Phylogeny

Question 1

What is the purpose of a phylogeny?

Answer 1

To show the relationships among evolutionarily related ‘objects’ - sequences, species, languages etc.

Question 2

What are the 2 components of a phylogenetic tree?

Answer 2

Branches and nodes

Question 3

What is an operational taxonomic unit (OTU)?

Answer 3

A node associated with an extand sequence

Question 4

What is the root of a phylogenetic tree?

Answer 4

The earliest described divergence in OTUs

Question 5

What are polytomies?

Answer 5

An internal node with more than 3 daughter branches

Question 6

What are bifurcations?

Answer 6

When an internal node has 2 daughter branches

Question 7

What is the difference between a polyphyletic group and a paraphyletic group?

Answer 7

polyphyletic does not include the most recent common ancestor, so these groups tend to be avoided by biologists

Question 8

What is the topology of a tree defined by?

Answer 8

It’s divergences

Question 9

According to Netwick, how many elements must be enclosed in the outermost bracket for an unrooted tree?

Answer 9

3

Question 10

Name 3 methods for inferring phylogenetic trees

Answer 10

1. Maximum parsimony
2. Distance methods
3. Maximum likelihood

Question 11

What is minimum parsimony?

Answer 11

Arranging a phylogenetic tree by the smallest number of evolutionary changes between nodes

Question 12

What are distance methods?

Answer 12

Computing a matrix of distances between each pair of sequences to search for a tree that best fits them

Question 13

What is the neighbour-joining (NJ) system?

Answer 13

Whereby a pair of sequences with the least distance is treated as a ‘unit’ which all other sequence distances are compared to

Question 14

What is the formula for likelihood?

Answer 14

Pr(data|hypothesis)

Question 15

Why is likelihood more reliable than distance methods?

Answer 15

• Uses all of the data to measure how well a tree fits the alignment
• completely probabilistic and so allows statistical methods to be used
• Parsimony has been shown to converge to a wrong tree when sequences are long

Question 16

What is the molecular clock hypothesis?

Answer 16

Idea that evolution is constant over time and among evolutionary lineages
supported by: haemoglobin, cytochrome and fribrinopeptides

Question 17

How is the molecular clock hypothesis useful?

Answer 17

Allows us to find a calibration point for evolutionary distances

Question 18

Name 4 problems with the molecular clock hypothesis?

Answer 18

• Clock is often stochastic with changes happening at random intervals
• Different proteins have their own clocks (different rates)
• Rate constancy may not hold globally
• Fossil calibrations always involve uncertainty such as dating errors and an incomplete record

Question 19

What information has the molecular clock shown about HIV?

Answer 19

• phylogenetic analysis shows that it is descended from primate virus
• shows that it has spread to humans more than once
• Molecular clock has shown spread to humans in 1930/1910

Question 20

Define a homology?

Answer 20

Phenotypic and genetic similarities (morphology) due to shared ancestry

Question 21

What are orthologs?

Answer 21

Orthologous genes - genes that are found in a single copy of the genome and are homologous between species, having diverged after speciation occured

Question 22

What are isofunctional homologs?

Answer 22

Orthologs that maintain the same function

Question 23

What are paralogous genes?

Answer 23

Genes that result from a duplication and are found on more than one copy of the genome which can diverge with speciation and evolve new functions. Increase the opportunities for evolutionary change

Question 24

What is the result of repeated gene duplications?

Answer 24

Gene families

Question 25

What is horizontal gene transfer and how can it occur?

Answer 25

• Movement of genes from one genome to the other

- Occurs via exchange of transposable elements and plasmids, viral infection and fusion

Question 26

Name 3 parametric methods to determine horizontal gene transfer

Answer 26

1. CG content
2. Conon bias
3. k-nucleotide frequencies