Devin F R Doud, Tanja Woyke
Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology...
June 7, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28582579/glowing-worms-biological-chemical-and-functional-diversity-of-bioluminescent-annelids
#10
Aida Verdes, David F Gruber
Bioluminescence, the ability to produce light by living organisms, has evolved independently in numerous lineages across the tree of life. Luminous forms are found in a wide range of taxonomic groups from bacteria to vertebrates, although the great majority of bioluminescent organisms are marine taxa. Within the phylum Annelida, bioluminescence is widespread, present in at least 98 terrestrial and marine species that represent 45 genera distributed in thirteen lineages of clitellates and polychaetes. The ecological diversity of luminous annelids is unparalleled, with species occupying a great variety of habitats including both terrestrial and marine ecosystems, from coastal waters to the deep-sea, in benthic and pelagic habitats from polar to tropical regions...
June 3, 2017: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/28570771/how-exaptations-facilitated-photosensory-evolution-seeing-the-light-by-accident
#11
REVIEW
Gregory S Gavelis, Patrick J Keeling, Brian S Leander
Exaptations are adaptations that have undergone a major change in function. By recruiting genes from sources originally unrelated to vision, exaptation has allowed for sudden and critical photosensory innovations, such as lenses, photopigments, and photoreceptors. Here we review new or neglected findings, with an emphasis on unicellular eukaryotes (protists), to illustrate how exaptation has shaped photoreception across the tree of life. Protist phylogeny attests to multiple origins of photoreception, as well as the extreme creativity of evolution...
June 1, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28569797/speciation-gradients-and-the-distribution-of-biodiversity
#12
Dolph Schluter, Matthew W Pennell
Global patterns of biodiversity are influenced by spatial and environmental variations in the rate at which new species form. We relate variations in speciation rates to six key patterns of biodiversity worldwide, including the species-area relationship, latitudinal gradients in species and genetic diversity, and between-habitat differences in species richness. Although they sometimes mirror biodiversity patterns, recent rates of speciation, at the tip of the tree of life, are often highest where species richness is low...
May 31, 2017: Nature
https://www.readbyqxmd.com/read/28554569/evolutionary-perspectives-on-ageing
#13
REVIEW
Martin Reichard
From an evolutionary perspective, ageing is a decrease in fitness with chronological age - expressed by an increase in mortality risk and/or decline in reproductive success and mediated by deterioration of functional performance. While this makes ageing intuitively paradoxical - detrimental to individual fitness - evolutionary theory offers answers as to why ageing has evolved. In this review, I first briefly examine the classic evolutionary theories of ageing and their empirical tests, and highlight recent findings that have advanced our understanding of the evolution of ageing (condition-dependent survival, positive pleiotropy)...
May 26, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28539388/an-evolutionary-perspective-on-cell-migration-digging-for-the-roots-of-amoeboid-motility
#14
Margaret A Titus, Holly V Goodson
Fritz-Laylin et al. (2017. J. Cell Biol. https://doi.org/10.1083/jcb.201701074) take advantage of the deep knowledge of mechanisms of actin-based motility and a growing number of sequenced genomes across the tree of life to gain insight into the machinery needed for pseudopod-based amoeboid motility and how it evolved.
June 5, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28535985/recalcitrant-deep-and-shallow-nodes-in-aristolochia-aristolochiaceae-illuminated-using-anchored-hybrid-enrichment
#15
Stefan Wanke, Carolina Granados Mendoza, Sebastian Müller, Anna Paizanni Guillén, Christoph Neinhuis, Alan R Lemmon, Emily Moriarty Lemmon, Marie-Stéphanie Samain
Recalcitrant relationships are characterized by very short internodes that can be found among shallow and deep phylogenetic scales all over the tree of life. Adding large amounts of presumably informative sequences, while decreasing systematic error, has been suggested as a possible approach to increase phylogenetic resolution. The development of enrichment strategies, coupled with next generation sequencing, resulted in a cost-effective way to facilitate the reconstruction of recalcitrant relationships. By applying the anchored hybrid enrichment (AHE) genome partitioning strategy to Aristolochia using an universal angiosperm probe set, we obtained 231-233 out of 517 single or low copy nuclear loci originally contained in the enrichment kit, resulting in a total alignment length of 154,756bp to 160,150bp...
May 20, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28533395/integrative-modeling-of-gene-and-genome-evolution-roots-the-archaeal-tree-of-life
#16
Tom A Williams, Gergely J Szöllősi, Anja Spang, Peter G Foster, Sarah E Heaps, Bastien Boussau, Thijs J G Ettema, T Martin Embley
A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution...
June 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28502981/mechanisms-of-gene-flow-in-archaea
#17
REVIEW
Alexander Wagner, Rachel J Whitaker, David J Krause, Jan-Hendrik Heilers, Marleen van Wolferen, Chris van der Does, Sonja-Verena Albers
Archaea are diverse, ecologically important, single-celled microorganisms. They have unique functions and features, such as methanogenesis and the composition of their cell envelope, although many characteristics are shared with the other domains of life, either through ancestry or through promiscuous horizontal gene transfer. The exchange of genetic material is a major driving force for genome evolution across the tree of life and has a role in archaeal speciation, adaptation and maintenance of diversity. In this Review, we discuss our current knowledge of archaeal mechanisms of DNA transfer and highlight the role of gene transfer in archaeal evolution...
May 15, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28502748/cytochrome-p450-diversity-in-the-tree-of-life
#18
David R Nelson
Sequencing in all areas of the tree of life has produced >300,000 cytochrome P450 (CYP) sequences that have been mined and collected. Nomenclature has been assigned to >41,000 CYP sequences and the majority of the remainder has been sorted by BLAST searches into clans, families and subfamilies in preparation for naming. The P450 sequence space is being systematically explored and filled in. Well-studied groups like vertebrates are covered in greater depth while new insights are being added into uncharted territories like horseshoe crab (Limulus polyphemus), tardigrades (Hypsibius dujardini), velvet worm (Euperipatoides_rowelli), and basal land plants like hornworts, liverworts and mosses...
May 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28496163/reshaping-the-tree-of-life
#19
Eva Heinz, Daryl Domman
This month's Genome Watch highlights how metagenomics is continuing to reveal the diversity of microorganisms in the environment and how it is challenging and expanding our understanding of how life evolved on Earth.
May 12, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28493998/metabolomics-analysis-finding-out-metabolic-building-blocks
#20
Ricardo Alberich, José A Castro, Mercè Llabrés, Pere Palmer-Rodríguez
In this paper we propose a new methodology for the analysis of metabolic networks. We use the notion of strongly connected components of a graph, called in this context metabolic building blocks. Every strongly connected component is contracted to a single node in such a way that the resulting graph is a directed acyclic graph, called a metabolic DAG, with a considerably reduced number of nodes. The property of being a directed acyclic graph brings out a background graph topology that reveals the connectivity of the metabolic network, as well as bridges, isolated nodes and cut nodes...
2017: PloS One
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