Hard to say anything specific, other than selective breeding through 2000 millenia (which is still a short time for real world genetics) have rendered Dûnyain sufficiently different from humans such as to make interbreeding hard.
As for the deformed child, I think Bakker was inspired by those numerous pictures of deformed babies (usually from India) which are to be found on the internet. I don't think it has any specific symbolism other than to show the incompatibility.
Still, interesting topic. Wouldn't mind if Bakker provided more info on Dûnyain genetics in future installments...
I had the same thought, everyone usually thinks 2000 years is a long time, but not for the effects of selective breeding to start being noticeable, it really has to be seen in perspective of human generations.
Let's see: the Dûnyain arrived on Ishuäl in 2147, and since that was during the Apocalypse, no babies would actually be born until 2156 at the earliest. Kellhus was born around 4076 (if he was 33 - age given in the appendices of TDTCB and TWP - when he left Ishuäl in 4109). That leaves us with around 1920 years of the Dûnyain breeding program until Kellhus was born, and even if we consider very short generations, for instance, lasting 15 years, that would only give us 128 generations (likely less because they most certainly were not having children by 15, there was the whole selection with the Thousand Thousand Halls, plus, a number of defective children could be born before they had one they were satisfied with, etc.). Which is not
that much for changes as drastic as the existence of Whale Mothers to take place.
But, as it has been stated in previous topics, we really can't look at this with the lens of real life genetics. Maybe in a "realistic" setting (genetics wise) whale mothers would only be possible with genetic engineering, but they did have Nonman blood (or at least the initial Anasûrimbor boy did), and we have no idea what that could result in taken together with what they were trying to achieve with their breeding program (the idea of whale mothers taking after the Tall has been floated around in previous threads, and is definitely possible).
Perhaps the concentration of Nonman genes (and here I'm speculating that at least one of the other original bloodlines the Dûnyain started with had Nonman ancestry as well - it's not impossible as we know of at least one other hybrid than the one in the Anasûrimbor line) is what ultimately resulted in them being genetically incompatible with regular women, almost like a different species? (I say "almost" here because there were still a few humans they could successfully breed with)
Regarding the deformed child - you might be right, I just found those specific deformities curious and was wondering if there was something more to it.
Though I remember that one little girl from India that was born with 8 limbs a few years back was that way due to a parasitic twin. There have been a few examples of Anasûrimbor twins in the series, maybe Kellhus and Esmenet's deformed child had a parasitic twin as well? Kelmomas, after all, had a parasitic twin in his soul in a way, it would be fitting that there was a sibling who had a "normal" physical one.
Sorry for the long post - we might not know enough to draw any meaningful conclusions, but it's always fun to speculate.
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