I don’t really see that as anti-Darwinian. Those genes successfully attach themselves to a new organism and provide advantages such that they are selected for in the population.
The selection is classical, but the mutations are supposed to be random, not skewed towards more useful genetic variants. One can speculate that a purely random (and otherwise neutral, say) prior mutation led to this directionality, but the actual resulting mechanism is AFAIK still unknown.
I don't think Darwin himself said anything about the randomness of the mutations, and of course was not aware of DNA and how things were encoded. I guess followers of Darwin may have said all sorts of things but the paper doesn't seem to contradict Darwinian evolution as described by Darwin.
I see the paper says "central tenet of neo-Darwinism that
mutations are random...". I'm not that up on neo-Darwinism whatever it is.
(I looked at Wikipedia and it seems neo-Darwinism is the term for the Darwin like thinking of the time so maybe the paper contradicts last years neo-Darwinism but not next years?)
Natural selection has nothing to do with randomness per se, it’s merely differential selection based on environmental fitness. The fitness function of a given environment can even narrow a range of existing genes without any mutation occurring during the period where the new fitness function is applied. The classic example of this is peppered moths shifting toward the darker range of their preexisting color range during the Industrial Revolution.
Horizontal gene transfer is another way organisms can acquire new traits.
