1. Agenda 10/8 Seashell Sort Phylogeny Lecture Phylogenetics Pracice
Homework:
1. Chp 26 Reading and Notes
2. Phylogeny Video and Notes

2. Seashell Sort How did your sort them into groups?
Did it feel accurate?
What additional data could you collect to learn more about the relationship between these organisms?

4. Macroevolution How do new species form? Why do new species form?
How do we classify a species?
What evidence do we have for evolution?

5. How are organisms classified?
Classifying living organisms began with Carolus Linnaeus (18th Century)
Classifications were based on structural similarities
A hierarchal scheme was made
Broadest group: Kingdom
Most specific: Species
This field is called taxonomy

6. Domains: A recent development
Carl Woese used a different type of evidence- genetic sequencing
He looked at a piece of rRNA that all living things possess, and compared the sequences
He noticed difference between prokaryotes and eukaryotes, but also that two distinct groups were within prokaryotes
3 Domain System
Eukarya
Archaea
Bacteria

7. Tree of Life

8. Phylogenetic Trees
Phylogeny is the study of evolutionary relationships among a group of organisms
Phylogenetic trees are like a family tree that shows the evolutionary relationships of a group of organisms through evolutionary time
Phylogenies are based on
Morphology and fossil record
Embryology
DNA, RNA, protein sequence similarities ***

10. Cladogram vs. Phylogenetic Trees
Most of the time these are used interchangeably but…
Cladogram: Hypothesis
Phylogenetic Tree: ‘True’

11. Parts of a Tree What could cause a branch point?

12. Classification over time
DNA and protein analysis have changed how we think about classification
The old Linnaean system might still match up with DNA/protein data, but a lot of changes occurred
For example, based on protein/DNA sequencing birds and now classified as true reptiles

13. Taxa
A taxon is any group of species designated by name. Every node should give rise to two lineages. If more than two linages are shown, it indicates an unresolved pattern of divergence or polytomy.
Graphic from Campbell
Be aware this unit introduces a lot of vocabulary such as polytomy. Explain polytomy is understood to be temporary, since the hope is that sometime future evidence will resolve the polytomy. The resolution will determine which group evolved from which group.
Also note that nodes have only two branches versus polytomy which have more than two branches.

14. Sister Taxa
Sister taxa are groups or organisms that share an immediate common ancestor. Also note the branches can rotate and still represent the same phylogeny.

15. Definition of a clade
A clade is any taxon that consists of all the evolutionary descendants of a common ancestor
Each different colored rectangle is a true clade.
Students need a clear understanding of cladistics. (Graphic: Understanding Evolution web site.)

16. With your elbow partner, describe 5 different techniques scientists can use to construct a cladogram or phylogenetic tree.

17. Molecular Clocks
Homologous structures are coded by genes with a common origin. These genes may mutate but they still retain some common and ancestral DNA sequences.
Genomic sequencing, computer software and systematics are able to identify these molecular homologies. The more closely related two organisms are, the more their DNA sequences will be alike.
The colored boxes represent DNA homologies.
 Shows two copies of the DNA base sequence (DNA 1 and DNA 2) for the original gene.
 Ask students what happened between  & : Hopefully they answer that the genes are experiencing mutations. DNA 1 has its first group showing a deletion (circled G) and the second group has an insertion of GTA.
 Comparing the two genes base by base shows they do not line up very well are a result of the two mutations.
 Careful analysis involving a computer program would reveal the homologous sequences and line them up accordingly.
Graphic Campbell 8th edition.

18. Molecular Clocks
The molecular clock hypothesis states: Among closely related species, a given gene usually evolves at reasonably constant rate.
These mutation events can be used to predict times of evolutionary divergence.
Therefore, the protein encoded by the gene accumulates amino acid replacements at a relatively constant rate.
Graphic Campbell 8th edition.
Here’s a nice reference website:

19. Molecular Clocks
The amino acid replacement for hemoglobin has occurred at a relatively constant rate over 500 million years.
What does the slope represent?
Different genes evolve at different rates and there are many other factors that can affect the rate.
Predict how many amino acid differences would be changed if 800 million years passed by.
Student may have to interprets molecular clocks on the AP exam. They should know that a linear graph represents a constant rate of change and that the slope of the line allows them to predict how many amino acids would change over a given time span.
Ask the students to predict how many amino acid would be changed if 800 million years had passes by. (ANSWER: about 1.4—use a simple proportion, if 500 million years resulted in about 0.85 AA differences, then (800 x 0.85) ÷ 500 = 1.36 AA differences OR you can use points (0,0) and (500, 0.9) and use the 2-point slope formula to obtain the slope, then plug into y=mx + b and solve. Student’s know this lingo from math class! ) Either way, you arrive at about 1.4 AA differences.
Graphic

20. Molecular Clocks
Molecular clocks can be used to study genomes that change rather quickly such as the HIV-1 virus (a retrovirus).
Using a molecular clock, it as been estimated that the HIV-1 virus entered the human population in 1960’s and the origin of the virus dates back to the 1930’s.

21. Making a Cladogram Based on Traits
Examine the data given.
Propose a cladogram depicting the evolutionary history of the vertebrates.
The lancet is an outgroup which is a group that is closely related to the taxa being examined but is less closely related as evidenced by all those zeros!
The taxa being examined is called the ingroup.
Let the students use information in the table and construct a cladogram. Tell the student that using a 1 vs. a 0 is simply one convention with regard to presenting the data. Sometimes + and - are used or perhaps an X and nothing at all in the table.

22. Making a Cladogram Based on Traits
Note that each trait exists only after the group divides into two.
Graphic from Campbell.