Theoretically after 20 years of breeding the frog genome could be hardly in the dna after generations of generations. Ntm the lysine deficiency could also be in fact eradicated if at the time of the 2nd Generation having lysine when born which in such cases makes the each generation stronger and more immune to the old bio-engineered alterations of 1st generation. Honestly I hate JP3 like everyone else, but I think that's what Joe Johnson was trying to show that the Dinosaurs actually had mutated back to almost their past selfs. Which is why we see color variations from the previous films and such. Now if in turn this will continue in JW.
But imo I really feel like their should be some sort of clan color variations. I think I good homage is if we see a JP skin toned Raptor fight a rival clan Raptor from TLW or JP3. These things occur irl like in Africa with plains Lions. I mean it's not like all the Raptors would agree to one Female leader, that's why Muldoon said, "They're extremely intelligent, especially the lead one; we bred 8 originally but when she came around she killed all but 2 of the others." So imo why should their be one dominate Alpha Raptor? If you notice very briefly in the TLW as Sarah Harding escapes for the Helicopter, the 2 raptors fighting we're different clans. One had Red Tiger Stripes the Other a Blue.
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