- Organelles evolving from other living organisms as described in this article - Bacteria in and on our bodies - Fungal mycelium in relation to plants
I am sure there are many more.
The old metaphor of a tree of life has completely broken down with crosslinks everywhere at all levels, far beyond what even Barbara McClintock wrote about.
It's not completely true (but in the area what is "completely true") that only the mitochondria and chloroplasts are captures or symbionts. Flagella and cilia are examples of others! Though technically they aren't considered organelles.
The book I mentioned above is really good! It doesn't simply talk about how current understanding has momved beyond the tree metaphor, it talks about how that came about, as well. Of course, being a book for the general public at talks a lot about the people involved too.