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authors raise the possibility that “diverging species that remain incompletely iso-
lated reproductively (such as D. simulans and D. mauritiana ) may be permeable to
introgression over a large portion of their genomes.” Because only a small region
near each “speciation locus” is impermeable, the exchange may continue for
some time until reproductive isolation is complete.
Michel et  al. (2010) evaluated the genetic diversity of Rhagoletis pomonella ,
a species known to have speciated sympatrically by moving from hawthorn to
apple hosts in North America within the past 250 years. They found “widespread
divergence throughout the Rhagoletis genome, with the majority of loci display-
ing host differences, latitudinal clines, associations with adult eclosion time, and
within-generation responses to selection.”
Many questions about speciation remain unanswered ( Howard and Berlocher
1999, Mallet 2006, Schluter and Conte 2009, Via 2009, Johnson 2010, Cutter
2012 ). How important are conventional gene mutations compared to novel
genetic elements, such as repeated sequences, symbiotic microorganisms such as
Wolbachia , or transposable elements? How often are “speciation” genes altered
in their coding sequence compared to changes in noncoding regulatory regions?
How often is reproductive isolation based on polyploidy, or on chromosomal
rearrangements of chromosomes? If transposable elements, polyploidy, or infec-
tious microorganisms such as Wolbachia cause speciation, would they produce
a rapid change without significant genetic change in the arthropod genome?
Cloning and characterizing genes important in speciation may provide informa-
tion on how reproductive isolation occurs at the molecular level.
12.10.3 Detecting Cryptic Species
One can argue that morphological methods are faster, easier, and cheaper than
molecular methods for many taxonomic studies. However, molecular methods
often provide the only method for detecting cryptic species. The ability to detect
cryptic species may have ecological and economic importance.
RAPD-PCR may provide an inexpensive method for detecting cryptic spe-
cies. For example, two populations of the encyrtid parasitoid Ageniaspis
citricola were imported into the United States from Taiwan and Thailand as part
of a classical biological control program directed against an invasive pest of cit-
rus, Phyllocnistis citrella ( Hoy et  al. 2000 ). Slight differences in the biology and
behavior of the two populations led us to evaluate them with RAPD-PCR and
the results indicated the two populations were genetically distinct ( Hoy et  al.
2000 ). Subsequently, analysis of two highly conserved actin genes confirmed
the distinctiveness of these populations. Analysis of ribosomal ITS2 sequences
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