Roots are usually included in the term "vegetables."
Yeah, it's true that modern people have some adaptations due to what they call "niche construction" which appears to be a fancy term for "agriculture" + "cooking" when it comes to diet.
For example, most modern people can digest milk, whereas our paleolithic ancestors mostly couldn't, and some populations of humans have developed heightened tolerance for carbohydrate-heavy diets that probably would have given our paleolithic ancestors diabetes. They still do that to many people today.
And the fact that we can tolerate foods our ancestors couldn't doesn't necessarily mean they're better for us than the kinds of foods they ate are for us. Humans never lost the ability to digest meat, fish, fruit and vegetables. All evidence shows that a diet heavier in fruits and vegetables with some fish and meat (not as much as most Americans eat) is optimal, and whether you attribute that to the adaptations of two million years of evolution or not doesn't really change the bottom line.