Biol 415: Lecture 16 (10/22/15)

Front 1

Define: Homologous characters

Back 1

Characters whose traits are shared between two or more taxa or clades because of inheritance from a common ancestor

Front 2

Provide an example of homology

Back 2

The pouch shared between Koalas and Possums

Front 3

T/F: Homologous characters can be useful in identifying monophyletic clades

Back 3

True

Front 4

Define: Convergence (A.K.A. homoplasious characters)

Back 4

Characters whose traits are shared between two or more taxa but evolved independently

Front 5

Provide an example of homoplasies

Back 5

Fins in dolphins and fish + sharks aer homoplasy

Front 6

Which of the following is synonymous with evolutionary convergence

A. Non homologous

B. Analogous traits

C. Homoplasious

D. All of the above

Back 6

D. All of the above

Front 7

Define Reversals

Back 7

A Homoplasious character in which the traits independently returned to their original (Ancestral state)

Front 8

Why are homoplasies not useful for phylogeny construction

Back 8

Homoplasies contain both convergence and reversals making it difficult to identify common ancestry and construct acurate phylogenies.

Front 9

The evolution of armor plates in cichlids were due to convergence

Back 9

False. it was due to reversal

Front 10

T/F: Character state changes are useful in helping to group species together

Back 10

True

Front 11

What is the difference between Unique Derived Characters and Shared Characters

Back 11

Unique derived characters are unique for a single clade while Shared derived characters are unique to two or more clades.

Front 12

What is the difference between Shared Primitive Characters and Shared Derived Characters

Back 12

Shared Primitive characters are ancestral traits shared amongst a group of clades. Shared Derived Character is a recent trait appearing in a common ancestor and in later descendants. Shared Primitive traits are not useful in determining monophyletic groups because it is difficult to determine how far back the shared primitive trait really goes.

Front 13

What two types of characters are not usefull in diagnosing a monophyletic group?

Back 13

Unique derived characters and shared primitive characters

Front 14

Also known as synapomorphis, this type of character is the only one that can be used in diagnosing monophyletic groups

Back 14

Shared derived characters.

Front 15

T/F: CMT1A in chimps and humans is a type of unique derived character

Back 15

False. it is a synapomorphy (shared derived character) which can infer that chips and humans are a form of monphyletic clade

Front 16

What are the purpose of outgroups in a phylogeny?

Back 16

To polarize primitive to derived direction of character state changes in the group

Front 17

Define Apomorph

Back 17

Any new derived character or trait

Front 18

Define Plesiomorph

Back 18

Any ancestral (old) character within a set of tax

Front 19

T/F: A clade is any monophyletic group

Back 19

True

Front 20

What method should you use in order to create a phylogenetic tree without knowing the sequence of apomorphs or know of a common ancesotr?

Back 20

1. Begin with an outgroup analysis. Choose an outgroup based on group and assume that the outgroup has not evolved relative to the ancestral condition of the group.

2. Explore possible ordering of new characters for the taxa based on parsimony

Front 21

Define: Parsimony

Back 21

The hypothesis with the fewest number of evolutionary changes is evolutionarily preferred.

Front 22

Which of the following is correct about parsimony?

A. The optimal tree is the one that minimizes the sum of the lengths of all characters in terms of evolutionary steps

B. A tre with the minimum length

C. Provides the bet fit of the data set.

D. All of the above

Back 22

D. All of the above

Front 23

Back 23

A. Wings

Front 24

Why is it difficult to categorize whales on a phylogenetic tree

Back 24

Artiodactyls and mammals are the two groups that whales would fall under, but are unable to accurately place because of their fuse/fragmented astragalus.

Front 25

Describe the Distance method

Back 25

A faster method of building phylogenetic trees than parsimony

Front 26

Describe the process of the distance method

Back 26

1. Make pairs of species

2. For each pair, calculate the distance. the distance is the difference in character states. For DNA, it can be the number of changes required to go from one sequence to another

3. Join the species pairs following the order of shortest distance (neighbor joining)

Front 27

T/F: Under the distance method, closely related organisms will share more nucleotide homologies

Back 27

True

Front 28

T/F: Under the distance method, the greater the separation from a common ancestor, the more homologies

Back 28

False. the greater the separation from a common ancestor, the less homologies

Front 29

Use the distance matrix to find the closest relative to the outgroup

Back 29

Camal

Front 30

What are the three methods of building a phylogeny?

Back 30

1. Parsimony

2. Distance based method

3. Likelihood method

Front 31

Describe the likelihood method

Back 31

A probability based method of building a phylogenetic tree.

Front 32

What methods are used to measure the confidence in a phylogenetic tree?

Back 32

Bootstrapping

Front 33

Explain bootstrapping

Back 33

A method of measuring the confidence of a phylogenetic ree by creating artifical datasets simulated from the original data, sampling at random with replicates, and finding the best phylogeny for each simulated data. Find how many times each clade is supported among the newly found phylogeny. If it is supported 70 out of 100, the bootstrap supports the branch leading to that clade is 70%

Front 34

Based on the image, what is the bootstrap percent of whales and hippos

Back 34

Because they are grouped together 4/5 based on their base pairs they have an 80% bootstrap