Biology Reference
In-Depth Information
Classifications are often represented in graphical forms as tree-like dichoto-
mous branching graphs or
dendrograms
. A dendrogram produced from phe-
netic information is called a
phenogram
. A phenogram shows how similar the
group is, but it does not provide information about probable lines of descent.
When a dendrogram is produced from cladistic information it is called a
clado-
gram
. A cladogram shows the sequence of origin of clades and indicates the
times at which the various cladogenic events have taken place. If the dendro-
gram includes both phenetic and phylogenetic data it is a phylogram, or
phylo-
genetic tree
, and indicates the cladistic branching, as well as the relative amount
of change that has occurred. Those species that show the closest relationship
are grouped together into larger, more-inclusive groups or genera. Genera are
grouped into families, and families into orders, classes, and phyla.
12.6.4 Project Goals and Appropriate DNA Sequences
The first step is to consider carefully the project goals and to evaluate pub-
lished information as to which genes/DNA sequences may be most appropriate
to answer the question (
Figure 12.4
). Analysis of the evolution of orders will
require different approaches than analysis of species within a genus. Whether a
specific DNA sequence is appropriate for a particular project can be difficult to
predict in advance unless a survey has been, or can be, conducted to determine
whether the appropriate level of variability is present.
Analyses of different DNA sequences provide information about different lev-
els of phylogenetic analyses over a broad range of taxa. For example, ribosomal
genes are widely used because they are highly conserved, but have regions that
change rapidly and regions that change slowly. Once the target gene or other
DNA sequence has been chosen, primers must be designed or made to amplify
the target sequence by the PCR or a cloning strategy developed. Cloning of tar-
get DNA may be required if inadequate sequence information is available in the
literature or GenBank and if “universal primers” are unavailable.
Once insects have been obtained by collecting or from museums, DNA must
be extracted. As noted in Chapter 8, PCR results vary with the preservation
method. Old, dried museum specimens are likely to contain degraded DNA, so
using DNA sequences that are present in multiple copies (such as mitochondrial
or ribosomal DNA) may be more appropriate than using single-copy nuclear
genes. DNA extraction results are easier with freshly collected, frozen (at
−
80°C),
or alcohol-preserved (95% ethanol [EtOH]) insects. However, a method devel-
oped for isolating DNA from fossils without destroying the specimen has been
adapted to arthropods (
Hoss and Paabo 1993, Rowley et al. 2007, Jeyaprakash
and Hoy 2010
). This method involves soaking intact specimens in a guanidinium
