Lecture 7: Phylogenetics Flashcards
Monophyletic
Includes one ancestor and all descendants of that ancestor
Paraphyletic
Includes an ancestor and only some of its descendants
Polyphyletic
Any random grouping of ancestors and descendants
Synapomorphy
Shared derived trait
Plesiomorphy
Ancestral trait (evolved in a deeper ancestor)
T or F: Vertebral column is a plesiomorphy of terrestrial (land) animals.
True
What is maximum parsimony? What are the assumptions?
Best tree uses fewest number of transitions to account for gain/losses of traits
I.e., best tree is tree with fewest tick marks
Assumes homoplasies (convergent traits) are rare
Assume it evolved once
What is the problem with maximum parsimony?
Homoplasies/convergent evolution (maximum parsimony approach does not always reveal true evolutionary relationships among taxa)
What is Occam’s razor?
Make fewest assumptions to explain a phenomenon
What is Molecular clock? Assumptions, strengths, weakness.
• Assumption: mutation in genomes occur at the same rate on all branches (i.e., assumes constant mutation rate)
Give an examples of molecular clock
- Ancestor x to species A (8 ticks)
- Ancestor x to species B (8 ticks)
- 16 ticks total
A monophyletic group is also known as a _______.
Clade
What are the assumptions of maximum parsimony?
• Homoplasies (convergent traits) are rare
• Traits evolved once
Why are humans non variable?
Bottleneck (reduction in population size and genetic diversity; humans have gone through many series of bottleneck events
What is adaptive radiation? Give an example.
Natural selection favoring rapid diversification of population (i.e., rapid adaptive divergence of traits) (e.g., Hawaiian fruit flies)
Nucleotide (DNA) sequence example
Nucleotide substitutions:
A mutated to G in Species C and A
Outgroup: T in 2
Substitution: T to C (all descendants - Species D, C, B, A)
Outgroup: A in position 3
Shared by all species/descendants
Useless position
Outgroup: position 4 (T)
T to G occurred in Species B (4T -> G)
Not shared by any other species
Outgroup: position 5 C
5C → A (Species A & C)
Outgroup: position 6
C to G occurred in Species D, C, and A
4C → G
Outgroup: position 7 (not informative)
Outgroup: position 8
8T → C (Species A & B)
Outgroup: position 9
Substitution in SPecies D, C, & A
9A → G
What is an outgroup?
Most ancestral group on tree
What is homoplasy?
shared derived character state that has not been inherited from a common ancestor exhibiting that character state
What is the principle of parsimony?
favors hypothesis that requires fewest assumptions
What is molecular clock?
States that rate of evolution of a molecule is constant through time
What is the goal of phylogenetics?
To reconstruct evolutionary relationships among organisms
A & B differ by 200 nucleotides. How old is MRCA of A and B?
Mutation rate = 1 mut/1,000 yrs
Ancestor of A & B: 1/1000 = 200/x = 200,000 years old
__________________ reflects rapid adaptive divergence of species (adaptive radiation).
Polytome/star phylogeny
