1. Agenda Microevolution Test Reflection
Seashell sort and ‘Click and Learn’
Phylogeny lecture/practice
Warm up: Begin working on ‘Microevolution Review’ sheet
Turn in: Video notes

2. Ms. Poole’s 5 Takeaways 1. Math Review 2. Reading Carefully 3. Timing
Any math we cover previously is far game
Remember- I am prepping you for the AP bio test, not just one unit at a time.
2. Reading Carefully
If it ask for an example in plants, don’t give an example in animals
3. Timing
No need to restate question
Underline important information

3. Ms. Poole’s 5 Takeaways 4. Choose the best answer 5. Content Review
Don’t make huge assumptions
Think about what conclusions they are expecting you to draw
5. Content Review
If we spend a class day on it, read about it, and watch a video, it is probably pretty important

4. Macroevolution Part I:
Phylogenies

5. With your elbow partner, beginning sorting the seashells into groups
With your elbow partner, beginning sorting the seashells into groups. Write down your rationale for your groups on your dry erase board. Be sure to also look at the back of the cards

6. On your board, write a summary of how your groups differed from the actually cladogram of the seashells after completing the click and learn

7. What does macroevolution mean? What will we be studying?

8. Taxonomy
Classification originated with Carolus Linnaeus in the 18th century.
Based on structural (outward and inward) similarities
Hierarchal scheme, the largest most inclusive grouping is the kingdom level
The most specific grouping is the species level
Point out that Linnaeus had the kingdom as the highest or largest grouping. The domain concept is recent. Relate to the students that at first there were just two kingdoms. The addition of the third kingdom, Protista occurred The addition of the fourth kingdom Monera occurred in The addition of the fifth kingdom, Fungi occurred in Finally, in 1977 the Monerans were split into the Bacteria and Archeabacteria.

9. Taxonomy
Taxonomy is the classification of organisms based on shared characteristics.
Under the three-domain system of taxonomy, which was established in 1990 and reflects the evolutionary history of life as currently understood, the organisms found in kingdom Monera have been divided into two domains, Archaea and Bacteria (with Eukarya as the third domain). The term "moneran" is the informal name of members of this group and is still sometimes used (as is the term "prokaryote") to denote a member of either domain.

10. Domains- A Recent Development
Carl Woese proposed three domains based the rRNA differences prokaryotes and eukaryotes. The prokaryotes were divided into two groups Archaea and Bacteria.
Organisms are grouped from species to domain, the groupings are increasingly more inclusive.
The taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species.
Why is taxonomy important to evolution?
Point out that Archaea was thought to be very ancient but many are beginning to believe that is not the case because of rRNA evidence. The graphic indicates that Eukarya and Archaea had a more recent common ancestor than Bacteria and Eukarya. Also mention that Archaea often live in some very extreme environments. Some species can tolerate very high temperatures, others high salinity, and others low pH.

11. Phylogenetic Trees
Phylogeny is the study of the evolutionary relationships among a group of organisms.
A phylogenetic tree is a construct that represents a branching “tree-like” structure which illustrates the evolutionary relationships of a group of organisms.
Phylogenies are based on
Morphology and the fossil record
Embryology
DNA, RNA, and protein similarities
The importance of students understanding cladograms and phylogenetic trees cannot be over emphasized. Many biologist use them interchangeably. The subtle difference is cladogram is used to represent a hypothesis about the evolutionary history of a group of organisms. A phylogenetic tree represents the true evolutionary history of a group of organisms.

12. Phylogenetic Trees Basics
Phylogenies can be illustrated with phylogenetic trees or cladograms. Many biologist use these constructs interchangeably.
A cladogram is used to represent a hypothesis about the evolutionary history of a group of organisms.
A phylogenetic tree represents the “true” evolutionary history of the organism. Quite often the length of the phylogenetic lineage and nodes correspond to the time of divergent events.
This slide is simply explaining some phylogenetic tree basics. Explain that a node may occur because the group was divided in two by geographic isolation. Since they are no longer together, they are experiencing the “founder effect”, different selection pressures, and different mutations.

13. Predict what could cause a node or branch point.

14. Phylogenetic Trees of Sirenia and Proboscidea
Point out to students that elephants are closely related to manatees. Also, that manatees are more closely related to elephants than they are to seals and walruses. Pinnidpedia (a widely distributed and diverse group of fin-footed marine mammals which are semiaquatic) are more closely related to bears and are carnivores. Manatees, like elephants, are herbivores. Additionally, emphasize that phylogenetic trees and cladograms can be oriented vertically or horizontally.
Any organism not shown across the top of the page is an extinct species.
Explain three conclusions we can make from this image.

15. Traditional Classification and Phylogenies
This phylogenetic tree is a reflection of the Linnaean classification of carnivores, however with the advancements in DNA and protein analysis, changes have been made in the traditional classification of organisms and their phylogeny.
For example, birds are now classified as true reptiles.
Emphasize that classification began by using only physical traits and quite often that was a reflection of the phylogeny of the organisms . Subsequent use of both embryology and biochemistry evidence has caused changes in such phylogenies and often results in changing classifications.

16. Taxa
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.
A taxon is any group of species designated by name. Example taxa include: kingdoms, classes, etc. Every node should give rise to two lineages. If more than two linages are shown, it indicates an unresolved pattern of divergence or polytomy.

17. 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.

18. 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.
Explain how we know each is a true clade
Students need a clear understanding of cladistics. (Graphic: Understanding Evolution web site.)

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

20. Recreating Phylogenies
The formation of the fossil record is illustrated below.
Note the location at which fossils are found is indicative of its age which can be used to recreate phylogenies.
Be sure to point out that the deeper the fossil is buried, the older it is. Radioactive carbon-14 dating is used to determine the age of the fossil. The fossil record served as the first evidence that evolution occurs and helps illustrate that species do indeed change over time. Additionally, extinct species were also discovered.

21. Using Homologous Features
Once a group splits into two distinct groups they evolve independently of one another. However, they retain many of the features of their common ancestor.
Any feature shared by two or more species and inherited from a common ancestor are said to be homologous.
Compare and constrast Cladogenesis vs. Anagenesis
Emphasize that homologous physical structures along with evidence from the fossil record serve as the basis for traditional classification. Graphic

22. Analogous Structures
Analogous structures are those that are similar in structure but are not inherited from a common ancestor.
While the bones found in the wings of birds and bats are homologous, the wing itself is analogous. The wing structure did not evolve from the same ancestor.
It’s tricky to verbally distinguish between fore limbs and four limbs! Student hear both words as 4 limbs, thus it is a good idea to say, “fore limbs, as in f-o-r-e (spelling it out) limbs” as you discuss these concepts with students. Also, ask students if they know what part of speech four and fore belong to—they are homonyms which sound alike but mean something different. It makes a nice segue into a discussion of “homologous” structures vs. analogous structures.
Graphic
Graphic
While the bones are the same, point out how different the construction of the wings are
Attachment of the wing bats to that of a bird
Feathers as opposed to stretched skin
Point out how the overall shape is the same and ask why that might be the case.\
The physics necessary for flight is the selection pressure responsible for the similar shape of the wings. Examine airplane wings! Analogous structures should NOT be used in establishing phylogenies . Why?

23. How can scientists determine the length of time that evolution takes?

24. 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.

25. 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:

26. 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

27. 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.

28. 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.

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