To clarify my last comment.
Suppose two species have sequence as follows:
Species A -- ATTCTGAGCG
Species B -- ATCCTGTGCG
Directly sequencing PCR products derived from a primary hybrid will give
you:
hybrid -- ATNCTGNGCG
This is because the PCR products contain equal amounts of T and C at
position 3, and equal amounts of A and T at position 7. This sequence could
not be used in a phylogenetic analysis, because there are no informative
sites -- the variable sites are ambiguous.
In the F2 or F3 generation of a cross, recombination between the two
parental sequences could give an intermediate sequence like ATTCTGTGCG, but
this is only likely if the two variable positions are much further apart
than the 917 bp that Yukawa sequenced. Recombination within a single gene
is unlikely.
Assuming that Yukawa is honest and moderately competent, I think his
phylogeny is fairly strong evidence that D. suzukii is not D. Peng Seng.
Nick
--
Nicholas Plummer
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