Apex progressionShards are earned inside one species' own Techtree, and an Apex is paid for with them. Avatar Shards are a holdings counter, not a shop purchase.
Research one species' Techtree slot by slot. Filling a slot took 1 Research Vial, and a recorded prompt on a Category 3 or higher tree asked for 2 Advanced Research Vials instead. Finishing a group of three nodes is the step that pays one Avatar Shard into the same strip that holds Research Vials, Advanced Research Vials, DNA and Cores.
The only Apex price read on screen so far is 40 Avatar Shards for the Helezhura Apex. The community records one Apex per species, so open that species' own unlock panel and read its cost rather than assuming 40 carries across.
The three-node group is the rule creators and players both repeat, and no official rule page states it, so confirm the counter on your own panel after your first finished group. The full step list, the subspecies shortcut and the four questions no source answers are on the Avatar Shards and Apex reference, and the creature roster shows which species have a recorded Apex form.