What is the root of a tree?
1 unique internal node that is the ancestor of all the sequences
What 2 types of data can be used in phylogenetic inference?
- Character-based methods: Use aligned character (protein/DNA) directly during construction
- Distance-based methods: Transform sequence into pairwise distances (dissimilarities) then use the matrix for construction
What is a tree?
A mathematical structure which represents a model of an actual evolutionary histiry of a group of sequences or organisms; ie an evolutionary hypothesis
What do internal nodes of a tree represent?
Hypothetical ancestors
Give 3 features of bootstrapping
- Refers to distance method
- Re-sample from original site
- Repeat original analysis on each pseudoreplicate data set
What is the main step in the Neighbour Joining method?
At each step, each pair of possible neighbours are considered and the one producing the shortest tree is chosen
Give 2 strengths and 3 weaknesses of distance methods
Strengths:
- Computationally simple and quick
- Distance correction (Implies a model of evolution)
Weaknesses:
- No insight about actual evolutionary changes
- UPGMA (Not NJ) assumes molecular clock
- For longer timescales distnces are non-linear and require correction
What is an additive tree?
A cladogram with branch lengths; also called phylograms and metric trees
What are the features of a tree when it is altrometric?
OTUs are equal distances from the root
What is the problem with numerical taxinomy?
Not entirely objective
What do terminal nodes represent?
Sequences or organisms for which there is data; typically called an Operational Taxonomical Unit (OTU)
What is an ultrametric tree?
A special kind of additive tree where the tips (OTUs) are all equidistant from the root
What is the fundamental step in the UPGMA method?
- Choose the most similar pair
- Cluster them together (Half the resulting value is attributed to the branch length)
- Calculate the new distance matrix
What is a cladogram?
A tree showing relative order of common ancestry
What is included in the character-based method for tree construction?
- The state of a specific (aa/nt) is considered
- A tree that minimizes number of changes required to explain the data is chosen (maximum parisomy, minimum evolution)
What does a tree consist of?
Nodes connected by branches
Maximum parisomy is an example of what?
- Occam's razor: simplest hypotheses are preferable to more complicated ones
- ie finding a tree that requires the smallest number of evolutionary changes among the sequences
What assumptionabout speciation is made in tree construction?
That it is a rare event, occuring only once at a node,, generating only two branches (bifurcating) as opposed to multifurcating where there is polytomy at the node
Give 3 advantages of maximum parisomy
Advantages:
- Doesn't reduce sequence information to a single number (might give info on specific changes in protein/regulatory sequence)
- Tries to provide information on ancestral sequences
- Evaluates different trees
What is an advantage of the UPGMA method?
It identifies the root of the tree
When phylogonies are used as analytical frameworks, what 3 things can be learned from character analysis?
- When specific episodes of positive Darwinian selection occured during history
- The genetic changes which are unique to human lineage
- Likely geographical location of the common ancestor of African apes and Humans
What is a network?
More thanone path between any pair of nodes
List 3 things that can be inferred from phylogenetic trees built from DNA or protein sequence data
- Species that are the closest living relative to humans
- Forensics (Florida Dentist)
- Origins of specific transposable elements
What is included in the distance method for tree construction?
- Evolutionary distances are computed for all pairs of sequences (bases on number of substitutions)
- The tree is based on a relationship among distances (ie UPGMA, Neighbour-joining)
What are neighbours?
When OTUs are connected through a single internal node
When does the UPGMA method fail?
When the rates of evolution are not constant; shown by distances between roots and OTUs varying; Neighbour joining usually gets the right tree
Give 4 disadvantages of maximum parisomy
Disadvantages:
- Computationally expensive (exact searches increasinly impractical due to rapid increase in taxa)
- Doesn't correct for multiple mutations (doesn't imply evolution model)
- Evolution is not necessarily parasimonious
- Doesn't provide onformation on branch lengths