What if Natives were of a different species? How would this affect cultural assimilation/branding?

I was watching Distric-9 the other day and I had an interesting thought. How would New World relations have been different if the Native American population had evolved into another hominid, or even another species? Although this concept is far fetched, lets consider culturally they were the same as in reality. It would present a huge barrier in the American’s ability to assimilate to European culture. Perhaps it would have resulted in the complete extermination of the native population. Or perhaps some American born disease could have ravaged the European population—but I’m getting sidetracked. In colonial New England, John Rolfe probably wouldn’t have married Pocahontas. John Smith might have described her and the other natives as demons. We might have never even considered to “play Indian” and government symbols could be purely European.

Disclaimer- not high/drunk

If interested here’s a link to a pbs page about human evolution. http://www.pbs.org/wgbh/evolution/humans/humankind/index.html