Agriculture Reference
In-Depth Information
Molecular Genetic Tools
Microsatellite markers
Microsatellites are the most popular genetic
markers in molecular ecology because of
their broad scope of applicability, ranging
from the study of local breeding structures
and parentage to global population genetics
(Sunnucks, 2000; Zhang and Hewitt, 2003).
Microsatellites are generally nuclear
markers that are simple sequence motifs of
one to six nucleotides that are repeated
typically between 5 and 40 times (Selkoe
and Toonen, 2006). Repeat units have a
considerable mutation rate (1 × 10
-2
- 10
-6
per locus and generation) because of slip
strand mispairing and proofreading errors
during replication (Eisen, 1999). The high
allelic diversity and biparental mode of
inheritance of microsatellite loci make them
especially useful genetic markers to study
the hierarchical population genetic struc-
ture in social insects from large-scale gene
fl ow and migration rates to the degree of
inbreeding within and among colonies, and
for assigning individuals to colonies and
populations (Vargo and Husseneder, 2011).
Genetic relationships and levels of gene
fl ow among populations are generally
quantifi ed using
F
-statistics (Wright, 1965),
particularly
F
ST
, which compares allele
frequencies among populations;
F
ST
varies
between zero when there are no genetic
differences among populations to one when
populations are genetically unrelated,
sharing no alleles in common.
There is an increasing arsenal of molecular
techniques for detecting and quantifying
the genetic structure of individuals, popu-
lations and species. The two most commonly
used markers in urban entomology, and
much of molecular ecology, are mito-
chondrial DNA (mtDNA) markers and
microsatellites. This section provides a very
brief overview of these techniques. More
complete discussions of genetic markers
used in the fi eld of molecular ecology are
available in reviews written by Loxdale and
Lushai (1998), Sunnucks (2000) and Avise
(2004). In addition Vargo and Husseneder
(2011) have reviewed molecular markers
used in studies of colony and population
genetic structure in termites.
Mitochondrial genes
Mitochondrial genes are generally mater-
nally inherited and are commonly used in
studies of population genetic structure and
evolutionary relationships. Several genes
have been used but most studies employ
the cytochrome oxidase I or II genes (COI
and COII) or the 16S ribosomal gene (16S
rDNA). At the species level, the COI gene is
most commonly used and it has been
designated as the offi cial DNA barcoding
gene for species identifi cation (Hebert
et
al.
, 2003). Most commonly, sequence data
are obtained for the genes and then analysed
for similarity and phylogenetic relation-
ships. Because mtDNA is maternally
inherited and tends to evolve rapidly owing
to a higher mutation rate than nuclear DNA,
it has a smaller effective population size
and therefore tends to be more diagnostic
at the population level than nuclear
markers. Mitochondrial DNA markers are
therefore highly informative for dis-
tinguishing among species, for detecting
population genetic structure and for deter-
mining geographic sources of introduced
populations.
Taxonomy and Species Identifi cation
One of the most important steps in the
management of any urban pest is proper
species identifi cation. This can be quite
challenging, however, in the case of many
urban pest species, especially subterranean
termites. Species in this group are
notoriously diffi cult to identify, with few
distinguishing traits, particularly among the
workers and soldiers, the most commonly
encountered castes. Thus it is not surprising
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