DOCSLIB.ORG

The Hybrid Nature of the Eukaryota and a Consilient View of Life on Earth

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Hybrid Nature of the Eukaryota and a Consilient View of Life on Earth Nature Reviews Microbiology | AOP, published online 12 May 2014; doi:10.1038/nrmicro3271 PERSPECTIVES of eukaryogenesis have been proposed. OPINION There is substantial molecular support for endosymbiosis4,14, and the mechanism (that The hybrid nature of the Eukaryota is, selective advantage) for this model has also been explored6,9,20–22. By contrast, autog- and a consilient view of life on Earth enous models, which imply that eukaryotes arose by stepwise mutations without the external acquisition of genetic material, James O. McInerney, Mary J. O’Connell and Davide Pisani require an excessive amount of ad hoc expla- 23 Abstract | The origin of the eukaryotic cell, which is known as eukaryogenesis, has nation . In addition, as it has been found that amitochondriate eukaryotes, such as puzzled scientists for more than 100 years, and many hypotheses have been microsporidia24 and Giardia spp.25, are not proposed. Recent analyses of new data enable the safe elimination of some of primitively amitochondriate but are instead these hypotheses, whereas support for other hypotheses has increased. In this derived from mitochondrion-bearing ances- Opinion article, we evaluate the available theories for their compatibility with tors, the evidence suggests that acquisition empirical observations and conclude that cellular life consists of two primary, of the mitochondrion occurred early in eukaryotic evolution and certainly predates paraphyletic prokaryotic groups and one secondary, monophyletic group that has the origin of all known extant eukaryotes. symbiogenic origins — the eukaryotes. The details of the process of mitochon- drial acquisition are still debated. Much of In 1905, Konstantin Mereschkowski pos- bioenergetics, and modern cell biology and our understanding of the nature of life on tulated a symbiotic origin of plastids and biochemistry — each of which has contrib- Earth and the deepest philosophical rami- animal cells1, and in 1923, Ivan Wallin argued uted important and surprisingly congruent fications of this knowledge depend almost for a bacterial origin of the mitochondrion2. insights relating to this argument. It is the entirely on a precise understanding of the Since then, dozens of scenarios have been put consilience of these lines of evidence that origin of the mitochondrion4,14,22,26. One sce- forward to explain eukaryogenesis3–10. How leads us to conclude that eukaryotes are nario that is commonly seen in textbooks27 then should the different lines of evidence be not a primary lineage of life; rather, they describes Eukaryota as a lineage that sepa- viewed and how should their contributions are a relatively late innovation, are perhaps rated from the Archaebacteria before the to the arguments be weighted? younger than any of the two prokaryotic diversification of the Archaebacteria. In this Although many readers will be familiar groups and emerged from both of them. scenario, mitochondrial origins merely cor- with Karl Popper11, who advocated falsifi- Indeed, the ‘eukaryotes-late’ hypotheses respond to the introgression28 of a symbiont ability — that is, generating, testing and imply that there was a merger between an into an otherwise well-defined eukaryotic rejecting hypotheses — as the framework for archaebacterium and a eubacterium. lineage. This is known as the three‑domains generating knowledge, the framework by A recent report focusing on the evidence hypothesis27 (FIG. 1a). The three‑domains tree which we understand evolution to be a that supports a paraphyletic organization of recognizes Eubacteria, Archaebacteria and strong theory is that of consilience12. Con- the Archaebacteria13 has indicated that life is Eukaryota as three primary, monophyletic silience is said to be the ‘jumping together’ divided into two domains. In this Opinion lineages of ancient origins. The rooting of of facts or, in other words, the analysis of article, we explore the evidence for eukaryotic this tree, which was achieved using deeply whether there is agreement across different origins for all parts of the eukaryotic cell. diverging paralogues29, identified Eukaryota classes of evidence, thereby amounting to as the sister lineage to the Archaebacteria. a single unifying theory12. For example, Background: the proposed models An alternative rooting of the three‑domains evolution is a strong theory because there is The origin of eukaryotes is intimately inter- tree places the Eukaryota as the sister line- consilience between empirical observations twined with the study of endosymbiosis, age to a monophyletic prokaryotic group from genetics, palaeontology, chemistry, particularly with the origin of the mitochon- (which consists of the Archaebacteria and physics and behaviour, and together, these drion. Various endosymbiotic hypotheses the Eubacteria)5,30. This is known as the observations support an overall theory of for eukaryogenesis have been suggested, ‘eukaryotes-early’ hypothesis (FIG. 1b). In this evolution. and specific prokaryotic groups have scenario, an ancient complex eukaryotic cell In this Opinion article, we argue that been proposed as the sister groups of the underwent various reduction events to give hypothesis testing and inductive reasoning mitochondrion and the plastid4,7,8,14–17. The rise to prokaryotes5; no recent phylogenetic are consilient with a symbiogenic hypothesis origin of the mitochondrion is key to dis- analysis has provided convincing support for the origin of the Eukaryota. We address tinguishing between alternative hypotheses for this hypothesis. Other alternatives to the eukaryogenesis from four perspectives — regarding the origins of eukaryotes. Both three‑domains tree include a phagotrophic molecular phylogenetics, palaeontology, endosymbiotic4,14 and autogenous18,19 models hypothesis18, hypotheses that suggest an NATURE REVIEWS | MICROBIOLOGY ADVANCE ONLINE PUBLICATION | 1 © 2014 Macmillan Publishers Limited. All rights reserved PERSPECTIVES a Three-domains Eubacteria Other autogenous theories include the the mitochondrion or identical to it. In its hypothesis gradual evolution of eukaryotes from within original definition36, Eocyte simply referred the Archaebacteria32 or from the Eubacteria, to those organisms that are a sister group to Archaebacteria with some lateral gene transfer (LGT) from the Eukaryota within the Archaebacteria. the Archaebacteria33. The ring of life hypothesis argues that the Eukaryota Current, viable alternatives to autoge- Eukaryota emerged from within the Archae- neous models are represented by a set of bacteria8,9,34,37 at the same time as from hypotheses in which the eukaryotic lineage within the Eubacteria and that the Eocytes b Eukaryotes-early was established as a consequence of a are the archaebacterial sister group of the hypothesis Eukaryota merger in which two (or more) prokaryotes Eukaryota. either fused or entered a process of sym- Regardless of the placement of the root biosis7–9,15,20,21,34,35. These hypotheses differ of life, whether it is within the Eubacteria38 Archaebacteria in the number of mergers they assume, the or between the Eubacteria and Archaebacte- phylogenetic affinities of the mergers and ria29,39, the ring of life and the three‑domains Eubacteria the order in which the mergers occurred. tree are mutually incompatible. Indeed, the Nevertheless, they all imply that the Eukary­ ring of life type of model has a profound ota are not a primary lineage of life, and implication for how we view life, as it sug- c Eocyte hypothesis hence — in contrast to the three‑domains gests that the Eukaryota are not a primary Eubacteria hypothesis — they do not entail the existence lineage but are a secondary lineage of life of a proto-eukaryotic lineage as old as the and that the Archaebacteria and Eubacteria Archaebacteria. are not monophyletic (FIG. 2). The first step Other Archaebacteria It is important to note that not all towards understanding the origins of eukary­ Eukaryota hypotheses that propose the existence of otes is therefore to clarify whether the cur- Eocytes only two primary lineages of life are equally rent evidence supports the Eocyte–eukaryote well supported. Although many homologues grouping, which is compatible with the ring are shared by Eukaryota and Archaebacteria, of life, or the three‑domains grouping, which d Ring of life hypothesis Eubacteria the observed contribution to eukaryotic is not. genomes from specifically hydrogen- dependent archaebacteria is limited, which Evidence from phylogenetic analyses Eukaryota weakens support for the hydrogen hypoth- The phylogenetic relationships of eukaryotes esis20 and for sulphur-syntrophy hypotheses21. have been analysed using both genome-scale Eocytes 3,8,39 Other Furthermore, the contributions from Delta­ data sets and smaller sets of genes (vary- 7 15,35 Archaebacteria proteobacteria and Spirochaetes are not ing from one to approximately 85 genes, significant in number17 and are probably and often encoding ribosomal proteins) Figure 1 | Competing scenarios for the origin limited to individual LGTs. This effectively that are assumed to be ‘genealogy-defining’ of the eukaryotesNature and the Reviews highest-level | Microbiology struc- argues against the serial endosymbiotic (REFS 27,37,40,41). Woese originally pro- ture for describing the diversity of cellular 15,35 life. a | The ‘three‑domains’ phylogenetic tree, theory (SET) of Margulis and the syn- posed ribosomal RNA genes to be the ideal 27 which is also known as the three‑domains tree of trophy hypothesis of López–García and
Load more

Recommended publications
  • Novel Insights Into the Thaumarchaeota in the Deepest Oceans: Their Metabolism and Potential Adaptation Mechanisms
    Zhong et al. Microbiome (2020) 8:78 https://doi.org/10.1186/s40168-020-00849-2 RESEARCH Open Access Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms Haohui Zhong1,2, Laura Lehtovirta-Morley3, Jiwen Liu1,2, Yanfen Zheng1, Heyu Lin1, Delei Song1, Jonathan D. Todd3, Jiwei Tian4 and Xiao-Hua Zhang1,2,5* Abstract Background: Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans—the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the “shallower” deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water. Results: In this study, metagenomic data were obtained from 0–10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1000–4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+ and Na+ respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition.
    [Show full text]
  • Origin and Evolution of Eukaryotic Compartmentalization
    TESI DOCTORAL UPF 2016 Origin and evolution of eukaryotic compartmentalization Alexandros Pittis Director Dr. Toni Gabaldon´ Comparative Genomics Group Bioinformatics and Genomics Department Centre for Genomic Regulation (CRG) To my father Stavros for the PhD he never did Acknowledgments Looking back at the years of my PhD in the Comparative Genomics group at CRG, I feel it was equally a process of scientific, as well as personal development. All this time I was very privileged to be surrounded by people that offered me their generous support in both fronts. And they were available in the very moments that I was fighting more myself than the unsolvable (anyway) comparative genomics puzzles. I hope that in the future I will have many times the chance to express them my appreciation, way beyond these few words. First, to Toni, my supervisor, for all his support, and patience, and confidence, and respect, especially at the moments that things did not seem that promising. He offered me freedom, to try, to think, to fail, to learn, to achieve that few enjoy during their PhD, and I am very thankful to him. Then, to my good friends and colleagues, those that I found in the group already, and others that joined after me. A very special thanks to Marinita and Jaime, for all their valuable time, and guidance and paradigm, which nevertheless I never managed to follow. They have both marked my phylogenomics path so far and I cannot escape. To Les and Salvi, my fellow students and pals at the time for all that we shared; to Gab and Fran and Dam, for
    [Show full text]
  • Radical Views of the Tree of Life
    Environmental Microbiology (2009) doi:10.1111/j.1462-2920.2009.01895.x Genomics update Radical views of the Tree of Life Howard Ochman* been posited over the years (Embley and Martin, 2006; Department of Biochemistry and Molecular Biophysics, Poole and Penny, 2007). University of Arizona, Tucson, Arizona 85718, USA. To examine the origin of the eukaryotes, Pisani et al. (2007) applied a supertree approach to each of three The tripartite division of cellular organisms into three large overlapping data sets containing either 0, 8 or 21 domains – the Bacteria, the Archaea and the Eukarya – eukaryotic genomes, in order to monitor the effects of has become so ingrained that most of us have all but taxon sampling on the resulting branching orders. Super- forgotten (or did not even know) that the ancestry and trees are phylogenies that are assembled by merging sets relationships among these ancient lineages are far from of more limited trees, each based on a gene that is not settled. The most widely accepted view, which emerged necessarily present in all taxa. Their results resolved bac- primarily from analyses of anciently duplicated genes teria and archaea as separate groups, but favour a chi- (Gogarten et al., 1989; Iwabe et al., 1989), places Bacte- meric origin of eukaryotes, as the majority of eukaryotic ria as the basal lineage and distinct from the common genes with prokaryotic homologues derive from multiple ancestor of archaea and eukaryotes. Accordingly, these symbioses. These findings help explain how different studies frame the Archaea, despite their appellation, as genes originated and why particular genes show distinct archaic but not primordial, and the three domains are phylogenetic histories, but they do not ascertain whether each viewed as separate lineages, with archaea and the cellular lineage leading to eukaryotes – i.e.
    [Show full text]
  • Archaea and the Origin of Eukaryotes
    REVIEWS Archaea and the origin of eukaryotes Laura Eme, Anja Spang, Jonathan Lombard, Courtney W. Stairs and Thijs J. G. Ettema Abstract | Woese and Fox’s 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features. Although it has been generally accepted for some time that mitochondria descend from endosymbiotic alphaproteobacteria, the precise evolutionary relationship between eukaryotes and archaea has continued to be a subject of debate. In this Review, we outline a brief history of the changing shape of the tree of life and examine how the recent discovery of a myriad of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes. Furthermore, we revisit central questions regarding the process of eukaryogenesis and discuss what can currently be inferred about the evolutionary transition from the first to the last eukaryotic common ancestor. Sister groups Two descendants that split The pioneering work by Carl Woese and colleagues In this Review, we discuss how culture- independent from the same node; the revealed that all cellular life could be divided into three genomics has transformed our understanding of descendants are each other’s major evolutionary lines (also called domains): the archaeal diversity and how this has influenced our closest relative.
    [Show full text]
  • Downloaded from the NCBI FTP Site [37]
    Life 2015, 5, 818-840; doi:10.3390/life5010818 OPEN ACCESS life ISSN 2075-1729 www.mdpi.com/journal/life Article Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales Kira S. Makarova *, Yuri I. Wolf and Eugene V. Koonin National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA; E-Mails: [email protected] (Y.I.W.); [email protected] (E.V.K.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-301-435-5913; Fax: +1-301-435-7793. Academic Editors: Hans-Peter Klenk, Michael W. W. Adams and Roger A. Garrett Received: 12 January 2015 / Accepted: 28 February 2015 / Published: 10 March 2015 Abstract: With the continuously accelerating genome sequencing from diverse groups of archaea and bacteria, accurate identification of gene orthology and availability of readily expandable clusters of orthologous genes are essential for the functional annotation of new genomes. We report an update of the collection of archaeal Clusters of Orthologous Genes (arCOGs) to cover, on average, 91% of the protein-coding genes in 168 archaeal genomes. The new arCOGs were constructed using refined algorithms for orthology identification combined with extensive manual curation, including incorporation of the results of several completed and ongoing research projects in archaeal genomics. A new level of classification is introduced, superclusters that unit two or more arCOGs and more completely reflect gene family evolution than individual, disconnected arCOGs. Assessment of the current archaeal genome annotation in public databases indicates that consistent use of arCOGs can significantly improve the annotation quality.
    [Show full text]
  • Archezoa and the Origin of Eukaryotes Patrick J
    Problems and paradigms A kingdom’s progress: Archezoa and the origin of eukaryotes Patrick J. Keeling* Summary The taxon Archezoa was proposed to unite a group of very odd eukaryotes that lack many of the characteristics classically associated with nucleated cells, in particular the mitochondrion. The hypothesis was that these cells diverged from other eukaryotes before these characters ever evolved, and therefore they repre- sent ancient and primitive eukaryotic lineages. The kingdom comprised four groups: Metamonada, Microsporidia, Parabasalia, and Archamoebae. Until re- cently, molecular work supported their primitive status, as they consistently branched deeply in eukaryotic phylogenetic trees. However, evidence has now emerged that many Archezoa contain genes derived from the mitochondrial symbiont, revealing that they actually evolved after the mitochondrial symbiosis. In addition, some Archezoa have now been shown to have evolved more recently than previously believed, especially the Microsporidia for which considerable evidence now indicates a relationship with fungi. In summary, the mitochondrial symbiosis now appears to predate all Archezoa and perhaps all presently known eukaryotes. BioEssays 20:87–95, 1998. ௠ 1998 John Wiley & Sons, Inc. INTRODUCTION cyanobacteria and they also lack flagella and basal bodies Prior to the popularization of the endosymbiotic theory, it was (for discussion see Ref. 1). However, according to the widely believed that the evolutionary link between prokary- endosymbiotic theory, the reason photosynthesis is so simi- otes and eukaryotes was the presence of photosynthesis in lar in cyanobacteria and photosynthetic eukaryotes is that cyanobacteria and algae. The biochemistry of oxygenic the plastids of plant and algal cells are derived from a photosynthesis was considered too complicated and too cyanobacterial symbiont.
    [Show full text]
  • Structure and Function of Archaeal Histones
    REVIEW Structure and function of archaeal histones Bram Henneman1, Clara van Emmerik1¤, Hugo van Ingen1¤, Remus T. Dame1,2* 1 Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands, 2 Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands ¤ Current address: Bijvoet Center for Biomolecular Research, Utrecht University, the Netherlands * [email protected] Abstract The genomes of all organisms throughout the tree of life are compacted and organized in chromatin by association of chromatin proteins. Eukaryotic genomes encode histones, which are assembled on the genome into octamers, yielding nucleosomes. Post-translational modi- fications of the histones, which occur mostly on their N-terminal tails, define the functional a1111111111 state of chromatin. Like eukaryotes, most archaeal genomes encode histones, which are a1111111111 believed to be involved in the compaction and organization of their genomes. Instead of dis- a1111111111 crete multimers, in vivo data suggest assembly of ªnucleosomesº of variable size, consisting a1111111111 of multiples of dimers, which are able to induce repression of transcription. Based on these a1111111111 data and a model derived from X-ray crystallography, it was recently proposed that archaeal histones assemble on DNA into ªendlessº hypernucleosomes. In this review, we discuss the amino acid determinants of hypernucleosome formation and highlight differences with the canonical eukaryotic octamer. We identify archaeal histones differing from the consensus, OPEN ACCESS which are expected to be unable to assemble into hypernucleosomes. Finally, we identify Citation: Henneman B, van Emmerik C, van Ingen atypical archaeal histones with short N- or C-terminal extensions and C-terminal tails similar H, Dame RT (2018) Structure and function of to the tails of eukaryotic histones, which are subject to post-translational modification.
    [Show full text]
  • Evolution of Replicative DNA Polymerases in Archaea and Their Contributions to the Eukaryotic Replication Machinery Kira Makarova, Mart Krupovic, Eugene Koonin
    Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery Kira Makarova, Mart Krupovic, Eugene Koonin To cite this version: Kira Makarova, Mart Krupovic, Eugene Koonin. Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery. Frontiers in Microbiology, Frontiers Media, 2014, 5, pp.354. 10.3389/fmicb.2014.00354. pasteur-01977396 HAL Id: pasteur-01977396 https://hal-pasteur.archives-ouvertes.fr/pasteur-01977396 Submitted on 10 Jan 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License REVIEW ARTICLE published: 21 July 2014 doi: 10.3389/fmicb.2014.00354 Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery Kira S. Makarova 1, Mart Krupovic 2 and Eugene V. Koonin 1* 1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA 2 Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, France Edited by: The elaborate eukaryotic DNA replication machinery evolved from the archaeal ancestors Zvi Kelman, University of Maryland, that themselves show considerable complexity.
    [Show full text]
  • The Gospel According to LUCA (The Last Universal Common Ancestor)
    UC San Diego UC San Diego Electronic Theses and Dissertations Title The gospel according to LUCA (the last universal common ancestor) Permalink https://escholarship.org/uc/item/6pw6n8xp Author Valas, Ruben Eliezer Meyer Publication Date 2010 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO The gospel according to LUCA (the last universal common ancestor) A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics by Ruben Eliezer Meyer Valas Committee in charge: Professor Philip E. Bourne, Chair Professor William F. Loomis, Co-Chair Professor Russell F. Doolittle Professor Richard D. Norris Professor Milton H. Saier Jr. 2010 The Dissertation of Ruben Eliezer Meyer Valas is approved, and it is acceptable in quality and form for publication on microfilm and electronically: ______________________________________________________________________ ______________________________________________________________________ ______________________________________________________________________ ______________________________________________________________________ Co-chair ______________________________________________________________________ Chair University of California, San Diego 2010 iii DEDICATION I dedicate this work to Alexander “Sasha” Shulgin. Sasha is probably the wisest person I’ve met. He refuses to allow anything other than his own imagination dictates the rules of what is
    [Show full text]
  • Evaluating Evidence from Fossils and Molecular Clocks
    Downloaded from http://cshperspectives.cshlp.org/ on August 1, 2014 - Published by Cold Spring Harbor Laboratory Press On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks Laura Eme, Susan C. Sharpe, Matthew W. Brown and Andrew J. Roger Cold Spring Harb Perspect Biol 2014; doi: 10.1101/cshperspect.a016139 Subject Collection The Origin and Evolution of Eukaryotes On the Age of Eukaryotes: Evaluating Evidence Protein Targeting and Transport as a Necessary from Fossils and Molecular Clocks Consequence of Increased Cellular Complexity Laura Eme, Susan C. Sharpe, Matthew W. Brown, Maik S. Sommer and Enrico Schleiff et al. The Persistent Contributions of RNA to Eukaryotic Origins: How and When Was the Eukaryotic Gen(om)e Architecture and Cellular Mitochondrion Acquired? Function Anthony M. Poole and Simonetta Gribaldo Jürgen Brosius The Archaeal Legacy of Eukaryotes: A Origin of Spliceosomal Introns and Alternative Phylogenomic Perspective Splicing Lionel Guy, Jimmy H. Saw and Thijs J.G. Ettema Manuel Irimia and Scott William Roy How Natural a Kind Is ''Eukaryote?'' Protein and DNA Modifications: Evolutionary W. Ford Doolittle Imprints of Bacterial Biochemical Diversification and Geochemistry on the Provenance of Eukaryotic Epigenetics L. Aravind, A. Maxwell Burroughs, Dapeng Zhang, et al. What Was the Real Contribution of The Eukaryotic Tree of Life from a Global Endosymbionts to the Eukaryotic Nucleus? Phylogenomic Perspective Insights from Photosynthetic Eukaryotes Fabien Burki David Moreira and Philippe Deschamps Bioenergetic Constraints on the Evolution of The Dispersed Archaeal Eukaryome and the Complex Life Complex Archaeal Ancestor of Eukaryotes Nick Lane Eugene V. Koonin and Natalya Yutin Origin and Evolution of Plastids and Origins of Eukaryotic Sexual Reproduction Photosynthesis in Eukaryotes Ursula Goodenough and Joseph Heitman Geoffrey I.
    [Show full text]
  • With Inferred Horizontal Gene Transfers and Co-Occurrence Networks
    RESEARCH ARTICLE Deciphering Symbiotic Interactions of “Candidatus Aenigmarchaeota” with Inferred Horizontal Gene Transfers and Co-occurrence Networks Yu-Xian Li,a Yang-Zhi Rao,a Yan-Ling Qi,a Yan-Ni Qu,a Ya-Ting Chen,a Jian-Yu Jiao,a Wen-Sheng Shu,b Hongchen Jiang,c Brian P. Hedlund,d,e Zheng-Shuang Hua,f Wen-Jun Lia,g aState Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China bSchool of Life Sciences, South China Normal University, Guangzhou, People’s Republic of China cState Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People’s Republic of China dSchool of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA eNevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, Nevada, USA fDepartment of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People’s Republic of China gState Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, People’s Republic of China Yu-Xian Li and Yang-Zhi Rao contributed equally to this work. Author order was determined based on alphabetical order of authors’ last names. ABSTRACT “Candidatus Aenigmarchaeota” (“Ca. Aenigmarchaeota”) represents one of the earliest proposed evolutionary branches within the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, their ecological roles and potential host-symbiont interac- tions are still poorly understood. Here, eight metagenome-assembled genomes (MAGs) were reconstructed from hot spring ecosystems, and further in-depth com- parative and evolutionary genomic analyses were conducted on these MAGs and other genomes downloaded from public databases.
    [Show full text]
  • A Scientific Literature Review Comic by Lilja Strang
    A scientific literature review comic by Lilja Strang In Norse mythology all of life is contained within nine realms. These realms are connected by Yggdrasil, or the World Tree. A similar concept exists in biology. It’s called the tree of life and it shows the evolutionary connections between all life on earth. These two trees have more in common than most people think. To begin our story, think back to your earliest biology class. You probably saw either the 1959 tree of life, organized into Carl Woese—1990 either 5 kingdoms, or the 1990 tree with 3 domains. The 5 kingdoms tree compared life on the basis of how things looked. Microscopic organisms were too small to see easily, and were excluded. Whittaker’s 5 Kingdom Tree (1959) Woese’s 3 Domain Tree (1990) Plantae Fungi Animalia Bacteria Archaea Eucarya Carl Woese’s tree Protista was based on the best DNA evidence Monera of his time. Here, the microscopic Bacteria and Archaea were front and center. In fact, Woese realized that the Archaea were Níðhöggr (Nidhogg) is the dragon that gnaws at the roots of Yggdrasil. very special. In the 1990s, Archaea were thought to only be extremophiles living in very Methanosarcina mazeii produces the methane gas in cow farts. hot/cold, acidic/basic, or There are no known methane otherwise unusual habitats. producing Bacteria, only Archaea. Sulfolobus live in the Geysers of Yellowstone at temperatures of 40–55°C (104–131°F). Methane producers are found in humans too. Ferroplasma acidiphilum live They’re similar to those in the toxic byproducts of found in cows.
    [Show full text]