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PROTISTA
The paraphyletic, nonfungi, non-animal, nonplant Eucarya
+
Even MORE new words
to remember!
Key Points
•  Origin of eukaryotes via symbiosis
•  Origin of classification based on
functional (ecological) traits
•  Current classification based on
phylogenetic principles
•  Alternation of generations prominent
General
1.  Eukaryotes are mostly unicellular.
2.  Mixed history of classification:
“Protista” an informal term of
convenience for non-fungal, non-plant,
non-animal eukaryotes.
3.  From amoeba to giant kelp, arranged
functionally.
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Functional arrangements
a.  Animal-like heterotrophic protists:
Protozoa.
b.  Absorptive or fungus-like protists:
Pseudopodians.
c.  Plant-like photosynthetic protists:
Algae
d.  Mixotrophs
All of these groups are polyphyletic
Protists are…
1.  …the earliest
Eukaryotes
a.  True nucleus
b.  Cytoplasmic organelles
c.  ~2.2 bya
2.  …always associated
with water, dampness,
or body fluids
a.  Plankton, parasitic
Protists are…
3.  …aerobic (almost all)
and have
mitochondria for
cellular respiration.
4.  …photoautotrophs,
chemoheterotrophs,
or both (mixotrophs).
a.  Note NO
photoheterotrophs nor
chemoautotrophs.
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Protists are…
5.  …motile: most have
flagella or cilia or
pseudopodia at some
stage.
6.  …asexual or truly
sexual (true meiosis
and mitosis)
flagella
The Origin of Eukaryotes
“How to make a Eukaryote”
•  About 2.5 bya prokaryotes had
diversified into many types.
•  But the small size and limited genome
of prokaryotes constrained their
evolution.
•  So how did Eukaryotes become
possible?
The Origin of Eukaryotes
“How to make a Eukaryote”
•  Eukaryotic cell: true
nucleus, cytoplasmic
organelles
–  Membrane-enclosed
structures with specialized
function
–  Some with own genome
(mitochondria, chloroplasts)
•  This compartmentalization
allowed the evolution of
larger cells. But how?
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Ancestral Archaean &
evolution of nucleus
Endosymbiosis
•  A sequence of events in
which specialized
prokaryotes live within
larger prokaryotes in
symbiotic relationship.
•  Some became
mitochondria and some
chloroplasts.
•  Both were important in
an increasingly aerobic
world.
Aerobic
α-proteobacterium
è mitochondrion
Cyanobacterium
è chloroplast
Eukaryotic
chemoheterotroph
Eukaryotic
photoautotroph
Ancestral Archaean &
evolution of nucleus
Endosymbiosis
•  Model supported by
similarity in structure and
RNA between certain
prokaryotes and
corresponding eukaryote
organelles.
•  By alternative genetic code
(DNA sequence translation
to amino acids).
•  Mitochondria: αproteobacteria are
relatives.
•  Plastids (chloroplast and
some non-photosynthetic):
cyanobacteria are
relatives.
Aerobic
α-proteobacterium
è mitochondrion
Cyanobacterium
è chloroplast
Eukaryotic
chemoheterotroph
Eukaryotic
photoautotroph
Diatoms
Golden algae
Brown algae
Apicomplexans
Ciliates
“SAR” clade
Dinoflagellates
Alveolates
Forams
Rhizarians
Cercozoans
Radiolarians
Green
algae
Chlorophytes
Charophytes
Land plants
Archaeplastida
Red algae
Slime molds
Tubulinids
Entamoebas
Nucleariids
Opisthokonts
Fungi
Unikonta
Amoebozoans
•  Note that the vast majority
of eukaryotic diversity is
‘protistan’ and unicellular.
•  Is “Protista” monophyletic,
paraphyletic, or
polyphyletic?
•  How does this phylogeny
indicate that the difference
between paraphyletic and
polyphyletic is fuzzy?
Stramenopiles
Protist Diversity
Euglenozoans
Excavata
Diplomonads
Parabasalids
Choanoflagellates
Animals
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Euglenozoans
Stramenopiles
Diatoms
Golden algae
Brown algae
Apicomplexans
Ciliates
Forams
Rhizarians
Cercozoans
Radiolarians
Green
algae
Chlorophytes
Charophytes
Land plants
Amoebozoans
Slime molds
Tubulinids
Entamoebas
Fungi
Choanoflagellates
Animals
Euglenozoans
Stramenopiles
Diatoms
Golden algae
Brown algae
Apicomplexans
Ciliates
“SAR” clade
Dinoflagellates
Alveolates
Forams
Rhizarians
Cercozoans
Radiolarians
Green
algae
Chlorophytes
Charophytes
Land plants
Archaeplastida
Red algae
Amoebozoans
Slime molds
Tubulinids
Entamoebas
Fungi
Unikonta
Nucleariids
Opisthokonts
Choanoflagellates
Animals
Euglenozoans
Excavata
Parabasalids
Stramenopiles
Diatoms
Golden algae
Brown algae
Apicomplexans
Ciliates
“SAR” clade
Dinoflagellates
Alveolates
Forams
Rhizarians
Cercozoans
Radiolarians
Green
algae
Chlorophytes
Charophytes
Land plants
Archaeplastida
Red algae
Slime molds
Tubulinids
Entamoebas
Nucleariids
Opisthokonts
Fungi
Unikonta
Amoebozoans
Protozoans
• 
Excavata
I. 
Alveolata
II.  Opisthokonts (not
covered now)
Algal Protists
IV.  Stramenopiles
V.  Archaeplastids
Pseudopodians
VI.  Rhizarians
VII.  Amoebozoans
Excavata
Parabasalids
Diplomonads
Protist Diversity
Unikonta
Nucleariids
Opisthokonts
Protozoans
• 
Excavata
I. 
Alveolata
II.  Opisthokonts (not
covered now)
Algal Protists
IV.  Stramenopiles
V.  Archaeplastids
Pseudopodians
VI.  Rhizarians
VII.  Amoebozoans
Archaeplastida
Red algae
Diplomonads
Protist Diversity
“SAR” clade
Dinoflagellates
Alveolates
Protozoans
• 
Excavata
I. 
Alveolata
II.  Opisthokonts (not
covered now)
Algal Protists
IV.  Stramenopiles
V.  Archaeplastids
Pseudopodians
VI.  Rhizarians
VII.  Amoebozoans
Parabasalids
Excavata
Diplomonads
Protist Diversity
Choanoflagellates
Animals
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Excavata
•  Diplomonads
•  Parabasalids
•  Euglenozoans
Excavata: Parasites
•  Often anaerobic
•  What eukaryotic
feature could be
modified?
Giardia can be a severe
intestinal parasite
Excavata: Parasites
•  Diplomonads:
•  Small, simple
mitochondria
(mitosomes)
–  Not involved in cellular
respiration
–  Involved in maturation
of iron-sulfur proteins
•  Two separate nuclei
–  Function unclear, NOT
duplicated genomes
Giardia can be a severe
intestinal parasite
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Excavata: Parasites
•  Parabasilids with
reduced mitochondria:
hydrogenosomes
–  Responsible for some
anaerobic metabolism
•  Anaerobic, flagellated
protozoa
•  Include Trichomonas
vaginalis, the most
common protistan STD
Excavata: Euglenozoans
•  All characterized by
spiral, crystalline rod
inside flagella.
•  Kinetoplastids:
–  Heterotrophs including
Trypanosoma
–  Kinetoplastid: organelle
housing extraneous DNA
•  Euglenids:
–  Often mixotrophs
–  Photosynthesize in light
–  Heterotrophic via
phagocytosis in dark
Alveolata
•  What is its sister-clade?
•  Members of the
Chromalveolata probably
can photosynthesize
because of the
secondary
endosymbiosis of a red
alga.
•  Characterized by small,
membrane-bound
cavities, alveoli
Likely originated by
secondary endosymbiosis
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Figure 28.2
Plastid
Dinoflagellates
Membranes
are represented
as dark lines in
the cell.
Secondary
endosymbiosis
Apicomplexans
Red alga
Cyanobacterium
1 2
3
Primary
endosymbiosis
Heterotrophic
eukaryote
Stramenopiles
Secondary
endosymbiosis
One of these
membranes was
lost in red and
green algal
descendants.
Plastid
Euglenids
Secondary
endosymbiosis
Green alga
Chlorarachniophytes
Alveolata: Dinoflagellates
•  Marine & freshwater
–  photosynthetic (~50%)
phytoplankton
–  Some predators
–  Some parasitic on fish
•  Most unicellular
•  Cellulose “armor” and
paired flagella produce
spinning movement.
•  Explosive population
blooms result in red
tides.
Alveolata: Dinoflagellates
•  Zooxanthellae:
–  Important mutualists with
corals (also jellyfish, clams,
sea slugs, and other
protists).
•  Obligate mutualism for
many coral:
–  provide carbohydrates via
photosynthesis, get
protection.
•  Coral bleaching:
–  Death or expulsion of
zooxanthellae leads to
death of corals.
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Alveolata: Apicomplexans
•  Parasites of animals
•  Release tiny
infectious cells
(sporozoites) that
have specialized
ability to penetrate
into host cells and
tissues.
•  Complex life history
–  Sexual & Asexual
reproduction
–  Often multiple hosts
–  E.g. Plasmodium,
mosquitoes, and
humans
Alveolata: Ciliates
•  Move and feed by cilia.
•  Very diverse group with
complex cells.
–  Manage to be aggressive
predators and unicellular
•  Two types of nuclei:
macronucleus and
micronuclei (convert back
and forth).
•  Asexual reproduction via
mitosis and cytokinesis.
•  Sexual reproduction via
meiosis and conjugation
Brown algae
“SAR” clade
Dinoflagellates
Apicomplexans
Ciliates
Forams
Cercozoans
Radiolarians
Green
algae
Chlorophytes
Charophytes
Land plants
Archaeplastida
Red algae
Slime molds
Tubulinids
Entamoebas
Nucleariids
Opisthokonts
Fungi
Unikonta
Amoebozoans
•  Account for 1/2 of global
photosynthetic production
•  Various life cycles, but
alternation of generations is
key
Golden algae
Rhizarians
Accessory pigments:
Carotenoids: yellow-orange
Xanthophylls: brownish
Phycobilin: red and blue
Diatoms
Alveolates
– 
– 
– 
– 
Euglenozoans
Stramenopiles
•  Single-celled, colonial, or truly
multicellular (“seaweeds”)
•  Freshwater or marine
•  Important in aquatic food webs
•  All have chlorophyll a (the primary
pigment)
Parabasalids
Excavata
Diplomonads
Algal Protists
Choanoflagellates
Animals
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Stramenopila
•  Sister-clade to
Alveolates
•  Hair-like projections on
flagellae
•  Photoautotrophs
–  Chloroplasts derived
from eukaryotic symbiont
(recall 2’ endosymbiosis)
•  Oomycetes have lost
chloroplasts and are
heterotrophic
Stramenopila: Diatoms
(Bacillariophyta)
•  Olive-brown or
yellow
–  What pigments are
responsible for
these?
Stramenopila: Diatoms
(Bacillariophyta)
•  Olive-brown or yellow
–  Xanthophylls &
carotenoids
•  Freshwater & marine
•  Distinctive cell structure
based on silica wall
matrix.
•  Excellent index fossils.
•  Form massive
sediments.
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Stramenopila: Brown algae
(Phaeophyta)
•  Carotenoids; xanthophylls
•  Why do so many marine
photosynthesizers use
auxiliary pigments?
•  Marine, multicellular.
•  Common in cool coastal
water.
•  Some giant (100m) have
fastest linear growth of
any organism (60m/
season); e.g. Macrocystis,
giant bladder kelp.
Stramenopila: Brown algae
(Phaeophyta)
•  Truly multicellular thallus,
independently derived
separate tissue
specialization:
–  Holdfast: rootlike anchor
–  Stipe: stemlike structure
–  Blades: leaflike structure
where majority of
photosynthesis occurs
•  True alternation of
generations
Alternation of Generations
•  Life cycles in which
both haploid and
diploid stages are
multicellular.
•  Also evolved
independently in plants
and fungi.
•  Divided into haploid
gametophyte
generation and diploid
sporophyte generation
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Stramenopila: Oomycetes
•  Water molds, white rusts,
mildews
•  Heterotrophs, lack
chloroplasts
•  Important in organic
decomposition in aquatic
environments
•  Some (especially mildews)
harmful plant pathogens.
–  Potato blight Phytophthora
infestans
Archaeplastids
(the non-plant ones)
•  Rhodophyta (Red Algae)
•  Chlorophyta (Green Algae)
Archaeplastids: Red Algae
(Rhodophyta)
•  (not all red, red to black).
•  Multicellular, most marine
(some fresh).
•  Abundant in warm coastal
tropics.
•  Some in very deep water (ca
250m).
•  No flagellated stages in life
cycle.
•  Chloroplasts from primary
cyanobacteria symbiont.
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Archaeplastids: Green Algae
(Chlorophyta)
•  7,000 species, most diverse
Protista after diatoms.
•  Shared common ancestry with
plants.
•  Like red algae, chloroplasts
from primary cyanobacteria
symbiont.
–  Synapomorphy of Archaeplastids
•  Mostly unicellular
•  Mostly fresh water
Chlamydomonas, a single-cellular
freshwater green alga
Green algae life histories
•  But have quite a diversity
in life history
•  Can inhabit damp soils.
•  Can live symbiotically with
protozoa, invertebrates,
fungi
•  Note that lichens can also
be associations between
fungi and cyanobacteria or
brown algae or yellowgreen algae (a
stramenopile we didn’t
cover)
Green algae life histories
• 
Larger size and greater
complexity evolved by
three different
mechanisms:
1.  Colony formation (e.g.
Volvox in pond scum)
2.  True multicellularity,
complete with alternation
of generations (e.g. the
sea lettuce, Ulva)
3.  Supercellularity: repeated
division of nuclei with no
cytoplasmic division,
similar to fungal hyphae or
slime molds (e.g. in
Caulerpa)
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Golden algae
Brown algae
“SAR” clade
Dinoflagellates
Apicomplexans
Ciliates
Forams
Rhizarians
Cercozoans
Radiolarians
Green
algae
Chlorophytes
Charophytes
Land plants
Archaeplastida
Red algae
Slime molds
Tubulinids
Entamoebas
Nucleariids
Opisthokonts
Fungi
Unikonta
Amoebozoans
• 
Diatoms
Alveolates
• 
Eukaryotes with
Pseudopodia that move
and feed by cellular
extensions.
Pseudopodia is a generic
term for extensions that
can bulge from any portion
of the cell.
Much like “wing”, this
does not indicate
homology.
Euglenozoans
Stramenopiles
• 
Parabasalids
Excavata
Diplomonads
Pseudopodians
Choanoflagellates
Animals
Rhizarians
•  Originally united by DNA sequence data.
•  Pseudopodia are threadlike.
Rhizaria: Foraminiferans
“Forams”
•  All marine, primarily in sand,
attached to algae, or occur as
plankton.
•  Encased in multichambered,
coiled, snail-like shells (tests)
made of Calcium Carbonate
(CaCO3)
–  More than 90% of known
diversity are from fossils
–  Deposition of CaCO3 tests
creates limestones and chalks.
•  Cytoplasm can be uninucleate or
multinucleate and extends
through tests as pseudopodia.
•  Some tests >5cm in diameter.
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Rhizaria: Radiolaria
•  “ray feet” or axopodia:
numerous slender
pseudopodia reinforced by
microtubules.
•  Used for flotation and
feeding: food sticks to
axopods, engulfed and
transported by cytoplasm
•  Important component of
plankton:
–  Heliozoans in freshwater
–  Radiolarians in marine
•  Shells of silica often
deposited in sediments
Amoebozoans
• 
• 
• 
• 
“root-like foot”
Pseudopodia are lobe- or tube-shaped
Simple, naked, or shelled
Unflagellated cells that move via pseudopodia and feed
by surrounding and engulfing food (phagocytosis)
•  Sister group of lineages including fungi and animals
Amoebozoans :
Gymnamoebas & Entamoebas
•  More typical amoebas.
•  Gymnamoeba:
–  Free-living heterotrophs
on bacteria or detritus.
•  Entamoebas:
–  All parasitic;
–  No meiosis, reproduce
using various asexual
modes
–  Include Entamoeba
histolytica, responsible
for amoebic dysentery
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Amoebozoans: Slime Molds
(Mycetozoans)
•  Superficially resemble fungi
•  In cellular organization and reproduction
are obviously amoebozoans.
Plasmodial slime molds
(Myxomycota)
•  All heterotrophs, often
brightly colored.
•  Feeding stage is a large
amoeboid mass called the
plasmodium (!).
–  Not multicellular, but
multinucleated.
–  Via the process of
coenocytosis: repeated
division of nuclei without
cytoplasmic division.
Plasmodial slime molds:
“Alternation of generations”
Environmental
stress
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Cellular slime molds
(Acrasiomycota)
•  Aggregates of individual
cells that keep their
identity while feeding.
•  Haploid.
•  NOT coenocytic.
•  Reproduce asexually with
fruiting bodies.
•  Reproduce sexually as
giant cell (grows via
consuming other haploid
amoebas).
•  Probable inspiration for
scene from Terminator 3
Comparative Biology &
Cellular Slime molds
•  Researchers at UCSD
studying Dictyostelium, a
cellular slime mold, found
that two genes used to
guide the amoeba to food
sources are also used used
to guide human white blood
cells to the sites of
infections.
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