1. Schedule Cultural connection Introduction to evolution
Introduction to phylogenetic trees
Build a phylogeny 1
Build a phylogeny 2
Applying phylogenetic trees

2. Learning objectives
Be able to read a phylogenetic trees and predict evolutionary relationships
Be able to construct phylogenetic trees and use parsimony to evaluate which tree is the most likely
Be able to identify shared derived traits and distinguish this from convergence.

3. Evolution What is it? Is it controversial? If so, why?
Do scientists think it is controversial?

4. Evolution
Any change in the inherited traits of a population that occurs from one generation to the next The process of descent with modification that is responsible for the origin, maintenance and diversity of life

5. Biodiversity 1,700,000 described (and climbing)
conservative estimate is that only 1/3 are described > 5,000,000 species
Note our accuracy in estimates for most
taxa is very low
For example there are ~ 10,000 species of birds
23 new bird species described in 2013!
- Junin Tapaculo found in the Andes in Peru

6. Broad applications Medical research and public health
Personalized medicine
Development of vaccines & therapeutics
Agriculture
Increase genetic diversity
Include refuge area
Ecology and conservation
Captive breeding
Inbreeding depression

7. Patterns of change through time
Evolution
Descent with modification
time
Phenotype

8. Phylogenetics
Phylogeny: A visual representation of the evolutionary history of populations, genes, or species.
Phylogenies represent hypotheses about evolutionary relationships that we can test by collecting more data

9. Phylogenetics
More closely related species should share more traits in common

10. Reading phylogenetic trees
Describe Root, Nodes, Tips or terminal nodes, branches. Can you guess, which is more closely related the Snow leopard, the Canada Lynx or the Jaguar? Why?

11. Reading phylogenetic trees
Trees can be rooted or unrooted
Birds
Crocodiles
Turtles
Amphibians
Mammals
Lizards
Snakes
Birds
Crocodiles
Turtles
Amphibians
Mammals
Lizards
Snakes
root
an unrooted tree shows relationships, but not time
root establishes a point of common ancestry - outgroup
where the root is put can drastically change the meaning of the tree

12. Reading phylogenetic trees
trees can be slanted or bracket style A B C A B C

13. Reading phylogenetic trees
Trees can be oriented in different ways, but the relationships remain the same
Birds
Crocodiles
Turtles
Amphibians
Mammals
Lizards
Snakes
Birds
Crocodiles
Snakes
Lizards
Turtles
Mammals
Amphibians

14. Reading phylogenetic trees
Taxa can rotate around interior nodes without changing the relationships
Turtles
Amphibians
Mammals
Lizards
Snakes
Crocodiles
Birds
Birds
Crocodiles
Turtles
Amphibians
Mammals
Lizards
Snakes

15. Reading phylogenetic trees
Taxa can rotate around interior nodes without changing the relationships
Turtles
Amphibians
Mammals
Lizards
Snakes
Crocodiles
Birds
Birds
Crocodiles
Turtles
Amphibians
Mammals
Lizards
Snakes

16. Reading phylogenetic trees
Taxa can rotate around interior nodes without changing the relationships
Turtles
Amphibians
Mammals
Lizards
Snakes
Crocodiles
Birds
Birds
Crocodiles
Turtles
Amphibians
Mammals
Lizards
Snakes
The order of branching is important

17. Are these two trees equivalent?

18. Is the frog more closely related to the fish or the cat?

19. Constructing phylogenies
groups species based on shared characters
“Shared”: All (or most) members of the group and their common ancestor have the trait

20. Constructing a phylogeny

21. Constructing a phylogeny

22. Constructing a phylogeny

23. How do we pick the best tree?
In general, parsimony is our guide
Fewest evolutionary changes necessary to explain the data
Some datasets can’t generate one best tree

25. Candy Phylogeny
Step 1: Pick traits (1= has the trait, 0= does not have the trait) Step 2: Now draw 2 hypothetical trees. Do not worry about whether it is the best tree. Step 3: Now map each of your traits onto the two trees. Put a plus or minus to indicate whether it is a gain or loss of the trait. Step 4: Use parsimony to evaluate which is the better tree.

26. Homologous vs. convergent characters

27. Not all shared traits are due to common descent
Convergence: character state similarity not due to common descent
Imaging forming camera eye similar in octopuses and other vertebrates

28. Not all shared traits are due to common descent

29. Not all shared traits are due to common descent
Parsimony is used to select the best tree – 2 vs 6 changes!

30. Broad applications Medical research and public health
Personalized medicine
Development of vaccines & therapeutics
Agriculture
Increase genetic diversity
Include refuge area
Ecology and conservation
Captive breeding
Inbreeding depression

31. Broad applications Where did HIV come from?
When were cows domesticated?
Do different populations of elephants require conservation?

33. Bos indicus
Bos taurus
Each species was a
separate domestication
event

34. Conservation application
African elephants – formerly classified as 1 species, but morphological and phylogenetic evidence now suggests that there may be two species: one which inhabits forests and one which inhabits grassland savannahs.
Because elephant population are in decline, this research may help with conservation efforts to preserve these species.
African elephants that inhabit the forest and savannahs look different – but because they do not have many opportunities to interact it is difficult to assess the BSC
Collected tissue samples from 195 elephants in 21 pops throughout Africa
Critical because elephants are in decline and means that both pops need to be preserved
is a combination of alleles (DNA sequences) at adjacent locations (loci) on a chromosome that are inherited together. A haplotype may be one locus, several loci, or an entire chromosome depending on the number of recombination events that have occurred between a given set of loci.
A second meaning of the term haplotype is a set of single-nucleotide polymorphisms (SNPs) on a single chromosome of a chromosome pair that are associated statistically.