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I think the issues currently are first, how to show them. From my observation and manual survey, a sizable dominate species usually consist of a few large clans, but many small families and plenty of single mutation creatures if purely using genetic distance as the measurement, how do we reasonably define clans/subspecies without creating so many branches of branches, and the merging of branches? If we are talking about subspecies that can mate with each other, then diverging lineages can merge back together like in braided stream model, that I think would require some intense rewrite of the current clade tree data structure.
The second problem I think is about computation efficiency, the current speciation algorithm is a separate running thread behind the scene independent of other processes, and for a long running simulation it tends to lag behind (clustering algorithm tends to require some intense computation), we would need some very efficient algorithms for subspecies identification or the issue of lagging behind would be even more severe.