There is no accurate count of the number of Native American languages. While thousands went extinct after Europeans arrived in 1492, unknown and undocumented thousands more had already gone extinct, as cultures grew and collapsed throughout North and South America.
Different sites break up Native American languages in different ways. There are always languages that seem to not belong to any known group. Some sites name the language families differently.
In general, a language family is believed to have a common ancestor language. As people moved, dialects developed, often referring to plants, animals, or religious components specific to that particular region. In the early stages of dialect changes, these groups could communicate easily, with only a few words that confused each other. As centuries, and generations passed, the languages became more different, and verbal communication between them less likely.
Native Americans had other forms of language. Recognized written language was rare among the Americans. However, there are other forms of written language. Story blankets, pots, and more were as common as Egyptian hieroglyphics. Much like the funny faces used in text messages today, those picture messages could share meaning across the verbal language barrier.
Also, as great hunters, they developed versions of sign language. Tribes that hunted together could communicate with each other over long distances with sign language and blankets.
As a writer, I hope to portray how language changes over time in my Trails series. Even though I can’t push it as far as I’d like, as that would make it unreadable, I try to give hints to the reader that words change. And their meanings change. Much as the Native Americans of today struggle to maintain the memory of the languages the governments attempted to wipe out, my characters struggle to maintain the language as they know it.