Had not thought of the similarity of the tune with The Prisoner's Song and glad to have that brought to our attention.

On the meanings of the Great Speckled Bird, fortunately, people keep singing the song and do so because it strikes some chord of appeal and has done so for many generations.

A couple of observations. Several species of birds are "speckled" when they are young. Bluebirds and Robins come to mind. The Ugly Duckling tale is based upon rejection based upon the difference in appearance. Neither of these concepts are related to 'meaning' but both might involve a sense of recognition.

The song does relate to a specific passage from the Bible, but it is also based upon imagery and analogy and neither requires a literal interpretation. The suggestion is that the people of God are different from those around them and there is persecution because of the difference. The historical context suggests the people are the nation of Israel, but that is only one level of interpretation. The basic underlying truth is that people who are different do risk ill treatment.