In order to properly understand the mechanisms involved during fossilization, here is a brief reminder of the structure of bone.

Bone receives a continuous blood supply and is comprised of different types of cells, the most important being osteocytes (mature bone cells), osteoblasts (responsible for bone formation) and osteoclasts (responsible for bone resorption). The extracellular matrix is made up of organic and inorganic elements:

The organic phase is comprised of 90 % collagen, secreted by the osteoblasts that link together to form fibres. This is what gives bone its flexibility as well as its resistance to pressure, tension and torsion.

The inorganic phase consists of small slightly crystallised carbonate hydroxylapatite crystals [Ca₅(PO₄CO₃)₃(OH)]. It is responsible for the hardness of the bone and partly for its resistance to compression. It is the small size of the crystals that differentiates biological apatite from mineral apatite.

Mature bone forms two types of structure:

(1) a central part (spongy bone) composed of trabeculaeseparated by spaces that contain bone marrow.

(2) a peripheral part (compact bone), densely mineralised and composed of units known as osteons. Every osteon is comprised of several layers of concentric bone lamellae surrounding the Haversian canal in the middle. The Haversian canals contain nerves and blood vessels above all.

Bone diagenesis is a complex phenomenon during which many minerals are formed. It can be divided into several phases.

Decomposition of organic matter: intense bacterial activity that starts shortly after an animal dies, which decomposes tissue. The collagen is destroyed through the intervention of specific enzymes called collagenases. The acids produced locally during the decomposition of soft tissue and the collagen will help to dissolve the bone apatite (inorganic phase of fresh bone) and allow the collagenases to penetrate more deeply into the bone structure leading to an acceleration of the chemical decomposition of the organic compounds.

After several months, the bacterial activity stops and environmental factors take over the fossilisation processes. Then come the following phases:

Recrystallisation of the bone apatite: the bone matrix recrystallises by integrating external chemical elements. The carbonate hydroxylapatite of the fresh bone [Ca₅(PO₄CO₃)₃(OH)] is replaced by the better crystallized carbonate-fluorapatite [Ca₅(PO₄CO₃)₃F] or fluorapatite [Ca₅(PO₄)₃F]. In general, recrystallisation keeps the bone's microstructure intact but a partial destruction of the more delicate structures may also be observed.

Enrichment in trace elements: the external chemical elements that penetrate the bone depend on the type of sediment and infiltrated water.

Permineralization: new minerals, dissolved in the infiltrated water, precipitate and fill the bone cavities and fractures. These minerals gradually reduce the exchanges between the bone and the surrounding environment.

Compaction/fracturing process: as the fossilized bone become buried, it is subject to an increasing amount of pressure leading to deformations and fractures. These new fractures can later be replaced by various minerals, depending on the type of sediment.

Early diagenesis refers to phenomena that begin with bacterial activity and end with the recrystallization of the bone apatite; late diagenesis refers to phenomena that occur after this recrystallization.