There's a scene in the film set in India. A group of people are chanting the tones over and over. When asked where they heard that sound, they pointed to the sky in unison. The Frenchman played the sounds before a panel, along with a report on how to couple the sounds with hand signals in order to communicate with the aliens.

During interviews Spielberg said it was a basic greeting, like saying hello.

I don't think it was ever made clear what the tones meant, and I wondered about that too. They were probably a simple greeting, but they could have been for the purpose of synchronizing subsequent messageskind of like the initial noise that an old dial-up modem makes. They could also have been part of a basic test that the aliens gave to any beings that they encounteredif the beings can receive the tone and mimic it back to them, it proves that the beings have some intellectual capability that includes language.
Having said that, none of those possibilities are very compelling to me. The aliens obviously knew that humans were capable of communication because they had been studying them for at least 30 years based on the date when they abducted the navy airmen. Considering all of their incredible technology and access to study subjects and presumably human TV and radio broadcasts, they really should have been able to learn English or French and just be clearer with their communications.

It was the alien's method of communication. It gathered everyone to Devil's Tower.
"I will not go down in history as the greatest mass-murderer since Adolf Hitler!" - Merkin Muffley

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