Biology Reference
In-Depth Information
are most congruent with the observed data. However, all will be
estimates
of
the “true” tree; we cannot be sure that our estimate is truly accurate in depict-
ing the evolutionary relationships. Many reviews of phylogenetic methods are
available (
Felsenstein 1988, 2004; Swofford and Olson 1990; Stewart 1993; Hillis
et al. 1996; Swofford et al. 1996; Pagel 1999; Shoemaker et al. 1999; Fox et al.
1999; Steel and Penny 2000; Fortna and Gardiner 2001; Huelsenbeck et al. 2001;
Arbogast et al. 2002; Gibson and Muse 2002; Swofford 2002; Bergsten 2005; Hall
2011; Ronquist and Deans 2010)
, and providing detailed procedures for con-
structing phylogenies is beyond the scope of this chapter. Only a brief outline of
the different approaches is provided. Details of phylogenetic methods should be
obtained from the above-cited reviews, topics, and “how-to” manuals. Be aware
that the methods for inferring phylogenetic relationships from molecular data
continue to evolve. Phylogenetic analysis involves knowledge of statistics, com-
puters, and mathematics, including calculus and matrix algebra; previous expo-
sure to the theory of quantitative genetics is useful (
Felsenstein 2004
).
Inferring a phylogeny is an estimation procedure and is based on incomplete
information. Any study of DNA sequences sampled from different species or dif-
ferent individuals in a population is likely to start with a phylogenetic analysis.
Thus, phylogenetic analysis is now common in biology, but a novice will be frus-
trated by the fact that there are so many different approaches and differences
among experts.
The selection of one or more trees from among the set of possible phyloge-
nies is based on one of two approaches: 1) defining a specific sequence of steps,
an algorithm, for constructing the best tree; or 2) defining a criterion for com-
paring alternative phylogenies to one another and deciding whether they are
equally good, or one is better. Some methods of phylogeny construction are
based on different explicit evolutionary assumptions, whereas others are not.
Phylogenetic trees represent evolutionary pathways and there is a difference
between species trees and gene trees (
Goldstein and Harvey 1999
). Branches in
a species tree join extant species to an ancestral species and represent the time
since those species diverged. The data used to construct the tree often represent
a single region of the genome of those species. A gene tree constructed from a
short region of the genome may not be the same as the species tree. Two spe-
cies may carry genes that diverged before the species split, or introgression or
transposition may have resulted in genes having diverged after the species split.
Phylogenies are presented as rooted or unrooted trees. A
rooted tree
conveys the
temporal ordering of the species or genes on a tree, but an
unrooted tree
reflects
the distances between units with no notion of which was ancestral to which. Some
