The earthquakes are caused by the Queen Metroid
Right after you kill all the Metroid larvae in the Metroid nest, another earthquake occurs that signals the emergence of the Queen Metroid (and if you go into this room prior to killing all the larvae, the Queen won't appear), implying that it has been the Queen causing all the earthquakes throughout the game. This explains why the earthquakes occur after you kill all the Metroids in an area: It's the Queen reacting to the deaths of her offspring. The Chozo based the Metroids on Arachnus
The Arachnus looks very similar to the Metroids, especially the Omega Metroid - they're both reptilian creatures with four limbs, reddish pink skin, large mouths, and hard green shells on their backs. It's possible that the Chozo created the Metroids based on the DNA of some native Arachnuses. This would explain why they look so similar.- This may actually be supported by the Mawkin in Dread, who combined the local fauna of ZDR such as Corpius to create the chimera Experiment No. Z-57. If they did it with Corpius, maybe the Thoha did it with Arachnus.
- Alternatively, their resemblance to Arachnus is a side-effect of the Metroids being on SR388, since they are known to evolve differently depending on their environment.
