Define ‘phylogeny’.
The evolutionary history of a group.
Define ‘phylogenetic tree’.
A graphical summary of a groups evolutionary history.
Define ‘cladogram’.
Diagram which shows branching order. Branch lengths are meaningless.
Define ‘phylograms’.
Diagram shows branch order and branch length.
What are the stages within the phylogenetic process?
Data aquisition > alignment > phylogenetic reconstruction > hypothesis testing.
What is the most important step within the phylogenetic process?
Data aquisition.
Describe the mitochondrial genome.
Closed, circular and double stranded molecule/ approx 17,000 bases long/ haploid/ does not recombine/ maternally inherited.
Define ‘homologue’.
The same organ under every variety of form and function (true or essential correspondence).
Why is mitochondrial DNA useful?
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.
What are the different methods of phylogenetic reconstruction?
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.
What are the stages within a distance analysis?
- 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.
What is an additive tree?
When branch lengths in the matrix and the tree path lengths match perfectly.
Define ‘analogy’.
Superficial and misleading similarity.
What is the molecular clock hypothesis?
- 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.
What are the molecular clock assumptions?
- DNA sequences tick metronomically - Rate variation across genes is similar/identical - Rate variation across taxa is similar/identical.
What are the sources of erroe with phylogenetics?
- Stochastic variability in population size - Incorrect tree - Lack of rate consistency - Imprecision of calibration points.
