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\b[<taphonomy> studies the transformation of biological remains from death or production into the material ultimately recovered and interpreted.] It explains how a living organism or community becomes an incomplete geological sample. For shed structures or <trace fossils>, production of the evidence need not involve the death of the producer. Its relevance therefore extends beyond asking whether a skeleton was buried intact.
Three primary process classes are \b[decay; physical <disarticulation> and transport; and burial alteration, including <diagenetic mineralization>]. The boundaries are operational and the mechanisms interact: <post-mortem decay> can continue after burial, and previously buried remains can be reworked and transported again. <biostratinomy> groups events before final burial, whereas <diagenesis> groups subsequent physical and chemical changes. Those are stages or settings, rather than three mutually exclusive mechanisms.
First, <post-mortem decay> transforms tissues by <autolysis>, microbial decomposition and associated chemical reactions. Soft tissues, <connective tissues> and different <phylogenetic characters> disappear at different rates. The important result is not simply that hard parts survive longer: a partly decayed organism can acquire a misleading anatomical combination. Experiments on <amphioxus> and <lamprey> larvae followed recognizable characters through decomposition. Derived diagnostic features tended to disappear before some more general chordate features, producing a directional bias. Coding every unobserved diagnostic character as ancestrally absent can push a genuinely derived <fossil> toward an earlier position on a <phylogenetic tree>, the effect called <stemward slippage>.<Non-random decay of chordate characters causes bias in fossil interpretation by Robert S. Sansom and others>[Nature 463, pp. 797–800; amphioxus and ammocoete decay sequences and stemward slippage]{ref}
Experiments on adult <hagfish> and <lampreys> extended the comparison beyond larvae. They documented transformations as well as disappearance, so a residual stain or collapsed structure should not automatically be identified as an intact organ. Replicate specimens sampled through time are needed because destructive observations cannot follow every internal character in the same individual. For a new experimental test, temperature, water chemistry, microbial conditions and starting condition should be recorded and, where tested, varied independently. A laboratory sequence supplies constraints on interpretations; it is not a universal clock assigning an exact post-mortem duration to every <fossil>.<Decay of vertebrate characters in hagfish and lamprey (Cyclostomata) and the implications for the vertebrate fossil record by Robert S. Sansom and others>[Results and Discussion; transformations during decay and non-random loss of diagnostic characters]{ref}
Second, <disarticulation>, fragmentation and <taphonomic transport> alter which elements occur together and where they accumulate. Loss of <ligaments> releases <bones>, while currents or scavengers can move them. Shape, density, size, articulation and orientation influence transportability, so a concentration of robust elements need not represent the most abundant living species or the original place of death. Flow experiments and comparison of element representation, as developed in <Michael R. Voorhies>'s <vertebrate> assemblage study, provide a basis for testing such alternatives. A useful comparison measures elements under specified flow and <sediment> conditions, with articulated versus disarticulated material distinguished. <hydraulic sorting> cannot be transferred unchanged between all animals and environments.<Taphonomy and Population Dynamics of an Early Pliocene Vertebrate Fauna, Knox County, Nebraska by Michael R. Voorhies>[transport experiments and bone assemblage interpretation; transportability varies among skeletal elements]{ref}
The consequences include mixing habitats and ages. An apparently coherent <bone> bed may combine local and transported animals; <reworking of fossils> can place older remains in younger <sediment>; <time averaging> can combine successive communities into one assemblage. None implies that every <fossil> assemblage is hopelessly mixed. Articulation, abrasion, orientation, size distributions, sedimentary context and independent age information can instead delimit the plausible history. Abrasion alone is an imperfect transport-distance meter because material properties and the transport medium also matter.
Third, burial changes both preservation and geometry. Rapid isolation can reduce <scavenging>, but burial does not halt all decomposition. <sedimentary compaction> flattens and fractures remains; <dissolution> removes mineralized tissues; <precipitation (chemistry)> can infill pores or replicate tissues; <fossil recrystallization> can erase original microscopic detail. A <fossil> can therefore retain an excellent outline but lack its original chemistry, or preserve <histology> while its overall shape has been distorted. Mineralized replacement is not the only route to <fossilization>, and surviving original hard parts need not have undergone complete replacement.
Experiments by <Derek E. G. Briggs> and <Amanda J. Kear> illustrate constructive as well as destructive <diagenesis>. Decaying shrimps developed <diagenetic mineralization> by <calcium phosphate> preserving <muscle> detail, particularly in oxygen-restricted systems, with the animal itself supplying <phosphate>. <diagenetic mineralization> began on a timescale of weeks. This demonstrates a mechanism by which decay-associated chemistry can stabilize fine structures before they disappear. It does not show that low <oxygen> guarantees preservation: chemical availability, acidity, tissue composition and the relative rates of destruction and <precipitation (chemistry)> still control the outcome.<Fossilization of soft tissue in the laboratory by Derek E. G. Briggs and Amanda J. Kear>[Science 259, pp. 1439–1442; shrimp decay, endogenous phosphate and early muscle phosphatization]{ref}
These mechanisms are indispensable for reconstructing the history of life. A <fossil>'s first occurrence is a minimum observation of a lineage, not automatically its evolutionary origin. A sudden appearance of soft-bodied organisms can reflect a new window of <exceptional preservation>, while disappearance of a <phylogenetic character> can reflect its destruction rather than evolutionary loss. Relative <fossil> abundance reflects both biological abundance and the probabilities of production, preservation, exposure and recovery. Comparisons of diversity through time must therefore consider changes in environments, preservational pathways and sampling. \b[The <fossil record> is filtered evidence whose reliability can be tested; <taphonomy> identifies which biological conclusions that evidence can support.]
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