In the session “Incremental backups available with Xtrabackup and Percona Server” Vladislav Lesin and George Lorch from Percona went over differential backups.  There are three ways to get the delta; full scan, use redo logs, or a combination of the two.  For full scan you scan all pages and backup any pages with last change LSN newer than a specific LSN.  Advantages are that you only store changed pages and there are no server changes required.  The downside if you have the overhead of a full scan. The redo logs can be used to restore a database to/from a specific point since it has the change data.  Advantage of using redo log are that there is no full scan.  The downsize is the space consumed.

In the combined method they store the LSN information on pages in the server in a RB-tree utilizing a separate thread that checks the redo logs on checkpoint.  This is to avoid the full scan.  They shared an edge case where size can be an issue with this approach.