And Now Begins Our Tour of The Kingdoms.

Bacteria - the "true" bacteria

Archaea - the archaebacteria

Eukarya - the eukaryotes

The evolutionary relationships have been determined via comparison of DNA, mRNA and rRNA sequences.

Signature sequences are oligonucleotides (i.e., short sequences of nucleic acids) of unique sequence found in 16S ribosomal RNA. These are characteristic to particlar prokaryote groups, and can help to link them, phylogenetically.

These have yielded strong evidence that Archaea (specifically, thermophiles) and Eukarya are more recently descended from a common ancestor than either taxon is descended from a common ancestor with Bacteria.

We've already seen that prokaryotes display a wide array of metabolic pathways, with a variety of elements/compounds used as oxidizing agents and terminal electron acceptors.

Eukarotes use only two pathways:

• aerobic cellular respiration (oxygen as terminal electron acceptor)

• fermentation
  

This, too, suggests that prokaryotes may have evolved several times, whereas eukaryotes are more likely to share a common ancestor.

There are two models that can be combined to explain eukaryotic origin:

• The Autogenous Model
  Eukaryotes arose when the outer membranes of ancestral prokaryotes underwent extensive inpocketing and pinching off to form complex internal network of membranes.
  • Evidence: some extant species of cyanobacteria (e.g., Gloeocapsa) have complex internal membrane systems and resemble simple chloroplasts.

• The Endosymbiont Model
  Proposed by Lynn Margulis (University of Massachusetts), this model holds that small, energy-transducing prokaryotes were either
  • ingested as prey
  • internal symbionts
  inside larger prokaryotes, where they survived and thrived. Eventually, host and symbiont became inextricably linked in a symbiotic relationship.

  Evidence:

  • such symbioses exist today (e.g. Giardia, a basal (i.e., very primitive) flagellated protist has symbiotic, energy-transducing bacteria instead of mitochondria and two haploid nuclei.)

  • there are extant species of cyanobacteria and heterotrophic bacteria that strongly resemble chloroplasts and mitochondria, respectively.

  • the enzymes embedded in mitochondrial and chloroplast internal membranes are more similar to those of prokaryotes than they are to other enzymes found in eukaryotes

  • ribosome enzymes in the mitochondria and chloroplasts are more like those of prokaryotes than those of eukaryotes

  • mitochondria and chloroplasts have their own genome, separate from and largely independent of the nuclear genome.

  • mtDNA and cpDNA are circular, and though there may be multiple copies, all are genetically identical within a given cell (hence, these organelles are--like bacteria--essentially haploid
  • mtDNA and cpDNA circular chromosomes have no associated histones or RNA

  • cytochromes and other transport proteins used in mitochondria and chloroplasts are made in situ, without cooperation from nuclear genome enzyme products.

  • mitochondria and chloroplasts reproduce via binary fission very similar to that seen in prokaryotes.

  • nucleus, mitochondria and chloroplasts all have a double membrane.

Here's an overview of the two models and how they both contributed to eukaryotic origin:

The typical cladogram we saw earlier could be modified to account for this combining of ancestral lineages:

And only recently has the important role of viruses become clear in the evolution of eukaryote genomes.

The Earliest Eukaryotes

The Earliest Eukaryotes were Protists

The oldest known eukaryote fossils (2.1 billion years old, found in pre-Cambrian fossil beds in Michigan) are called acritarchs.

acrit = "confused" (Gr)

arch = "beginning" (Gr.)

What do protists have in common?

Protists may be

• unicellular
• colonial
• colonial with a division of labor among cells

• planktonic (free-floating in a marine or freshwater water column)
• terrestrial

• photoautotrophic
• chemoheterotrophic, including
  • predatory
  • parasitic
  • commensal
  • mutualistic
  • detritivorous (feeding on dead, organic matter and turning it into smaller organic molecules, but NOT decomposing it)

A Sampling of Interesting Protists

Very Ancient Protists of Uncertain Evolutionary Affinity

This is a polyphyletic assemblage akin to the former "Kingdom Protista," as it contains a variety of protists whose evolutionary affinities are not clear. A broad, non-committal overview of the most primitive protists can be seen here.

Diplomonads and Parabasalids

• it is flagellated (though flagellum has typical eukaryote morphology: two central microtubules surrounded by nine paired microtubules)

• pathogenic; causes giardiasis
• mitochondria are reduced, and lack DNA
• Giardia lacks any type of plastids
• lacks electron transport chain proteins or any enzymes associated with aerobic respiration.
• usually lives in anaerobic conditions
• has a very simple cytoskeleton
• contains two haploid nuclei
• Is Giardia's anatomy a holdover of its ancestor's autogeny? Or endosymbiosis? Or both?

Did the diplomonads and parabasalids branch off the evolutionary tree before mitochondrial incorporation and before karyogamy of an ancestral eukaryote? (Remember: prokaryotes are essentially haploid).

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Euglenozoa

This includes

• euglenoids
• kinetoplastids (such as Trypanosoma spp., the causative agents of such deadly diseases as Chaga's Disease, leishmaniasis and "Sleeping Sickness", more accurately known as African Trypanosomiasis.)

  Along with many other flagellum-bearing protists, euglenoids and kinetoplastids were once lumped in the now-defunct, polyphyletic taxon Mastigophora (mastig = "whip"; phor = "to bear").

  This should be a reminder about that symplesiomorphies are not informative when one is trying to construct monophyletic taxa. The flagellum (and its shorter cousin, the cilium is a very ancient, widespread eukaryotic structure. It gives little information useful for classifying anything with a flagellum into a less inclusive taxon.

  However, the flagellum of the euglenozoans has a unique feature: a spiral or crystalline rod inside the protein filaments. It's function is unknown, but this unique feature of the flagellum is derived, and so its presence has been used as a synapomorphy that links the Euglenoids into a single, putatively monophyletic taxon.

  Also unique to euglenoids are disk-shaped cristae in the mitochondria. The two very basic characters suggest monophyly of the euglenoids, kinetoplastids, and a few other small groups of Euglenozoans.

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Alveolata

These are linked by the presence of alveoli under the plasma membrane, which is highly complex in function and anatomy.

This group includes the

• dinoflagellates
  (check out some nice dinoflagellate images
• economicall important apicomplexans (parasits formerly known as "sporozoans")
• the hugely diverse ciliates (among the most complex protists)

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Stramenopila

Their name comes from the Latin stramen ("straw") and pilos ("hair")). The taxon gets its name from its fuzzy flagellum, which is often paired with a smooth one. Flagellated cells occur in all members of this taxon, though in some highly derived groups, they occur only during reproductive cycles and function as gametes. This group includes the

• Diatoms - (Bacillariophyta)

• Brown Algae - (Phaeophyta)

• Golden Algae - (Chrysophyta)

• Water "molds" - (Oomycota)

The diversity of their names reflects that biosystematists once thought these organisms belonged to taxa as diverse and different as "algae" (whatever that means) and fungi. They now are believed to be monophyletic.

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