If I highlight and annotate a PDF in iBooks, will those highlights be kept if in Adobe Acrobat?

If I highlight a PDF in iBooks on an iPhone and save the PDF, will those highlights be present if I open the PDF in Adobe Acrobat? Or vice versa?

The PDF specification explicitly describes annotations and highlights, so any app that can read PDFs should be able to display them, and any app that saves PDFs should save them.

Apple's PDFKit produces annotations and highlights that are to spec, so they should be compatible with other readers. I would suggest it's a bug if they aren't.

The only non-standard implementation that I know of is that MacOS's Preview uses proprietary Bookmarks, which cannot be read by other non-Apple applications. Bookmarks from Acrobat and other PDF apps will appear in the Table of Contents sidebar in Preview and other Apple PDFKit-based apps.