The octopus is one of Earth's most striking creatures, able to exert fine control over a complex and flexible body all while constantly adjusting its coloration through specialized organs on its skin. The creatures also appear to be rather smart; researchers have found evidence of complex problem solving and observational learning. All of this from an animal that is part of the mollusks, a group we often associate with things like clams.

Of course, mollusks started diversifying back when the only vertebrates were fishes, so that's plenty of time for them to evolve some distinctive features. To get a better glimpse of what, exactly, evolved, researchers have now sequenced the genome of the California two-spot octopus. The answer to the octopus' surprising smarts seems to be the expansion of two types of genes, along with the generation of hundreds of new ones.

Sequencing the genome wasn't an easy task. Unlike some invertebrates like Drosophila, the octopus' genome is roughly the same size as many mammals (2.7 billion bases long, about 90 percent the size of the human genome). But a team of researchers has managed to get 83 percent of those bases, covering almost all of the organism's 33,700 genes. According to author Daniel Rokhsar, the California two-spot octopus (Octopus bimaculoides) was chosen simply because it's easy to work with in a lab.

Most of what we know about the formation of body plans comes from organisms with symmetric left and right sides (called bilaterians). Here, the arrangement of organs and appendages along the body's long axis is controlled by clusters of genes called Hox. The octopus clearly has a radically different body plan, and the Hox genes reflect it. While they're present, none of them are next to each other—any clusters the octopus' ancestors inherited have been scattered.

There's some hint that the complex body plan is put together by equally complex gene interactions. One family of genes that controls the activity of other genes (the C2H2 zinc finger transcription factors) has expanded dramatically in the octopus' lineage. While some of their relatives have about 200 of these genes, the octopus has over a thousand, nearly double the number found in a typical mammal.

Some big nerves In mammals, long nerve cords are possible in part because of myelin, a fatty material that acts as electrical insulation, keeping neighboring nerves from interfering with each other. Cephalopods lack the ability to produce myelin, but there are still situations where long nerve cords are useful. To manage this, cephalopods grow big nerves—the longer nerves are also larger in diameter, and cords bundle fewer of these large nerves together. This turned out to be useful for early neurobiology researchers. A squid giant axon turned out to be big enough that they could stick crude electrodes into it, allowing the first direct measure of electrical activity in nerves.

The octopus' nervous system is also rather complex, with a relatively large brain that surrounds its esophagus and dedicated optic lobes; there are also nerve cords running down each arm. Like mammals, the octopus has expanded a family of molecules (protocadherins) that help nerve cells stick to each other. It has 168 of these, while other invertebrates typically have about 20.

There are other hints of adaptations, like relatives of the receptor for the nerve signaling molecule acetylcholine that seem to have evolved to sense touch within the suckers. But the biggest find is a large collection of completely new genes, which the authors number in the hundreds—and possibly thousands. "It's hard to pin down an exact number, but there are hundreds that meet all the criteria of a bona fide gene, with evidence for expression, and some similar cephalopod sequence in the available transcript databases," Rokhsar told Ars. "These are the ones we are most confident in, but there are thousands more that look like bona fide genes."

Not all of them will turn out to be real, but the haul of new genetic information is likely to be substantial as we have little idea what many of them do. The DNA sequences provide some hints—there's a large family of genes involved in skin coloration, for example. But all we can say about a lot of them is that they are often expressed in the octopus' distinctive features: its nerves, multi-hued skin, and suckers.

The researchers don't even speculate what these genes might be doing, and it will be hard to test since nobody's managed to do octopus genetic breeding yet. Some hints might come if we manage to sequence a squid genome, since they have a number of similar traits. But the squid and octopus lineages diverged over 270 million years ago, back when our ancestors were strange-looking fish that could sort of prop themselves up on their front fins. So there's a good chance that some of these genes are unique to the octopus and will maintain their aura of mystery for quite some time.

Nature, 2015. DOI: 10.1038/nature14668 (About DOIs).