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Ray McAllister posted a question regarding the stability of
integumentary colors. Carotenoids, of course, are not very stable (as
are most other highly unsaturated molecules. Feather caroteonids, for
example, can be destroyed by exposure to sunlight (even in the dry
feather). Melanins, a very common pigment also fades or abrades. This
has been sstudied in birds but not to my knowledge in reptiles.
I believe there are some reports of plant pigments preserved in
the fossil record, but do not have references at hand.
Molecules that contain pyrroles (a tetra-pyrrole is heme-the same
as in hemoglobin) are quite stable. Porphyins (rarely found in
feathers) are stable enough to apparently have survived from the
Silurian! Pyrroles/porphyins are often (but not always conjugated to a
protein). Examples, beside HB include bile pigments, vitamin B12,
etc. These are highly colored molecules. Cytochrome is another
example. These are other pigments are abundant in tissues throughout
the animal kingdom.
An unusual feature of many pigments is that they exist in
essentially a solid state. Theis means their chemistry can be
modified. Secondary changes may occur after deposition. Still, melanin
is recoveder from ink sacs of squids so there may be hope.