Biology Reference
In-Depth Information
lineages of R2 elements evolved in arthropods and these have been maintained
(
Eickbush 2002
).
12.5.3 Satellite DNA
Satellite DNA may comprise a large fraction of the total DNA in an arthropod.
Microsatellites are usually species specific, perhaps because this DNA evolves at a
very high rate. There are only a few cases in which the same satellite sequences
have been found throughout an entire genus. Satellite DNA can be used for
species diagnoses or analyses of populations (
Bachmann et al. 1993, Lunt et al.
1999, Caterino et al. 2000, Lumley and Sperling 2011
). Satellite DNA has most
often been used in population ecology and is discussed in Chapter 13.
12.5.4 Introns
Introns within single-copy nuclear genes are perceived to be highly variable and
can be used in taxonomic studies (
Caterino et al. 2000
). The use of introns to
resolve origins of invasive populations of the Mediterranean fruit fly is described
in Chapter 13.
12.5.5 Nuclear Protein-Coding Genes
A variety of protein-coding loci have been used in molecular systematics
(
Friedlander et al. 1992, Caterino et al. 2000
). Nuclear genes exhibit a wide range
of evolutionary rates, and the availability of entire genome sequences for many
arthropod species has dramatically increased the number and type of genes that
can be used in phylogenetic analyses.
Problems with nuclear DNA sequences used for phylogenetic analysis include
the fact that they may be heterozygous; they also are present in low copy num-
ber, which may make them difficult to amplify by the PCR. Furthermore, many
genes contain large introns that make it difficult to amplify more than one exon
unless
Reverse Transcriptase-PCR
(
RT-PCR
) is carried out on mRNA. Caution also
is warranted: many single-copy loci actually are present in more than one copy.
Furthermore, pseudogenes (inactive forms of a gene) may create problems if
comparisons are made inadvertently between genes and pseudogenes.
12.5.6 Rare Genomic Changes
DNA sequence data are used most often to construct phylogenies. However,
Rokas and Holland (2000)
suggest that single-nucleotide substitutions may not
always be informative and argue that rare genomic changes such as
indels
(an insertion or deletion), retroposon integrations, signature sequences,
