What is the purpose of a phylogeny?
To show the relationships among evolutionarily related ‘objects’ - sequences, species, languages etc.
What are the 2 components of a phylogenetic tree?
Branches and nodes
What is an operational taxonomic unit (OTU)?
A node associated with an extand sequence
What is the root of a phylogenetic tree?
The earliest described divergence in OTUs
What are polytomies?
An internal node with more than 3 daughter branches
What are bifurcations?
When an internal node has 2 daughter branches
What is the difference between a polyphyletic group and a paraphyletic group?
polyphyletic does not include the most recent common ancestor, so these groups tend to be avoided by biologists
What is the topology of a tree defined by?
It’s divergences
According to Netwick, how many elements must be enclosed in the outermost bracket for an unrooted tree?
3
Name 3 methods for inferring phylogenetic trees
- Maximum parsimony
- Distance methods
- Maximum likelihood
What is minimum parsimony?
Arranging a phylogenetic tree by the smallest number of evolutionary changes between nodes
What are distance methods?
Computing a matrix of distances between each pair of sequences to search for a tree that best fits them
What is the neighbour-joining (NJ) system?
Whereby a pair of sequences with the least distance is treated as a ‘unit’ which all other sequence distances are compared to
What is the formula for likelihood?
Pr(data|hypothesis)
Why is likelihood more reliable than distance methods?
- 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
What is the molecular clock hypothesis?
Idea that evolution is constant over time and among evolutionary lineages
supported by: haemoglobin, cytochrome and fribrinopeptides
How is the molecular clock hypothesis useful?
Allows us to find a calibration point for evolutionary distances
Name 4 problems with the molecular clock hypothesis?
- 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
What information has the molecular clock shown about HIV?
- 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
Define a homology?
Phenotypic and genetic similarities (morphology) due to shared ancestry
What are orthologs?
Orthologous genes - genes that are found in a single copy of the genome and are homologous between species, having diverged after speciation occured
What are isofunctional homologs?
Orthologs that maintain the same function
What are paralogous genes?
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
What is the result of repeated gene duplications?
Gene families
