MSA- multiple sequence alignment. Aligning many sequences is often preferable to pairwise comparisons. Problem- Computational complexity of multiple alignments grows rapidly with the number of sequences being aligned. .
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*Phylogeny- the evolutionary history of a group
3 types possible:
Phylogenetic analysis is controversial. There are a wide variety of different methods for analyzing the data, and even the experts often disagree on the best method for analyzing the data.
Parking lot “A” at 4:00 How many cars changed spaces during this 2 hour interval?
Parking lot “A” at 4:00 #2- Molecular Phylogeny requires statistical estimations.
It is critical to phylogenetic analysis that homologous characters be compared across species.
Webster’s New Collegiate- Fundamental similarity of structure due to descent from a common ancestral form.
(same region analyzed only 1 difference)
fewer homoplasies than DNA
Nodes: branching points Branches: lines
Topology: branching pattern
Distance- a measure of the overall pairwise difference between two data sets.
The raw material for tree reconstruction is tabular summaries of the pairwise differences between all data sets to be analyzed
“There is no denying that distance-based methods “look at the big picture” and pointedly ignore much potentially valuable information.”
Analysis of individual characters are translated into evolutionary trees.
Character- a well-defined feature that can exist in a limited number of different states. (Ex. DNA and protein sequences)
After sequences are aligned, algorithms model each tree.
The method is computationally time consuming as all possible trees are examined.
The aim is to find the tree (among all possible trees)
that has the highest likelihood of producing the observed data (statistical methods).
are similar to maximum parsimony methods but also take into account the likelihood of specific mutations (ex. A G).
Every ‘tree drawing program’ will generate a tree. The important question is whether or not the tree drawn is the right one.
Inferred tree is constructed from data set.
Re-run the calculation on subsets of the data (resampling).
Resampling is repeated several (100-1000) times.
Bootstrap trees are constructed from the resampled data sets.
Bootstrap tree is compared to original inferred tree.
% of bootstrap trees supporting a node are determined for each node in the tree.
Addition of time to phylogenetic tree. Units of time are often in millions of years.
Assumption- substitution rates are constant over millions of years.
Rates of molecular evolution for genes with similar functional constraints can be quite uniform. (Clock may run at different rates in different proteins.)