I could not find any reason for this so I guess it is just down to differences in genetics between the species, the ones with the spikes are less likely to be eaten
The spikes are just an adaption for delivering the poison and also for appearing dangerous.
Some pufferfish without spikes aren’t poisonous – and are routinely eaten by predators, others that are poisonous rely on colouration to advertise their venom.
It’s a case of divergence – the environments and ecology the different species of pufferfish evolved in are reflected by their level of poison and presence of spikes.
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