1. History of Protistology
Zacharias
Janssen
1580-1638
(together with his father
Hans Janssen)
Antoni
van Leeuwenhoek
1632-1723
Carolus Linnaeus
1707-1778
CRYPTOGAMIA
One of 25 classes of plants, containing
all plants with ‘concealed’ reproductive
organs, i.e. all plants lacking both seeds
and flowers.
1. Algae
2. Fungi
3. Bryophyta (mosses and liverworts)
4. Pteridophyta (ferns and relatives)
Carolus Linnaeus, 1754
ALGAE
-(Mostly) aquatic, photosynthetic organisms
-Originally defined by characters that they LACK, not
by characters that they have
-Algal groups are NOT closely related to one-another
-The term ‘alga’ is very useful in an ecological sense,
but not at all in a systematic/taxonomic sense
PROTOZOA
-Term coined by Georg August Goldfuß in 1818:
PROTO: First
ZOON: Living Creature, later ‘animal’
-Current usage introduced by Carl Theodor von
Siebold (1845) to describe what he thought were
unicellular animals
-We now know that most protozoans are NOT closely
related to multicellular animals
Ernst Häckel
1834-1919
Monophyletic Tree
of Organisms
Ernst Häckel
1866
PROTISTS
All unicellular eukaryotes, including the
protozoa and all unicellular, eukaryotic
algae
Problems with the definition
of protists (1)
• Multicellularity evolved several times in
the history of life, not only in the branches
that lead to animals, plants and fungi.
There are multicellular heterokonts (i.e.
brown algae), dinoflagellates, etc. Should
we consider them protists?
Problems with the definition
of protists (2)
• Yeasts, microsporidians and
myxozoans are all examples of
unicellular eukaryotes with
multicellular ancestors. If we agree to
consider them protists, the group
becomes polyphyletic
Problems with the definition
of protists (3)
• There are types of cellular organization in
protists that are not unequivocally uni- or
multicellular
– Cellular Slime Moulds
– Plasmodia, e.g. in dinoflagellates, plasmodial slime
moulds, apicomplexans
– Obligate colonial forms, sometimes with cell
differentiation, eg. in ciliates (Zoothamnion) and in
many lineages of green algae
An alternative definition
• Protists are all eukaryotes that are
not animals, plants or fungi
• BUT: We’ve moved back to a
negative definition, based on
characters that these organisms
LACK and not on those they SHARE
What protistologists do
given all this…
• We don’t worry too much about
definitions and focus on the
organisms instead. And we relish on
the morphological and genetic
diversity of the organisms that we
get to study
Traditionally (i.e. until
1960’s)
• PROKARYOTES
– Monera (bacteria)
• EUKARYOTES
– Animals, incl. Protozoa (sarcodines,
flagellates, ciliates and sporozoans)
– Plants, incl. Fungi and Algae (greens,
reds, browns, diatoms and many kinds
of flagellates)
Problem Groups
• Dinoflagellates
• Euglenoids
• “Claimed” by both zoologists and
botanists
Charles Darwin
1809-1882
“I have called this
principle, by which
each slight variation,
if useful, is preserved,
by the term natural
selection”
Linnaean Classification
• Based exclusively on morphological
similarity
• Hierarchical system independent of
evolutionary theory, no assumptions
on ‘relatedness’ are made
Phylogeny:
Evolutionary history of
organisms, both living
and extinct
(Häckel, 1866)
Phylogenetic Classification
• Attempts to reflect the evolutionary
history of organisms; taxa thought to
be closely related are classified
together
• Morphological similarity is a tool to
investigate phylogeny, not the sole
criterion for classification
How?
• Distinguish between HOMOLOGOUS
and ANALOGOUS structures
(convergent evolution)
• Distinguish between SHAREDDERIVED (useful) and either
ANCESTRAL or UNIQUE characters
(not useful)
Why?
• A phylogenetic classification lets you
make PREDICTIONS about some of the
characteristics of the members of the
group
• A phylogenetic tree gives you a framework
on which one can trace the evolution of
particular characteristics
Phylogeny vs. taxonomy
• PHYLOGENY: Evolutionary history of
organisms, often represented as a
tree. There is just one true phylogeny
of organisms.
• TAXONOMY/CLASSIFICATION refers
to the way we CHOOSE to carve the
phylogenetic tree into groups we find
useful. A very subjective thing.
Monophyletic Group
• Includes the most
recent common
ancestor of a group
of organisms and all
of its descendents
• Plants, diatoms,
primates, alveolates,
opisthokonts
Polyphyletic Group
• A collection of organisms
in which the most recent
common ancestor is not
included (usually because
it is not likely to share the
characteristics of the
group)
• Algae, worms, trees,
amoebae, flagellates
Paraphyletic Group
• Includes the most
recent common
ancestor of a group
of organisms and
some but not all of its
descendents
• Reptiles, green algae,
dinosaurs, fish
Problem
• The term “monophyletic” is sometimes
used for all groups that share a common
ancestor, whether all its descendents are
included or not (i.e it CAN include
paraphyletic groups)
• Many people consider it an ambiguous
term
• They use the term “holophyletic” instead
But…
• In order to know whether a group is
mono-, para- or polyphyletic, one
needs to know the topology of the
underlying phylogenetic tree
• And exactly that is the problem…
Covered with cilia, in the past they were considered to be
strange ciliates, but details of their ultrastructure are very
different from those of ciliates. But what are they?
HETEROKONTS
Morphological data has its
limitations
• It is not always easy to distinguish
between homologies and instances
of convergent evolution (analogies)
• Some groups, in particular within the
protists, have very little morphology
to work with (the little-brown-ball
syndrome)
Molecular Phylogeny
Eric Streitwieser
“Endless DNA”
Advantages of molecular data
for phylogenetic studies (1)
• Many molecular markers are shared in all
life, allowing for direct comparisons of
very distantly related groups
• There is a very large pool of characters to
compare; the total data set is as large as
the genome size
Advantages of molecular data
for phylogenetic studies (2)
• Morphological change and molecular
divergence are relatively independent
from each other
• Different degrees of variation exist in
different molecules, they can be used to
investigate phylogenetic questions at
different levels
Alignment
Archaezoans
• Eukaryotes that never had
mitochondria. Originally included:
– Microsporidians
– Archamoebae (e.g. pelobionts)
– Metamonads (incl. Diplomonads and
Trichomonads)
The collapse of the
Archaezoans
• Mitochondrial genes were found in the
nucleus of all groups of archaezoans; this
means that they all had mitochondria and
have lost them secondarily
• Phylogenetic trees based on protein
genes don’t put any of the archaezoan
groups at the base of the phylogenetic
tree
Our current view
• There are no living archaezoans
• The common ancestor of all living
eukaryotes was mitochondriate
We have a problem!
• Molecular phylogenetic trees
based on different genes are not
always congruent with each
other!
Limitations of molecular data
for phylogenetic studies
• Methodological problems of tree construction
(e.g. long branch attraction, mutational
saturation, etc.)
• Molecular data can’t normally be obtained from
fossils. This puts 99% of the organisms that have
ever lived out of reach
• In many cases, even very large amounts of data
(whole genomes) have failed to provide strong
support for any particular topology of the
phylogenetic tree
• Genes have sometimes a different evolutionary
history than the organisms they are found in!
(e.g. lateral gene transfer)
Will we ever be able to determine the
topology of the phylogenetic tree of
life?
• Maybe. But this is not at all a certainty.
• The topologies of branches that involve
rapidly-evolving taxa (for example in rapid
radiation events) are going to be
extremely difficult to resolve, because
rapid speciation events leave little time for
informative mutations to be established in
genes.
Trends for the future
• We’ve only started to tap into the wealth on
information provided by molecular data. Expect
many more gene sequences from a greater
variety of organisms in the future
• New types of phylogenetic data will become more
important, for example positions of genes within
chromosomes (genomics)
• New kinds of morphological data are also starting
to become available from the fields of cell biology
and protein biology
Back to the past
• BUT: it is surprising the amount of very
basic biology that we still DON’T know
about many protists, things like
development, life cycles, cell ploidies and
the presence or absence of sex.
• One of the best ways of learning new
things about protists is one of the oldest
ones: sitting in front of the microscope
and LOOKING
Conclusions (1)
• Our understanding of the biology of
protists has been determined to a very
large degree by the technologies that have
been available to study them
• Molecular methods have proved to be very
powerful for resolving phylogenetic
questions, but they also have important
limitations.
Conclusions (2)
• The best phylogenetic studies are
those that use ALL kinds of data
available. Both morphological and
molecular methods have important
advantages and disadvantages, and
they work best when they are used to
complement each other