the biological link between Beforans and Alternians is difficult. Meenah and Feferi are clones of each other, so they’re the same species; if Beforans are different from Alternians, then Meenah and all her friends would be considered mutants there. if Alternians are different from Beforus then Feferi and co. are all mutants instead, which is even more problematic given Alternia’s culture.

the first stumbling block is that we don’t really know “where” life comes from in Homestuck’s cosmology. for a lack of any other information, we might assume evolution and natural selection rule, as in real life; but how can there be any “natural” selection in a world where paradox clones exist? Jake doesn’t have parents or a family tree; he’s not descended from any human being. so was he intelligently designed? and if he was, does that mean the rest of humanity was “intelligently designed” to be like him?

we can’t be totally sure this isn’t the case, as per. Book 3, p. 459:

Skaia sacrifices the planet of origin so that its child (a new universe) may have a chance to be born. But it simultaneously seeds the dead planet with the potential for new life and civilization (exiles), and retroactively seeds the planet with the children who would fertilize Skaia with the new universe. This is the essence of the universal creation cycle. Sacrifice the old to make way for the new. Life rises again from the ashes of the old. Rinse and repeat. Something else to wonder: how often has Earth itself been through this process before humanity came along?

exiles arrive on the destroyed Earth with all the technology they need to start everything all over again; so if this has happened before, who’s to say carapacians didn’t engineer humankind in a lab?

but gl'bgolyb was introduced at the dawn of trollkind’s sentience - anywhere between thousands and hundreds of millions of years in the past, depending on how Scratch interprets the nebulous concept of ‘sentience’ - and when Becquerel first arrived on Earth, pterosaurs still soared the skies. so when a scratch happens, there’s the potential for the evolutionary tree to branch significantly before the paradox clones are even meteoric twinkles in the sky. so when those carapacians were designing trolls in a lab, were they designing the trolls that would come to exist on Beforus, or the trolls that Feferi and her friends would live amongst?

@raguna-blade points out that “genes are in themselves a kind of idea” (coincidentally something I found I had also said in the past while I was searching for the above Book 3 commentary); so in the way that ideas tend to sink into the void and then rise back up again throughout time in Homestuck, it wouldn’t be too farfetched to assume that, given enough time, the same genetic ideas would eventually assert themselves on both Beforus and Alternia. but Alternia has also been subject to a pervasive eugenics program for an unknown stretch of time; and Scratch knows that as a scratch doctor, his job isn’t to totally rewrite every part of Alternia, but to make sure the broad strokes remain the same while altering the details to fit his own narrative. Alternia’s history isn’t an original work, it’s only his fanfiction of what the trolls should be like. (we also see this philosophy at work in the history of Skaianet Systems, where Scratch’s protege Meenah crosses over to the post-scratch Earth and works behind the scenes to make sure events take place in roughly the same way, right down to cloning John’s father to act as an identical father to Jane).

Meenah was a teenager in Beforus’ modern day; so when her meteor arrived on Alternia, centuries or thousands or millions of years in the past, was she advanced for her race? had trolls been selectively bred in preparation for her arrival, or did her arrival mark the initiation of a new ideal troll form, sending subsequent generations of her race on a trajectory that would lead to the perfect conditions for her identical descendant Feferi? in either case the long con of Scratch’s eugenic master plan is revealed; there is no perfect Alternian warrior race. Meenah’s trolls aren’t being bred “toward” anything, to be good at conquering or playing games; they’re being bred to make sure they stay exactly the same as they always were, and never become anything new.