Penguins live in places besides Antartica, such as South America and Africa. Marsupials also live in the Americas. So the premise of your question is misplaced.
Animals migrate and also evolve constantly. Darwin’s theory was largely based on observing how common animals, horses and cattle, had evolved during the previous 1000 years (this becomes an issue in kashruth, since some people are nervous about eating beef since the presumptions for slaughtering cattle developed when domestic cattle were only slightly larger than sheep, but they evolved into something bigger during the last 2000 years – in this case with clever farmers rather than Ha-Shem directing the evolution).
Note that I’m not discussing the concept of what is “time” which involves issue of kaballah we can’t discuss publicly. Also I want to point out that the idea of “random” mutation driving evolution is the only thing that is really apikorisdik in the theory of evolution. Animals evolving, migrating, and the rules of “survival of the fitest” are in ways questionable from a halachic perspecttive. The shailoh isn’t whether, or how fast, a Raptorsaurus evolve into a chicken – but only if that occured “randomly” or under Ha-Shem’s direction.