TruffleRuby and JRuby have always been separate projects, but TR kinda "grew up" as part of JRuby for a couple years. Eventually we decided the goals were becoming too different so TR split back off into its own project.
We still communicate, we share several support libraries, and I'm sure we'll mimic some of their optimizations just like they've mimicked some of our features, but there's not a lot of commonality between the projects anymore.