This is what i got from my advisor ...
Genetic cause:Statistically, for 2 unrelated rays to have a recessive gene to cause this is extremely improbable, for this gene to express itself in all of the pups is also extremely improbable, I mean millions to one against, there are mathematical formulas to work out the exact odds, but it pretty much proves that the 'batman' defect is not genetic from a statistical point of view.
So, if its not 'Nature' ( genetic) then it must be 'Nurture'( environmental)
This kind of defect and a host of other diseases and malformations can be commonly caused in all animal species by something called Gene Transcription Error ( GTE) . This means that the parents genes are good but some external factor has caused the genes to be 'mis-written' in the offspring. In parents this is a 2 way reversable trait, meaning the effect goes away when the underlying cause goes away and if the batman pups ever reproduce the effect is unlikely to repeat, unless the same environmental reason for the GTE is present.( this question will be answered in the next generation)
Things that commonly cause GTE are : Environmental stress from things such as pollutants such as bad water , over medication etc.
Disruption of circadian rhythms such as lights on 24/7 or off 24/7, (Amazonia is approx 12/12.
Improper diet/lack of proper nutrients.
Temperature ( too hot for too long) overcrowding.
No escape from aggressive males
and a whole host of other factors, almost anything you can think of that might cause any kind of stress.
Regarding specifically the question of Temperature:
I am convinced that most people keep their rays too hot.
As an example: the Xingu river ( where most of our favorite black rays and scobinas are from) day time water temp averages approx 82F and night time approx 72F, you can work out the mean temp from that obviously ( 77F). You see here a rhythm like a sin wave. Most ray keepers keep them at a nearly constant 82F-86F.
The day/night temperature variation is actually greater than the seasonal variation. Small pools and lakes can get hotter for periods during the 'dry' season but usually anything trapped in those seasonal places dies as their oxygen runs out. The other places do not get much hotter or if they do it is only for short periods of time.
Also rays, living for the most part on the bottom,usually are in the cooler parts of the water. Rays are adapted to the rhythm and are largely prompted to breed by the cues from temperature and pressure changes.
Keeping rays at a temperature higher than their evolutionary 'normal' is like revving the engine of a car non-stop, you will go faster but the engine will eventually seize up.
In the short term, yes it makes pups grow faster and parents reproduce more often in a year but in the long term will inevitably have an adverse effect on their health, be it only living shorter lives, but more probably things like you have experienced with your pups.
I think this is why we see this much more often with captive bred rays than in the wild.
I also think the parent killed the other pup because of this deformity, and would probably have killed ( and maybe eaten) the rest pretty quickly. This behaviour is very common in the animal kingdom when offspring are 'wrong'.
I am also convinced that most people over-medicate their rays when simple better water would be a preferable route to take. I frequently see recommendations on MFK for 4X dose of praziquantel for instance! WHY? there is NO extra benefit but plenty of potential side effects that rays, as long-lived animals, would be prone to. Kidney damage, liver damage, DNA transcription damage with invisible effects as well as 'batman' etc.GTE can also be caused by bacteria and viruses, which may otherwise do nothing to the apparent health of the animal