Your article refers to allopatry. This process is commonly refered to as character displacement and may be morphological or ecological.
The author presumes that since the mice species referenced had lost chromozomes, and since they could not interbreed, that a new species had been created. Scientific consensus does not agree. That logic equates to stating that since lions and tigers can interbreed, they must be the same species.
Many species evolve characteristics, but at the end of the day, they are still the same species.
Chromozome count and placement is how we all get different colors of hair and eyes, are short or tall, etc. And as bad as you hate to admit it, we are all the same species.