Chapt 28: EUKARYOTES: CELLULAR DIVERSITY

OUTLINE

I. History -- Geological History <<>> Biological History

II. WHAT IS A EUKARYOTE?

LIFE CYCLES

III. WHERE DID THE NUCLEUS COME FROM?

IV. WHERE DID ORGANELLES COME FROM?

V. CLASSIFICATION: PROTISTS

VI. PHYLOGENETIC TREES

VII. THE TAKE HOME LESSON...

I. History -- Geological History <<>> Biological History

 

Age of Earth	4.5 billion years	radioisotopic dating of meteorites formed during formation of solar system
Earliest Common Ancestor	3.5-4 billion years	formation of solid crust vs. observation of oldest fossils; carbon isotopes indicate 3.8by metebolic activity (Greenland)
Oldest Prokaryotic Fossils	3.5 billion years	possible cyanobacteria bacteria (autotrophic - photosynthetic). Western Austrailia stromatolites (Fig 26.1)
Oldest Eukaryotic Fossils	2.1 billion years	possible eukarytic algae, Michigan (Han & Runnegar, 1992, Science 257:232) Giardia - "intermediate form" ...two nuclei, no mitochondria
Multicellular Eukaryotes	1-1.2 billion years	projected from on DNA sequence analysis
Cambrian "Explosion" (Animals)	500 million years	Burgess Shale Fossils Many of current animal phyla (echinoderms, annelids, arthropods, chordates). appearance of skeletons thought to be in response to predation. Summary of animal evolution: Fig. 32.3. Summary of chordate evolution: Fig. 34.6.
Origins of Plants from green algae	460 million years	Fossil Record Summary of Plant evolution: Fig. 29.3.
Vascular Plants	400 million years
Gymnosperms	360 million years	"naked seeds", conifers, etc.
Angiosperms	130 million years	"contained seeds", flowering plants
Oldest Vertebrates	500 million years	jawless, fishlike, fig. 34-36
Oldest Jawed Vertebrates	500 million years	Hox gene duplications
Oldest Bony Fishes	425-450 million years
Oldest Amphibians	365 million years	fig. 34-36
Oldest Reptiles	300 million years	fig. 34-36
Oldest Birds	150 million years	fig. 34-36
Oldest Mammals	220 million years	fig. 34-36
Homo erectus	1-2 million years	fig. 34.30, 34.33
Homo sapien	100,000 years	fig. 34.30, 34.33

II. WHAT IS A EUKARYOTE?

             |------- Bacteria < PROKARYOTES
             |
             |                  NO Nucleus, No Organelles
Earliest     |
Common ------|   |--- Archaea  < PROKARYOTES
Ancestor     |   |            (extreme: thermophyles, etc.)
             |---|
                 |
                 |--- Eucarya  < EUKARYOTES (Nucleus, organelles)
                               Microsporidia, Diplomonads,
                               Trichomonads, Flagellates,
                               Entamoebae, Slime molds,
                               Cilliates, Fungi,
                               Plants, Animals 

---

1. Cells. (Review Chapter 7; Figure 7.7, 7.8)

2. Nuclear membrane - compartmentalizes genome,

linear DNA, introns, chromosome pairs, diploid / haploid

3. Intracellular membrane network (endomembrane)

endoplasmic reticulum - protein synthesis, secretion, plasma membrane proteins
golgi apparatus - secretion

4. cytoskeleton - microtubules, actin

5. mitochondria - organelle, mit. DNA, double membrane -- electron transport / ATP

6. chloroplasts - organelle, chlor. DNA, inner / outer membranes -- photosynthesis

7. cilia (microtubules), flagella (9+2 microtubules)

8. mitosis - meiosis

---

LIFE CYCLES

1. Haploid (N) vs. Diploid (2N)
Eukaryotic genomes are organized into linear chromosomes.
At some point in their life, Eukaryotic species have two copies of each chromosome.
"N" is used to symbolically represent the "single copy complement" or haploid condition.
"2N" is used to represent the "double copy complement" or diploid condition.

2. Life Cycle is a description of the haploid and diploid states (forms) of the organism, and the transitions between. The organism "alternates" between the haploid and diploid condition in an ongoing cycle.

3. A significant component of this course will focus on these haploid and diploid stages.

4. Examples: Fig. 28.9, 28.13, 28.20, 28.24, 28.25

sexual vs. asexual reproduction, spores, gametes, meiosis, mitosis, haploid, diploid, syngamy

III. WHERE DID THE NUCLEUS COME FROM?

Ancient lineages?: Giardia, pair of nuclei but no organelles (Fig. 28.4)

Nuclei but no organelles suggests that a nucleus may have been acquired first, and organelles second, and suggests that Giardia represents an early and transitional state of the Eukarya. Situating Giardia at the base of the Eukaryotic lineage is further supported by nucleic acid analyses (rRNA) suggesting that Giardia is the product of a very early division of the Eucharya. However, DNA analysis indicates that Giardia once possessed mitochondria. Giardia contains mitochondrial genes. Presumably some mitochondiral genes were transferred to the Giardia nuclear genome and the trait of possessing mitochondria secondarily lost. Giardia has in interesting if unclear record of its long history written in its genome.

Suggestion: Nuclear membrane a consequence of infolding of the plasma membrane. Selective Advantage? Compartmentalization?

nuclear envelope
• holes (nuclear pores) to let mRNA out, nucleotides, ATP, hormones and nuclear hormone receptors in.
• must dissemble and reassemble for mitosis / meiosis.

IV. WHERE DID ORGANELLES COME FROM?

Support for Endosymbiont Theory:
Mitochondria and Chloroplasts are of similar size as bacteria.

Mitochondria and Chloroplasts have complex double membrane systems, similar to bacteria.

Mitochondria and Chloroplasts are somewhat self-contained, as if they derived from functional cells.

Mitochondria and Chloroplasts divide by binary fission, similar to bacteria.

Mitochondria and Chloroplasts contain circular DNA, like bacteria, which contains genes encoding organelle specific proteins.

Mitochondria and Chloroplast DNA contains no Introns, same as bacteria (Eukaryotic genes contain introns).

Mitochondria and Chloroplasts contain tRNAs, ribosomes, etc. to translate their own mRNAs into protein.

Molecular evidence.

1. Mitochondrial rRNA is most similar to rRNA of Agrobacterium (symbiontic nitrogen fixing bacteria of plant roots.

2. Chloroplast rNRA is most similar to rRNA of Cyanobacteria (photosynthetic bacteria).

3. One subset of Mitochonrial proteins are encoded by mitochondrial genes and a second subset of mitochondrial proteins are encoded by nuclear genes. Interestingly, the mitochondrial genes contain NO introns, while the nuclear genes DO contain introns. Even more interesting, both the nuclear and mitochondrial genes which encode mitochondrial proteins are more similar to prokaryotic homologues than they are to eukaryotic homologues. Together, this suggests that nuclear mitochondria genes originated in their mitochondrial precursor prokaryote, and migrated to the nucleus where they later incorporated introns by whatever mechanism caused introns.

V. CLASSIFICATION: PROTISTS

                 Named       Estimated
                 Extant      Number
                 Species     Species

Prokaryotes        5K       400K - 4M
Eukaryotes
  Protists        60K          
  Plants          300K 
  Fungi           100K        1.5M
  Animals         1.5M         30M

What is a Protist? I don't know what it means but I know one when I see it! (?)

"Protist" refers to simple eukaryotic organisms, and includes the unicellular eukaryotes as well the uni-cellular and multi-cellular algae. It does not include Plants, Animals, or Fungi.

Major Divisions: Kingdoms

Old Scheme: Five Kingdoms

1. Monera - Prokaryotes, bacteria-like organisms (awkward designation)

2. Protista - Eukaryotes, but single celled or "simple" (awkward designation)

3. Plants - Plants - Autotrophic, complex

4. Fungi - Fungi

5. Animals - Everything else... Animals - Heterotrophic, Eukaryotic

Problem: Divisions should be monophyletic, the Five Kingdom scheme is not.
Separating Plants, Fungi and Animals from the Protista makes Protista NOT monophyletic, they share their common ancestor with Plants, Fungi and Animals. So, either reduce the number of Kingdoms to Prokaryote vs. Eukaryote, or increase the number of Kingdoms so that each Kingdom is monophyletic. Kingdoms really become a division of convenience. (see Campbell, Fig. 26.26, p. 542)

Summarized from Campbell: Four of the Five Kingdoms: From the Five Kingdom Scheme (ARTIFICIAL!!!!! / AWKWARD!!!!!)

VI. PHYLOGENETIC TREES

Phylogenetic Trees are Hypotheses of the True relationships (Evolutionary relationships) of organisms.

Phylogenetic Trees may be based on physical/morphological characters (traits or features) and/or DNA sequences.

Some characters and sequences are considered more appropriate than others for use in constructing these trees.

The resulting Hypothesis is therefore subject to (biased by) the individual choices made by the person constructing the Tree.

Phylogenetic Trees may never be True (represent the true evolutionary history); but if they are done carefully, they can be very close to the true history.

If a Phylogenetic Tree is based on Derived Traits (called Synapomorphy, p. 483), then the branch points and branch lengths imply time. How much time is not clear, since we can not always say how fast certain changes have occured. But an earlier branch point implies that the change occured at an ealier time in the history of the earth.

Woese, (1996), rRNA sequences

           EUCARYA
   |------------------------Microsporidia
   |
 ==|  |---------------------Diplomonads (Giardia,fig.28.4)
   |  |
   |--|  |------------------Trichomonads
      |  |
      |--|  |---------------Flagellates (Euglena)
         |  |
         |--|  |------------Entamoebae (Rhizopoda, Amoebas)
            |  |
            |--|  |---------Slime molds (Dictyostelium)
               |  |
               |--|  |------Ciliates (Paramecium, Stentor)
                  |  |
                  |--|  |---Plants
                     |  |
                     |--|---Animals
                        |
                        |---Fungi (yeast, mushrooms, etc)

   |-----------------------------------------Diplomonads (Giardia)
   | 
 ==|  |--------------------------------------Microsporidians
   |  |
   |==|  |-----------------------------------Trichomonads
      |  |
      |==|  |--------------------------------Euglenoids (Euglena)
      |  |  |
         |==|  |-----------------------------Kinetoplastids
            |  |
            |==|  |--------------------------Amastigote amoebae
               |  |  
               |==|  |-----------------------Entamoebae
                  |  |
                  |==|  |--------------------Slime molds
                     |  |
                     |==|  |-----------------Red algae
                        |  |
                        |==|  |--------------Apicomplexans
                           |  |
                           |==|  |-----------Dinoflagellates, Ciliates
                              |  |
                              |  |  |--------Chromophytes 
                              |==|  |   (Brown algae, Chrysophytes, 
                                 |  |  Xanthophytes),Oomycetes, Diatoms
                                 |==|
                                    |  |-----Green algae, Plants
                                    |  |
                                    |==|  |--Fungi
                                       |==|
                                          |--Animals

                                     P
     |-----------------------------------Archezoans (Giardia)
     |  (1)                          P
     |              P  |-----------------Eugleoids 
     |     |-----------|             P
     |     | (2)       |-----------------Kinetoplastids
=====|     |     
     |     |                         P
     |     |        P  |-----------------Ciliates
     |=====|     |-----|             P
           |     | (3) |-----------------Dinoflagellates 
           |     |
           |     |                   P
           |     |              P  |-----Brown Algae
           |     |        P  |-----| P
           |     |     |-----|     |-----Water Molds
           |     |  P  |     |       P
           |     |-----|     |-----------Golden Algae
           |     | (4) |             P
           |     |     |-----------------Diatoms
           |     |
           |     |                   P
           |=====|-----------------------Red Algae
                 |
                 | (5)               P?
                 |                 |-----Green Algae
                 |=================|        
                 | (6)             |-----PLANT KINGDOM
                 |         
                 |
                 |-----------------------FUNGI KINGDOM
                 | (7)  
                 |
                 |-----------------------ANIMAL KINGDOM
                   (8)

Monophyletic Divisions

1. Archaezoa
2. Euglenozoa
3. Alveolata
4. Stramenopila
5. Rhodophyta
6. Plant
7. Fungus
8. Animal

"P" = Protist Group (descriptive, not monophyletic)

The numbered branches above represent branches containing major monophyletic groupings of taxa. Taxa within these branching patterns are presumed to share a common ancestor which was distinct from other major groupings.

VII. THE TAKE HOME LESSON...

1. that organisms are many and diverse.

2. that diversity is a consequence of evolution, of lineage by descent.

3. that lineages should be defined based on their monophyletic origins (common ancestry).

4. that understanding these lineages allows us to understand the true relationships between diverse organisms.