In a handful of fossilized teeth and bones, scientists say they’ve found evidence of a previously unknown human species that lived in what is now the Philippines about 50,000 years ago. The discovery deepens the mystery of an era when the world was a melting pot of many different human kinds on the move.

Small-jawed with dainty teeth, able to walk upright but with feet still shaped to climb, these island creatures were a mix-and-match patchwork of primitive and advanced features in a unique variation of the human form, the...