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Taphonomy is the study of decaying organisms over time and how they become fossilized (if they do). The term taphonomy (from the Greek taphos, τάφος meaning burial, and nomos, νόμος meaning law) was introduced to paleontology in 1940 by Russian scientist Ivan Efremov to describe the study of the transition of remains, parts, or products of organisms, from the biosphere, to the lithosphere, i.e. the creation of fossil assemblages.
Taphonomists study such phenomena as biostratinomy, decomposition, diagenesis, and encrustation and bioerosion by sclerobionts. (Sclerobionts are organisms which dwell on hard substrates such as shells or rocks.)
One motivation behind taphonomy is to better understand biases present in the fossil record. 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 either infer that that 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.
Archaeologists study taphonomic processes in order to determine how plant and animal (including human) remains accumulate and differentially preserve within archaeological sites. This is critical to determining whether these remains are associated with human activity. In addition, taphonomic processes may alter biological remains after they are deposited at a site. Some remains survive better than others over time, and can therefore bias an excavated collection.
Forensic taphonomy is concerned with the study of the decomposition of human remains, particularly in the context of burial sites.
Experimental taphonomy testing usually consists of exposing the remains of organisms to various altering processes, and then examining the effects of the exposure.
Taphonomy has undergone an explosion of interest since the 1980s, with research focusing on certain areas.
- microbial, biogeochemical, and larger-scale controls on the preservation of different tissue types; in particular, exceptional preservation in Konzervat-lagerstatten. Covered within this field is the dominance of biological versus physical agents in the destruction of remains from all major taxonomic groups (plants, invertebrates, vertebrates)
- processes that concentrate biological remains; especially the degree to which different types of assemblages reflect the species composition and abundance of source faunas and floras
- the spatio-temporal resolution and ecological fidelity of species assemblages, particularly the relatively minor role of out-of-habitat transport contrasted with the major effects of time-averaging
- the outlines of megabiases in the fossil record, including the evolution of new bauplans and behavioral capabilities, and by broad-scale changes in climate, tectonics, and geochemistry of Earth surface systems.
Taphonomic biases in the fossil record
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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, that the former are much overrepresented relative to the latter.
Characteristics of the habiatat
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 amount 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 intrisically obviously allocthonous, 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 is very little endemic organisms to be preserved. This is a particular problem in palynology.
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 lagerstatte).
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 tens of thousands 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 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 behavior in relation to other organisms or shifts in the global environment, can cause secular or long-term cyclic changes in preservation (megabias).
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,
- Search images: field experiments have shown that paleontologists working on, say fossil clams are better at collecting clams than anything else, because their search images has been shaped to bias them in favour of clams.
- Relative ease of extraction: fossils that are easy to obtain (such as many phosphatic fossils that are easily extracted en mass by dissolution in acid) are overabundant in the fossil record.
- Taxonomic bias: fossils with easily discernable morphologies will be easy to distinguish as separate species, and will thus have an inflated abundance.
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 (resistant chemical in brackets) 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.
Plants and algae produce the most preservable compounds, which are listed according to their preservation potential by Tegellaar (see reference).
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 likelier to be found fully articulated. However, erosion also tends to destroy smaller fossils more easily.
- Beecher’s Trilobite type preservation
- Bitter Springs type preservation
- Burgess Shale type preservation
- Doushantuo type preservation
- Ediacaran type preservation
- Fossil record
- Trace fossils
- Efremov, I. A. (1940) "Taphonomy: a new branch of paleontology" Pan-American Geology 74: pp. 81-93
- Martin, Ronald E. (1999) "1.1 The foundations of taphonomy" Taphonomy: A Process Approach Cambridge University Press, Cambridge, England, p. 1, ISBN 0-521-59833-8
- See Taylor and Wilson, 2003[page needed]
- Behrensmeyer, A. K; S. M Kidwell, R. A Gastaldo (2009), Taphonomy and paleobiology.
- Briggs, D.E.G.; Kear, A.J. (1993), "Decay and preservation of polychaetes; taphonomic thresholds in soft-bodied organisms", Paleobiology 19 (1): 107–135
- Briggs, D.E.G. (1999), "Molecular taphonomy of animal and plant cuticles: selective preservation and diagenesis", Philosophical Transactions of the Royal Society B: Biological Sciences 354 (1379): 7–17, doi:10.1098/rstb.1999.0356
- Butterfield, N.J. (1990), "Organic preservation of non-mineralizing organisms and the taphonomy of the Burgess Shale", Paleobiology 16 (3): 272–286, JSTOR 2400788.
- Conway Morris, S. (2008), "A Redescription of a Rare Chordate, Metaspriggina walcotti Simonetta and Insom, from the Burgess Shale (Middle Cambrian), British Columbia, Canada", Journal of Paleontology 82 (2): 424–430, doi:10.1666/06-130.1
- Tegelaar, E.W.; De Leeuw, J.W.; Derenne, S.; Largeau, C. (1989), "A reappraisal of kerogen formation", Geochim. Cosmochim. Acta 53 (3): 03–3106, Bibcode:1989GeCoA..53.3103T, doi:10.1016/0016-7037(89)90191-9
- Behrensmeyer, A. K.; Kidwell, S. M.; Gastaldo, R. A. (2000). "Taphonomy and Paleobiology". Paleobiology 26 (4): 103–147. doi:10.1666/0094-8373(2000)26[103:TAP]2.0.CO;2. ISSN 0094-8373.
- Emig, C. C. (2002). Death: a key information in marine palaeoecology. In: Current topics on taphonomy and fossilization, Valencia. Col.lecio Encontres, 5: 21-26.
- Greenwood, D. R. (1991), The taphonomy of plant macrofossils. In, Donovan, S. K. (Ed.), The processes of fossilisation, p. 141-169. Belhaven Press.
- 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.
- Taylor, P. D. and Wilson, M. A. (2003), Palaeoecology and evolution of marine hard substrate communities. Earth-Science Reviews 62: 1-103. 
- The Shelf and Slope Experimental Taphonomy Initiative is the first long-term large-scale deployment and re-collection of organism remains on the sea floor.
- The Journal of Taphonomy
- Bioerosion Website at The College of Wooster
- Comprehensive bioerosion bibliography compiled by Mark A. Wilson