1. Macroevolution Part I:
Phylogenies

2. 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.

3. Taxonomy
A specie’s scientific name is Latin and composed of two names: Genus followed by species
So, the cheetah’s scientific name is Acinonyx jubatus
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.

4. 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.
A taxonomic unit at any level of hierarchy is called a taxon.
As it turns out, classifying organisms according to their shared characteristics is also indicative of their evolutionary history.
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.

5. 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.

6. 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.

7. 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.
This phylogenetic tree represents the “true” evolutionary history of elephants. The nodes and length of a phylogenetic lineage indicate the time of divergent events. Also any organism not shown across the top of the page is an extinct species.

8. 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.

9. 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.

10. 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.

11. Rotating Branches
Emphasize that inverting the diagram top to bottom does not “change” the evolutionary history. The common ancestor remains the same.
The two phylogenetic trees illustrate the same evolutionary relationships. The vertical branches have been rotated.

12. 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.)

13. True Clade
A true clade is a monophyletic group that contains a common ancestor and all of its descendants.
A paraphyletic group is one that has a common ancestor but does not contain all of the descendants.
A polyphyletic group does not have a unique common ancestor for all the descendants.
Make certain students can differentiate between these types of clades and reinforce the concept of what is a true clade and what is not a true clade.

14. Anagenesis vs. Cladogenesis
Anagenesis (phyletic change) is the accumulation of changes in one species that leads to speciation over time.
It is the evolution of a whole population.
When certain changes have accumulated, the ancestral population can be considered extinct. A series of such speciation over time constitutes an evolutionary lineage.
Anagenesis, also known as "phyletic change", is the evolution of species involving an entire population rather than a branching event, as in cladogenesis. When enough mutations have occurred and become stable in a population so that it is significantly differentiated from an ancestral population, a new species name may be assigned. A key point is that the entire population is different from the ancestral population such that the ancestral population can be considered extinct. A series of such species is collectively known as an evolutionary lineage.

15. Anagenesis vs. Cladogenesis
Cladogenesis- is the budding of one or more new species from a species that continues to exists.
This results in biological diversity.
Usually, cladogenesis involves the physical separation of the group to allow them to evolve separately.
Simply put, anagenesis involves no budding whereas cladogenesis involves the formation of clades. Cladogenesis has been much more common in the history of life on Earth.

16. 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.

17. 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.
Homologous features can be heritable traits, such as anatomical structures, DNA sequences, or similar proteins.
Emphasize that homologous physical structures along with evidence from the fossil record serve as the basis for traditional classification. Graphic

18. Ancestral vs. Derived Traits
During the course of evolution, traits change. The original shared trait is termed the ancestral trait and the trait found in the newly evolved organism being examined is termed the derived trait.
Any feature shared by two or more species that is inherited from a common ancestor is said to be homologous.
Graphic
While homologous structures are important, latter on molecular homologies are also very important. These structures are homologous structures. They all have the same bones (some are fused) in the forelimbs.
The limbs above are homologous structures, having similar bones.

19. 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 .

20. Why Analogous Structures Exist
Analogous structures evolve as a result of similar selection pressures. These two animals are both burrowing mammals, yet are not closely related.
The top animal is a placental mole and the bottom animal is a southern marsupial mole from Australia.
Both have large claws for digging, thick skin in the nose area for pushing dirt around and an oval body which moves easily through tunnels.
As students to cite other examples of convergent evolution. Interesting the kangaroo and deer fit into the same niche but there are some differences that exists.
Graphic Campbell 8th edition

21. Why Analogous Structures Exist
Another reason analogous structures exists is due to evolutionary reversals.
Fish gave rise to tetrapods.
Cetaceans (whales and dolphins) are tetrapods that returned to the ocean.
Ask students what a tetrapod is? Hopefully they know “tetra” is a prefix meaning four and “pod” is a root word meaning “foot”. While your at it, ask them what kind of “pod” we are! Hopefully they supply you with a correct answer of biped which is a variation on the root word “pod”.
Graphic from:

22. Why Analogous Structures Exist
A selection pressure for flippers or fin like structures was exerted for survival in an aquatic environment.
Thus the flipper of a whale or dolphin is very similar to the fin of a fish.
These are analogous structures or homoplasies.

23. Other Analogous Structures Examples

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.
The slope of the line represents the average rate of change in the amino acid sequence of the molecular clock.
Different genes evolve at different rates and there are many other factors that can affect the rate.
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

28. 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.

29. Putting It All Together

30. Reconstructing Phylogenies
The following rules apply to reconstructing a phylogeny:
Maximum likelihood states that when considering multiple phylogenetic hypotheses, one should take into account the one that reflects the most likely sequence of evolutionary events given certain rules about how DNA changes over time.
Maximum parsimony states that says when considering multiple explanations for an observation, one should first investigate the simplest explanation that is consistent with the facts.
Graphic from Campbell.

31. Reconstructing Phylogenies
Based on the percentage differences between gene sequences in a human, a mushroom, and a tulip two different cladograms can be constructed.
The sum of the percentages from a point of divergence in a tree equal the percentage differences as listed in the data table.
Ask students:
Which organism is more closely related to humans given the data in the table?
Ans: The mushroom. WHY? Ans: Because it has fewer differences in DNA sequences.

32. Reconstructing Phylogenies
For example in Tree 1, the human–tulip divergence is
15% + 5% + 20% = 40%
In tree 2, the divergence also equals 40%
15% + 25% = 40%
BUT, if the genes have evolved at the SAME RATE in the different branches, Tree 1 is more likely since it is the simplest.

33. 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.

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

35. Created by:
Carol Leibl
Science Content Director
National Math and Science