Lecture 4: Methods Of Tree Reconstruction

Front 1

Phylogenetics is the science of ________.

Back 1

recontructing evolutionary trees

Front 2

What's the first method of tree reconstuction?

Back 2

1) Phenetics (based on grouping populations according to their similarities)

Front 3

What are the steps involved in phenetics?

Back 3

1) list similarities
2) group by counts of similarities
3) remember homology vs. homoplasy

Front 4

What's the 2nd method of tree reconstruction?

Back 4

cladistics (taxa grouped based on shared derived characters)

Front 5

What are the assuptions of cladistics?

Back 5

1) all taxa related by descent from a common ancestor
2) THese relationships take the form of a tree
3) Lineages within the tree change through time

Front 6

Phenetic methods are also called _______ methods, especially when data are molecular.

Back 6

Distance.. phenetics:
1) is computationally simple
2) ignores the fact that similarity can result from convergent evolution (homology vs. homoplasy)
3) has been replaced by newer and better methods

Front 7

What is true about cladogenesis and shared-derived character states (synapomorphies)?

Back 7

when a lineage splits after the evolution of a derived character state, both daughter lineages will have the derived character.

Front 8

Define Synapomorphy

Back 8

a shared-derived character
shared: occurs in 2 or more taxa
derived: a trait that has changed since the earliest common ancestor of the group

Front 9

What are cladistic phylogenies solely based on?

Back 9

synapomorphies

Front 10

What are 2 alternate pathways to similarity that can confound (throw into disorder)the recognition of synapomorphies?

Back 10

1) symplesiomorphy: a primitive character state shared by 2 or more taxa. or apomorphy: a derived state found in only one taxon

2) Homoplasy: similarity resulting from convergent or parallel evolution

Front 11

What are 2 strategies for avoiding homoplasy?

Back 11

1. Choose characters that change rarely
2. Use many, many characters and hope to swamp any homoplasy with lots of synapomorphies

Front 12

What are the steps of the OUTGROUP COMPARISON principle (of the cladistic method)?

Back 12

1. choose an OUTGROUP known (on the basis of other evidence) to be OUTSIDE the group of interest
2. Character states present in the outgroup are assumed to be ancestral
3. Characater states present only in the ingrouup are synapomorphies (or apomorphies if only seen in one taxon)

Front 13

What kinds of outgroups are most useful?

Back 13

closely related ones...but still the outgroup must be outside the group of interest.

Front 14

The second Cladistic methods principle is ?

Back 14

Parsimony principle--the simplest answer is the best. Applied to phylogenetics: the evolutionary tree that requires the least amount of change is the most likely.

Front 15

Determining whether character states are ancestral or derived via OUTGROUP COMPARISON is called _______

Back 15

polarizing your characters

Front 16

What are the difficulties with the parsimony principle?

Back 16

finding the shortest tree

Front 17

What are solutions to this problem?

Back 17

1) use a computer to compare many trees
2) use a search algorithm to focus on only a subset of trees