Because Rony’s results from her PCR did not match her previous results for the positive controls, I ran the PCRs myself on the controls and the hybrids. Anneal temp 50C. PCR set up, samples, etc. are here.
Results: The positive controls still do not match the results Rony got in two consecutive PCR attempts. However, the Bay_Actin_Rv2 and Sea_Actin_Rv3 primers do result in clearly distinguishable differences between bay and sea scallop gDNA. Lane 2 (bay gDNA/bay actin primer) has a large, ~1000bp band and lane 7 (sea gDNA/sea actin primer) produces a ~300bp band. Unfortunately, this does provide us with any useful info. Something needs to be reworked (i.e. possibly new target gene) in order to start getting some useful results.
However, the results we did get definitely confirm that the hybrids are NEITHER hybrids nor bay scallop, due to the fact that no bands are present in any other sample than the bay scallop gDNA samples.