Thank you for the reply, I think it's helped guide me into the right direction. I found two articles related to transceivers in Arria V devices:
Transceiver Basics for Arria V Devices (
http://bimansirphysics.webs.com/documents/av_54002transreceiver%20basic%20aletra.pdf)
Arria V Device Handbook - Volume 2: Transceivers (
https://www.altera.com/content/dam/altera-www/global/en_us/pdfs/literature/hb/arria-v/av_5v3.pdf)
However, I can't find a clear explanation on what protocol the PMA uses to deserialize data coming from the PCML pins. How does the deserializer in the PMA decide how to convert serial data into parallel data?