It looks like your players are generating chunks. Pre-generating the world (within a world border) can remove a lot of the lag associated with that. There is also an optimisation guide made by a third party you might make use of, which has a Pixelmon focus. Performance Guide
Lag spikes happening every 2.5 minutes looks like something going on with world saving; is a mod or plugin handling that?
Overall, most of the lag is Entiity tick. You have 20,000 tile entities loaded - and with 49 players online, that’s about the sort of thing you should expect. There’s only so much plugins can do; when there’s a big player count on a modded server, the impact can be huge. If you really need to drill down into causes, you could try using Spark profiler.