Species Diverstiy tells you the number of unique extant genomes that exist within the sim for that species. Every bot of a species gets assigned a "subspecies" number when the sim is started. They all get the same number as they are all exactly the same geneitcally. They are all the same sub-species. At that point in time, the Species Diversity graph will give you a 1 for the species as a whole as it will if you are running a sim with bots that have mutations disabled. Bots inherent the sub-species number of their parent (or mother in the case of sexual reproduction) but once bots start mutating, I increment this number monotomically in such a way that every unique genome will have a unique number. Note that I don't go so far as to actualy compare genomes so it is possible (but very unlikely) that two bots could mutate independently in the same way and end up with the same genome in which case the number of unique subspecies in the sim would be over estimated, but this is so improbable as to be ignored. Note also that IIRC, viral infection will also bump the sub-species number for an individual. So, not only does this graph give you an idea of how diverse a mutating population has become but it also gives you a means to detect how many individuals in a non-mutating population have experienced unique virus infections.
Subspecies Distance is a half completed attempt to give you some idea as to the genetic distance between the two most distantly related individuals within the species. It's kind of broken at the moment. Currently, it is based on sub-species number, which is the wrong way to do it. Imagine a bot A with sub species number 500. It has 100 children, all which mutate uniquely. They will have subspecies numbers 501-601. They all are only 1 mutation distance from their parent but the graph will give a subspeceis distance of 101.
I've recently implimented a more robust means for tracking the relatedness of individuals where I maintain an ancestor list for every extant bot over the past 100 generations. Besides switching over the Subspecies Distance graph to use this information (on my to-do list) this should enable a host of interesting features in this area including generational distance and exact phylological trees for bots which may not have an extant common ancestor.
