Chaetognaths
Chaetognaths, or arrow worms, are invertebrate creatures that feed on plankton. They are found worldwide, from the shallows to the depths and from the polar regions to the warmest ones. What makes them so important when it comes to the history of crayfish and squid is the classification. It is a sister group to the creatures that would become mollusks, including the squid, but has several characteristics of the creatures that would become arthropods, such as the crayfish. Genetics puts it in with mollusks, although the debate is still raging as to what relationship it may have with the other species.
Urbilaterian or PDA Ancestor Mystery
Science has a fair knowledge and bulk of information regarding the relationship of squid and crayfish ancestors. They classify the branches of their tree as deuterostomes and protostomes, with the former being all those creatures whose mouths developed after the anuses, and the protostomes being all those creatures whose anuses developed after the mouths. Vertebrates and starfish are deuterostomes, while mollusks and arthropods are are protostomes. The Urbilaterian ancestor, or the PDA (protostome-deuterostome ancestor), is the hypothesized creature that both of those developed from millions of years ago. The problem is that, because it most likely had no hard shell or anything to fossilize well, it left no record of itself. Because of this, many scientists debate that it even existed. If it did, then it would be one of the ancestors linking squid and crayfish together.
Protostome Lineage
Both mollusks and arthropods are housed together under protostomes along with annelids (worms). Protostomes are further broken down into Ecdysozoa, Platyzoa and Lophotrochozoa: the superphylum with arthropods, the one with rotifers, and the one with mollusks and annelids. The result is that a common ancestor may exist in the protosome fossil record that connects the ecdysozoans (crayfish family line) and Lophotrochozoans (squid family line). Again, the trouble is in finding one of the ancient protostomes to use as evidence.
Problematic Diversification
Most biologists are well aware there must be some form of link between the ancestors of squid and crayfish. What is unclear to them is how the two are actually related or when the diversification took place that separated them. They believe that, along with a lot of other life on Earth, the first diversification occurred during the Cambrian Explosion, but before some 555 million years ago with the appearance of the mysterious Kimbrella, thought to be a mollusk. If a mollusk existed by that point, then the protostomes had to have evolved away from one another, creating the three branches. Many species seem to end in the Cambrian Explosion area, and their lineage cannot be traced further back. Obviously, finding a common ancestor between a squid and a crayfish will take more time to discover.