In this context, it means established deeply or firmly, like the roots of a tree. "Respect for the freedom of speech is rooted in American culture."

Yes, it carries similar ideas to "based on" and "originating from." Notice that something simply sits on a base, while the roots of a tree go into the ground, so "rooted in" suggests something even stronger and more stable than "based on." Similarly, in a sense you can say that a tree "originates from" its roots... and also that it depends on or gets its nourishment from its roots. "X is rooted in Y" contains a sense that something gets its power from Y. Here are some other examples of use. "So long as an opinion is strongly rooted in the feelings, it gains rather than loses in stability by having a preponderating weight of argument against it."--John Stuart Mill "China is old, with a deep history rooted in tradition and a strong concentration on elders, culture, and family values." Describing the job of the "National Security Advisor" in the United States: "Unlike the jobs of their cabinet counterparts, their position is neither rooted in law nor accountable to Congress." "Architecture, which is rooted in physics, is fully cognizant of the implication of force acting on one's building."

Yes, Luiz, I agree with what you suggested and with what Justin wrote in reply. "Rooted" means that something has come from something else in an exclusive way. In your example, there is a suggestion of systems of communication that are NOT rooted in human nature, and that languages are the ones that are rooted in human nature. Another example: The right to the preservation of one's own life is rooted in human nature. Another example: A person's abuse of alcohol is rooted in his experience of trauma and rejection earlier in life. As you can see, it expresses a philosophical understanding of things.