Editing Taphonomy (section)

==Research areas==
[[File:Skull burial.jpg|thumb|Actualistic taphonomy seeks to understand taphonomic processes through experimentation, such as the burial of bone.<ref name=":2">{{cite journal |last1=Carpenter |first1=Kenneth |title=Hydraulic modeling and computational fluid dynamics of bone burial in a sandy river channel |journal=Geology of the Intermountain West |date=30 April 2020 |volume=7 |pages=97–120 |doi=10.31711/giw.v7.pp97-120 |doi-access=free }}</ref>]]
Taphonomy has undergone an explosion of interest since the 1980s,<ref name=behrens>{{Citation
| last = Behrensmeyer
| first = A. K
 |author2=S. M Kidwell |author3=R. A Gastaldo
| title = Taphonomy and paleobiology
| year = 2009
| postscript = .
}}</ref> with research focusing on certain areas.
* [[microbe|Microbial]], [[biogeochemical]], and larger-scale controls on the preservation of different tissue types; in particular, exceptional preservation in [[lagerstätte|Konzervat-lagerstätten]]. 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.
*Actualistic taphonomy uses the present to understand past taphonomic events. This is often done through controlled experiments,<ref>{{Cite journal|last=Andrews|first=P.|date=1995|title=Experiments in taphonomy|url=https://www.sciencedirect.com/science/article/abs/pii/S0305440385700167|journal=Journal of Archaeological Science|volume=22|issue=2|pages=147–153|doi=10.1006/jasc.1995.0016|bibcode=1995JArSc..22..147A |via=Elsevier Science Direct|url-access=subscription}}</ref> such as the role microbes play in fossilization,<ref name="Briggs1993" /> the effects of mammalian carnivores on bone,<ref name=":3" /> or the burial of bone in a water flume.<ref name=":2" /> Computer modeling is also used to explain taphonomic events.<ref name=":2" /><ref>{{cite journal |last1=Olszewski |first1=Thomas D. |title=Modeling the Influence of Taphonomic Destruction, Reworking, and Burial on Time-Averaging in Fossil Accumulations |journal=PALAIOS |date=2004 |volume=19 |issue=1 |pages=39–50 |doi=10.1669/0883-1351(2004)019<0039:MTIOTD>2.0.CO;2|bibcode=2004Palai..19...39O |s2cid=130117819 |url=https://pubs.geoscienceworld.org/sepm/palaios/article-abstract/19/1/39/99941/Modeling-the-Influence-of-Taphonomic-Destruction |url-access=subscription }}</ref> Studies on actualistic taphonomy gave rise to the discipline [[conservation paleobiology]].
* The spatio-temporal resolution{{clarify|date=February 2018}} and ecological fidelity{{clarify|date=February 2018}} of species assemblages, particularly the relatively minor role of out-of-habitat transport contrasted with the major effects of time-averaging.{{clarify|date=February 2018}}
* The outlines of [[megabias]]es in the [[fossil record]], including the evolution of new [[bauplan]]s and behavioral capabilities, and by broad-scale changes in climate, tectonics, and geochemistry of Earth surface systems.
* The [[Mars Science Laboratory]] mission objectives evolved from assessment of ancient Mars habitability to developing predictive models on taphonomy.{{clarify|date=February 2018}}<ref name='Science 01-24-2014'>{{cite journal |last1=Grotzinger |first1=John P. |title=Habitability, Taphonomy, and the Search for Organic Carbon on Mars |journal=Science |date=24 January 2014 |volume=343 |issue=6169 |pages=386–387 |doi=10.1126/science.1249944 |pmid=24458635 |bibcode=2014Sci...343..386G |doi-access=free }}</ref>

=== Paleontology ===
One motivation behind taphonomy is to understand biases present in the [[fossil]] record better. Fossils are ubiquitous in sedimentary rocks, yet [[Paleontology|paleontologist]]s 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 fossil]]s) and [[biostratigraphy]]. By coming to understand the [[oceanographic]] and [[Ethology|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,<ref>{{cite book |last1=Cherns |first1=Lesley |last2=Wheeley |first2=James R. |last3=Wright |first3=V. Paul |chapter=Taphonomic Bias in Shelly Faunas Through Time: Early Aragonitic Dissolution and Its Implications for the Fossil Record |title=Taphonomy |series=Topics in Geobiology |date=2010 |volume=32 |pages=79–105 |doi=10.1007/978-90-481-8643-3_3|isbn=978-90-481-8642-6 }}</ref> poses a major challenge in reconstructing past environments from the modern,<ref>{{cite journal |last1=Bialik |first1=Or M. |last2=Coletti |first2=Giovanni |last3=Mariani |first3=Luca |last4=Commissario |first4=Lucrezi |last5=Desbiolles |first5=Fabien |last6=Meroni |first6=Agostino Niyonkuru |title=Availability and type of energy regulate the global distribution of neritic carbonates |journal=Scientific Reports |date=11 November 2023 |volume=13 |issue=1 |page=19687 |doi=10.1038/s41598-023-47029-4|doi-access=free |pmid=37952059 |pmc=10640608 |bibcode=2023NatSR..1319687B |hdl=10281/453746 |hdl-access=free }}</ref> notably in settings such as [[carbonate platform]]s.  

=== 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.<ref>{{Cite journal|last=Passalacqua|first=Nicholas|title=Introduction to Part VI: Forensic taphonomy|url=https://www.academia.edu/1566948|language=en}}</ref>

There are two different branches of forensic taphonomy: [http://www.itsgov.com/forensic-taphonomy.html biotaphonomy] and [http://www.itsgov.com/forensic-taphonomy.html 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.<ref name=":0">{{Cite news|title=Forensic taphonomy|date=2011-12-08|work=Crime Scene Investigator (CSI) and forensics information|language=en-US}}{{verify source|date=April 2021}}</ref>

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 ([https://naturalhistory.si.edu/sites/default/files/media/file/wibperimortemfinal.pdf perimortem]) and after death ([https://naturalhistory.si.edu/sites/default/files/media/file/wibperimortemfinal.pdf postmortem]). This can make a huge difference when considering what can be used as evidence in a criminal investigation.<ref>{{cite book |doi=10.1201/b15424-1 |chapter=Front Matter |title=Manual of Forensic Taphonomy |year=2013 |pages=i-xiv |isbn=978-1-4398-7841-5 |last1=Pokines |first1=James |last2=Symes |first2=Steven A. |doi-broken-date=2024-11-12 }}</ref>

=== 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.<ref name=":8">{{Cite book |last1=Grant |first1=Jim |url=https://www.taylorfrancis.com/books/9781317541110 |title=The Archaeology Coursebook |last2=Gorin |first2=Sam |last3=Fleming |first3=Neil |date=2015-03-27 |publisher=Routledge |isbn=978-1-317-54111-0 |edition=0 |language=en |doi=10.4324/9781315727837}}</ref> 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.<ref>{{Cite book |last=Lyman |first=R. Lee |url=https://www.cambridge.org/core/product/identifier/9781139878302/type/book |title=Vertebrate Taphonomy |date=1994-07-07 |publisher=Cambridge University Press |isbn=978-0-521-45215-1 |edition=1 |doi=10.1017/cbo9781139878302}}</ref> 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.<ref>{{Cite journal |last1=Rainsford |first1=Clare |last2=O’Connor |first2=Terry |date=June 2016 |title=Taphonomy and contextual zooarchaeology in urban deposits at York, UK |url=http://link.springer.com/10.1007/s12520-015-0268-x |journal=Archaeological and Anthropological Sciences |language=en |volume=8 |issue=2 |pages=343–351 |doi=10.1007/s12520-015-0268-x |bibcode=2016ArAnS...8..343R |s2cid=127652031 |issn=1866-9557|url-access=subscription }}</ref> When the artifact is deposited, [[abiotic]] and [[Ecosystem#Definition|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.<ref name=":1" /> Interpretation of the post-mortem, pre-, and post-burial histories of faunal assemblages is critical in determining their association with hominid activity and behaviour.<ref>{{Citation |last=Forbes |first=Shari |title=Taphonomy in Bioarchaeology and Human Osteology |date=2014 |url=http://link.springer.com/10.1007/978-1-4419-0465-2_137 |encyclopedia=Encyclopedia of Global Archaeology |pages=7219–7225 |editor-last=Smith |editor-first=Claire |access-date=2023-05-12 |place=New York, NY |publisher=Springer New York |language=en |doi=10.1007/978-1-4419-0465-2_137 |isbn=978-1-4419-0426-3|url-access=subscription }}</ref>

For instance, to distinguish the bone assemblages that are produced by humans from those of non humans, much [[Ethnoarchaeology|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 [[Excavations, Archaeological|excavation]] of animal dens and burrows to study the discarded bones and experimental breakage of bones with and without stone tools.<ref name=":9">{{Cite book |last1=Renfrew |first1=Colin |title=Archaeology Theory Methods and Practice |last2=Bahn |first2=Paul |publisher=Thames & Hudson |year=2020 |isbn=9780500843208 |edition=8th |location=London |pages=89–90 |language=en-gb}}</ref>
[[File:Australopithecus africanus - Cast of taung child.jpg|thumb|265x265px|Taphonomic study of the Taung child skull claims they were likely killed by a large bird, indicated by traces of talon cuts.<ref>{{Cite journal |last=Berger |first=Lee R. |date=October 2006 |title=Brief communication: Predatory bird damage to the Taung type-skull ofAustralopithecus africanus Dart 1925 |url=https://onlinelibrary.wiley.com/doi/10.1002/ajpa.20415 |journal=American Journal of Physical Anthropology |language=en |volume=131 |issue=2 |pages=166–168 |doi=10.1002/ajpa.20415 |pmid=16739138 |issn=0002-9483|url-access=subscription }}</ref>]]
Studies of this kind by [[C.K. Brain]] in South Africa have shown that bone fractures previously attributed to "[[Killer ape theory|killer man-apes]]" were in fact caused by the pressure of overlying rocks and earth in limestone caves.<ref name=":9" /> His research has also demonstrated that early hominins, for example [[australopithecine]]s, were more likely preyed upon by carnivores rather than being hunters themselves, from cave sites such as [[Swartkrans]] in South Africa.<ref name=":9" />

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 bone|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.<ref name=":9" /> In practice John Speth applied these criteria to the bones from the [[Garnsey kill site|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.<ref>{{Cite book |last1=Speth |first1=John D. |url=https://www.fulcrum.org/concern/monographs/6t053h67j |title=Late Prehistoric Bison Procurement in Southeastern New Mexico: The 1977 Season at the Garnsey Site |last2=Parry |first2=William J. |date=1978 |publisher=U OF M MUSEUM ANTHRO ARCHAEOLOGY |isbn=978-0-932206-73-2 |location=Ann Arbor, MI |language=en |doi=10.3998/mpub.11395480}}</ref>

One of the most important elements in this methodology is replication, to confirm the validity of results.<ref name=":8" />

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.<ref name=":9" /> 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.<ref name=":8" />

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 mat]]s and microbial activity influence the formation of fossils and the preservation of soft tissues.<ref name=":4">{{Cite journal |last1=Iniesto |first1=M. |last2=Villalba |first2=I. |last3=Buscalioni |first3=A. D. |last4=Guerrero |first4=M. C. |last5=López-Archilla |first5=A. I. |date=May 2017 |title=The Effect Of microbial Mats In The Decay Of Anurans With Implications For Understanding Taphonomic Processes In The Fossil Record |journal=Scientific Reports |language=en |volume=7 |issue=1 |pages=45160 |doi=10.1038/srep45160 |pmid=28338095 |pmc=5364532 |bibcode=2017NatSR...745160I |issn=2045-2322}}</ref><ref name=":5">{{Cite journal |last1=Iniesto |first1=Miguel |last2=Buscalioni |first2=Ángela D. |last3=Carmen Guerrero |first3=M. |last4=Benzerara |first4=Karim |last5=Moreira |first5=David |last6=López-Archilla |first6=Ana I. |date=2016-05-10 |title=Involvement of microbial mats in early fossilization by decay delay and formation of impressions and replicas of vertebrates and invertebrates |journal=Scientific Reports |language=en |volume=6 |issue=1 |pages=25716 |doi=10.1038/srep25716 |issn=2045-2322 |pmc=4861970 |pmid=27162204|bibcode=2016NatSR...625716I }}</ref> In these studies, microbial mats entomb animal carcasses in a sarcophagus of microbes—the sarcophagus entombing the animal's carcass delays decay.<ref name=":4" /> 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.<ref name=":4" /> The environment within the entombed carcasses is typically described as anoxic and acidic during the initial stage of decomposition.<ref name=":4" /><ref name=":6">{{Cite journal |last1=INIESTO |first1=MIGUEL |last2=LAGUNA |first2=CELIA |last3=FLORIN |first3=MAXIMO |last4=GUERRERO |first4=M. CARMEN |last5=CHICOTE |first5=ALVARO |last6=BUSCALIONI |first6=ANGELA D. |last7=LÓPEZ-ARCHILLA |first7=ANA I. |title=The Impact of Microbial Mats and Their Microenvironmental Conditions in Early Decay of Fish |date=2015 |url=https://www.jstor.org/stable/44708731 |journal=PALAIOS |volume=30 |issue=11/12 |pages=792–801 |doi=10.2110/palo.2014.086 |jstor=44708731 |bibcode=2015Palai..30..792I |s2cid=73644674 |issn=0883-1351|url-access=subscription }}</ref> 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.<ref name=":4" /><ref name=":5" /> The anoxic and acidic conditions created by that mats also inhibit the process of autolysis within the carcasses delaying decay even further.<ref name=":7">{{Cite journal |last1=Butler |first1=Aodhán D. |last2=Cunningham |first2=John A. |last3=Budd |first3=Graham E. |last4=Donoghue |first4=Philip C. J. |date=2015-06-07 |title=Experimental taphonomy of Artemia reveals the role of endogenous microbes in mediating decay and fossilization |journal=Proceedings of the Royal Society B: Biological Sciences |volume=282 |issue=1808 |pages=20150476 |doi=10.1098/rspb.2015.0476 |pmc=4455810 |pmid=25972468}}</ref>  Endogenous gut bacteria have also been described to aid the preservation of invertebrate soft tissue by delaying decay and stabilizing soft tissue structures.<ref name=":7" /> Gut bacteria form pseudomorphs replicating the form of soft tissues within the animal. These [[pseudomorph]]s are possible explanation for the increased occurrence of preserved guts impression among invertebrates.<ref name=":7" /> 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]].<ref name=":4" /><ref name=":5" />

Microbial mats additionally play a role in the formation of molds and impressions of carcasses. These molds and impressions replicate and preserve the [[Integumentary system|integument]] of animal carcasses.<ref name=":4" /> 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.<ref name=":4" /> 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.<ref name=":5" /> 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.<ref name=":6" />