In the movie, the codex appears to be an old skull, and it doesn't look like it's from a homo-sapient like creature. So, where did it come from? Why a skull? Is there any canon information about it?
There is no canonical answer, however, we can draw insight from the film and from non-canonical sources, such as director, Zack Snyder.
"Man of Steel" Q&A With Henry Cavill, Amy Adams & Zack Snyder hosted by Kevin Smith to promote the release of the Blu-Ray originally broadcast November 6, 2013, includes a question posed by Steve Younis of the Superman Homepage asking for clarification about the Codex.
Snyder shares a number of points:
- The codex is an ancient prehistorical being that represents the epitome of their natural evolution.
- The skull provides the raw genetic material from which their entire race is born, while the birthing matrix applies the variation and speciation and specialization into different roles.
- The carvings in the skull come from the fact that Kryptonian society was NOT monolithic (and, in fact, Jor-El and Zod may have fought side-by-side in the relatively recent past) and different factions, sects, religions, and governments have fought over this fragment over the ages. The carvings are the product of a particular religious sect engraving their sayings of significance into the skull.
- The skull is merely ONE of the fragments of this being, but as the crown jewel, it is kept in Krypton's capital city. Other cities in the world may have a femur or a bone chip in order to run their own birthing matrices.
Note that such replication, while antithetical to our typical approach to genetic resiliency (born through natural replication and mutation), there is justification for artificial replication if sufficiently reliable. See the Neal Stephenson novel "Snow Crash" for more on the concept of "Informational Hygiene" as a means of preserving more than genetic information (such as culture, ideals, etc) and a justification for using the same artifact repeatedly.
"Man of Steel Prequel"
The Prequel was an originally digitally released comic with story credits shared by Zack Snyder, David Goyer, and Geoff Johns while the script was written by Sterling Gates. Despite being "official", the canonicty is reasonably questioned because of the gap between the story and script. Future creators and filmmakers within the DC Cinematic Universe are unlikely to lose sleep if their material were to contradict this comic or to be handcuffed by its contents.
That said, from the Prequel comic, we learn that every Scout Ship was equipped with its own Growth Codex and, of course, the Genesis Chamber that we see in the film.
Film Based Speculation
Irrespective of the above insights coming from outside the film. Using the film itself, it is plausible to speculated and arrive at many of these same conclusions. First, that the Codex is mainly a database with the skull being used as a storage medium. This is consistent with the fact that Jor-El was able to use his son as the same and that Jax-Ur was able to determine Jor-El's actions (incidentally, Zod's crew's ability to adapt using Jor-El's novel technologies is addressable by the fact that, presumably, Jor-El was a good scientist and actually publishing his findings for the benefit of all). Second, some of the logistics of the film are possibly addressed by the possibility of more than one Codex on Krypton. For example, the readiness of the Sword of Rao to fire upon Jor-El and Zod's readiness to "bring that ship down" with less than kid gloves. Third, the Scout Ship and its Genesis Chamber strongly imply more than one Codex (or at least ability to input genetic data into the Chamber without THE Codex on Krytpon). Fourth, the appearance of the Codex indicates that Kryptonians did indeed evolve on planet (as opposed to being imported from another world). Fifth, the artifact belies a hidden history with culture, values, interests, etc.