Lecture 12 - 13 Flashcards
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)