Assignments for Today
- Take-home exam #5 is due
- Read the discussion below, who is right? (A Hennigian comb is a comb like phylogeny named after Willi Hennig, the father of cladistics.)
- Read through:
- From previous reading assignments: How can one root a tree that includes all living cellular oganisms?
Assignments for next Monday
- Read Walter Fitch's article on types of homology (available on HuskyCT or here)
----- Original Message -----
Sent: Thursday, July 11, 2002 6:47 PM
Subject: Re: New finds
> > --+--+-----------A
> > | `--+--+-----B
> > | | `--+--C
> > | | `--D
> > | `--------E
> > `--------------F
> This is >not< a Hennigian comb. Only the entire ABCDE clade and the F
> make a (two-toothed) Hennigian comb in this cladogram. In a Hennigian comb
> the side branches are left unbranched, like the teeth of a comb. Hence the
This _is_ a Hennigian comb, because in a cladogram, _only_ topology counts.
A cladogram is a mobile. Look at the following -- it's exactly the same
cladogram as above:
... what a side branch is lies completely in the hand of the presentator.
All I did was I rotated a few stems around their long axes.
PPT Slides for today continued
to phylogenetic reconstruction
|Compilation of sequence dataset|
|Determination of substitution model|
Why phylogenetic reconstruction of molecular evolution?
A) Systematic classification of organisms
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?
B) Evolution of molecules
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)
C) Identification of organisms
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.
Goals Class 18: