The sibling tephritid fruit flies B. tryoni and B. neohumeralis are sympatric species that provide a unique Australian model for the genetics of speciation.  The species are genetically extremely similar but are reproductively isolated by time of mating, a trait which is genetically controlled and sensitive to light intensity.   A previous, candidate gene approach revealed that cryptochrome, which encodes a light sensitive protein with input into the circadian clock, is differentially expressed in brain and antennae (An et al., 2004).  We have now prepared replicated quantitative transcriptomes of brain and antennae, sampled at morning and night, from the sibling speicies.   The raw reads were assembled de novo using Trinity, with a separate assembly for each tissue, but combining the two species due to the extreme similarity of the genomes, thus enabling a direct comparison of read counts for each transcript.   ANOVA was used to test the difference in gene expression between (i) time of day, (ii) the two species and (iii) the interaction ie where the time-of-day pattern of expression is different between B. tryoni and B. neohumeralis.  Data will be presented from the brain analysis revealing candidate genes that are differentially expressed between the species.   However, due to the large number of statistical analyses, very few time-of-day differences and no interaction differences reach significance.