Taphonomy is the study of the post-mortem, pre-burial and post-burial histories of faunal remains  and can best be described as the collective sum of all biotic and abiotic temporal and spatial processes an organism (or part of it) undergoes from the time of death until its discovery as a fossil.
The term taphonomy comes from the Greek taphos meaning death or burial, and nomos meaning law, i.e. the law of burial. It was introduced to palaeontology in 1940 by the Russian scientist Ivan Efremov to describe the study of the creation of fossil assemblages through the transition of parts, remains, or products of organisms from the biosphere or living world to the lithosphere or sedimentary record. 
Very few organisms become preserved and represented in the fossil record. One of several reasons is that a large percentage of all biological entities end up as food for other organisms. The low probability of becoming fossilized is also due to aerobic decay, saprophytic and saprozoic decomposition, and recycling of their chemical components from exposure to the elements. Dead organisms that do manage to become buried and fossilised, and are later discovered, all contribute to the overall understanding of taphonomy.
Necrology is the first stage in the fossilisation process and involves the death or loss of a part of an organism. As parts of an organism can be shed, death is not always essential as the first step in the formation of fossils. Plants especially can shed leaves in autumn, branches during a storm, and fruit and seeds during the dispersal process, but will continue to thrive. Similarly, stags may shed their antlers, male antelope may loose one of their horns during the establishment of territorial dominance, young mammals display tooth replacement, lizards can loose their tails and starfish one of their limbs. So within plants and animals, parts of the organism may become incorporated into the fossil record without the actual death of the organism having occurred.
All interactions involving the transferral of an organism (or part of it) from the living state to the inorganic world is known as biostratinomy. Burial is an important aspect of biostratinomy and is an essential part of the fossilisation process as it protects the dead organism against scavengers and the elements. Once buried, an oxygen-free environment prevents decay and inhibits bacterial activity. Soft tissue and soft-bodied organisms are seldom preserved and usually vanish without a trace, and these are therefore poorly represented in the fossil record. Extremely rare conditions are required for their preservation, such as rapid burial in anaerobic, extremely fine grained sediments.
Diagenesis involves all of the physical and/or chemical processes responsible for the lithification of the sediment and chemical interactions with the water residing between clasts. During the fossilisation process, chemicals within the organism are replaced by minerals which crystallize within the existing structures and preserve the original detail. The minerals involved in this process are dissolved within the water percolating through the sediments enclosing the buried organisms, and this mineral replacement process may occur at different times during a prolonged period of burial.
Processes affecting preservation
The collective processes of death, burial and preservation result in the formation of fossils, but a dead organism may undergo several other modification processes before, during and after fossilisation, affecting the ultimate preservation of the specimen. This depends on several factors, including amongst others, how long the dead organism was exposed on the surface before being buried, as well the chemical composition of the soil. Various taphonomic processes will affect an organism before it becomes buried, resulting in implications for the state of preservation. Some of the main processes affecting the eventual completeness of the original skeleton are summarised below.
Environmental settings having a high energy, such as beaches with continuous wave action or strong currents within a river, will cause significant abrasion to the skeletal material. Within such an environment, a skeleton behaves as a sedimentary particle and is transported and sorted with respect to the carrying capacity of river currents, waves, and tides. The degree to which a skeleton is disarticulated will indicate its exposure to the energy within the depositional environment and the size of the disarticulated skeletal elements can therefore be an effective indicator of the flow capacity in a hydraulic or wind-driven system. The hard parts of a disarticulated skeleton tend to orientate with the long axis parallel to the unidirectional flow in a current-dominated environment and perpendicular to wave crests on wave-dominated bottoms.
Articulated skeletons generally indicate rapid burial of the organism and if the skeleton is oriented in a life-like position this could indicate that it was attached to a firm substrate or could indicate the death of an in-place infauna.
Bioerosion includes the many different biological processes that cause the dead organism to corrode or degrade. Chemicals secreted by root activity etch the bone surface and accelerate the weathering process, whereas living organisms may feed on and bore into the dead organism. Therefore fragmentation of skeletal elements can be the result of abrasion or bioerosion in the form of scavenging or predation. Although bioerosion may erase information, it leaves identifiable traces in the form of trace fossils and therefore adds information to the overall interpretation of an assemblage.
When an organism becomes buried, over time mineral replacement starts to take place until some form of equilibrium is reached. But changes in the chemical conditions within the substrate surrounding the organism, including fluctuations in temperature, pH or pCO2 in calcium carbonate skeletons, may cause the skeleton to dissolve. The movement of molecules from a high concentration, saturated environment to one that is undersaturated can therefore result in dissolution.
Another form of modification a skeleton may undergo is known as rounding. This is when the broken edges of bone attain a more rounded edge through a combination of abrasion, bioerosion and dissolution, and the degree of edge rounding can give an indication of the time since the breakage occurred.
Within different environments, different biota may cause variable growth patterns of encrustation on skeletons. Encrustation may indicate a particular environment, and points to the fact that at some point the skeleton was exposed above a sediment-water interface. Encrustation may actually help to preserve certain detail on the surface of the skeleton substrate by forming a protective layer.
Advantages of taphonomic studies
The study of taphonomy helps to reconstruct faunal composition, palaeoenvironments, and the process of faunal community succession. It is also used to determine the ages of different communities, and where there were hominids present, it is a useful tool to infer aspects of their behaviour. Important factors to consider within the study of taphonomy include determining which agents and processes were collectively responsible for the creation of certain fossil assemblages in question. Scientists studying taphonomy therefore strive to determine how the fossil accumulation resulted and what agents modified it to resemble its current state. As an example, within a southern African context, several agents of accumulation and modification may be present in the fossil assemblage of a Plio-Pleistocene cave setting. These include:
1) felids (leopards, sabre-tooth and false sabre-tooth cats)
2) hominids (Australopithecus africanus, Paranthropus robustus & Homo habilis)
4) raptors (eagles & owls)
5) hyenas (brown & spotted)
6) canids (wolf-like creatures)
7) hill-wash & gravity
Each of these will produce characteristic patterns of modification to the bones present within an assemblage, but aspects of these patterns may not be unique due to the fact that there is a degree of overlap in the patterns produced by different agents of modification. In order to determine which of these, or a combination of them, could have modified an assemblage, various factors need to be considered. These include surface modification  and breakage patterns on bones, skeletal parts and elements represented, taxonomy of the faunal assemblage present, and weathering patterns on the bones. Breakage patterns can result in several different types of bone fractures and when the bone is fresh it results in spiral fractures, but weathered bone produces longitudinal fractures. Therefore a problem to consider with surface modification of bones is equifinality. This is when several different processes can produce the same result when viewed from a macroscopic level. This can often be clarified with careful examination of the bone surface modification at a microscopic level.
When looking at skeletal elements and taxonomy of the faunal assemblage, various criteria need to be investigated. These include the minimum number of individuals, the representation of different size classes of animals present, and ontogeny of the skeletal elements. The latter refers to the growth and development of organisms; immature individuals can be distinguished from adults by the fact that they will display unfused epiphyses and their dental composition consists of a temporary set of milk teeth. Ontogeny is therefore useful to determine whether an assemblage is attritional in nature, that is to say prime animals will be absent with only old and young individuals present. Dental characteristics of old individuals will include very worn down grinding surfaces.
Lastly, rates of weathering and weathering patterns on bones can indicate how long certain skeletal elements were exposed to the elements. In a savannah environment, weathering stages of bone are given values, with zero indicating fresh bone and higher values representing increasingly cracked and fractured bone surfaces. Cracking of the surface results in surface exfoliation, and the loss of the outermost surface causes the bone to have a fibrous appearance. With increasing exposure there is an increase in coarseness until the bone looses integrity. Different taxa, classes of animals, and age groups will display different weathering patterns on their bone surfaces. The different classes of animals have different internal structures making up there bones, with bird bones being more hollow and mammals having a structured network of dense canals. The bone structure of the latter class may therefore give it an advantage in terms of being more resistant to weathering. Due to their strength and thickness, compact bones are very resistant to weathering and may therefore have a higher representation in the faunal assemblage than other skeletal elements, creating a bias within the assemblage.
All of the above mentioned factors need to be carefully investigated to clarify how they may have contributed to the observed patterns and biases present within a fossil assemblage. It is therefore important to use a multi-disciplinary approach in order to comprehensively understand the taphonomy of a site and to eliminate researcher bias. Site context is important because in terms of spatial and temporal variation, different processes will produce different patterns. For example, by keeping the temporal component constant but shifting the spatial component to the Northern Hemisphere, cave taphonomy in North America will vary in certain aspects to that observed in southern Africa. Importantly hominids will be absent and ursids will be present, eliminating the possibility of cultural artefacts and influencing the faunal composition, as well as overall characteristics of the site.
Models to test observed taphonomic patterns
There are two models to test observed taphonomic patterns and they are summarised briefly as follows:
1) The palaeo-taphonomic model
The steps described above for the cave taphonomy example refer to this model. This entails examining the content and context of a faunal assemblage, including surface modification and breakage patterns on bones, bone size and type, skeletal part representation, taxonomy of the faunal assemblage present, and weathering patterns on the bones. Data sets are collected as measurements or descriptions of features within the assemblage.
2) Actualistic models
Also called Neotaphonomy and Middle Range research, these models are comparative and involve extrapolating modern findings back into the past, so they are based on the use of analogy and on the principle of Uniformitarianism. There are two forms of actualistic research:
a) Experimental: this involves replication studies conducted by humans to reproduce observed patterns in the fossil record
b) Naturalistic: this involves studying the modification of bone by animals, for example giving a hyena a bone to crush with its powerful jaws and collecting the fragments to compare with fossil bone fragments. Other forms of bone modification include socio-ecological/ behavioural or ethnographic models whereby modern hunter-gatherers perform experimental butchering on animals and the cut marks on the bones are compared to those on the bones from archaeological sites. Another naturalistic approach entails exposing the remains of organisms to various natural, altering processes such as sedimentary abrasion or wind erosion, and then recollecting the remains of the organism to examine the effects of the exposure.
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 Lyman, R.L. 1994. Vertebrate Taphonomy. Cambridge University Press.
- ↑ Shipman, P. 1981. Life history of a fossil: An introduction to taphonomy and paleoecology. Harvard University Press.
- ↑ 3.0 3.1 3.2 Gastaldo, Savrda & Lewis. 1996. Deciphering Earth History: A laboratory Manual with Internet Exercises.Contemporary Publishing Company of Raleigh, Inc.
- ↑ 4.0 4.1 Dixon, D. et al. 2001. Cassell’s Atlas of Evolution. Andromeda Oxford Limited.
- ↑ McRoberts, C. 1998. Laboratory Notes. Invertebrate Paleontology. State University of New York, College at Cortland.
- ↑ 6.0 6.1 6.2 6.3 Brain, C.K. 1981. The Hunters or the Hunted? An introduction to African Cave Taphonomy. The University of Chicago Press, Chicago.
- ↑ d'Errico, F. & Backwell, L.R. 2005. The origin of bone tool technology and the identification of early hominid cultural traditions. From Tool to Symbols: From Early Hominids to Modern Humans: 238-275. Witwatersrand University Press, Johannesburg.
- ↑ Behrensmeyer, A. K. 1978. Taphonomic and ecologic information from bone weathering. Paleobiology 4:150-162.