Evaluating Evidence from Fossils and Molecular Clocks

Total Page:16

File Type:pdf, Size:1020Kb

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. McFadden For additional articles in this collection, see http://cshperspectives.cshlp.org/cgi/collection/ Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved Downloaded from http://cshperspectives.cshlp.org/ on August 1, 2014 - Published by Cold Spring Harbor Laboratory Press The Pre-Endosymbiont Hypothesis: A New The Impact of History on Our Perception of Perspective on the Origin and Evolution of Evolutionary Events: Endosymbiosis and the Mitochondria Origin of Eukaryotic Complexity Michael W. Gray Patrick J. Keeling For additional articles in this collection, see http://cshperspectives.cshlp.org/cgi/collection/ Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved 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. Brown1, and Andrew J. Roger Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax B3H 4R2, Canada Correspondence: [email protected] Our understanding of the phylogenetic relationships among eukaryotic lineages has im- proved dramatically over the few past decades thanks to the development of sophisticated phylogenetic methods and models of evolution, in combination with the increasing avail- ability of sequence data for a variety of eukaryotic lineages. Concurrently, efforts have been made to infer the age of major evolutionary events along the tree of eukaryotes using fossil- calibrated molecular clock-based methods. Here, we review the progress and pitfalls in estimating the age of the last eukaryotic common ancestor (LECA) and major lineages. After reviewing previous attempts to date deep eukaryote divergences, we present the results of a Bayesian relaxed-molecular clock analysis of a large dataset (159 proteins, 85 taxa) using 19 fossil calibrations. We show that for major eukaryote groups estimated dates of divergence, as well as their credible intervals, are heavily influenced by the relaxed molec- ular clock models and methods used, and by the nature and treatment of fossil calibrations. Whereas the estimated age of LECA varied widely, ranging from 1007 (943–1102) Ma to 1898 (1655–2094) Ma, all analyses suggested that the eukaryotic supergroups subsequently diverged rapidly (i.e., within 300 Ma of LECA). The extreme variability of these and previ- ously published analyses preclude definitive conclusions regarding the age of major eukary- ote clades at this time. As more reliable fossil data on eukaryotes from the Proterozoic become available and improvements are made in relaxed molecular clock modeling, we may be able to date the age of extant eukaryotes more precisely. ur conception of the tree of eukaryotes has came clear that the deep structure of the rRNA Ochanged dramatically over the last few tree was the result of a methodological artifact decades. In the 1980s and early 1990s, prevailing known as long branch attraction (LBA) (Budin views were based on small subunit ribosomal and Philippe 1998; Roger et al. 1999; Philippe RNA (SSU rRNA) gene phylogenies (e.g., Sogin et al. 2000a,b). Analyses based on multiple pro- 1991). However, as multiple protein-coding tein genes instead hinted at the existence of gene datasets were developed and more sophis- higher-level eukaryotic “supergroups” that en- ticated phylogenetic methods were used, it be- compassed both protistan and multicellular eu- 1Current address: Department of Biological Sciences, Mississippi State University, Mississippi State, MS. Editors: Patrick J. Keeling and Eugene V. Koonin Additional Perspectives on The Origin and Evolution of Eukaryotes available at www.cshperspectives.org Copyright # 2014 Cold Spring Harbor Laboratory Press; all rights reserved; doi: 10.1101/cshperspect.a016139 Cite this article as Cold Spring Harb Perspect Biol 2014;6:a016139 1 Downloaded from http://cshperspectives.cshlp.org/ on August 1, 2014 - Published by Cold Spring Harbor Laboratory Press L. Eme et al. karyotic lineages (Baldauf et al. 2000). More THE EUKARYOTIC TREE OF LIFE recently, a better understanding of protistan ultrastructural diversity and the development Estimates of divergence dates from molecular of phylogenomic approaches have refined this clock analyses are only meaningful if the phy- picture and further delineated these groups (see logeny on which they are based is correct. How- also Fig. 1) (Bapteste et al. 2002; Burki et al. ever, recovering deep phylogenetic relationships 2007; Hampl et al. 2009; Brown et al. 2012; among eukaryotes has proven to be an extreme- Zhao et al. 2012). ly challenging task. As our understanding of eukaryote phylog- The most recent conceptions of the eukary- eny improved, fossil-calibrated molecularclock- otic tree of life feature five or six “supergroups” based methods were beginning to be applied to (Keeling et al. 2005; Roger and Simpson 2009; date the major diversification events in this do- Burki 2014) including Opisthokonta, Amoebo- main (Hedges et al. 2001; Douzery et al. 2004; zoa, Excavata, the SAR group, Archaeplastida, Hedges and Kumar 2004; Berney and Pawlowski and Hacrobia (Haptophyta and Cryptophyta). 2006; Parfrey et al. 2011). Molecular clock anal- Whereas phylogenomic analyses robustly re- yses were first introduced by Zuckerkandl and cover the monophyly of Opisthokonta, Amoe- Pauling (1965). Theyshowed that the differences bozoa and SAR, the phylogenetic coherence of between homologous proteins of different spe- Excavata, Archaeplastida, and Hacrobia is less cies are approximately proportional to their di- certain (see also Fig. 1) (Burki et al. 2008, 2012; vergence time. Since then, sophisticated RMC Hampl et al. 2009; Parfrey et al. 2010; Brown methods have been developed that combine fos- et al. 2012; Zhao et al. 2012; Burki 2014). sil data with molecular phylogenies for the in- Another challenge inherent to dating an- ference of divergence times. However, attempts cient events in eukaryotic evolution is the cur- to estimate the age of deep divisions within rent uncertainty regarding the location of the eukaryotes using these methods have yielded root (Stechmann and Cavalier-Smith 2002, vastly different estimates (e.g., see Douzery et al. 2003a,b; Cavalier-Smith 2010; Derelle and 2004 vs. Hedges et al. 2004). These discrepan- Lang 2012; Katz et al. 2012). Tackling this ques- cies can be explained by a myriad of sources of tion is made especially difficult by the absence variability and error including (1) the assumed of closely related outgroups to eukaryotes. The phylogeny of eukaryotes, (2) the sparse fossil large phylogenetic distance between sequences record of protists and other organisms lacking from eukaryotes and their archaeal or bacterial hard structures for fossilization, (3) how fossil orthologs makes their use as outgroups highly constraints are applied to phylogenetic trees, prone to phylogenetic artefacts like LBA (Fel- (4) methods and models used in RMC analysis, senstein 1978; Roger and Hug 2006). Conse- and (5) the selection of taxa and genes included. quently, various alternative methods have been Here, we review the progress and pitfalls in used in the last decade, yielding different results estimating the age of the last eukaryotic com- regarding the placement of the root; between mon ancestor (LECA) and supergroups using Amorphea (or “unikonts”) and all othereukary- molecular clock-based analyses. We first discuss otes (i.e., “bikonts”) (Richards and Cavalier- recent progress in our understanding
Recommended publications
  • Download This Publication (PDF File)
    PUBLIC LIBRARY of SCIENCE | plosgenetics.org | ISSN 1553-7390 | Volume 2 | Issue 12 | DECEMBER 2006 GENETICS PUBLIC LIBRARY of SCIENCE www.plosgenetics.org Volume 2 | Issue 12 | DECEMBER 2006 Interview Review Knight in Common Armor: 1949 Unraveling the Genetics 1956 An Interview with Sir John Sulston e225 of Human Obesity e188 Jane Gitschier David M. Mutch, Karine Clément Research Articles Natural Variants of AtHKT1 1964 The Complete Genome 2039 Enhance Na+ Accumulation e210 Sequence and Comparative e206 in Two Wild Populations of Genome Analysis of the High Arabidopsis Pathogenicity Yersinia Ana Rus, Ivan Baxter, enterocolitica Strain 8081 Balasubramaniam Muthukumar, Nicholas R. Thomson, Sarah Jeff Gustin, Brett Lahner, Elena Howard, Brendan W. Wren, Yakubova, David E. Salt Matthew T. G. Holden, Lisa Crossman, Gregory L. Challis, About the Cover Drosophila SPF45: A Bifunctional 1974 Carol Churcher, Karen The jigsaw image of representatives Protein with Roles in Both e178 Mungall, Karen Brooks, Tracey of various lines of eukaryote evolution Splicing and DNA Repair Chillingworth, Theresa Feltwell, refl ects the current lack of consensus as Ahmad Sami Chaouki, Helen K. Zahra Abdellah, Heidi Hauser, to how the major branches of eukaryotes Salz Kay Jagels, Mark Maddison, fi t together. The illustrations from upper Sharon Moule, Mandy Sanders, left to bottom right are as follows: a single Mammalian Small Nucleolar 1984 Sally Whitehead, Michael A. scale from the surface of Umbellosphaera; RNAs Are Mobile Genetic e205 Quail, Gordon Dougan, Julian Amoeba, the large amoeboid organism Elements Parkhill, Michael B. Prentice used as an introduction to protists for Michel J. Weber many school children; Euglena, the iconic Low Levels of Genetic 2052 fl agellate that is often used to challenge Soft Sweeps III: The Signature 1998 Divergence across e215 ideas of plants (Euglena has chloroplasts) of Positive Selection from e186 Geographically and and animals (Euglena moves); Stentor, Recurrent Mutation Linguistically Diverse one of the larger ciliates; Cacatua, the Pleuni S.
    [Show full text]
  • Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life
    Smith ScholarWorks Biological Sciences: Faculty Publications Biological Sciences 10-1-2010 Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life Laura Wegener Parfrey University of Massachusetts Amherst Jessica Grant Smith College Yonas I. Tekle Smith College Erica Lasek-Nesselquist Marine Biological Laboratory Hilary G. Morrison Marine Biological Laboratory See next page for additional authors Follow this and additional works at: https://scholarworks.smith.edu/bio_facpubs Part of the Biology Commons Recommended Citation Parfrey, Laura Wegener; Grant, Jessica; Tekle, Yonas I.; Lasek-Nesselquist, Erica; Morrison, Hilary G.; Sogin, Mitchell L.; Patterson, David J.; and Katz, Laura A., "Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life" (2010). Biological Sciences: Faculty Publications, Smith College, Northampton, MA. https://scholarworks.smith.edu/bio_facpubs/126 This Article has been accepted for inclusion in Biological Sciences: Faculty Publications by an authorized administrator of Smith ScholarWorks. For more information, please contact [email protected] Authors Laura Wegener Parfrey, Jessica Grant, Yonas I. Tekle, Erica Lasek-Nesselquist, Hilary G. Morrison, Mitchell L. Sogin, David J. Patterson, and Laura A. Katz This article is available at Smith ScholarWorks: https://scholarworks.smith.edu/bio_facpubs/126 Syst. Biol. 59(5):518–533, 2010 c The Author(s) 2010. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: [email protected] DOI:10.1093/sysbio/syq037 Advance Access publication on July 23, 2010 Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life LAURA WEGENER PARFREY1,JESSICA GRANT2,YONAS I. TEKLE2,6,ERICA LASEK-NESSELQUIST3,4, 3 3 5 1,2, HILARY G.
    [Show full text]
  • Identification of a Novel Fused Gene Family Implicates Convergent
    Chen et al. BMC Genomics (2018) 19:306 https://doi.org/10.1186/s12864-018-4685-y RESEARCH ARTICLE Open Access Identification of a novel fused gene family implicates convergent evolution in eukaryotic calcium signaling Fei Chen1,2,3, Liangsheng Zhang1, Zhenguo Lin4 and Zong-Ming Max Cheng2,3* Abstract Background: Both calcium signals and protein phosphorylation responses are universal signals in eukaryotic cell signaling. Currently three pathways have been characterized in different eukaryotes converting the Ca2+ signals to the protein phosphorylation responses. All these pathways have based mostly on studies in plants and animals. Results: Based on the exploration of genomes and transcriptomes from all the six eukaryotic supergroups, we report here in Metakinetoplastina protists a novel gene family. This family, with a proposed name SCAMK,comprisesSnRK3 fused calmodulin-like III kinase genes and was likely evolved through the insertion of a calmodulin-like3 gene into an SnRK3 gene by unequal crossover of homologous chromosomes in meiosis cell. Its origin dated back to the time intersection at least 450 million-year-ago when Excavata parasites, Vertebrata hosts, and Insecta vectors evolved. We also analyzed SCAMK’s unique expression pattern and structure, and proposed it as one of the leading calcium signal conversion pathways in Excavata parasite. These characters made SCAMK gene as a potential drug target for treating human African trypanosomiasis. Conclusions: This report identified a novel gene fusion and dated its precise fusion time
    [Show full text]
  • New Horizons the Microbial Universe of the Global Ocean
    New Horizons The Microbial Universe of the Global Ocean BIGELOW LABORATORY FOR OCEAN SCIENCES 2012-13 ANNUAL REPORT BIGELOW LABORATORY FOR OCEAN SCIENCES • ANNUAL REPORT 2012–13 1 “Without global ocean color satellite data, humanity loses its capacity to take Earth’s pulse and to explore its unseen world. The fragility of the living Earth and its oceans has been noted by astronaut Sally Ride, who speaks of the changes in land, oceans, and atmosphere systems as witnessed from space, and the challenge that a changing climate presents to our beloved Earth. It is our duty to provide a long-term surveillance system for the Earth, not only to understand and monitor the Earth’s changing climate, but to enable the next generations of students to make new discoveries in our ocean gardens, as well as explore similar features on other planets.” —Dr. Charles S. Yentsch Bigelow Laboratory Founder 1927–2012 2 NEW HORIZONS: THE MICROBIAL UNIVERSE OF THE GLOBAL OCEAN Welcoming the Future A Message from the Chairman of the Board igelow Laboratory has just finished an exceptional and transformative period, a time that has witnessed the accomplishment of an array of Bprojects that will take the organization to new levels of achievement. The most obvious of these has been the completion of the $32 million Bigelow Ocean Science and Education Campus in East Boothbay. Shortly following the dedication of the new facilities in December, all of Bigelow Laboratory’s management, scientists, and staff were on board and operational on the new site, enabling a higher level of scientific and operational efficiency and effectiveness than ever before.
    [Show full text]
  • Multigene Eukaryote Phylogeny Reveals the Likely Protozoan Ancestors of Opis- Thokonts (Animals, Fungi, Choanozoans) and Amoebozoa
    Accepted Manuscript Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opis- thokonts (animals, fungi, choanozoans) and Amoebozoa Thomas Cavalier-Smith, Ema E. Chao, Elizabeth A. Snell, Cédric Berney, Anna Maria Fiore-Donno, Rhodri Lewis PII: S1055-7903(14)00279-6 DOI: http://dx.doi.org/10.1016/j.ympev.2014.08.012 Reference: YMPEV 4996 To appear in: Molecular Phylogenetics and Evolution Received Date: 24 January 2014 Revised Date: 2 August 2014 Accepted Date: 11 August 2014 Please cite this article as: Cavalier-Smith, T., Chao, E.E., Snell, E.A., Berney, C., Fiore-Donno, A.M., Lewis, R., Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa, Molecular Phylogenetics and Evolution (2014), doi: http://dx.doi.org/10.1016/ j.ympev.2014.08.012 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. 1 1 Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts 2 (animals, fungi, choanozoans) and Amoebozoa 3 4 Thomas Cavalier-Smith1, Ema E. Chao1, Elizabeth A. Snell1, Cédric Berney1,2, Anna Maria 5 Fiore-Donno1,3, and Rhodri Lewis1 6 7 1Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
    [Show full text]
  • Protist Phylogeny and the High-Level Classification of Protozoa
    Europ. J. Protistol. 39, 338–348 (2003) © Urban & Fischer Verlag http://www.urbanfischer.de/journals/ejp Protist phylogeny and the high-level classification of Protozoa Thomas Cavalier-Smith Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK; E-mail: [email protected] Received 1 September 2003; 29 September 2003. Accepted: 29 September 2003 Protist large-scale phylogeny is briefly reviewed and a revised higher classification of the kingdom Pro- tozoa into 11 phyla presented. Complementary gene fusions reveal a fundamental bifurcation among eu- karyotes between two major clades: the ancestrally uniciliate (often unicentriolar) unikonts and the an- cestrally biciliate bikonts, which undergo ciliary transformation by converting a younger anterior cilium into a dissimilar older posterior cilium. Unikonts comprise the ancestrally unikont protozoan phylum Amoebozoa and the opisthokonts (kingdom Animalia, phylum Choanozoa, their sisters or ancestors; and kingdom Fungi). They share a derived triple-gene fusion, absent from bikonts. Bikonts contrastingly share a derived gene fusion between dihydrofolate reductase and thymidylate synthase and include plants and all other protists, comprising the protozoan infrakingdoms Rhizaria [phyla Cercozoa and Re- taria (Radiozoa, Foraminifera)] and Excavata (phyla Loukozoa, Metamonada, Euglenozoa, Percolozoa), plus the kingdom Plantae [Viridaeplantae, Rhodophyta (sisters); Glaucophyta], the chromalveolate clade, and the protozoan phylum Apusozoa (Thecomonadea, Diphylleida). Chromalveolates comprise kingdom Chromista (Cryptista, Heterokonta, Haptophyta) and the protozoan infrakingdom Alveolata [phyla Cilio- phora and Miozoa (= Protalveolata, Dinozoa, Apicomplexa)], which diverged from a common ancestor that enslaved a red alga and evolved novel plastid protein-targeting machinery via the host rough ER and the enslaved algal plasma membrane (periplastid membrane).
    [Show full text]
  • Extensive Molecular Tinkering in the Evolution of the Membrane Attachment Mode of the Rheb Gtpase
    www.nature.com/scientificreports OPEN Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb Received: 14 December 2017 Accepted: 15 March 2018 GTPase Published: xx xx xxxx Kristína Záhonová1, Romana Petrželková1, Matus Valach 2, Euki Yazaki3, Denis V. Tikhonenkov4, Anzhelika Butenko1, Jan Janouškovec5, Štěpánka Hrdá6, Vladimír Klimeš1, Gertraud Burger 2, Yuji Inagaki7, Patrick J. Keeling8, Vladimír Hampl6, Pavel Flegontov1, Vyacheslav Yurchenko1 & Marek Eliáš1 Rheb is a conserved and widespread Ras-like GTPase involved in cell growth regulation mediated by the (m)TORC1 kinase complex and implicated in tumourigenesis in humans. Rheb function depends on its association with membranes via prenylated C-terminus, a mechanism shared with many other eukaryotic GTPases. Strikingly, our analysis of a phylogenetically rich sample of Rheb sequences revealed that in multiple lineages this canonical and ancestral membrane attachment mode has been variously altered. The modifcations include: (1) accretion to the N-terminus of two diferent phosphatidylinositol 3-phosphate-binding domains, PX in Cryptista (the fusion being the frst proposed synapomorphy of this clade), and FYVE in Euglenozoa and the related undescribed fagellate SRT308; (2) acquisition of lipidic modifcations of the N-terminal region, namely myristoylation and/ or S-palmitoylation in seven diferent protist lineages; (3) acquisition of S-palmitoylation in the hypervariable C-terminal region of Rheb in apusomonads, convergently to some other Ras family proteins; (4) replacement of the C-terminal prenylation motif with four transmembrane segments in a novel Rheb paralog in the SAR clade; (5) loss of an evident C-terminal membrane attachment mechanism in Tremellomycetes and some Rheb paralogs of Euglenozoa.
    [Show full text]
  • Phylogenomics Supports the Monophyly of the Cercozoa T ⁎ Nicholas A.T
    Molecular Phylogenetics and Evolution 130 (2019) 416–423 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Phylogenomics supports the monophyly of the Cercozoa T ⁎ Nicholas A.T. Irwina, , Denis V. Tikhonenkova,b, Elisabeth Hehenbergera,1, Alexander P. Mylnikovb, Fabien Burkia,2, Patrick J. Keelinga a Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada b Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia ARTICLE INFO ABSTRACT Keywords: The phylum Cercozoa consists of a diverse assemblage of amoeboid and flagellated protists that forms a major Cercozoa component of the supergroup, Rhizaria. However, despite its size and ubiquity, the phylogeny of the Cercozoa Rhizaria remains unclear as morphological variability between cercozoan species and ambiguity in molecular analyses, Phylogeny including phylogenomic approaches, have produced ambiguous results and raised doubts about the monophyly Phylogenomics of the group. Here we sought to resolve these ambiguities using a 161-gene phylogenetic dataset with data from Single-cell transcriptomics newly available genomes and deeply sequenced transcriptomes, including three new transcriptomes from Aurigamonas solis, Abollifer prolabens, and a novel species, Lapot gusevi n. gen. n. sp. Our phylogenomic analysis strongly supported a monophyletic Cercozoa, and approximately-unbiased tests rejected the paraphyletic topologies observed in previous studies. The transcriptome of L. gusevi represents the first transcriptomic data from the large and recently characterized Aquavolonidae-Treumulida-'Novel Clade 12′ group, and phyloge- nomics supported its position as sister to the cercozoan subphylum, Endomyxa. These results provide insights into the phylogeny of the Cercozoa and the Rhizaria as a whole.
    [Show full text]
  • Evolution of the Eukaryotic Membrane Trafficking System As Revealed
    Evolution of the eukaryotic membrane trafficking system as revealed by comparative genomic and phylogenetic analysis of adaptin, golgin, and SNARE proteins by Lael Dan Barlow A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Physiology, Cell, and Developmental Biology Department of Biological Sciences University of Alberta c Lael Dan Barlow, 2019 Abstract All eukaryotic cells possess a complex system of endomembranes that functions in traffick- ing molecular cargo within the cell, which is not observed in prokaryotic cells. This membrane trafficking system is fundamental to the cellular physiology of extant eukaryotes, and includes or- ganelles such as the endoplasmic reticulum, Golgi apparatus, and endosomes as well as the plasma membrane. The evolutionary history of this system offers an over-arching framework for research on membrane trafficking in the field of cell biology. However, the evolutionary origins of this system in the evolution from a prokaryotic ancestor to the most recent common ancestor of extant eukaryotes is a major evolutionary transition that remains poorly understood. A leading paradigm is described by the previously proposed Organelle Paralogy Hypothesis, which posits that coordi- nated duplication and divergence of genes encoding organelle-specific membrane trafficking pro- teins underlies a corresponding evolutionary history of organelle differentiation that produced the complex sets of membrane trafficking organelles found in extant eukaryotes. This thesis focuses
    [Show full text]
  • Protists – a Textbook Example for a Paraphyletic Taxon
    ARTICLE IN PRESS Organisms, Diversity & Evolution 7 (2007) 166–172 www.elsevier.de/ode Protists – A textbook example for a paraphyletic taxon$ Martin Schlegela,Ã, Norbert Hu¨lsmannb aInstitute for Biology II, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany bFree University of Berlin, Institute of Biology/Zoology, Working group Protozoology, Ko¨nigin-Luise-Straße 1-3, 14195 Berlin, Germany Received 7 September 2004; accepted 21 November 2006 Abstract Protists constitute a paraphyletic taxon since the latter is based on the plesiomorphic character of unicellularity and does not contain all descendants of the stem species. Multicellularity evolved several times independently in metazoans, higher fungi, heterokonts, red and green algae. Various hypotheses have been developed on the evolution and nature of the eukaryotic cell, considering the accumulating data on the chimeric nature of the eukaryote genome. Subsequent evolution of the protists was further complicated by primary, secondary, and even tertiary intertaxonic recombinations. However, multi-gene sequence comparisons and structural data point to a managable number of such events. Several putative monophyletic lineages and a gross picture of eukaryote phylogeny are emerging on the basis of those data. The Chromalveolata comprise Chromista and Alveolata (Dinoflagellata, Apicomplexa, Ciliophora, Perkinsozoa, and Haplospora). Major lineages of the former ‘amoebae’ group within the Heterolobosa, Cercozoa, and Amoebozoa. Cercozoa, including filose testate amoebae, chlorarachnids, and plasmodiophoreans seem to be affiliated with foraminiferans. Amoebozoa consistently form the sister group of the Opisthokonta (including fungi, and with choanoflagellates as sister group of metazoans). A clade of ‘plants’ comprises glaucocystophytes, red algae, green algae, and land vascular plants. The controversial debate on the root of the eukaryote tree has been accelerated by the interpretation of gene fusions as apomorphic characters.
    [Show full text]
  • Evolution: Revisiting the Root of the Eukaryote Tree
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Dispatch R165 cytokinesis and are enhanced by Rho 18. Yamada, T., Hikida, M., and Kurosaki, T. (2006). and RGA-4 in the germ line and in the early and suppressed by Rac. J. Cell Biol. 166, Regulation of cytokinesis by mgcRacGAP in B embryo of C. elegans. Development 134, 61–71. lymphocytes is independent of GAP activity. 3495–3505. 16. Severson, A.F., Baillie, D.L., and Bowerman, B. Exp. Cell Res. 312, 3517–3525. (2002). A formin homology protein and a 19. Schonegg, S., Constantinescu, A.T., Hoege, C., profilin are required for cytokinesis and and Hyman, A.A. (2007). The Rho GTPase- Department of Molecular Genetics and Cell Arp2/3-independent assembly of cortical activating proteins RGA-3 and RGA-4 are Biology, University of Chicago, Chicago, microfilaments in C. elegans. Curr. Biol. 12, required to set the initial size of PAR domains IL 60637, USA. 2066–2075. in Caenorhabditis elegans one-cell E-mail: [email protected] 17. Zhang, W., and Robinson, D.N. (2005). Balance embryos. Proc. Natl. Acad. Sci. USA of actively generated contractile and resistive 104, 14976–14981. forces controls cytokinesis dynamics. Proc. 20. Schmutz, C., Stevens, J., and Spang, A. (2007). Natl. Acad. Sci. USA 102, 7186–7191. Functions of the novel RhoGAP proteins RGA-3 DOI: 10.1016/j.cub.2008.12.028 Evolution: Revisiting the Root of the been controversial since they were first proposed [6]. Now, with the Eukaryote Tree rapid accumulation of genome-scale data for diverse protist species, a flurry of phylogenomic analyses A recent phylogenomic investigation shows that the enigmatic flagellate [7–9] are putting these hypotheses Breviata is a distinct anaerobic lineage within the eukaryote super-group to the test.
    [Show full text]
  • Phylogenomics Invokes the Clade Housing Cryptista, Archaeplastida, and Microheliella Maris
    bioRxiv preprint doi: https://doi.org/10.1101/2021.08.29.458128; this version posted August 31, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Phylogenomics invokes the clade housing Cryptista, 2 Archaeplastida, and Microheliella maris. 3 4 Euki Yazaki1, †, *, Akinori Yabuki2, †, *, Ayaka Imaizumi3, Keitaro Kume4, Tetsuo Hashimoto5,6, 5 and Yuji Inagaki6,7 6 7 1: RIKEN iTHEMS, Wako, Saitama 351-0198, Japan 8 2: Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 236-0001, 9 Japan 10 3: College of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan. 11 4: Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan 12 5: Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305- 13 8572, Japan 14 6: Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 15 Ibaraki, 305-8572, Japan 16 7: Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, 17 Japan 18 19 †EY and AY equally contributed to this work. 20 *Correspondence addressed to Euki Yazaki: [email protected] and Akinori Yabuki: 21 [email protected] 22 23 Running title: The clade housing Cryptista, Archaeplastida, and Microheliella maris. 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.08.29.458128; this version posted August 31, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]