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This _is_ a Hennigian comb, because in a cladogram, _only_ topology counts.
... what a side branch is lies completely in the hand of the presentator.
to phylogenetic reconstruction
|Compilation of sequence dataset|
|Determination of substitution model|
Why phylogenetic reconstruction of molecular evolution?
Who were the first angiosperms? (i.e. where are the first angiosperms located
Where in the tree of life is the last common ancestor located?
e.g.: domain shuffling, reassignment of function, gene duplications, horizontal gene transfer, drug targets, detection of genes that drive evolution of a species/population (e.g. influenca virus, see here for more examples)
1) Obtain sequences
Databank Searches -> ncbi a) entrez, b) BLAST, c) blast of pre-release data
2) Determine homology (see notes for earlier classes for practical implementation)
Reminder on Definitions:
3) Align sequences
4) Reconstruct evolutionary history
(e.g.: smallest error between distance matrix
and distances in tree, or use
ii) algorithmic approaches (UPGMA or neighbor joining)
find that tree that explains sequence data with minimum number of substitutions
(tree includes hypothesis of sequence at each of the nodes)
given a model for sequence evolution, find the tree that has the highest probability under this model.
This approach can also be used to successively refine the model.
Bayesian statistics use ML analyses to calculate posterior probabilities for trees, clades and evolutionary parameters. Especially MCMC approaches have become very popular in the last year, because they allow to estimate evolutionary parameters (e.g., which site in a virus protein is under positive selection), without assuming that one actually knows the "true" phylogeny.
- ...) Else:
5) Interpret the result.