Lecture 16 - Molecular Phylogeny Flashcards
Give an example of an immunological method.
Sarich and Wilson (1967).
Human albumin purified and used to raise antibodies in rabbits.
Anti-serum used to test albumin from other Hominids.
The amount of anti-serum require to produce a reaction was measured.
What is DNA-DNA hybridisation based on?
Based on measuring the melting temperature of hybrid DNA.
The more closely related the genomes of the two species, the higher the melting temperature.
What is a reversal?
A reversion in the DNA sequence.
How can we minimise the effect of reversals?
- use DNA sequences that are evolving slowly
- use long stretches of DNA
- align sequences and use parts that show a high degree of conservation
- rDNA sequences often used.
Give the steps to rRNA sequence analysis.
1) Extract DNA from organisms of interest
2) Amplify rDNA sequence using PCR and universal primers
3) Purify and sequence amplicons
4) Align sequences
5) Calculate phylogeny
What is Multiple Sequence Alignment?
Alignment of sequences that have an evolutionary relationship so as to maximise sequence identity.
Name three multiple sequence alignment programmes.
- ClustalW
- T-Coffee
- MUSCLE
Name some different statistical methods used to calculate phylogenies.
- Maximum Likelihood
- Bayesian
- Maximum Parsimony
- Neighbour-Joining
- Minimum Evolution
What is the Maximum Likelihood method?
Choose the tree which makes the data most probable.
How do we carry out a Maximum Likelihood method?
Use a mathematical model of rates of nucleotide substitution and a given phylogenetic tree with known branch lengths.
Calculate how likely you are to obtain a particular set of DNA sequences.
What proportion of single nucleotide polymorphisms (SNPs) are transitions?
2/3
What is the DNA substitution model?
A model describing the relative rates of different changes.
Relative rates of each substitution are calculated and used in maximum likelihood calculations.
What is branch support (bootstrapping)?
A test of how reliable each branch of a tree is.
What does the bootstrap support of a branch indicate?
The percentage of times it appears in trees calculated from resampled datasets.
What is polytomy?
Unresolved branches
