Taphonomy

Taphonomy is the study of how organisms decay and become fossilized or preserved in the archaeological record. The term "taphonomy" (from the Greek , meaning "burial", and , meaning "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.
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.
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). It should be added that 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 organism (vegetal or animal) is dead because it has 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.
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.
Environmental archaeology.
Archaeologists study taphonomic processes in order to determine how plant and animal (including human) remains accumulate and differentially preserve within archaeological sites. Environmental archaeology is a multidisciplinary field of study that focuses on understanding the past relationships between groups and their environments. The main subfields of environmental archaeology include zooarchaeology, paleobotany, and geoarchaeology. Taphonomy allows specialists to identify what artifacts or remains encountered before and after initial burial. Zooarchaeology, a focus within environmental archaeology investigates taphonomic processes on animal remains. The processes most commonly identified within zooarchaeology include thermal alteration (burns), cut marks, worked bone, and gnaw marks. Thermally altered bone indicate the use of fire and animal processing. Cut marks and worked bone can inform zooarchaeologists on tool use or food processing. When there is little to no written record, taphonomy allows environmental archaeologists to better comprehend the ways in which a group interacted with their surrounding environments and inhabitants.
The field of environmental archaeology provides crucial information for attempting to understand the resilience of past societies and the great impacts that environmental shifts can have on a population. Knowledge gained from the past through these studies can be used to inform present and future decisions for human-environment interactions.
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 diversity, which may exclude groups such as fungi and entire animal phyla from the fossil record. Many animals that moult, on the other hand, are overrepresented, as one animal may leave multiple fossils due to its discarded body parts. Among plants, wind-pollinated species produce so much more pollen than animal-pollinated species, the former being overrepresented relative to the latter.
Characteristics of the habitat.
Most fossils form in conditions where material is deposited to the bottom of water bodies. Especially shallow sea coasts produce large amounts of fossils, so organisms living in such conditions have a much higher chance of being preserved as fossils than organisms living in non-depositing conditions. In continental environments, fossilization is especially likely in small lakes that gradually fill in with organic and inorganic material and especially in peat-accumulating wetlands. The organisms of such habitats are therefore overrepresented in the fossil record.
Mixing of fossils from different places.
A sedimentary deposit may have experienced a mixing of noncontemporaneous remains within single sedimentary units via physical or biological processes; i.e. a deposit could be ripped up and redeposited elsewhere, meaning that a deposit may contain a large number of fossils from another place (an allochthonous deposit, as opposed to the usual autochthonous). Thus, a question that is often asked of fossil deposits is to what extent does the fossil deposit record the true biota that originally lived there? Many fossils are obviously autochthonous, such as rooted fossils like crinoids, and many fossils are intrinsically obviously allochthonous, such as the presence of photoautotrophic plankton in a benthic deposit that must have sunk to be deposited. A fossil deposit may thus become biased towards exotic species (i.e. species not endemic to that area) when the sedimentology is dominated by gravity-driven surges, such as mudslides, or may become biased if there are very few endemic organisms to be preserved. This is a particular problem in palynology.
Temporal resolution.
Because population turnover rates of individual taxa are much less than net rates of sediment accumulation, the biological remains of successive, noncontemporaneous populations of organisms may be admixed within a single bed, known as time-averaging. Because of the slow and episodic nature of the geologic record, two apparently contemporaneous fossils may have actually lived centuries, or even millennia, apart. Moreover, the "degree" of time-averaging in an assemblage may vary. The degree varies on many factors, such as tissue type, the habitat, the frequency of burial events and exhumation events, and the depth of bioturbation within the sedimentary column relative to net sediment accumulation rates. Like biases in spatial fidelity, there is a bias towards organisms that can survive reworking events, such as shells. An example of a more ideal deposit with respect to time-averaging bias would be a volcanic ash deposit, which captures an entire biota caught in the wrong place at the wrong time (e.g. the Silurian Herefordshire lagerstätte).
Gaps in time series.
The geological record is very discontinuous, and deposition is episodic at all scales. At the largest scale, a sedimentological high-stand period may mean that no deposition may occur for millions of years and, in fact, erosion of the deposit may occur. Such a hiatus is called an unconformity. Conversely, a catastrophic event such as a mudslide may overrepresent a time period. At a shorter scale, scouring processes such as the formation of ripples and dunes and the passing of turbidity currents may cause layers to be removed. Thus the fossil record is biased towards periods of greatest sedimentation; periods of time that have less sedimentation are consequently less well represented in the fossil record.
A related problem is the slow changes that occur in the depositional environment of an area; a deposit may experience periods of poor preservation due to, for example, a lack of biomineralizing elements. This causes the taphonomic or diagenetic obliteration of fossils, producing gaps and condensation of the record.
Consistency in preservation over geologic time.
Major shifts in intrinsic and extrinsic properties of organisms, including morphology and behaviour in relation to other organisms or shifts in the global environment, can cause secular or long-term cyclic changes in preservation (megabias).
Human biases.
Much of the incompleteness of the fossil record is due to the fact that only a small amount of rock is ever exposed at the surface of the Earth, and not even most of that has been explored. Our fossil record relies on the small amount of exploration that has been done on this. Unfortunately, paleontologists as humans can be very biased in their methods of collection; a bias that must be identified. Potential sources of bias include,
Preservation of biopolymers.
The taphonomic pathways involved in relatively inert substances such as calcite (and to a lesser extent bone) are relatively obvious, as such body parts are stable and change little through time. However, the preservation of "soft tissue" is more interesting, as it requires more peculiar conditions. While usually only biomineralised material survives fossilisation, the preservation of soft tissue is not as rare as sometimes thought.
Both DNA and proteins are unstable, and rarely survive more than hundreds of thousands of years before degrading. Polysaccharides also have low preservation potential, unless they are highly cross-linked; this interconnection is most common in structural tissues, and renders them resistant to chemical decay. Such tissues include wood (lignin), spores and pollen (sporopollenin), the cuticles of plants (cutan) and animals, the cell walls of algae (algaenan), and potentially the polysaccharide layer of some lichens. This interconnectedness makes the chemicals less prone to chemical decay, and also means they are a poorer source of energy so less likely to be digested by scavenging organisms. After being subjected to heat and pressure, these cross-linked organic molecules typically "cook" and become kerogen or short (<17 C atoms) aliphatic/aromatic carbon molecules. Other factors affect the likelihood of preservation; for instance scleritisation renders the jaws of polychaetes more readily preserved than the chemically equivalent but non-sclerotised body cuticle.
It was thought that only tough, cuticle type soft tissue could be preserved by Burgess Shale type preservation, but an increasing number of organisms are being discovered that lack such cuticle, such as the probable chordate "Pikaia" and the shellless "Odontogriphus".
It is a common misconception that anaerobic conditions are necessary for the preservation of soft tissue; indeed much decay is mediated by sulfate reducing bacteria which can only survive in anaerobic conditions. Anoxia does, however, reduce the probability that scavengers will disturb the dead organism, and the activity of other organisms is undoubtedly one of the leading causes of soft-tissue destruction.
Plant cuticle is more prone to preservation if it contains cutan, rather than cutin.
Plants and algae produce the most preservable compounds, which are listed according to their preservation potential by Tegellaar (see reference).
Disintegration.
How complete fossils are was once thought to be a proxy for the energy of the environment, with stormier waters leaving less articulated carcasses. However, the dominant force actually seems to be predation, with scavengers more likely than rough waters to break up a fresh carcass before it is buried. Sediments cover smaller fossils faster so they are likely to be found fully articulated. However, erosion also tends to destroy smaller fossils more easily.
Significance.
Taphonomic processes allow researchers of multiple fields to identify the past of natural and cultural objects. From the time of death or burial until excavation, taphonomy can aid in the understanding of past environments. When studying the past it is important to gain contextual information in order to have a solid understanding of the data. Often these findings can be used to better understand cultural or environmental shifts within the present day.