Study of decomposition and fossilization of organisms
Taphonomy is the study of how organisms decay and become fossilized or preserved in the paleontological record. The term "taphonomy" (from Greek , 'burial' and , 'law') was introduced to paleontology in 1940 by Soviet scientist Ivan Efremov to describe the study of the transition of remains, parts, or products of organisms from the biosphere to the lithosphere.
The term taphomorph is used to describe fossil structures that represent poorly-preserved, deteriorated remains of a mixture of taxonomic groups, rather than of a single one.
Description.
Taphonomic phenomena are grouped into two phases: biostratinomy, events that occur between death of the organism and the burial; and diagenesis, events that occur after the burial. Since Efremov's definition, taphonomy has expanded to include the fossilization of organic and inorganic materials through both cultural and environmental influences. Taphonomy is now most widely defined as the study of what happens to objects after they leave the biosphere (living contexts), enter the lithosphere (buried contexts), and are subsequently recovered and studied.
This is a multidisciplinary concept and is used in slightly different contexts throughout different fields of study. Fields that employ the concept of taphonomy include: 
There are five main stages of taphonomy: disarticulation, dispersal, accumulation, fossilization, and mechanical alteration. The first stage, disarticulation, occurs as the organism decays and the bones are no longer held together by the flesh and tendons of the organism. Dispersal is the separation of pieces of an organism caused by natural events (i.e. floods, scavengers etc.). Accumulation occurs when there is a buildup of organic and/or inorganic materials in one location (scavengers or human behavior). When mineral rich groundwater permeates organic materials and fills the empty spaces, a fossil is formed. The final stage of taphonomy is mechanical alteration; these are the processes that physically alter the remains (i.e. freeze-thaw, compaction, transport, burial). These stages are not only successive, they interplay. For example, chemical changes occur at every stage of the process, because of bacteria. Changes begin as soon as the death of the organism: enzymes are released that destroy the organic contents of the tissues, and mineralised tissues such as bone, enamel and dentin are a mixture of organic and mineral components. Moreover, most often the organisms (vegetal or animal) are dead because they have been killed by a predator. The digestion modifies the composition of the flesh, but also that of the bones.
Research areas.
Taphonomy has undergone an explosion of interest since the 1980s, with research focusing on certain areas.
Paleontology.
One motivation behind taphonomy is to understand biases present in the fossil record better. Fossils are ubiquitous in sedimentary rocks, yet paleontologists cannot draw the most accurate conclusions about the lives and ecology of the fossilized organisms without knowing about the processes involved in their fossilization. For example, if a fossil assemblage contains more of one type of fossil than another, one can infer either that the organism was present in greater numbers, or that its remains were more resistant to decomposition.
During the late twentieth century, taphonomic data began to be applied to other paleontological subfields such as paleobiology, paleoceanography, ichnology (the study of trace fossils) and biostratigraphy. By coming to understand the oceanographic and ethological implications of observed taphonomic patterns, paleontologists have been able to provide new and meaningful interpretations and correlations that would have otherwise remained obscure in the fossil record. In the marine environment, taphonomy, specifically aragonite loss, poses a major challenge in reconstructing past environments from the modern, notably in settings such as carbonate platforms. 
Forensic science.
Forensic taphonomy is a relatively new field that has increased in popularity in the past 15 years. It is a subfield of forensic anthropology focusing specifically on how taphonomic forces have altered criminal evidence.
There are two different branches of forensic taphonomy: biotaphonomy and geotaphonomy. Biotaphonomy looks at how the decomposition and/or destruction of the organism has happened. The main factors that affect this branch are categorized into three groups: environmental factors; external variables, individual factors; factors from the organism itself (i.e. body size, age, etc.), and cultural factors; factors specific to any cultural behaviors that would affect the decomposition (burial practices). Geotaphonomy studies how the burial practices and the burial itself affects the surrounding environment. This includes soil disturbances and tool marks from digging the grave, disruption of plant growth and soil pH from the decomposing body, and the alteration of the land and water drainage from introducing an unnatural mass to the area.
This field is extremely important because it helps scientists use the taphonomic profile to help determine what happened to the remains at the time of death (perimortem) and after death (postmortem). This can make a huge difference when considering what can be used as evidence in a criminal investigation.
Archaeology.
Taphonomy is an important study for archaeologists to better interpret archaeological sites. Since the archaeological record is often incomplete, taphonomy helps explain how it became incomplete. The methodology of taphonomy involves observing transformation processes in order to understand their impact on archaeological material and interpret patterns on real sites. This is mostly in the form of assessing how the deposition of the preserved remains of an organism (usually animal bones) has occurred to better understand a deposit.
Whether the deposition was a result of human, animals and/or the environment is often the goal of taphonomic study. Archaeologists typically separate natural from cultural processes when identifying evidence of human interaction with faunal remains. This is done by looking at human processes preceding artifact discard in addition to processes after artifact discard. Changes preceding discard include butchering, skinning, and cooking. Understanding these processes can inform archaeologists on tool use or how an animal was processed. When the artifact is deposited, abiotic and biotic modifications occur. These can include thermal alteration, rodent disturbances, gnaw marks, and the effects of soil pH to name a few.
While taphonomic methodology can be applied and used to study a variety of materials such as buried ceramics and lithics, its primary application in archaeology involves the examination of organic residues. Interpretation of the post-mortem, pre-, and post-burial histories of faunal assemblages is critical in determining their association with hominid activity and behaviour.
For instance, to distinguish the bone assemblages that are produced by humans from those of non humans, much ethnoarchaeological observation has been done on different human groups and carnivores, to ascertain if there is anything different in the accumulation and fragmentation of bones. This study has also come in the form of excavation of animal dens and burrows to study the discarded bones and experimental breakage of bones with and without stone tools.
Studies of this kind by C.K. Brain in South Africa have shown that bone fractures previously attributed to "killer man-apes" were in fact caused by the pressure of overlying rocks and earth in limestone caves. His research has also demonstrated that early hominins, for example australopithecines, were more likely preyed upon by carnivores rather than being hunters themselves, from cave sites such as Swartkrans in South Africa.
Outside of Africa Lewis Binford observed the effects of wolves and dogs on bones in Alaska and the American Southwest, differentiating the interference of humans and carnivores on bone remains by the number of bone splinters and the number of intact articular ends. He observed that animals gnaw and attack the articular ends first leaving mostly bone cylinders behind, therefore it can be assumed a deposit with a high number of bone cylinders and a low number of bones with articular ends intact is therefore probably the result of carnivore activity. In practice John Speth applied these criteria to the bones from the Garnsey site in New Mexico. The rarity of bone cylinders indicated that there had been minimal destruction by scavengers, and that the bone assemblage could be assumed to be wholly the result of human activity, butchering the animals for meat and marrow extraction.
One of the most important elements in this methodology is replication, to confirm the validity of results.
There are limitations to this kind of taphonomic study in archaeological deposits as any analysis has to presume that processes in the past were the same as today, e.g that living carnivores behaved in a similar way to those in prehistoric times. There are wide variations among existing species so determining the behavioural patterns of extinct species is sometimes hard to justify. Moreover, the differences between faunal assemblages of animals and humans is not always so distinct, hyenas and humans display similar patterning in breakage and form similarly shaped fragments as the ways in which a bone can break are limited. Since large bones survive better than plants this also has created a bias and inclination towards big-game hunting rather than gathering when considering prehistoric economies.
While all of archaeology studies taphonomy to some extent, certain subfields deal with it more than others. These include zooarchaeology, geoarchaeology, and paleoethnobotany.
Microbial Mats.
Modern experiments have been conducted on post-mortem invertebrates and vertebrates to understand how microbial mats and microbial activity influence the formation of fossils and the preservation of soft tissues. In these studies, microbial mats entomb animal carcasses in a sarcophagus of microbes—the sarcophagus entombing the animal's carcass delays decay. Entombed carcasses were observed to be more intact than non-entombed counter-parts by years at a time. Microbial mats maintained and stabilized the articulation of the joints and the skeleton of post-mortem organisms, as seen in frog carcasses for up to 1080 days after coverage by the mats. The environment within the entombed carcasses is typically described as anoxic and acidic during the initial stage of decomposition. These conditions are perpetuated by the exhaustion of oxygen by aerobic bacteria within the carcass creating an environment ideal for the preservation of soft tissues, such as muscle tissue and brain tissue. The anoxic and acidic conditions created by that mats also inhibit the process of autolysis within the carcasses delaying decay even further.  Endogenous gut bacteria have also been described to aid the preservation of invertebrate soft tissue by delaying decay and stabilizing soft tissue structures. Gut bacteria form pseudomorphs replicating the form of soft tissues within the animal. These pseudomorphs are possible explanation for the increased occurrence of preserved guts impression among invertebrates. In the later stages of the prolonged decomposition of the carcasses, the environment within the sarcophagus alters to more oxic and basic conditions promoting biomineralization and the precipitation of calcium carbonate.
Microbial mats additionally play a role in the formation of molds and impressions of carcasses. These molds and impressions replicate and preserve the integument of animal carcasses. The degree to which has been demonstrated in frog skin preservation. The original morphology of the frog skin, including structures such as warts, was preserved for more than 1.5 years. The microbial mats also aided in the formation of the mineral gypsum embedded within the frog skin. The microbes that constitute the microbial mats in addition to forming a sarcophagus, secrete an exopolymeric substances (EPS) that drive biomineralization. The EPS provides a nucleated center for biomineralization. During later stages of decomposition heterotrophic microbes degrade the EPS, facilitating the release of calcium ions into the environment and creating a Ca-enriched film. The degradation of the EPS and formation of the Ca-rich film is suggested to aid in the precipitation of calcium carbonate and further the process of biomineralization.
Taphonomic biases in the fossil record.
Because of the very select processes that cause preservation, not all organisms have the same chance of being preserved. Any factor that affects the likelihood that an organism is preserved as a fossil is a potential source of bias. It is thus arguably the most important goal of taphonomy to identify the scope of such biases such that they can be quantified to allow correct interpretations of the relative abundances of organisms that make up a fossil biota. Some of the most common sources of bias are listed below.
Physical attributes of the organism itself.
This perhaps represents the biggest source of bias in the fossil record. First and foremost, organisms that contain hard parts have a far greater chance of being represented in the fossil record than organisms consisting of soft tissue only. As a result, animals with bones or shells are overrepresented in the fossil record, and many plants are only represented by pollen or spores that have hard walls. Soft-bodied organisms may form 30% to 100% of the biota, but most fossil assemblages preserve none of this unseen