Molecular Phylogenetics. Dan Graur. Molecular phylogenetic approaches: 1. distance-matrix (based on distance measures) 2. character-state (based on character states) 3. maximum likelihood (based on both character states and distances). DISTANCE-MATRIX METHODS
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1. distance-matrix (based on distance measures)
2. character-state (based on character states)
3. maximum likelihood (based on both character states and distances)
In the distance matrix methods, evolutionary distances (usually the number of nucleotide substitutions or amino-acid replacements between two taxonomic units) are computed for all pairs of taxa, and a phylogenetic tree is constructed by using an algorithm based on some functional relationships among the distance values.
*Units: Numbers of nucleotide substitutions per 1,000 nucleotide sites
Unweighted pair-group method with arithmetic means
The neighbors-relation method (Sattath & Tversky)
The neighbor-joining method (Saitou & Nei)
Similarities among OTUs can be due to:
(Plurality should not be posited without necessity.)
William of Occam or Ockham (ca. 1285-1349)
English philosopher & Franciscan monk
Excommunicated by Pope John XXII in 1328.
Officially rehabilitated by Pope Innocent VI in 1359.
Maximum parsimony involves the identification of a topology that requires the smallest number of evolutionary changes to explain the observed differences among the OTUs under study.
In maximum parsimony methods, we use discrete character states, and the shortest pathway leading to these character states is chosen as the best or maximum parsimony tree.
Often two or more trees with the same minimum number of changes are found, so that no unique tree can be inferred. Such trees are said to be equally parsimonious.
1. Identify all the informative sites.
2. For each possible tree, calculate the minimum number of substitutions at each informative site.
3. Sum up the number of changes over all the informative sites for each possible tree.
4. Choose the tree associated with the smallest number of changes as the maximum parsimony tree.
Thus, the tree supported by the largest number of informative sites is the most parsimonious tree.
All other informative sites are deemed to be homoplasies.
Wagner-Fitch: Unordered. Character state changes are symmetric and can occur as often as neccesary.
Camin-Sokal: Complete irreversibility.
Dollo: Partial irreversibility. Once a derived character is lost, it cannot be regained.
Weighted: Some changes are more likely than others.
Transversion: A type of weighted parsimony, in which transitions are ignored.
The set at an internal node is the intersection () of the two sets at its immediate descendant nodes if the intersection is not empty.
The set at an internal node is the union () of the two sets at its immediate descendant nodes if the intersection is empty.
When a union is required to form a nodal set, a nucleotide substitution at this position must be assumed to have occurred.
number of unions = minimum number of substitutions
Fitch’s (1971) method for inferring nucleotides at internal nodes
Branch-and-Bound = Examine some trees, get the best tree (guaranteed).
Heuristic = Examine some trees, get a tree that may or may not be the best tree.
Descendant trees of tree 2
Obtain a tree by a fast method. (e.g., the neighbor-joining method)
Compute minimum number of substitutions (L).
Turn L into an upper bound value.
Rationale: (1) the maximum parsimony tree must be either equal in length to L or shorter. (2) A descendant tree is either equal in length or longer than the ascendant tree.
How to calculate ML score for a tree :
1... j ... ...N
... ... ...
Seq x: C...GGACGTTTA...C
Seq y: C...AGATCTCTA...C
... ... ...