1. Evolutionary history of a group of organisms
Phylogeny
Evolutionary history of a group of organisms

2. Phylogenetic tree: ancestor-descendant relationships among populations/species

3. =Outgroup
Root
Branch
Node
Tip

4. Each phylogenetic tree is a hypothesis
Approaches
Phenetic – overall similarities between populations (genetic distance – summarizes average percentage of bases in a DNA sequence that differ) More divergent populations are on more distant branches
Cladistic: based on shared derived characters (synapomorphies)

5. Synapomorphy: a trait that exists in a certain group of organisms but exists in no others (due to common ancestry)
Monophyletic group: an ancestral species and ALL of its descendants (based on synapomorphy)
AKA: lineage, clade
ONE Snip test: if you cut a branch and all the branches and tips fall off, then it is monophyletic

6. 5 of the 6 trees listed describe the same relationship
5 of the 6 trees listed describe the same relationship. Which tree is different?

7. Homology (same source): derived from a common ancestor
Homoplasy (same form): similar but not due to common ancestry.

8. Homologous (1) or Homoplasy (2)
a. the dorsal fins of a dolphin (mammal) and a salmon (fish) b. the flippers of a dolphin and arm of a human c. a rhesus monkey’s tail and a human’s coccyx d. the bracts (red leaves) of a poinsettia and green leaves of a rose e. the bracts (red leaves) of a poinsettia and red petals of a rose f. the scales on a reptile and the feathers on a bird

9. Why don’t we place homologous characteristics on a tree twice?
Basics of Phylogeny: Cladograms
Why don’t we place homologous characteristics on a tree twice?
This implies the characteristic evolved more than once
Recall this involves a random mutation (rare event) that
happens to occur in an organism that is in an environment
where this mutation creates a favorable adaptation.
This kind of thing takes millions of years (ex. limbs evolving
on fish). Very low probability it would happen more than
once:
But if this does happen, it is called convergent evolution
Place analogous characteristics on trees, but don’t CREATE
trees using them. (Fig 27.2 )

10. Using the basics of phylogeny to construct the Tree of Life
Organism Classification: Before the Tree of Life
Linneaus
Organisms that didn’t move, made their own food: Plants.
Organisms that moved, ate others for food: Animals.
Problems with this system?

11. Organism Classification: Before the Tree of Life
II. Then…fundamental division at the cellular level between prokaryotes and eukaryotes discovered
Eukaryote: “true-kernel”
Prokaryote: “before-kernel”
~_no nucleus__
~__smaller_____________
~__Nucleus (membrane bound)___
~__larger______________

12. Organism Classification: Before the Tree of Life
III. 1960s = 5 kingdoms
prokaryotes
Set of shared characteristics defined kingdom members.
eukaryotes
Most Characteristics:
_______morphological________

13. Major Changes in Organism Classification:
The Tree of Life
Carl Woese et al: __RNA_____to study relationships
Compared gene sequence for ____16S and 18 S RNA___________
in all cells
make up part of ribosomes
location of protein synthesis
Eukaryote
Prokaryote
ribosomes

14. Why compare sequence for rRNA gene?
Ribosomes found in ALL organisms and serve
the same function
Ribsosomal RNA (rRNA) therefore in ALL organisms
The DNA that encodes for rRNA in ALL organisms
This gene happens to be HIGHLY conserved (similar)
among species but not identical
The amount of change in the DNA sequence of this gene
over time is consistent and understood

15. So what happens when organisms are
classified this way?
Major division among organisms NOT between prokaryotes and eukaryotes but between Bacteria, Archaea, Eukarya
I. Bacteria
II. Archaea
III. Eukarya
Prokaryotes
~no memb-bound organelles
(no nucleus,mitochondria, etc.)
~circular chromosomes
~single-celled
Eukaryotes
~memb-bound organelles
~linear chromosomes

16. So what happens when organisms are
classified this way?
BUT, Molecular Data conflicts with morphological data…
I. Bacteria
II. Archaea
III. Eukarya
Prokaryotes
~no nucleus,
mitochondria, etc.
~circular chromosomes
~single-celled
Molecularly Similar
~rRNA sequence
~RNA polymerase
~How DNA is
packaged in the cell

17. FYI: You should be able to
Draw both types of trees
Place characteristics on trees in correct location
Be able to recall specific characteristics that create one
tree versus the other (ex. circular vs linear chromosomes and
complex versus simple RNA polymerase) so if a tree was
drawn for you, you could come up with the correct characteristics
to place on a specific tree
Understand how work of Woese et al changed how we
classify organisms

18. Which of the following is more closely related to green algae?
Red algae because they share the MRCA
Land plants because they share the MRCA
Red algae because it is also an algae
Land plants because they also have chlorophyll (green)

19. Which of the following is more closely related to land plants?
Chordates b/c they share the MRCA at the root of the tree
Mollusks b/c they share the MRCA at the root of the tree
Land plants are equally related to Chordates and Mollusks b/c they share the MRCA at the root of the tree
Neither b/c they don’t share a MRCA

20. Jellyfish are more closely related to chordates than to fungi?
True because the MRCA of jellyfish and chordates is above the MRCA of jellyfish and fungi
True because the MRCA of jellyfish and chordates is below the MRCA of jellyfish and fungi
False because the MRCA of jellyfish and chordates is above the MRCA of jellyfish and fungi
False because jellyfish are equally as related to chordates and fungi based on their equal MRCA

21. Identify the tree that shows a different set of relationships between the 9 taxa than the other two trees.
The difference is in tree 1
The difference is in tree 2
The difference is in tree 3

22. If species a–i are a group of flowering plants, assume taxa a–d have red flowers,
taxa f–i have blue flowers, and taxa e has white flowers. Draw the locations of
flower color changes on trees 1–3. How are the three trees similar? How are they
different?

23. How do we know about the “history” in the phylogenies?
Fossil record is the only DIRECT evidence
Fossil record is biased though
Habitat bias
Taxonomic bias
Tissue bias
Temporal bias
Abundance bias

24. How do we get the “branches” on our phylogenetic trees?
Evolution.
Sometimes there is fast and huge divergence from a single ancestor
=Adaptive radiation
Why?
Ecological opportunity
Morphological innovation

25. Why don’t we see ALL the species that ever evolved?
Extinction
Background rates
Normal environmental change
Emerging disease
competition
Mass extinction (above background average)
Sudden, extraordinary environmental change