L1 Phylogenetics

Question 1

Phenetics

Answer 1

Classify organisms on how similar they are

Question 2

Linnean Taxonomy

Answer 2

classifying organisms into various ranks e.g. phylum, kingdom, class, order, genus, species

Question 3

Cladists

Answer 3

See OneNote diagram

Classifying organisms on their evolutionary history, “shared derived characters”
- share the same evolutionary derived characteristics that the ancestral species does not have

Question 4

Molecular Phylogenetics

Answer 4

• protein electrophoresis
• DNA:DNA hybridisation
• Sequences

Question 5

How is phylogeny determined?

Answer 5

• identify homologous characters

- homology: derived from a common ancestor

Question 6

Alignments and homology

Answer 6

See OneNote

• Asserting homology based on alignment
• the alignment problem

Question 7

Taxa

Answer 7

Species

Question 8

Node

Answer 8

point at the end of the tree or where the tree branches

Question 9

Clade

Answer 9

grouping e.g. mammals grouped together

Question 10

Phylogenetic trees

Answer 10

depict the evolutionary history of the taxa

Question 11

Fundamental properties of Phylogenetic trees

Answer 11

• network without cycles, usually bifurcating
• polytomies, star phylogenies indicate failures to resolve the nodes into bifurcations, data set cannot resolve the correct order or the species has split into three

Question 12

Cladogram

Answer 12

• just the clades, topology

Question 13

Ultrametric tree

Answer 13

• has a root
• terminal nodes align
• time axis included

Question 14

Phylogram

Answer 14

• branch length proportional to distance/number of changes

Question 15

Topology

Answer 15

Grouping of tree

Trees can be drawn in different ways to represent the same thing as long as the topology is the same

Question 16

Root

Answer 16

See OneNote diagram

Rooting affects the interpretation of the tree

Deciding where the root should be:

• Assume out-root species to decide where to root the tree from
• Assert a molecular clock, assume rate of change e.g. amino acid/nucleotide changes, most divergent species would be the root

Question 17

Parsimony Principle

Answer 17

the one that takes the fewest steps is the most likely to have been the real scenario

Question 18

Are all variable sites equally useful in drawing the tree?

Answer 18

See OneNote

• parsimony informative
• singleton site

Question 19

Homoplasy

Answer 19

changing twice to go back to the same state

Question 20

Small parsimony problem

Answer 20

for a given tree what is the minimal number of steps required to explain the data

Question 21

Large parsimony problem

Answer 21

which of all the possible trees has the smallest minimum number of steps?

Question 22

Possible number of tree topologies

Answer 22

N = number of taxa
# of tree topologies = 2N-5

Question 23

Searching tree space

Answer 23

• branch and bound = exact method, will find the shortest tree
• heuristic method = branch swapping

Question 24

Nearest neighbour interchange

Answer 24

See OneNote

Question 25

Subtree pruning and regrafting

Answer 25

See OneNote

- all possible subtree removals and reattachment points are evaluated but the cut point is the reattachment point

Question 26

Tree bisection and reconnection

Answer 26

See OneNote

• all possible bisections and reattachment points are evaluated
• cut point is not necessarily the reattachment point

Question 27

What do you do when you have multiple trees that are equally short?

Answer 27

• build a consensus tree

Question 28

Strict consensus

Answer 28

See OneNote

Record the internal branches that are seen in all four trees, the other we collapse into a point of uncertainty - nodes collapsed to polytomy

Question 29

70% majority rule consensus

Answer 29

See OneNote

If a particular branch/clade is in at least 70% of the trees then it is represented in the consensus tree

Question 30

Distance methods

Answer 30

• lose info by reducing the data set to the distance matrix

- fast

Question 31

Distance Matrix

Answer 31

See OneNote

Question 32

Bootstrap

Answer 32

See OneNote diagram

• Sub-sampling your data
• Sample columns randomly to put into new data set to create pseudo-data set
• generate a consensus of bootstrapped datasets

Question 33

Assumptions

Answer 33

• sites evolve independently of each other
• all changes are equally likely
  BUT transitions usually occur more often than transversions

Question 34

Parsimony Informative Site

Answer 34

A site is parsimony-informative if it contains at least two types of nucleotides (or amino acids), and at least two of them occur with a minimum frequency of two.