It seems like if you look closely at the game a single widespread species, or I guess "ring species", can vary quite a bit between even though it has been classified or named as a single species nevertheless...Could there be certain penalties to maintaining a population as a widespread dominant species?
DISEASE PENALTIES INCREASING WITH A SPECIE'S POPULATION AND DENSITY
Like maybe there is a single disease to represent all diseases which starts off ineffective because it either has to adapt to a specific species or else the disease is just smart enough to know not to wipe out it's reproduction systems (animals) when they are weak.
The more widespread and long lasting a species is without any long lasting mutations the weaker it is against disease. At first a disease just slows an animal down making it harder for the creature to survive, but eventually it will go for the gusto and wipe out a species. The big thing is instead of becoming immune to a disease it would become more resistant simply by having a smaller population.
Maybe the disease could be an aspect of an animal so that it travels with it. That way a disease could be water born or land born to wipe out specific areas without being world wide (travelling through water removes land disease), but if it represents a whole slew of nasties then it can be pretty abstract I would think.
NATURAL DISASTERS AND WEATHER CHANGES (without specifically being tampered with by user)
This is pretty obvious, but maybe it could work alongside a disease factor so that it happens gradually enough to penalize or isolate a major species so that it is forced to change so the animal mutates and the disease then doesn't have the chance to wipe out a major species.
PLANTS THAT BECOME RESISTANT OR INEDIBLE
I don't think plants need to be very detailed like the animals as the focus of the game is not on them and I am fine thinking of them as 'fish food', but maybe if a species becomes too numerous the plants have an increased chance of becoming inedible or less nutritious. Maybe if an animal's diet is closer to 0 and an omnivore it is easier for food sources to become resistant and if it commits to plants it takes longer for plants to become resistant hopefully causing an omnivore species to diverge more and specialize. Perhaps a big herbivore species could be limited to only eating kelp, fruit, grass or whatnot as well to handicap its population.
The penalty or bonus would be attached to the animal rather than the plant so that as the animal changes the penalty goes down.
Meat would not be included since you have to catch prey first anyway.
So on and so on...
I was thinking basically that the less major species there are competing against each other the harder the world could be to survive in for those specific species and once that population is reduced the penalties could ease off a bit.
DISEASE LEVEL 1.1 (+0.01 per year due to world biodiversity)
PLANT RESISTANCE 0.7 ( +0.1 per year due to world biodiversity)
ENVIRONMENTAL STABILITY 1.05 (+0.05 due to species percentage of max pop or biodiversity)
But, I was also thinking though that maybe the parameters or dangers of the planet become altered by a species that dominates the world so that by changing its own environment it will phase itself out requiring some branching or for a marginal species to gain an advantage as it suits the parameters more closely.
DISEASE LEVEL 1.1 (+0.01 per year due to low biodiversity)
PLANT RESISTANCE 0.7 ( -0.1 per year due to biodiversity of plant eaters)
ENVIRONMENTAL STABILITY 1.05 (+0.01 due to low biodiversity because I said so)
Suggest a beneficial feature, or idea's for the future.
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