PokéBase - Pokémon Q&A
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I noticed after catching 1,000+ Pokemon, rarer Pokemon like the Starters that would only spawn during a Chain or with a Lure now occationally appear without a Chain or a Lure, and have spawned a bit more often after reaching the 2,000+ mark. Is this just a crazy coincidence, or do the spawn rates for rarer Pokemon actually increase after reaching milestones for Pokemon caught?

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A feature called the Catch Combo tracks how many of the same species of Pokémon is caught in a row without the Pokémon running away or the game turning off. The higher the combo, the stronger and rarer wild Pokémon become, and Shiny Pokémon become more common.

Yes, rarer Pokemon will have higher spawn rates the more Pokemon you've caught in LGPE. There's more information about this on the Bulbapedia and Serebii pages for Catch Combos.

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