Beehives are a place to house bees. Beehives need Beehive Frames inside them for the bees to live. Removing frames from an active hive will cause the bees to attack you, unless done at night, or with a Firepit underneath the hive active. Beehives can share flowers. The benefit of flowers diminishes after 60 flowers.
Beehives know about the area in a 5 block radius from them. If there are at least 10 flowers around the hive, there is a chance an empty frame will be populated with a Queen. This is indicated by bee particles flying around the hive. Having 4 empty frames in a hive greatly increases the chances of bees moving in.
If a beehive has two frames with queens, and an empty frame, the two colonies have a chance of Breeding and producing a new queen in the empty frame. This has the effect of passing on the Abilities of each parent to the offspring. Abilities are different traits bees have that change how they effect the world around them. They are on a scale of 1-10, with 10 being the max.
Bees also produce Honey. Using Right Click with an Empty Jar on a hive that visibly has honey gives you a Honey Jar. Opening a Honey Jar gives you Raw Honey, a Sugar substitute.
Pressing Right Click a filled frame in your inventory with a Knife gives you Beeswax, which has many uses. However, this kills the queen inside the frame so be careful!
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The most important use of beeswax is in creating Treated Lumber.
Bees with high Mutant ability have a chance of developing a Genetic Disease. Diseased bees pass on their disease to their offspring, and don't produce honey.