Protistan Systematics Ge197 Week 1 Winter 2013
Tuesday, January 22, 13 unidentified freshwater amoeba
Tuesday, January 22, 13 modified after an original by David Patterson Marine Biological Laboratory Woods Hole, Massachusetts USA
Tuesday, January 22, 13 modified after an original from Patrick Keeling University of British Columbia Vancouver, Canada
Tuesday, January 22, 13 5
Tuesday, January 22, 13 Arcella
Tubulinids
Kreutz, M. and Foissner , W. 2006: The Sphagnum ponds of Simmelried in Germany: a biodiversity hot-spot for microscopic organisms. Protozoological Monographs Vol. 3, Shaker Verlag, Aachen, Germany
Tuesday, January 22, 13 Paraquadrula
Tubulinids
Kreutz, M. and Foissner , W. 2006: The Sphagnum ponds of Simmelried in Germany: a biodiversity hot-spot for microscopic organisms. Protozoological Monographs Vol. 3, Shaker Verlag, Aachen, Germany
Tuesday, January 22, 13 Nebela vas
Tubulinids
courtesy of Wilhelm Foissner University of Salzburg, Austria
Tuesday, January 22, 13 Stramenopiles (tripartite hairs on flagella) *
Chrysophytes
opalines
Protsville Tuesday, January 22, 13 Stramenopiles (tripartite hairs on flagella) *
Chrysophytes
opalines
Cafeteria Protsville Tuesday, January 22, 13 Stramenopiles (tripartite hairs on flagella) *
Diatoms Chrysophytes
opalines
Cafeteria Protsville Tuesday, January 22, 13 Stramenopiles (tripartite hairs on flagella) *
macrophytic Diatoms brown Chrysophytes algae
opalines
Cafeteria Protsville Tuesday, January 22, 13 modified after an original from Patrick Keeling University of British Columbia Vancouver, Canada
Tuesday, January 22, 13 Chroomonas sp.
Cryptomonads
Kugrens, P. et al. 1986: Cell form and surface patterns in Chroomonas and Cryptomonas cells (Cryptophyta) as Revealed by scanning electron microscopy J. Phyc. 22: 512-522
Tuesday, January 22, 13 Emiliania huxleyi
Haptophytes
Hallegraeff, G. 1988: Plankton, a microscopic world Brill Academic Publishers, Leiden
Tuesday, January 22, 13 Pontosphaera discopora
Haptophytes
Hallegraeff, G. 1988: Plankton, a microscopic world Brill Academic Publishers, Leiden
Tuesday, January 22, 13 Ophiaster formosus
Haptophytes
Young, J. R. et al. 2009: Coccolith function and morphogenesis: insights from appendage-bearing coccolithophores of the family Syracosphaeraceae. J. Phycol. 45: 213-226
Tuesday, January 22, 13 Michaelsarsia elegans
Haptophytes
Young, J. R. et al. 2009: Coccolith function and morphogenesis: insights from appendage-bearing coccolithophores of the family Syracosphaeraceae. J. Phycol. 45: 213-226
Tuesday, January 22, 13 Synura petersenii
Synurophytes Ochrophytes
Tuesday, January 22, 13 Mallomonas sp.
Synurophytes Ochrophytes
courtesy of Yu Iokawa Joetsu University of Education Niigata, Japan
Tuesday, January 22, 13 Coscinodiscus
Diatoms
Tuesday, January 22, 13 Bacteriastrum furcatum
Diatoms
Hallegraeff, G. 1988: Plankton, a microscopic world Brill Academic Publishers, Leiden
Tuesday, January 22, 13 Stephanopyxis palmeriana
©Tamotsu Nagumo Diatoms Nippon Dental University Tokyo, Japan Image licensed to Phycological Images
Tuesday, January 22, 13 * Alveolates
dinoflagellates apicomplexans ciliates
Tetrahymena Pfisteria (red tide) (Plasmodium thermophila falciparum) malaria Alveolar membrane system: sacs (alveoli) underneath outer cell membrane Tuesday, January 22, 13 Gonyaulax spinifera
Dinoflagellates
Hallegraeff, G. 1988: Plankton, a microscopic world Brill Academic Publishers, Leiden
Tuesday, January 22, 13 Ceratocorys horrida
Dinoflagellates
courtesy of Maria Faust Smithsonian National Museum of Natural History Washington, DC, USA
Tuesday, January 22, 13 Dinophysis schuettii
Dinoflagellates
Hallegraeff, G. 1988: Plankton, a microscopic world Brill Academic Publishers, Leiden
Tuesday, January 22, 13 Ornithocercus thumii
Dinoflagellates
courtesy of Maria Faust Smithsonian National Museum of Natural History Washington, DC, USA
Tuesday, January 22, 13 Amphisolenia bidentata
Dinoflagellates
Hallegraeff, G. 1988: Plankton, a microscopic world Brill Academic Publishers, Leiden
Tuesday, January 22, 13 Pelagostrobilidium neptuni
Choreotrichs Spirotrichs Ciliates
Agatha et al. 2004: Pelagostrobilidium neptuni and Strombidium biarmatum: phylogenetic position inferred from morphology, ontogenesis and gene sequence data. Europ. J. Prot. 41: 65-83
Tuesday, January 22, 13 Codonella cratera
Choreotrichs (Tintinnids) Spirotrichs Ciliates
Tuesday, January 22, 13 Metopus es
Armophorids Ciliates
courtesy of Christian Bardele University of Tübingen Germany
Tuesday, January 22, 13 Didinium nasutum
Haptorians Litostomes Ciliates
Foissner et al. 1995 Taxonomische und ökologische Revision der Ciliaten des Saprobiensystems, Band 4 Bazerisches Landesamt für Wasserwirtschaft Munich, Germany
Tuesday, January 22, 13 * Rhizaria
testate amoebae
chlorarachnia cercomonads
Chlorarachnion reptans Paulinella ovalis Massisteria marina “nucleomorph”
Tuesday, January 22, 13 modified after an original from Patrick Keeling University of British Columbia Vancouver, Canada
Tuesday, January 22, 13 Acanthometra
Acantharians Radiolarians
©Peter Parks, ImageQuest Ltd. Witney, Oxon, UK
Tuesday, January 22, 13 Lychnaspis miranda
Acantharians Radiolarians
Ernst Haeckel Kunstformen der Natur
Tuesday, January 22, 13 Dictyacantha
Acantharians Radiolarians
Hallegraeff, G. 1988: Plankton, a microscopic world Brill Academic Publishers, Leiden
Tuesday, January 22, 13 Hexastylus triaxonius
Spumellarians Radiolarians
www.radiolarian.com
Tuesday, January 22, 13 Lamprocyclas maritalis
Nasellarians Radiolarians
www. radiolaria.org
Tuesday, January 22, 13 Reticulomyxa filosa
Foraminiferans
Hausmann et al. 2003: Protistology, 3rd edition ©Schweizerbart’sche Verlagsbuchhandlung
Tuesday, January 22, 13 Globigerina bulloides
Foraminiferans
Hallegraeff, G. 1988: Plankton, a microscopic world Brill Academic Publishers, Leiden
Tuesday, January 22, 13 Globigerinella sp.
Foraminiferans
©O. Roger Anderson, image licensed to micro*scope
Tuesday, January 22, 13 modified after an original from Patrick Keeling University of British Columbia Vancouver, Canada
Tuesday, January 22, 13 Giardia lamblia
Diplomonads
Tuesday, January 22, 13 Spironucleus elegans
Diplomonads
courtesy of Guy Brugerolle Blaise Pascal University of Clermont-Ferrand, France
Tuesday, January 22, 13 Trichomonas vaginalis
Trichomonads Parabasalians
Tuesday, January 22, 13 Streblomastix strix
Oxymonads
Leander, B. S. and Keeling, P. J. 2004: Symbiotic innovation in the oxymonad Streblomastix strix. J. Eukaryot. Microbiol. 51: 291-300
Tuesday, January 22, 13 Devescovina striata
Cristamonads Parabasalians
Kirby, H. 1941: Devescovenid flagellates of termites. II The genus Devescovina. Univ. Calif. Publ. Zool. 45: 1-92
Tuesday, January 22, 13 Staurojoenina assimilis
Hypermastigotes Parabasalians
Dolan, M. et al. 2004: Cysts and symbionts of Staurojoenina assimilis Kirby from Neotermes. Europ. J. Protistol. 40: 257-264
Tuesday, January 22, 13 Eucomonympha imla
Hypermastigotes Parabasalians
Carpenter, K. J. and Keeling, P. J. 2007: Morphology and phylogenetic position of Eucomonympha imla. J. Euk. Micro. 54: 325-332
Tuesday, January 22, 13 Current problems with eukaryotic systematics
• “Phylogeny by fiat” • Morphology vs. molecular systematics • Discrepancies between phylogenetic markers (rRNA vs. other genes)
• Issues with statistics (LBA) • Lack of statistical support for monophyly of major “supergroups”
Tuesday, January 22, 13 * Ways to improve phylogeny
• Increased taxonomic sampling (break up long branches) !** add more organisms
• Concatenated gene phylogenies !**add more data (meaning more genes)
• Multicharacter data sets (gene phylogenies, morphology, etc.) !** add more non-molecular data
Tuesday, January 22, 13 Genome-enabled strategies for determining evolutionary relationships
•consensus phylogenies of single genes •consensus phylogenies of many genes •concatenated gene phylogenies
how do we assess statistical support?
do all genes have similar evolutionary
histories? (i.e., are all genes good proxies?)51
Tuesday, January 22, 13 How to read trees
Tuesday, January 22, 13 “natural” groups of organisms (or genes)
sister groups
descendants A B C
ancestor of A, B X descendant of Y
most recent common Y ancestor of A, B, C
think about your own geneology.....
Tuesday, January 22, 13 The anatomy of a tree
• Nodes • Branches • Leaves (taxa) 50 • Ingroups • Outgroups • Roots • Bootstraps • Scale bar
Tuesday, January 22, 13 Branches can rotate around nodes * Nodes are can rotate 360° - like a mobile
Tuesday, January 22, 13 Cladograms vs. phylograms
Cladograms show branching order - branch lengths are meaningless
Phylograms show branch order and branch lengths
Branch length is directly proportional to the amount of change
Tuesday, January 22, 13 57
Tuesday, January 22, 13 Rooting using an outgroup
Unrooted tree
rooted trees
Unrooted:“direction” of evolution unknown, or not inferred Rooted:“direction” of evolution known, or inferred
Tuesday, January 22, 13 Which of the four trees above depicts a different pattern?
Tuesday, January 22, 13 Which of the four trees above depicts a different pattern?
Tuesday, January 22, 13 How do we evaluate the quality of trees?
61
Tuesday, January 22, 13 How do we evaluate the quality of trees?
What parts of the tree are we confident in?
61
Tuesday, January 22, 13 Non-parametric bootstrapping
• Analyze original dataset • Generate new samples by resampling original data (n=# columns, n times) • Analyze new datasets like original • Summarize variation (“consensus”)
• Bootstrap values = variation in tree topologies (generally want >50)
Tuesday, January 22, 13 Bootstrapping
–The number of times a particular branch is formed in the tree (out of the X times the analysis is done).
–used to estimate probability and indicated on a consensus tree
–High bootstrap values don’t mean that your tree is the true tree!
Alignment and evolutionary assumptions are critical
Tuesday, January 22, 13 Monophyly, Paraphyly, and Polyphyly
“natural” groups = monophyletic
1. monophyletic: ancestor + all descendants (a.k.a. “clades”) 2. polyphyletic: multiple ancestries 3. paraphyletic: ancestor but not all descendants
check bootstrap support
What about dark groups to the right?
Tuesday, January 22, 13 Polytomy:
unresolved branching order, meaning either:
“unresolvable” using given phylogenetic methods (e.g., low bootstrap values) or multiple species diverged simultaneously
Polytomies are usually represented as more than two branches coming from a single node.
Tuesday, January 22, 13 1. monophyletic: ancestor + all descendants (a.k.a. “clades”) 2. polyphyletic: multiple ancestries 3. paraphyletic: ancestor but not all descendants
check bootstrap support
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Tuesday, January 22, 13 Xenologs: Horizontal gene transfer
E. coli
Horizontal gene transfer: genes acquired not through common “vertical” ancestry
Tuesday, January 22, 13