Phylogeny

Question 1

What is a taxon? What are sister taxa?

Answer 1

A taxon is a named group of organisms at any level of phylogeny

Sister taxa are lineages that diverge from the same ancestral node on a tree

Question 2

Define:
Monophyletic
Paraphyletic

Answer 2

All of the descendants of a common ancestor

A group that includes a common ancestor and all but one of it’s descendants

Question 3

What is homology? Why is it restricted?

Answer 3

Homology is structural similarity between species despite differences in function

It is restricted because homology is such strong evidence of common ancestry, they have to be sure similarity is caused by inheritance

Question 4

How are homologies organized in phylogenies?

Answer 4

Homologies are nested

Question 5

Define: 
synapomorphy
Autapomorphy
Sympliesiomorphy
Parsimony

Answer 5

synapomorphy - shared derived character (basis for reconstructing phylogeny)

Autapomorphy - derived character not shared with other taxa

Sympliesiomorphy - Shared ANCESTRAL character (not used to infer phylogeny)

Parsimony - the assumption that the phylogeny with the fewest number of steps is the correct one

Question 6

What are the steps of reconstructing a phylogeny?

Answer 6

Identify an outgroup - a group of organisms that is outside the group of interest

Determine polarity - Which way did transitions take place? Which character is ancestral?

Identify synapomorphy - Shared, derived charaters that arose in common ancestor and are present in descendants

Resolve conflicts with parsimony - fewest number of steps to be correct

Question 7

What is the relationship between transitions/transversions and parsimony?

Answer 7

Transversions are less common and easier for repair mechanisms to catch

Transitions are more likely

Question 8

What predictions can you make from phylogeny?

Answer 8

Order of trait evolution
Number of times a trait evolves
Rates of divergence in clades with different traits

Question 9

What are the definitions of dispersal and vicariance in terms of biogeography?

Answer 9

Dispersal - species come to their present ranges by dispersal across existing barriers

Vicariance - Ancestral species are divided when geological or other events create barriers

Question 10

what has to happen if a trait is said to evolve in response to a particular circumstance? What is most likely the actual cause of the development?

Answer 10

The trait must repeatedly evolve when the environment is met

Parallel evolution
Convergent evolution
Reversals

Question 11

What must be done to avoid confounding variables when looking at a trait?

Answer 11

Compare sister taxa and not just two changes