Instructions for printer-friendly copy.

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    Domain Eukarya

    Eukaryotes are unicellular or multicellular organisms
    made up of cells containing a membrane-bound nucleus and organelles.

    A vast diversity of
    unicellular and colonial
    Protists

    Plantae
    Fungi
    Animalia

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    A Domain in Flux

    What was once "Kingdom Protista" has since been determined
    to consist of many (monophyletic?) clades.

    These newer taxa undergo regular revision as new data
    reveal that some putatively monophyletic groups are...not so much.

    Only three eukaryote taxa are made up of truly
    multicellular organisms:

      Plantae
      Fungi
      Animalia

    The rest are (mostly) unicellular protists.
    They are shown on the cladogram in blue.

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Eukaryote Synapomorphies

A suite of important innovations sets eukaryotes apart from both Archaeans and Bacteria.


(click on pic for source)

    Cytoskeleton

    The eukaryotic cytoskeleton consists of
    • tubulin-based microtubules
    • actin-based microfilaments
    • various protein-based intermediate filaments

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(click on pic for source)

    Flagella

    The axoneme is the central strand of the flagellum (pl. flagella).

    Visible in cross section are
    • nine peripheral micotubule doublets
    • one central micotubule doublet
    • ("nine surrounding two")

    A cilium (pl. cilia) is a very short flagellum.
    Its axoneme structure is identical to that of a flagellum.

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(By LadyofHats, Wikimedia Commons)

    Endomembrane System

    The endomembrane system defines the
    • endoplasmic reticulum
    • Golgi bodies
    • vacuoles
    • lysosomes
    • peroxisomes
    • nuclear envelope

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    Genome Arrangement

    The primary genome of a prokaryote
    • is contained on a single, circular chromosome
    • consists of "naked" DNA unassociated with proteins

    The primary genome of a eukaryote
    • is contained on multiple, linear chromosomes
    • consists of DNA molecules wound around histone protein complexes

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(click on pic for source)

    Mitochondria

    Mitochondria are energy-transducing organelles bounded by a double membrane.

    They are derived from ancient, symbiotic prokaryotes.

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(click on pic for source)

    Derived Ribosomes

    Ribosomal RNA sequences and protein identities differ
    between prokaryotes and eukaryotes.

    Eukaryotic cells have characteristic 80S ribosomes,
    each consisting of four molecules of RNA complexed
    with many proteins.

    Ribosome-targeting antibiotics take advantage of these differences!

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    Mitosis

    Eukaryotic cells can reproduce asexually via mitosis.

    Prokaryotic cells undergo the less complex asexual process of fission.

    Lacking linear chromosomes, prokaryotes do not undergo mitosis or meiosis.

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    The Origin of Eukaryotes

    Two processes contributed to the origin of eukaryotic cells.

    Each occurred more than once in our evolutionary history.

    • autogeny
        Extensive inpocketing of the external plasma membrane formed a complex internal network of membranes.

    • endosymbiosis
        First proposed by Lynn Margulis, this model describes how small, energy-transducing prokaryotes
        • were ingested as prey, but not digested
        • took up residence as internal symbionts

    Eventually, host and internal resident became inextricably
    linked in a mutually beneficial symbiotic relationship.

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    Evidence of Endosymbisis: Retained Symbioses

    Giardia, a very primitive flagellated protist, contains
    • symbiotic, energy-transducing bacteria
    • two haploid nuclei

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    Evidence of Endosymbisis: Living "Pro-organelles"

    Several species of extant cyanobacteria and heterotrophic bacteria have internal membrane systems.

    These are reminiscent of mitochondrial and chloroplast internal membrane systems.

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(click on pic for source)

    Evidence of Endosymbisis: Organelle Structure

    Mitochondria and chloroplasts are bounded by two membranes, not one.

    This may be a remnant of ancient phagocytosis by the original host cell.

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    Evidence of Endosymbisis: Organelle Reproduction

    Both mitochondria and chloroplasts undergo fission to reproduce themselves.

    The process is similar to bacterial fission.

    Mitochondria reproduce indepenedently of other organelles.

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    Evidence of Endosymbisis: Organelle Ribosomes

    Mitochondria and chloroplasts have their own ribosomes.

    These are more similar to prokaryotic than to eukaryotic ribosomes.

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    Evidence of Endosymbisis: Organelle Genomes

    Mitochondria and chloroplast have their own genomes.
    • largely independent of the nuclear genome
    • chromosome is circular, not linear
    • DNA is not associated histones or RNA.

    Like prokaryotes, mitochondria and chloroplasts are haploid.

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    Secondary Endosymbiosis

    After the first eukaryotic cells had formed, additional endosymbioses
    led to further divergence of eukaryotic lineages
    .

    • Primary endosymbiosis - a larger cell engulfs a smaller cell,
      which then takes up residence to the benefit of both cells
      (as described above).

    • Secondary endosymbiosis - the product of primary endosymbiosis is engulfed by a larger cell, and then takes up residence to the benefit of both cells.

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    Secondary Endosymbiosis: The Descendants

    • Ancestral red algae endosymbiosis gave rise to

      • Dinoflagellates
      • Apicomplexans ("sporozoans")
      • Stramenopiles (brown algae and their relatives)

    • Ancestral green algae endosymbiosis gave rise to

      • Euglenoids
      • Viridiplantae (Green Plants)

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      Vertical Gene Transfer is the transfer of genes from parent to offspring.
      Lateral Gene Transfer is the transfer of genes between two extant, unrelated organisms.

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    Protists

    "No more pleasant sight has met my eye than this,
    of so many thousands of living creatures
    in one small drop of water."
    - Anton van Leeuwenhoek

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(Required Video!)

    Protist Diversity

    The term "protist" is descriptive, not phylogenetic.

    Protists...
    • have descended from multiple different ancestors
    • are diverse in form and natural history
    • may reproduce asexually and/or sexually, depending on species
    • may be
      • unicellular (one-celled)
      • coenocytic (multiple nuclei in one cytoplasmic mass)
      • aggregate (clumped together)
      • colonial (adhered in a more organized form)
      • truly colonial (with a cellular division of labor)

    Protists can vary in size from < 1 μm (Ostreococcus tauri)
    to > 20cm in diameter (coenocytic Syringammina fragilissima)!

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via GIPHY

    Protist Ecological Roles

    Protists are most commonly found in marine and freshwater habitats.
    They require moisture to survive, but also can live in terrestrial habitats.

    Various species of protists may be

    • photoautotrophs
    • chemoheterotrophs
      • predatory (see video!)
      • parasitic
      • commensal
      • mutualistic
      • detritivorous
      • mixotrophic

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    Acritarchs

    The oldest known eukaryote fossils (2.1 billion years old,
    from pre-Cambrian fossil beds in Michigan) are the
    acritarchs, from the Greek
      acrit = "confused"
      arch = "beginning"

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    Excavates

    A basal taxon is a lineage that evolved early and remains relatively unchanged.

    Excavates are considered basal with respect to more derived protist taxa.

    The name refers to a groove "excavated" on one side of the cell.

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(Watch only the first two minutes of the video. The rest is an advertisement for a Giardia detection test.)

    Excavates: Giardia lamblia

    Parasitic Giardia lamblia provides a showcase of basal characters.
    • has typical eukaryotic 9 + 2 flagella
    • two haploid nuclei
    • reduced mitochondria (a derived character)
    • no plastids
    • very simple cytoskeleton
    • is a facultative anaerobe
    • has no electron transport chain proteins or enzymes associated with aerobic respiration
    • can cause giardiasis

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    Excavates: Trichomonas

    Trichomonas vaginalis is another opportunistic parasite/pathogen.

    It shares many primitive characters with Giardia.

    It is the most common protist pathogen in humans in industrialized countries.

    Its name comes from the location where it was first discovered,
    but it shows up elsewhere, too.

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    Excavates: Trichonympha and Personympha

    Trichonympha and Personympha are intestinal endosymbionts in termites.

    Unlike termites, these protists can digest cellulose.

    Without them, their termite hosts would starve to death.

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    Excavates: Euglenozoans

    Euglena is popular in kids' science classes,
    where teachers often ask, "Is it a plant or an animal?"

    The answer, of course, is: Neither.

    Euglenoids are mixotrophs, meaning they can switch
    between photoautotrophy or heterotrophy, as necessary.

    They are NOT closely related to either plants or animals (review the cladogram).

    Euglena is a ubiquitous mixotroph that some of us remember from after Hurricane Andrew.

    When the power went off and filtration stopped,
    these guys turned local swimming pools a lovely emerald green.

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    SAR Clade

    The "SAR Clade" is a diverse assemblage
    that is probably not monophyletic.

    We will meet members of three representatives of the clade.

    • Stramenopila
    • Alveolata
    • Rhizaria

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    SAR Clade: Stramenopila

    The name comes from their fuzzy flagellum
    (stramen ("straw") and pilos ("hair"), Latin).

    The fuzzy flagellum is often paired with a smooth one.

    All stramenopiles have flagella, even if only during the reproductive cycle.

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(click on pic for source)

    Stramenopila: Bacillariophyta (Diatoms)

    The diatoms have a protoplast encased in a
    two-part shell composed of silica (glass)

    Tiny perforations in the shell allow contact
    between the cell and its aquatic environment.

    The spacing of the holes is so uniform that Swiss watchmakers
    once used them to calibrate their watches.

    Diatomaceous earth, the fossilized skeletons of millions of diatoms,
    is sometimes marketed as a safe insecticide to spread in your carpets to kill fleas:
    It makes tiny incisions in the exoskeleton that then causes the flea to desiccate.

    It is also the scouring component of "all natural" toothpastes.

    Diatoms are photoautotrophs with chloroplasts containing

    • chlorophyll a
    • chlorophyll c

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    Stramenopila: Chrysophyceae (Golden Algae)

    These are found primarily in fresh water.

    Their common name reflects the color produced by chlorophyll c.

    Prymnesium parvum can cause fish kills when it overgrows, producing a toxin called prymnesin.

    The toxin generally does not harm animals other than fish.

    The calcium carbonate "skeletons" of Emiliana huxleyi, a golden algal haptophyte, are the primary component of the iconic White Cliffs of Dover in England.

    Golden Algae are photoautotrophs with chloroplasts containing

    • chlorophyll a
    • chlorophyll c

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    Stramenopila: Phaeophyceae (Brown Algae)

    These marine algae form ecologically important kelp beds that serve as habitat for multitudes of mariune organisms.

    Floating species such as Sargassum provide habitat for animals in open ocean, where few other resources exist.

    The phaeophyte body consists of a

    • rootlike holdfast
    • stemlike stipe
    • leaflike blade
    • gas-filled floats

    Phaeophytes are photoautotrophs with chloroplasts containing

    • chlorophyll a
    • chlorophyll c
    • fucoxanthin (a brownish carotenoid)

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    SAR Clade: Alveolata

    Alveolates share a distinct synapomorphy:
    sac-like alveoli under the plasma membrane. These small vesicles form a pellicle that maintains the cell's shape.

    Various parts of the pellicle may be flexible and contractile
    or quite rigid.

    Alveolates include some of the most complex of all protists.

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    Alveolata: Dinoflagellates

    View some dinoflagellates.
    • Some species are responsible for seasonal red tides (<--required link) that can cause massive die-offs of fish and other marine animals.
    • They are responsible for the most common form of non-bacterial seafood poisoning in the U.S., ciguatera.

    Not all dinoflagellates are dangerous.

    • Symbiodinium spp. form one of the most vital symbiotic relationships on earth: zooxanthellae and coral(<--required link).
    • And some are just plain cool.

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    Alveolata: Apicomplexa

    These all-parasitic "sporozoans" have a modified Golgi apparatus, the apicoplast, at the apex of the cell.
    This structure facilitates invasion of a host cell.

    All apicomplexans are intracellular parasites of animals, and are usually host specific.

    Some of the diseases they cause include...

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    Alveolata: Ciliophora

    Commonly known as ciliates, these are the most
    anatomically complex protists.
    • covered in shortened flagella called cilia
    • one small, diploid micronucleus for reproduction only;
      its genes are not expressed
    • one large, polyploid macronucleus for regulation of cell functions.
      Produced by the micronucleus, it is not passed on to daughter cells.
    This are the most diverse protist group, with over 8000 species.

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    SAR Clade: Rhizaria

    This clade includes related shelled and unshelled amoebas
    that bear long, threadlink pseudopods.

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    Rhizaria: Foraminifera

    These aquatic amoebas secrete shells of calcium carbonate.

    Highly derived, threadlike pseudopods emerge from holes in the shell.

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    Rhizaria: Radiolaria

    These aquatic amoebas secrete shells of silica (glass).

    Threadlike pseudopods protrude from holes in the shell.

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    Amorphea

    This clade includes the protist groups
    • Amoebozoa
    • Slime Molds
    • Choanoflagellates

    As well as the multicellular Kingdoms

    • Fungi
    • Animalia.

      Amorphea's monophyly is not certain.
      But for now....

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    Amorphea: Amoebozoa

    We are closely related to amoebas.

    Most specifically, we are most closely related to parasitic entamoebas.

    Don't get this one up your nose. It will eat your brain.

    No wonder no one likes to have dinner with relatives on Thanksgiving.

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    Amorphea: Slime Molds

    We also share a relatively recent common ancestor with slime molds, whose phylogenetic relationships are still being determined.

    Once classified as Fungi, most of these are now believed to be Amoebozoans.

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    Amorphea: Choanoflagellates

    These stalked, sessile protists may be unicellular, but most are colonial.

    They are extremely similar to the choanocytes found in sponges,
    the most primitive proto-animals.

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    Plantae (= Archaeplastida)

    This ecologically vital clade includes
    • Rhodophyta (Red Algae)
    • Viridiplantae (Green Plants)

      A unifying characteristic is that all plants undergo an
      alternation of generations life cycle.

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(click on pic for source)

    Plantae: Rhodophyta (Red Algae)

    Rhodophyte synapomorphies
    • loss of flagella
    • loss of centrioles
    • chloroplasts containing
      • chlorophyll a
      • chlorophyll d
    • specialized light-collecting phycobilisomes containing
      photosynthetic phycobilin pigments:
      • phycoerythrin (red)
      • phycocyanin (blue-green)
      • allophycocyanins (blue-green)

      Chlorophyll d and the phycobilins are found only in Rhodophytes
      and cyanobacteria
      , evidence of their secondary endosymbiosis.

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(click on pic for source)

    Phycobilin Absorbance Spectra

    The phycobilins absorb regions of the spectrum
    not highly absorbed by carotenoids or chlorophylls.

    This allows red algae to utilize light that other plants
    simply reflect or transmit.

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(click on pic for source)

    Rhodophytes Can Be Deep

    • Chlorophyll d λmax = 710nm (far red)
    • phycoerythrin λmax = 495nm (blue) and 545nm (blue-green)
    • phycocyanins λmax = 621nm (yellow)

    Absorption of shorter wavelengths allows these algae to live in lower-light conditions than green algae can.


    Many species of red algae are coralline:
    They deposit calcium carbonate in their tissues.

    The hard, somewhat brittle thallus is a deterrent to herbivory.

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    Rhodophytes On Your Plate

    Red algae are the source of agar, an economically vital product.
    • component of many food items (to add smooth texture)
    • forms base for microorganism growth media in microbiology

    Your sushi wrap is Porphyra, a red alga.

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Coleochaete orbicularis, one of the closest relatives of land plants.

    Plantae: Viridiplantae

    The Green Plants form a diverse assemblage ranging in complexity
    from unicellular Chlamydomonas to giant Sequoia trees.

    Like all photoautotrophs, they use chlorophyll a as their primary electron acceptor.

    But they share a number of synapomorphies unique to green plants, including

    • energy stored as starch inside plastids
    • chlorophyll b (unique to Viridiplantae)

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Coenocytic Caulerpa

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progression from unicellularity --> colony: Volvocine algae
(Click on pic for more than you ever wanted to know about algae evolution.)

    Viridiplantae: Green Algae

    About 4300 green plant species are unicellular or multicellular green algae.

    Because they lack vascular tissues (which defines true plant organs)
    they do not have true stems, roots, or leaves, although some species have structural analogies:

    • stipe ("stem")
    • holdfast ("root")
    • blade ("leaf")

    Many species tend exhibit multicellularity via

    • aggregates and colonies
    • coenocytic thallus (multinucleate body with no cell walls)
    • true multicellular thallus

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    Viridiplantae: Charophyta

    Charophytes are the closest algal relatives of land plants.

    They share the following synapomorphies with land plants.

    • Cellulose synthesis occurs in hexameric protein rosettes.
    • Cell walls contain lignin-like compounds
    • Sporopollenin present (in Charophyte zygote cell walls)
    • Peroxisomes contain unique, specialized enzymes
    • Similar flagellated sperm are unlike those of other green algae
    • Phragmoplast forms near the end of mitosis, creating new cell walls

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