Epigenetic inclusions

Epigenetic inclusions are formed after the crystallization of the host mineral (from Greek “epi-“ after, “genesis” formation). Most frequently, they crystallize in fractures of the host mineral, within the limited space, providing flat crystals and aggregates, very different to well formed syngenetic inclusions. The fracture can be totally filled by epigenetic minerals or it can be healed (sealed) as a result of reprecipitation of the host mineral inside open fractures.

Example of epigenetic pyrite inclusions, forming flat crystals in a fissure inside quartz crystal. Compare these inclusions to euhedric syngenetic pyrite shown in previous section. Field of view 10 mm.


Iron oxides and hydroxides precipitated in a quartz fissure. Field of view 5 mm.


Another way to introduce new inclusions inside already formed crystal is by alteration of previously existing inclusions (protogenetic or syngenetic). A common example is quartz or topaz crystals with needles of syngenetic rutile or amphibole, altered and substituted by secondary iron oxides and hydroxides, forming so called “sageneitic” inclusions. Normally, only the needles that reach the surface of the host crystal are altered, while those completely enclosed in the host crystal conserved intact.

Sagenitic agate with totally altered inclusions, substituted by epigenetic minerals. Field of view 14 mm.


Inclusions formed by exsolution process are also classified as epigenetic. They appear after host crystal growth, as a result of slow cooling. A typical example of exsolution inclusions is rutile “silk” in ruby and sapphire; that in some cases can also cause asterism effect. In this process titanium ions, incorporated in corundum crystal structure as disseminated impurity at high temperature, migrate though the lattice to form individual solid rutile phase.

The orientation of exsolution rutile always corresponds to the symmetry of the crystal structure of the host mineral, forming needles in three directions crossing at 60º in the basal plane of corundum crystals. Other classic examples of exsolution process are the formation of perthites and antiperthites in fieldspar group minerals.

Exsolution rutile needles with interference colors in unheated sapphire from Tanzania.
Field of view 5 mm.


Exsolution rutile needles in unheated ruby from Mogok, Burma. Stone length 5 mm.


Not only rutile can form exsolution needles in corundums. In this case boehmite needles can be seen, oriented in three directions parallel to rhombohedron edges, in contrast to exsolution rutile needles lying in the basal plane of the host crystal. Field of view 2 mm.


Some treatments of gemstones generate solid substances in open fractures of gems. Such inclusions can be also classified in the category of epigenetic inclusions, not natural but artificially-produced. Some examples could be glass inclusions in heat treated and fracture filled corundums or diamonds and epoxy in fracture filled emeralds, among others.

Flash effect observed in fracture-filled diamond (Yehuda process or similar). Stone diameter 6 mm.