Lecture 7: Phylogenetics

Question 1

Define ‘phylogeny’.

Answer 1

The evolutionary history of a group.

Question 2

Define ‘phylogenetic tree’.

Answer 2

A graphical summary of a groups evolutionary history.

Question 3

Define ‘cladogram’.

Answer 3

Diagram which shows branching order. Branch lengths are meaningless.

Question 4

Define ‘phylograms’.

Answer 4

Diagram shows branch order and branch length.

Question 5

What are the stages within the phylogenetic process?

Answer 5

Data aquisition > alignment > phylogenetic reconstruction > hypothesis testing.

Question 6

What is the most important step within the phylogenetic process?

Answer 6

Data aquisition.

Question 7

Describe the mitochondrial genome.

Answer 7

Closed, circular and double stranded molecule/ approx 17,000 bases long/ haploid/ does not recombine/ maternally inherited.

Question 8

Define ‘homologue’.

Answer 8

The same organ under every variety of form and function (true or essential correspondence).

Question 9

Why is mitochondrial DNA useful?

Answer 9

It possesses a quarter (maternally inherited & haploid) of the effective population size of that of the nuclear locus. This means more drift occurs showing more sifferences between mtDNA and nDNA.

Question 10

What are the different methods of phylogenetic reconstruction?

Answer 10

Parsimony - Choose the tree that minimises the number of evolutionary changes. Distance - Choose the tree that best fits the estimated evolutionary distance. Likelihood - Choose the tree that makes your data most likely.

Question 11

What are the stages within a distance analysis?

Answer 11

1. Generating a pairwise half-matrix of genetic distance between all DNA sequences. 2. Producing a tree where the distance between taxa is the same as the distance in the matrix.

Question 12

What is an additive tree?

Answer 12

When branch lengths in the matrix and the tree path lengths match perfectly.

Question 13

Define ‘analogy’.

Answer 13

Superficial and misleading similarity.

Question 14

What is the molecular clock hypothesis?

Answer 14

• The amount of genetic difference between sequences is a function of time since separation. - Rate of molecular change is constant enough to predict times of divergence.

Question 15

What are the molecular clock assumptions?

Answer 15

• DNA sequences tick metronomically - Rate variation across genes is similar/identical - Rate variation across taxa is similar/identical.

Question 16

What are the sources of erroe with phylogenetics?

Answer 16

• Stochastic variability in population size - Incorrect tree - Lack of rate consistency - Imprecision of calibration points.