1. History of Protistology

Zacharias Janssen

1580-1638

(together with his fatherHans Janssen)

Antonivan Leeuwenhoek

1632-1723

                                           

Carolus Linnaeus 1707-1778

CRYPTOGAMIA

One of 25 classes of plants, containingall plants with ‘concealed’ reproductive organs, i.e. all plants lacking both seedsand flowers.

1. Algae2. Fungi3. 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 Treeof Organisms

Ernst Häckel1866

PROTISTS

All unicellular eukaryotes, including the protozoa and all unicellular, eukaryoticalgae

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 thisprinciple, by which each slight variation, if useful, is preserved,by the term naturalselection”

Linnaean Classification

• Based exclusively on morphological similarity

• Hierarchical system independent of evolutionary theory, no assumptions on ‘relatedness’ are made

Phylogeny:

Evolutionary history oforganisms, both livingand 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 SHARED-DERIVED (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 bestrange 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