CONSTRUCTING THE TREE OF LIFE

[The Central Scrutinizer]

Interesting article (http://www.bayarea.com/mld/mercurynews/news/5364411.htm)

In a bioinformatics class I wrote a final paper on constructing phylogenetic trees, and on various distance methods (the input is a matrix of distances between the species) Specifically, the paper focused on the Fitch-Margoliash algorithm.

Even though it was for a 600 level course, the paper is pretty math-lite and more geared for 'popular' reading because the paper is a general overview with some specific detaisl.

If anyone is interested just shoot me a PM.

From my paper-

some uses for phylogenetic trees:


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Species trees, gene duplication, partial internal duplications, recombination, reassortment, gene conversion, partial duplication with translocation, xenology, greatest rate, greatest change of rate, covarions, dating events, variation in rates, neutrality, positive Darwinism evolution, coevolution, origin of the genetic code, the cenancestor of everything alive today, tissue tropisms, geographic correlates, punctuated molecular equilibrium, climatological correlates, stress effects, and network alternatives.
(Fitch, 1995)

There are many more uses for phylogenetic trees than what is listed. The specifics of each use are very much beyond the scope of the subject of this paper. One particularly interesting, and surprising, example was to produce a tree to display the relationships between various tribes and castes of India (Fitch, 1967).
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And here are some useful references:

References
Uses for Evolutionary Trees, Walter M. Fitch, Philosophical Transactions: Biological Sciences, Volume 349, Issue 1327, New Uses for New Phylogenies (Jul. 29, 1995), 93-102.

Distance Methods for Inferring Phylogenies: A Justification, Joseph Felsenstein, 1984, Evolution, 38:16-24.

Construction of Phylogenetic Trees, Walter M. Fitch, Emanuel Margoliash, Science, New Series, Volume 155, Issue 3760, (Jan. 20, 1967), 279-284.

Phylogenetic Analysis and Intraspecific Variation: Performance of Parsimony, Likelihood, and Distance Methods, John J. Wiens, Maria R. Servedio, Systematic Biology, Volume 47, Issue 2 (Jun., 1998), 228-253.

Bioinformatics, Mount D.W., Cold Springs Harbor Press, 2001, 237-280.

An Alternating Least Squares Approach to Inferring Phylogenies from Pairwise Distances, Joseph Felsenstein, Systematic Biology, Volume 46, No. 1 (Mar. 1997), 101-111.

http://evolution.genetics.washington.edu/phylip/software.html