Molecular phylogenetics

Question 1

Apomorphy

Answer 1

Derived condition of a characteristic

Question 2

Autapomorphy

Answer 2

Apomorphy that only occurs in one taxon

Question 3

Clade

Answer 3

A branch or lineage

Question 4

Homoplasy

Answer 4

Parallelism and reversal in characters state transformation

Question 5

Monophyletic

Answer 5

Includes of the descendants of a common ancestor

Question 6

Parallelism

Answer 6

Type of homoplasy–character state transformation that occurs twice, once in each of 2 lineages

Question 7

Plesiomorphic

Answer 7

Ancestral state of a character

Question 8

Paraphyletic

Answer 8

Includes some but not all of the descendants of a common ancestor

Question 9

Polyphyletic

Answer 9

Includes different groups of taxa, derived from different common ancestors

Question 10

Reversal

Answer 10

Type of homoplasy–character state transformation that occurs twice, once from plesiomorphic to apomorphic condition, then back to plesiomorphic condition

Question 11

Sister group

Answer 11

Two clades that share a branch points

Question 12

Synapomorphy

Answer 12

A shared derived character state transformation

Question 13

Polytomy

Answer 13

Unresolved relationship

Question 14

Hard polytomy

Answer 14

Simultaneous divergence of multiple taxa

Question 15

Soft polytomy

Answer 15

Unknown relationship between multiple taxa

Question 16

Cladogram

Answer 16

x and y axis are meaningless, only relationships matter

Question 17

Additive tree

Answer 17

length of y axis = number of mutations or evolutionary events

Question 18

Ultrametric tree

Answer 18

y axis = time

Question 19

When do you use a rooted tree?

Answer 19

Rooted trees = you have some information on the ancestral state, so you can root your tree with whatever organism is most ancestral—affects inference of relationships

Question 20

How do you choose what gene to use for DNA sequence trees?

Answer 20

Example 1—recent divergence—you want to choose a gene with relatively fast
mutation rate
Example 2—ancient divergence—relatively slow mutation rate

Question 21

What is the neighbor joining method of phylogenetics

Answer 21

Neighbor joining methods—starts by assuming all sequences are “created equal”, then pull 2 sequences out and calculate distance across tree, repeat with every pair whichever pair has shortest distance is assumed to be most closely related

Question 22

What is the parsimony analysis method of phylogenetics?

Answer 22

Parsimony analysis—assumes that evolution is rare so the phylogeny that requires the fewest number of changes is the correct one

Question 23

What are the advantages of DNA based phylogenetics? Disadvantages?

Answer 23

• virtually unlimited characters
• can differentially weight character states
• discrete characters

However…gene tree may not match up with speciation events

Question 24

What are the 4 steps of tree reconstruction?

Answer 24

Select locus and perform sequence alignment
Tree reconstruction
Assessment of accuracy
Dating events using a molecular clock

Question 25

What is the problem with molecular clocks?

Answer 25

Implies a constant rate of mutation–may not give accurate divergence times

Question 26

What is bootstrapping?

Answer 26

Confidence in the reconstructed phylogeny—bootstrapping

Takes data matrix and randomly samples some of the columns, rebuilds the phylogeny from those—this is repeated

The percentage of times that the original relationships are upheld determines how confident you can be

Question 27

What is reticulate evolution? Why is it a problem? How can it occur?

Answer 27

Reticulate evolution, or network evolution, describes the origination of a lineage through the partial merging of two ancestor lineages, leading to relationships better described by a phylogenetic network than a bifurcating tree

Lack of independence between lineages

Hard to make a tree–more like a network

Recombination can contribute