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mitochondrial and chloroplast-gene order changes, or gene duplications and
genetic-code changes provide useful information with “enormous potential for
molecular systematics.”
As an example, Rokas and Holland (2000) reviewed research conducted
to resolve the relationship of the Strepsiptera, Diptera, and Coleoptera.
Strepsipteran forewings resemble the hind wing balancing organs (halteres)
of Diptera. Under one scenario, dipteran (hind wing) halteres could be homol-
ogous to the front wings of Strepsiptera if a homeotic mutation reversed the
position of the structures in Strepsiptera. By contrast, some would place the
Strepsiptera closer to the Coleoptera because both use the hind wings for flight.
Analysis of 18S rDNA sequence data did not resolve the question. However, a
unique intron insertion was found in the homeobox of the engrailed gene of
Diptera and Lepidoptera, that is absent from other insects and other outgroups.
If Strepsiptera had the intron, it would support a sister-group relationship with
Diptera, but its absence would not. Cloning of the strepsipteran homolog of
engrailed found the intron was absent, indicating that halteres of Strepsiptera
and Diptera are more likely a case of convergent evolution. Wiegmann et  al.
(2009) concluded that Strepsiptera are closely related to the Coleoptera (rather
than the Diptera) using both molecular and morphological data. As noted by
Minelli (2009) , the study by Wiegmann et  al. (2009) demonstrated the impor-
tance of integrating phylogeny and knowledge of the evolvability of devel-
opmental mechanisms. Minelli (2009) recommended that phylogenetics be
combined in the future with evolutionary developmental biology or “phylo-evo-
devo” to resolve other phylogenies.
Another example in which a rare genomic change may provide useful phyloge-
netic information involves the gene order in mitochondria of insects, Crustacea,
and Myriapoda ( Boore et  al. 1998 ). The mitochondria of both crustaceans and
insects share a changed gene order, suggesting that myriapods are an outgroup.
12.5.7 MicroRNAs
Erwin et al. (2011) pointed out that studies of comparative genomics and devel-
opmental patterning have changed our perception of the early evolution of
animals. “First whole-genome sequencing of dozens of metazoans has dem-
onstrated that any animal requires only about 20,000 protein-coding genes
for the production of its essential morphologic architecture. Second, much of
this protein-coding repertoire is conserved throughout all metazoans and is
even found today among single-celled opisthokonts.” Erwin et  al. (2011) fur-
ther state, “the last common ancestor of metazoans was a genetically com-
plex animal possessing all of the families of protein-coding genes used during
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