From Bulbapedia, the community-driven Pokémon encyclopedia.
The Tree of Beginning (Japanese: 世界のはじまりの樹 Tree of World's Beginning) is a rock formation that appears to be a gigantic tree. It is actually a living organism made up of crystal that feeds on sunlight. It has a symbiotic connection with a Mew that lives within it, and it is home to many kinds of ancient Pokémon thought to be extinct. It has a "circulatory system" of sorts that distributes nutrients to the crystals throughout is body. It also has a complex antibody system that takes the form of Fossil Pokémon that attack humans and machines within it, as well as guardians in the form of the Legendary Golems. The crystals of the tree actually seem to extend far beyond the formation itself, emerging from the ground like roots throughout the surrounding areas. The Tree of Beginning is located in a mountain range north of Pewter City and Mt. Moon, slightly outside of the borders of the Kanto region.
It appears to be based on the Norse myths of Yggdrasil, the world tree.