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Evolution of Dictyostelid Social Amoebas Inferred from the Use of Molecular Tools

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Dictyostelids

Abstract

Dictyostelid social amoebas are eukaryotic microbes distributed all around the globe. As with many other protist groups, one fundamental and revolutionary event in the study of dictyostelid (Amoebozoa) systematics has been the use of molecular tools. This has radically changed our understanding of evolution across the group and has greatly expanded the potential use of dictyostelids as model organisms for a wide range of areas including biomedicine, development, evolutionary biology, and molecular ecology. This is further supported by genome sequencing that has been carried out for at least one species in each of the major groups. Phylogenomic data are also essential to pinpointing the origin of diversification of dictyostelids in terrestrial ecosystems, which is basic for understanding the evolutionary history across eukaryotic amoeboid lineages.

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References

  • Adl SM, Simpson AGB, lane CE (2012) The revised classification of eukaryotes. J Eukaryot Microbiol 59:429–514

    Article  PubMed  Google Scholar 

  • Andersson JO, Roger AJ (2002) A cyanobacterial gene in non-hotosynthetic protists-an early chloroplast acquisition in eukaryotes? Curr Biol 12:115–119

    Google Scholar 

  • Archibald JM, O'Kelly CJ, Doolittle WF (2002) The chaperonin genes of Jakobid-like flagellates: implications for eukaryotic evolution. Mol Biol Evol 19:422–431

    Google Scholar 

  • Bass D, Richards TA, Matthai L, Marsh V, Cavalier-Smith T (2007) DNA evidence for global dispersal and probable endemicity of protozoa. BMC Evol Biol 13:162

    Article  Google Scholar 

  • Baldauf SL, Roger AJ, Wenk-Siefer TI, Doolittle WF (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972–977

    Article  PubMed  CAS  Google Scholar 

  • Benton MJ, Ayala FJ (2003) Dating the tree of life. Science 300:1698–1700

    Article  PubMed  CAS  Google Scholar 

  • Berney C, Pawlowski J (2006) A molecular time-scale for eukaryote evolution recalibrated with the continuous micro-fossil record. Proc Roy Soc B 273:1867–1872

    Article  CAS  Google Scholar 

  • Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR (2011) Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PLoS ONE 6:e16626

    Article  PubMed  CAS  Google Scholar 

  • Boenigk J, Ereshefsky M, Hoef-Emden K, Mallet J, Bass D (2012) Concepts in protistology: species definitions and boundaries. E J Protistl 48:96102

    Google Scholar 

  • Brown MW, Spiegel FW, Silberman JD (2009) Phylogeny of the “forgotten” cellular slime mold, Fonticula alba, reveals a key evolutionary branch within Opisthokonta. Mol Biol Evol 26(12):2699–2709

    Article  PubMed  CAS  Google Scholar 

  • Brown MW, Silberman JD, Spiegel FW (2011) “Slime molds” among the Tubulinea (Amoebozoa): molecular systematics and taxonomy of Copromyxa. Protist 162:277–287

    Article  PubMed  Google Scholar 

  • Brown MW, Kolisko M, Silberman JD, Roger AJ (2012) Aggregative multicellularity evolved independently in the eukaryotic supergroup Rhizaria. Curr Biol 22:1123–1127

    Article  PubMed  CAS  Google Scholar 

  • Caron DA, Countway PD, Savai P, Gast RJ, Schnetzer A, Moorthi SD, Dennett MR, Moran DM, Jones AC (2009) Defining DNA-based operational taxonomic units for microbial-eukaryote ecology. Appl Environ Microbiol 75:5797–5808

    Article  PubMed  CAS  Google Scholar 

  • Caron DA, Countway PD, Jones AC, Kim DY, Schnetzer A (2012) Marine protistan diversity. Annu Rev Mar sci 4:467–493

    Article  Google Scholar 

  • Cavalier-Smith T (2009) Megaphylogeny, cell body plans, adaptive zones: causes and timing of eukaryote basal radiations. J Eukaryot Microbiol 56:26–33

    Article  PubMed  Google Scholar 

  • Cavender J, Vadell E, Landolt J, Winsett K, Stephenson S & Romeralo M (2013) Ten new small cellular slime molds from Seasonal Rain Forest of Central America. Mycologia 105:610–635. doi:10.3852/11-332

    Google Scholar 

  • Douglas TE, Kronforst MR, Queller DC, Strassmann JE (2011) Genetic diversity in the social Amoeba Dictyostelium discoideum: population differentiation in Cryptic Species. Mol Phylogenet Evol 60:455–462

    Article  PubMed  Google Scholar 

  • Dunthorn M, Foissner W, Katz LA (2008) Molecular phylogenetic analysis of class Colpodea (phylum Ciliophora) using broad taxon sampling. Mol Phylogenet Evol 46:316–327

    Article  PubMed  CAS  Google Scholar 

  • Dunthorn MS, Foissner W, Katz LA (2011) Expanding character sampling for ciliate phylogenetic inference using mitochondrial ssu-rdna as a molecular marker. Protist 162:85–99

    Google Scholar 

  • Epstein S, Lopez-Garcia P (2008) “Missing” protists: a molecular prospective. Biodivers Conserv 17:261–276

    Article  Google Scholar 

  • Fenchel T, Finlay BJ (2004) The ubiquity of small species: patterns of local and global diversity. Bioscience 54:777–784

    Article  Google Scholar 

  • Fierer N, Breitbart M, Nulton J (2007) Metagenomic and small-subunit RNA analyses reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 73:7059–7066. doi: 10.1128/AEM.00358-07

    Google Scholar 

  • Fierer N (2008) Microbial biogeography: patterns in microbial diversity across space and time. In: Zengler K (ed) Accessing uncultivated microorganisms: from the environment to organisms and genomes and back. ASM Press, Washington DC, pp 95–115

    Google Scholar 

  • Finlay BJ (2002) Global dispersal of free-living microbial eukaryote species. Science 296:1061–1063

    Article  PubMed  CAS  Google Scholar 

  • Fiore-Donno AM, Berney C, Pawlowski J, Baldauf SL (2005) Higher-order phylogeny of plasmodial slime molds (Myxogastria) based on EF1A and SSU rRNA sequences. J Eukaryot Microbiol 52:201–210

    Article  PubMed  CAS  Google Scholar 

  • Fiore-Donno AM, Meyer M, Baldauf SL, Pawlowski J (2008) Evolution of dark-spored Myxpmycetes (slime-molds): molecules versus morphology. Mol Phylogenet Evol 46:878–889

    Article  PubMed  CAS  Google Scholar 

  • Fiore-Donno AM, Nikolaev SI, Nelson M, Pawlowski J, Cavalier-Smith T, Baldauf SL (2010a) Deep phylogeny and evolution of slime modls (Mycetozoa). Protist 161:55–70

    Google Scholar 

  • Fiz-Palacios O, Romeralo M, Ahmadzadeh A, Weststrand S, Ahlberg P & Baldauf SL (2013) Did terrestrial diversification of amoebas (amoebozoa) occur in synchrony with land plants? Plos One (in press)

    Google Scholar 

  • Foissner W (2006) Biogeography and dispersal of micro-organisms: a review emphasizing protists. Acta Protozoologica 45:111–136

    Google Scholar 

  • Foissner W (2008) Protist diversity and distribution: some basic considerations. Biodivers Conserv 17:235–242

    Article  Google Scholar 

  • Groussin M, Pawlowski J, Yang Z (2011) Bayesian relaxed clock estimation of divergence times in foraminifera. Mol Phylogenet Evol 61:157–166

    Article  PubMed  Google Scholar 

  • Hagiwara H (1989) The taxonomic study of Japanese Dictyostelid cellular slime molds. National Science Museum, Tokyo

    Google Scholar 

  • Handelsman J, Smalla K (2003) Conversations with the silent majority. Curr Opin Microbiol 6:271–273

    Article  Google Scholar 

  • Heidel AJ, Lawal HM, Felder M (2011) Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication. Genome Res 21:1882–1891

    Article  PubMed  CAS  Google Scholar 

  • Kalinsky T, Quake SR (2011) Single-cell genomics. Nat Methods 8:311–314

    Article  Google Scholar 

  • Kalinsky T, Blainey P, Quake SR (2011) Genomic analysis at the single-cell level. Annu Rev Genet 45:431–445

    Article  Google Scholar 

  • Kalla SE, Queller DC, Lasagni A, Strassmann JE (2011) Kin discrimination and possible cryptic species in the social amoeba Polysphondylium violaceum. BMC Evol Biol 11:31

    Article  PubMed  Google Scholar 

  • Keeling PJ, Doolittle WF (1996) Alpha-tubulin from early-diverging eukaryotic lineages and the evolution of the tubulin family. Mol Biol Evol 13:1297–1305

    Google Scholar 

  • Kenrick P, Crane PR (1997) The origin and early evolution of plants on land. Nature 389:33–39

    Article  CAS  Google Scholar 

  • Lahr DJ, Grant J, Nguyen T, Lin JH, Katz LA (2011) Comprehensive phylogenetic reconstruction of amoebozoa based on concatenated analyses of SSU-rDNA and actin genes. PLoS ONE 6(7):e22780

    Article  PubMed  CAS  Google Scholar 

  • Lara E, Berney C, Harms H, Chatzinotas A (2007) Cultivation-independent analysis reveals a shift in ciliate 18S rRNA gene diversity in a polycyclic hydrocarbon-polluted soil. FEMS Microbiol Ecol 62:365–373

    Article  PubMed  CAS  Google Scholar 

  • Lasek-Nesselquist E, Katz LA (2001) Phylogenetic position of Sorogena stoianovitchae and relationships within the Class Colpodea (Ciliophora) based on ssu rDNA sequences. J Eukaryot Microbiol 48:604–607

    Article  PubMed  CAS  Google Scholar 

  • Leander BS (2008) A hierarchical view of convergent evolution in microbial eukaryotes. J Eukaryot Microbiol 55:59–68

    Article  PubMed  Google Scholar 

  • Marcy Y, Ouverney C, Bik EM (2007) Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Nat Acad Sci 104:11889–11894

    Article  PubMed  CAS  Google Scholar 

  • Mehdiabadi NJ, Kronforst MR, Queller DC, Strassmann JE (2009) Phylogeny, reproductive isolation and kin recognition in the social amoeba, Dictyostelium purpureum. Evolution 63:542–548

    Article  PubMed  Google Scholar 

  • Mehdiabadi NJ, Kronforst MR, Queller DC, Strassmann JE (2010) Phylogeography and sexual macrocyst formation in the social amoeba Dictyostelium giganteum. BMC Evol Biol 10:17

    Article  PubMed  Google Scholar 

  • Moreira D, López-García P (2002) Molecular ecology of microbial eukaryotes unveils a hidden world. Trends Microbiol 10:31–38

    Article  PubMed  CAS  Google Scholar 

  • Nikolaev SI, Berney C, Fahrni JF, Bolivar I, Polet S, Mylnikov AP, Aleshin VV, Petrov NB, Pawlowski J (2004) The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proc Nat Acad Sci (USA) 101:8066–8071

    Google Scholar 

  • Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276(5313):734–740. doi:10.1126/science.276.5313.734

    Article  PubMed  CAS  Google Scholar 

  • Parfrey LW, Lahr DJG, Knoll AH, Katz LA (2011) Elucidating the timing of eukaryotic diversification. Proc Nat Acad Sci 108(33):13624–13629

    Article  PubMed  CAS  Google Scholar 

  • Pawlowski J, Burki F (2009) Untangling the phylogeny of amoeboid protist. J Eukaryot Microbiol 56:16–25

    Article  PubMed  CAS  Google Scholar 

  • Perrigo A, Baldauf SL, Romeralo M (2013) Dictyostelids of northern sweden and two new species: dictyostelium barbibulus and polysphondylium lilacinus. Fungal Diversity 58:185–198

    Google Scholar 

  • Porter S, Knoll AH (2000) Testate amoebae in the Neoproterozoic Era, evidence from vase-shaped microfossils in the Chuar Group, Grand Canyon. Paleobiology 26:360–385

    Article  Google Scholar 

  • Raper KB (1984) The dictyostelids. Princeton University Press, Princeton

    Google Scholar 

  • Rehm P, Borner J, Meusemann K, von Reumont BM, Simon S, Hadrys H, Misof B, Burmester T (2011) Dating the arthropod tree based on large-scale transcriptome data. Mol Phylogenet Evol 61:880–887

    Article  PubMed  Google Scholar 

  • Roger AJ, Smith MW, Doolittle RF, Doolittle WF (1996) Evidence for the Heterolobosea from phylogenetic analysis of genes encoding glyceraldehyde-3-phosphate dehydrogenase. J Euk Microbiol 43:475–485

    Google Scholar 

  • Romeralo M, Escalante R, Sastre L, Lado C (2007) Molecular systematics of dictyostelids: 5.8S ribosomal DNA and internal transcribed spacer region analyses. Eukaryot Cell 6:110–116

    Article  PubMed  CAS  Google Scholar 

  • Romeralo M, Baldauf SL, Cavender JC (2009) A new species of cellular slime mold from Southern Portugal based on morphology, ITS and SSU sequences. Mycologia 101:269–274

    Google Scholar 

  • Romeralo M, Spiegel FW, Baldauf SL (2010a) A fully resolved phylogeny of the social amoebas (Dictyostelia) based on combined SSU and ITS rDNA sequences. Protist 161:539–548

    Google Scholar 

  • Romeralo M, Rajguru S, Silberman J, Landolt J, Fiz O, Stephenson S (2010b) Population structure of the social Amoeba Dictyostelium rosarium based on rDNA. Fungal Ecol 3:379–385

    Article  Google Scholar 

  • Romeralo M, Cavender J, Landolt J, Stephenson S, Baldauf S (2011) The expanding phylogeny of social Amoebae defines new major lineages and emerging patterns in morphological evolution. BMC Evol Biol 11:84

    Article  PubMed  Google Scholar 

  • Romeralo M, Skiba A, Gonzalez-Voyer A, Schilde C, Lawal H, Kedziora S, Cavender J, Glöckner G, Urushihara H, Schaap P (2013) Analysis of phenotypic evolution in Dictyostelia highlights developmental plasticity as a likely consequence of colonial multicellularity. In: Proc R Soc B 7 August 2013, vol 280 no 1764 20130976. Published 19 June 2013. doi:10.1098/rspb.2013.0976

  • Rubinstein CV, Gerrienne P, de la Puente GS, Astini RA, Steemans P (2010) Early middle Ordovician evidence for land plants in Argentina (Eastern Gondwana). New Phytol 188:365–369

    Article  PubMed  CAS  Google Scholar 

  • Schaap P, Winckler T, Nelson M (2006) Molecular phylogeny and evolution of morphology in the social amoebas. Science 314:661–663

    Article  PubMed  CAS  Google Scholar 

  • Schmidt AR, Schonborn W, Schafer (2004) Diverse fossils amoebae in German Mesozoic amber. Palaeontology 47:185–197

    Article  Google Scholar 

  • Shadwick LL, Spiegel FW, Shadwick JDL, Brown MW, Silberman JD (2009) Eumycetozoa = Amoebozoa? SSU rDNA phylogeny of protosteloid Slime Molds and its significance for the supergroup Amoebozoa. PLoS ONE 4(8):e6754

    Article  PubMed  Google Scholar 

  • Smith HG, Wilkinson DM (2007) Not all free-living microorganisms have cosmopolitan distributions—the case of Nebela (Apodera) vas Certes (Protozoa: Amoebozoa: Arcellinida). J Biogeogr 34:1822–1831

    Article  Google Scholar 

  • Schnittler M, Novozhilov YK, Romeralo M, Brown MW, Spiegel FW (2012). Myxomycete-like organisms. In: Frey A. (ed) Engler’s syllabus der Planzenfamilien (Engler’s syllabus of plant families). Part 1: Blue-green Algae, Myxomycete-like organisms and Fungi. Science Publishers, Berlin

    Google Scholar 

  • Stechmann A, Baumgartner M, Silberman JD, Roger AJ (2006) The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic. BMC Evol Biol 6:101

    Google Scholar 

  • Stephenson SL, Fiore-donno AM, Schnittler M (2011) Myxomycetes in soil. Soil Biol Biochem 43:2237–2242

    Article  CAS  Google Scholar 

  • Sucgang et al (2011) Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol 12:R20

    Article  PubMed  CAS  Google Scholar 

  • Taylor JW, Berbee ML (2006) Dating divergences in the Fungal Tree of Life. Mycologia 98:838

    Article  PubMed  Google Scholar 

  • Vadell EM, Cavender JC, Romeralo M, Edwards SM, Stephenson SL, Baldauf SL (2011) New species of dictyostelids from Patagonia and Tierra del Fuego, Argentina. Mycologia 103:101–117

    Article  PubMed  Google Scholar 

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Acknowledgments

The authors want to thank R. Escalante, T. Heger, and A. Perrigo for valuable comments on this chapter. MR was supported by a Marie Curie Intra European Fellowship within the 7th European Community Framework Programme to MR (PIEF-GA-2009-236501).

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Romeralo, M., Fiz-Palacios, O. (2013). Evolution of Dictyostelid Social Amoebas Inferred from the Use of Molecular Tools. In: Romeralo, M., Baldauf, S., Escalante, R. (eds) Dictyostelids. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38487-5_9

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