Phylogenetic Trees

Question 1

What is represented by the root of the tree?

Answer 1

The common ancestor.

Question 2

What are represented by the internal nodes?

Answer 2

Hypothetical ancestors.

Question 3

What are represented by the terminal nodes?

Answer 3

Operational taxonomic units.

Question 4

What are the 3 main types of phylogenetic tree?

Answer 4

Cladogram, additive tree and ultrametric tree.

Question 5

What is shown in a cladogram?

Answer 5

Relative ancestry.

Question 6

What is shown in an additive tree?

Answer 6

It quantifies the amount of change between taxa using branch length.

Question 7

What is shown in an ultrametric tree?

Answer 7

It quantifies the evolutionary time between taxa. Terminal nodes must be in line if organisms are around at the same time.

Question 8

What is the benefit of using a rooted tree compared to an unrooted tree?

Answer 8

The root provides an evolutionary time axis which allows the ancestor-descendant relationships to be defined.

Question 9

What are polytomies?

Answer 9

Unresolved nodes resulting from insufficient resolution.

Question 10

Define an apomorphy.

Answer 10

A character trait that is different from the form found in the ancestor.

Question 11

Define a plesiomorphy.

Answer 11

An ancestral character trait.

Question 12

Define a synapomorphy.

Answer 12

A shared apomorphy in a single taxon.

Question 13

Define an autapomorphy.

Answer 13

An apomorphy in a single taxon.

Question 14

Define a homoplasy.

Answer 14

A character trait present in separate lineages.

Question 15

What is a monophyletic taxa?

Answer 15

A group containing a common ancestor and all its descendants.

Question 16

What is a paraphyletic taxa?

Answer 16

A group containing a common ancestor but does not contain all its descendants.

Question 17

What is a polyphyletic taxa?

Answer 17

A group that does not contain the most recent common ancestor of all the members.

Question 18

What is homoplasy?

Answer 18

A shared character between two or more animals that did not arise from a common ancestor.

Question 19

What is DNA saturation and why is it a problem?

Answer 19

When multiple substitutions at the same site in a sequence. This can mean the apparent divergence rate is lower than the actual mutation rate.

Question 20

What are the pros and cons of the clustering tree-building method?

Answer 20

Pros: inexpensive + fast + only a single tree produced.
Cons: can depend on the order sequences are added.

Question 21

What are the pros and cons of the search tree-building method?

Answer 21

Pros: can evaluate tree quality + can compare how hypotheses fit the data.
Cons: expensive + slow.

Question 22

What is the maximum parsimony tree-building method?

Answer 22

The programme searches for a tree that requires the least evolutionary changes to explain the differences among the sequences.

Question 23

What is long branch attraction and how can it be avoided?

Answer 23

Long branches cluster together due to homoplasy, not recent ancestry but can be overcome by adding more taxa.

Question 24

What is the maximum likelihood tree-building method?

Answer 24

The programme that makes the tree with the most likely evolutionary outcome.

Question 25

What is an outgroup?

Answer 25

A lineage that falls outside the clade being studied but is closely related to that clade. It roots the tree.