Questions (yours) and Answers (mine, i.e. J. Peter Gogarten)
What is phylogenetics? Does it mean building trees?
The equation between trees and phylogeny is a widely propagated misconception. The origins of the word phylo-geny are Greek phlon, race or class and Greek -geneia, from -gens, born. (from the American Heritage Dictionary). Phylogeny describes how the larger taxonomic categories came into existence (as opposed to ontogeny which describes how the individual organism comes into existence). Botanist discovered long ago that the origin of many species results from the fusion of genomes belonging to different parent species. They coined the term reticulate evolution. There is hardly any crop plant that is not aneupolyploid (i.e. every cell contains copies of genomes from two different parent species. More here.).
Every eukaryotic cell represents the result of a fusion between at least two independent ancestors, an alpha proteobacterium that evolved into the mitochondrion, but whose genes nowadays mostly reside in the nucleus, and a host cell that was a close relative of the archaea. (There might have been many more organisms contributing genes over time, but except for the cyanobacteria, these additional contributors currently are less well defined.)
Many organisms are in fact microbial communities, whose members live in close association (e.g., lichen), and many (all?) microbial communities can be viewed as higher order entities with a shared genetic resource (open source genetics J).
Especially for microorganisms (but see here
for recent examples of gene transfer between very divergent angiosperms) the
evolutionary history of organisms is not tree-like, at best, it can be
approximated by a tree. For more on
Gogarten, J. P., Doolittle, W. F., Lawrence, J. G. (2002). Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19, 2226-2238.
Zhaxybayeva, O., Gogarten, J. P. (2004). Cladogenesis, Coalescence and the Evolution of the Three Domains of Life. Trends in Genetics 20, 182-187
This is what Wikkipedia
currently says on phylogeny:
A phylogeny (or phylogenesis) is the origin and evolution of a set of organisms, usually of a species. A major task of systematics is to determine the ancestral relationships among known species (both living and extinct), and the most commonly used methods to infer phylogenies include cladistics, phenetics, maximum likelihood, and Bayesian.
During the late 19th century, the theory of recapitulation, or Haeckel's biogenetic law, was widely accepted. This theory was often expressed as "ontogeny recapitulates phylogeny", i.e. that the development of an organism exactly mirrors the evolutionary development of the species. The early version of this hypothesis has since been rejected as being oversimplified and misleading. However, modern biology recognizes numerous connections between ontogeny and phylogeny, explains them using evolutionary theory, and views them as supporting evidence for that theory. See the article on ontogeny and phylogeny.