Biology Reference
In-Depth Information
12.6 Steps in Phylogenetic Analysis of DNA Sequence Data
An ongoing need in molecular systematics and evolution studies is to resolve
which genes are informative for which questions. The wealth of information
obtained from DNA sequences can provide insights into evolution and specia-
tion, but how does one choose appropriate genes for a specific problem? How
can estimates of genetic distance be used to make judgments about species sta-
tus or date of speciation? Several concepts are important in using various phy-
logenetic programs to resolve the relationships of different taxa (
Gibson and
Muse 2002
).
12.6.1 Gene Trees or Species Trees
Phylogenetic analysis of a particular genetic locus may not agree with the spe-
cies phylogeny (
Caterino et al. 2000
). The incongruence may be due to the hori-
zontal movement of genes, duplication and extinction of one of the genes, or
to lineage sorting (deep coalescence). For example, the twospotted spider mite,
Tetranychus urticae
, has
fungal
carotenoid genes in its genome (
Altincicek et al.
2012
), as do aphids (
Moran and Jarvik 2010
), presumably through horizontal
transfer. Mitochondrial genes may be more reliable than nuclear genes for eval-
uating some recent divergences (
Caterino et al. 2000
).
12.6.2 Rooted or Unrooted Trees
Many phylogenetic methods produce unrooted trees. Information regard-
ing evolutionary rates or the most ancient relationships is needed to root the
inferred trees. A comparison of the two concepts is shown in
Figure 12.3
. For any
four taxa (the tips of the branches), there are three distinct unrooted trees (I, II,
and III). Each unrooted tree can be rooted on any of its five branches; two of the
possible rooted trees for the center, unrooted, tree are shown (IIA and IIB).
12.6.3 Tree Types
The immense diversity of insects and their long evolutionary history provides
a challenge for systematists. Due to mutation, high reproductive rates, natural
selection and stochastic events, populations change through time. A process of
gradual change through thousands of years can result in a different species; a
change within a single lineage is called
phyletic speciation
. Speciation also can
occur through
cladogenic speciation
, in which two populations of a species
become isolated and diverge genetically due to independent mutation, natu-
ral selection, and genetic drift. Other models for speciation include speciation
through hybridization and polyploidy, or by modification of regulatory genes.
The attributes of an organism used by systematists to establish their relationship
