Minecraft wiki entry for Development_versions, associated text: Biome information now is stored in sixty-four 4×4 arrays, allowing biomes to be changed based on height; previously, biome values corresponded to only the X and Z coordinates.
The  Biomes array in the  Level tag for each chunk now contains 1024 integers instead of 256. Each number in the array is the biome for a 4x4x4 volume in the chunk. These 4×4×4 volumes are arranged by Z, then X, then Y. That is, the first 4×4 values in the array are for the 16×16 chunk, at Y-levels 0–3, the next 4×4 is for Y-levels 4–7, etc.