Lecture 20. Molecular Phylogenetics

Question 1

What can evolution be represented as ?

Answer 1

A branching process

Question 2

What is the most recent common ancestor (MRCA) ?

Answer 2

The recent individual from which a set of biological entities descend

Question 3

What is anagenesis ?

Answer 3

Evolution of a new species without branching

Question 4

What is cladogenesis ?

Answer 4

An evolutionary splitting of one species into two descendent species

Question 5

What is extinction ?

Answer 5

The evolutionary termination of a biological entity

Question 6

What is a phylogenetic tree ?

Answer 6

A branching diagram showing the theorised relationships between different biological entities with respect to their evolutionary history

Question 7

What is a phylogeny ?

Answer 7

A guess based on observed data

Question 8

What are the major aims of phylogenetics ?

Answer 8

1. To reconstruct the correct evolutionary relationships between biological entities
2. To estimate the times of divergence between them
3. To describe the sequence of evolutionary changes along the lineage
4. To locate the geographic origins of ancestral lineages

Question 9

What are nodes ?

Answer 9

Represent taxonomic units - DNA sequences, genes, proteins, individuals, populations, species

Question 10

What are branches ?

Answer 10

Define the relationships between nodes in terms of descent and ancestry

Question 11

What are operation taxonomical units ?

Answer 11

The terminal nodes of the tree. They represent the actual data under study

Question 12

What are two operational taxonomic units separated by a single node called ?

Answer 12

Neighbours

Question 13

What are two operational taxonomic units separated by a single node called ?

Answer 13

Neighbours

Question 14

What is a hypothetical taxonomic unit ?

Answer 14

The internal nodes represent inferred ancestral units. We have no actual data for these

Question 15

What is a mulitfurcating node ?

Answer 15

More than two immediate descendants

Question 16

What is another name for a multifurcating node ?

Answer 16

Polytomous

Question 17

What is a bifurcating node ?

Answer 17

Only two immediate descendants

Question 18

What is another name for a bifurcating node ?

Answer 18

Dichotomous

Question 19

What is the root ?

Answer 19

The earliest node and anchors the tree in time

Question 20

What is an unrooted tree ?

Answer 20

A tree without a root node

Question 21

What does an unrooted tree specify ?

Answer 21

The degree of relatedness between taxonomic units, but does not define the direction of the evolutionary path

Question 22

What is topology ?

Answer 22

The branching pattern of the tree

Question 23

What is the topology of unrooted and rooted trees not affected by ?

Answer 23

Rotating branches around the internal nodes

Question 24

What is outgroup rooting ?

Answer 24

Uses external rooting to be more distantly related to everyone else

Question 25

What is an unscaled tree ?

Answer 25

The branch lengths are not proportional to the number of evolutionary changes which are indicated on the branches

Question 26

What is a cladogram ?

Answer 26

An unscaled tree

Question 27

What is a scaled tree ?

Answer 27

The branch lengths are proportional to the number of evolutionary changes

Question 28

What is a phylogram ?

Answer 28

A scaled tree

Question 29

What is cladistics ?

Answer 29

Biological classification based on shared descent

Question 30

What is a clade ?

Answer 30

A group of taxa composed of a common ancestor and all its descendants

Question 31

What is monophyletic ?

Answer 31

A taxonomic group in which all of the taxa are derived from a common ancestor and not shared by other taxa

Question 32

What type of clade is a monophyletic ?

Answer 32

A natural clade

Question 33

What is paraphyletic ?

Answer 33

A taxonomic group whose most recent common ancestor is shared by another taxa

Question 34

What type of clade is a paraphyletic ?

Answer 34

Not a true clade

Question 35

What is a polyphyletic ?

Answer 35

A grouping of taxa each more closely related to other taxa not in the grouping than they are to each other

Question 36

What type of clade is polyphyletic ?

Answer 36

Not a true clade

Question 37

What are the three steps in drawing a phylogeny ?

Answer 37

1. Identify homologous sequences
2. Align sequences and identify variant sites
3. Calculate tree

Question 38

What are the methods of calculating a tree ?

Answer 38

1. Distance based
2. Maximum parsimony
3. Maximum likelihood
4. Bayesian

Question 39

How do you calculate the tree using the distance method ?

Answer 39

1. Calculate a measure f molecular distance between pairs of operational taxonomic units and enter the value into a distance matrix
2. Sequentially cluster samples in a bottom up manner identifying pairs that are most similar first and placing them in a clade together
3. Calculate new average distances between this clade an other operational taxonomic units

Question 40

What is the calculating the tree method for maximum parsimony aim to achieve ?

Answer 40

Identify the trees that require the fewest number of evolutionary changes

Question 41

How do you calculate the tree using the maximum parsimony method ?

Answer 41

1. Identify character states for each variant site for all operational taxonomic units
2. Scroll through the trees and find the one that require the fewest number of character state changes

Question 42

What is phylogeography ?

Answer 42

Describes the geographical distribution of operational taxonomic units and attempting to make inferences about the geographic location of hypothetical taxonomic units