Phylogeny

Question 1

What is a phylogenetic tree

Answer 1

A diagram that depicts the lines of evolutionary descent of different species from a common ancestor

Question 2

What are terminal taxa?

Answer 2

The branches that occur at the tips of the tree

Question 3

What are internal nodes?

Answer 3

Nodes within the tree identifying different common ancestors

Question 4

What is a root node?

Answer 4

The node at the bottom of the phylogenetic tree usually the last common ancestor

Question 5

What are internal branches?

Answer 5

Branches that occur between internal nodes

Question 6

Cladogram?

Answer 6

A phylogenetic tree that only shows the ancestral history of the branches

Question 7

Phylogram?

Answer 7

A phylogenetic tree in which the branch lengths represent the amount of evolutionary divergence

Question 8

Chronogram?

Answer 8

A phylogenetic tree where the lengths of the branches are based on time (usually has a time scale)

Question 9

What is a monophyletic group?

Answer 9

A clade that includes the most recent common ancestor and all of its descendants

Question 10

What is a paraphyletic group?

Answer 10

A monophyletic group that excludes SOME of the descendants

Question 11

What is a polyphyletic group?

Answer 11

A monophyletic group that excludes the most recent common ancestor

Question 12

What is a synapomorphy?

Answer 12

A trait that is present in a ancestral species and is shared ONLY with its descendants

Question 13

What is an ancestral trait?

Answer 13

A trait that comes from a distant common ancestor with that trait

Question 14

What is a derived trait?

Answer 14

A trait that appears in one branch proabably from mutation

Question 15

What is convergence?

Answer 15

It is when two separate branches on a tree independently evolve similar traits

Question 16

What is reversal?

Answer 16

It occurs when a trait appears and disappears again and again on a tree

Question 17

What is homology?

Answer 17

A similarity due to ancestry between two branches

Question 18

What is a homoplasy?

Answer 18

A similar structure that has evolved independently in two species

Question 19

Sister groups?

Answer 19

Two descendants of a speciation event, close relatives

Question 20

Ingroups?

Answer 20

The group of taxa in a study that is actually being analyzed

Question 21

Outgroups?

Answer 21

The taxa or group of taxa in a study that is acting as a control and is not being analyzed

Question 22

What is the relationship between phylogeny and classification?

Answer 22

Phylogeny is a type of classification that includes organizing various groups based on similar/different characteristics

Question 23

What is a rooted tree?

Answer 23

A tree where one branch corresponds to the common ancestor of all the species included in the tree

Question 24

What is an unrooted tree?

Answer 24

A tree that portrays relationships among species, but doesn’t depict their common ancestor

Question 25

What is the parsimony principle?

Answer 25

It states that the best tree is the one that requires the fewest evolutionary changes

Question 26

What is the maximum likelihood model?

Answer 26

The process of developing a probabilistic model of character evolution and search for the most likely tree under that model (two trees that are both parsimonious)

Question 27

What are parsimony-uninformative characters?

Answer 27

Character traits that will always have the same number of changes on any tree

Question 28

What are parsimony-informative characters?

Answer 28

Character traits that vary in number of changes from tree to tree

Question 29

What is an invariant character?

Answer 29

Parsimony uninformative
Same state in all species CCCC
ZERO CHANGE

Question 30

What is a transition?

Answer 30

It is a change from purine to purine (A-T)

Question 31

What is a transversion?

Answer 31

It is a change from purine to pyrimadine (A-G)

Question 32

What are synonymous substitutions?

Answer 32

They don’t change the phylogenetic relationship (same amino acid)

Question 33

What are non-synonymous substitutions?

Answer 33

They change the phylogenetic relationship (different amino acid)

Question 34

What is a polytomy?

Answer 34

Uncertainty in the phylogeny demonstrated by 2+ branches meeting at one node

Question 35

What is the molecular clock?

Answer 35

States that DNA and protein sequences evolve at a rate that is relatively constant over time
How old a recent common ancestor is based on genetic differences

Question 36

How do you calculate internal nodes?

Answer 36

N = species
internal nodes = N-1

Question 37

What are the different phylogenetic applications?

Answer 37

Studying temp and mode of evolution
Coevolution
Biogeography
Community phylogenetics
Conservation biology

Question 38

How have phylogenies been applied to coevolution?

Answer 38

How and to what extent interacting organisms from different clades evolve together

Question 39

How have phylogenies been applied to biogeography?

Answer 39

Use phylogenies to infer where taxa originated and history of dispersal to other areas

Question 40

How can phylogenies be used in conservation biology?

Answer 40

identify previously unsuspected diversity
emphasize conservation of old lineages and/or multiple lineages

Question 41

What is the best strategy for conservation?

Answer 41

Conserve old lineages
Preserve greatest diversity of lineages