Fossilization

@article{gratacap1896fossils,
    author = "Gratacap, L. P.",
    title = "Fossils and Fossilization",
    year = "1896",
    journal = "The American Naturalist",
    url = "https://doi.org/10.1086/276499",
    doi = "10.1086/276499",
    number = "359",
    openalex = "W2023980066",
    pages = "902-912",
    volume = "30"
}

@book{doi105962bhltitle45787,
    author = "Schuchert, Charles and Schuchert, Charles",
    title = "A synopsis of American fossil Brachiopoda: including bibliography and synonymy",
    year = "1897",
    booktitle = "United States Geological Survey eBooks",
    url = "https://doi.org/10.5962/bhl.title.45787",
    doi = "10.5962/bhl.title.45787",
    openalex = "W4248099698"
}

Abstract I — On the Factors which Influence the External Form of Fossil Plants Most writers of general treatises on Palaeobotany give an introductory chapter on fossilization, and this as a rule includes an account of the various kinds of fossil plants and the circumstances under which plants may become incorporated in sediments. The differences between the external form of the fossil and the original plant fragment are not often mentioned in relation to the factors which operate in the production of a fossil. It is often implied that fossil plants of the “ incrustation ” or “ impression ” type are produced in much the same way as herbarium specimens. That such a crude analogy does not satisfactorily explain the forms found among fossil plants of this type is obvious to those who have applied transfer methods to the examination of such fossils. In the writer’s opinion, the reason why so little precision has been given to descriptions of fossil-plant forms is that insufficient attention has been paid to the properties of sediments and the role played by the matrix. While many writers recognize that the differences in shape between a fossil and the original plant are due to the compressibility of the plant tissues the writer is not aware of any reference in the literature to the importance of the compressibility of the matrix in determining the form of a fossil embedded in it. It will be shown that the alteration in shape of a plant in undergoing fossilization in many cases may be best described as the result first of the collapse of the plant tissues and second of a more or less uniform vertical strain of the fossil and the surrounding matrix together.

@article{doi101098rstb19360008,
    author = "Walton, John",
    title = "VII - On the factors that influence external form of fossil plants; with descriptions of the foliage of some species of the Palaeozoic Equisetalean Genus Annularia Sternberg",
    year = "1936",
    journal = "Philosophical transactions of the Royal Society of London. Series B, Biological sciences",
    abstract = "Abstract I — On the Factors which Influence the External Form of Fossil Plants Most writers of general treatises on Palaeobotany give an introductory chapter on fossilization, and this as a rule includes an account of the various kinds of fossil plants and the circumstances under which plants may become incorporated in sediments. The differences between the external form of the fossil and the original plant fragment are not often mentioned in relation to the factors which operate in the production of a fossil. It is often implied that fossil plants of the “ incrustation ” or “ impression ” type are produced in much the same way as herbarium specimens. That such a crude analogy does not satisfactorily explain the forms found among fossil plants of this type is obvious to those who have applied transfer methods to the examination of such fossils. In the writer’s opinion, the reason why so little precision has been given to descriptions of fossil-plant forms is that insufficient attention has been paid to the properties of sediments and the role played by the matrix. While many writers recognize that the differences in shape between a fossil and the original plant are due to the compressibility of the plant tissues the writer is not aware of any reference in the literature to the importance of the compressibility of the matrix in determining the form of a fossil embedded in it. It will be shown that the alteration in shape of a plant in undergoing fossilization in many cases may be best described as the result first of the collapse of the plant tissues and second of a more or less uniform vertical strain of the fossil and the surrounding matrix together.",
    url = "https://doi.org/10.1098/rstb.1936.0008",
    doi = "10.1098/rstb.1936.0008",
    openalex = "W1986483944"
}

@article{doi101130001676061960711075mamfao20co2,
    author = "Johnson, Ralph Gordon",
    title = "MODELS AND METHODS FOR ANALYSIS OF THE MODE OF FORMATION OF FOSSIL ASSEMBLAGES",
    year = "1960",
    journal = "Geological Society of America Bulletin",
    url = "https://doi.org/10.1130/0016-7606(1960)71[1075:mamfao]2.0.co;2",
    doi = "10.1130/0016-7606(1960)71[1075:mamfao]2.0.co;2",
    openalex = "W2063150735"
}

The calcareous shells of recent articulate brachiopods and fossils of the same class dating back to the Mississippian are investigated for their crystal form, $$O^{18}/O^{16}$$ ratios, and $$SrCO_{3}$$ and $$MgCO_{3}$$ contents. In the case of recent forms it is shown that temperature affects $$O^{18}/O^{16}$$ ratios, $$SrCO_{3}$$ and $$MgCO_{3}$$ contents, and consequently Sr/Ca and Mg/Ca ratios. The $$SrCO_{3}$$ and $$MgCO_{3}$$ contents are investigated in samples from waters of 35‰ ± 1.5‰ salinity over the range of temperatures from 10° C. to 26° C. As is true for the $$O^{18}$$ concentrations, the uptake of Sr and Mg in the shells is shown to be sensitive also to changes in the concentrations of the two trace elements in sea water. The $$O^{18}/O^{16}$$ ratios and the $$SrCO_{3}$$ and $$MgCO_{3}$$ contents in fossil samples of Pliocene, Cretaceous, Permian and Mississippian age were determined. Samples as old as the early Permian have been found in which the relationship of $$O^{18}/O^{16}$$ ratios and the $$SrCO_{3}$$ and $$MgCO_{3}$$ contents are similar to recent species. The relation of the $$O^{18}/O^{16}$$ ratios to the $$SrCO_{3}$$ contents in a late Mississippian sample is also similar to that in recent species. These findings make it probable that the original $$O^{18}/O^{16}$$ ratios and $$SrCO_{3}$$ and $$MgCO_{3}$$ contents in these fossils are the original ones. In other samples the relations of the relative concentrations of one, two, or all three constituents indicate diagenetic alterations by fresh water. The significance of the chemical similarity of the fossil samples to recent shells is discussed. It is concluded that the results are best explained if it is assumed that the $$O^{18}$$, Sr and Mg contents, and the Sr/Ca and Mg/Ca ratios in the oceans have remained essentially constant during the last 2.0 to $$2.5 \times 10^{8}$$ years.

@article{doi101086626740,
    author = "Lowenstam, Heinz A.",
    title = "Mineralogy, O 18 /O 16 Ratios, and Strontium and Magnesium Contents of Recent and Fossil Brachiopods and Their Bearing on the History of the Oceans",
    year = "1961",
    journal = "The Journal of Geology",
    abstract = "The calcareous shells of recent articulate brachiopods and fossils of the same class dating back to the Mississippian are investigated for their crystal form, $$O^{18}/O^{16}$$ ratios, and $$SrCO\_{3}$$ and $$MgCO\_{3}$$ contents. In the case of recent forms it is shown that temperature affects $$O^{18}/O^{16}$$ ratios, $$SrCO\_{3}$$ and $$MgCO\_{3}$$ contents, and consequently Sr/Ca and Mg/Ca ratios. The $$SrCO\_{3}$$ and $$MgCO\_{3}$$ contents are investigated in samples from waters of 35‰ ± 1.5‰ salinity over the range of temperatures from 10° C. to 26° C. As is true for the $$O^{18}$$ concentrations, the uptake of Sr and Mg in the shells is shown to be sensitive also to changes in the concentrations of the two trace elements in sea water. The $$O^{18}/O^{16}$$ ratios and the $$SrCO\_{3}$$ and $$MgCO\_{3}$$ contents in fossil samples of Pliocene, Cretaceous, Permian and Mississippian age were determined. Samples as old as the early Permian have been found in which the relationship of $$O^{18}/O^{16}$$ ratios and the $$SrCO\_{3}$$ and $$MgCO\_{3}$$ contents are similar to recent species. The relation of the $$O^{18}/O^{16}$$ ratios to the $$SrCO\_{3}$$ contents in a late Mississippian sample is also similar to that in recent species. These findings make it probable that the original $$O^{18}/O^{16}$$ ratios and $$SrCO\_{3}$$ and $$MgCO\_{3}$$ contents in these fossils are the original ones. In other samples the relations of the relative concentrations of one, two, or all three constituents indicate diagenetic alterations by fresh water. The significance of the chemical similarity of the fossil samples to recent shells is discussed. It is concluded that the results are best explained if it is assumed that the $$O^{18}$$, Sr and Mg contents, and the Sr/Ca and Mg/Ca ratios in the oceans have remained essentially constant during the last 2.0 to $$2.5 \times 10^{8}$$ years.",
    url = "https://doi.org/10.1086/626740",
    doi = "10.1086/626740",
    openalex = "W2284192460"
}

@article{doi101130001676061961721817camcof20co2,
    author = "Turekian, Karl K. and Armstrong, R. L.",
    title = "Chemical and Mineralogical Composition of Fossil Molluscan Shells from the Fox Hills Formation, South Dakota",
    year = "1961",
    journal = "Geological Society of America Bulletin",
    url = "https://doi.org/10.1130/0016-7606(1961)72[1817:camcof]2.0.co;2",
    doi = "10.1130/0016-7606(1961)72[1817:camcof]2.0.co;2",
    openalex = "W1968729505"
}

@article{doi101130001676061964751197fciptr20co2,
    author = "Fagerstrom, J. A.",
    title = "Fossil Communities in Paleoecology: Their Recognition and Significance",
    year = "1964",
    journal = "Geological Society of America Bulletin",
    url = "https://doi.org/10.1130/0016-7606(1964)75[1197:fciptr]2.0.co;2",
    doi = "10.1130/0016-7606(1964)75[1197:fciptr]2.0.co;2",
    openalex = "W2066399383"
}

@article{doi10113000167606196475217cotcof20co2,
    author = "Pilkey, Orrin H. and Goodell, H",
    title = "Comparison of the Composition of Fossil and Recent Mollusk Shells",
    year = "1964",
    journal = "Geological Society of America Bulletin",
    url = "https://doi.org/10.1130/0016-7606(1964)75[217:cotcof]2.0.co;2",
    doi = "10.1130/0016-7606(1964)75[217:cotcof]2.0.co;2",
    openalex = "W1977610530"
}

@article{doi1010160025322767900515,
    author = "Seilacher, Adolf",
    title = "Bathymetry of trace fossils",
    year = "1967",
    journal = "Marine Geology",
    url = "https://doi.org/10.1016/0025-3227(67)90051-5",
    doi = "10.1016/0025-3227(67)90051-5",
    openalex = "W1975115126",
    references = "doi1010079783662010204, doi101007bf01820746, doi101007bf02986976, doi101086626811, doi101126science150369260, doi10130674d70c452b2111d78648000102c1865d, doi1023071483846, openalexw2049573044, openalexw2343619380, openalexw574363047"
}

@article{openalexw2603991543,
    author = "Durham, J. Wyatt",
    title = "The incompleteness of our knowledge of the fossil record",
    year = "1967",
    journal = "Journal of Paleontology",
    openalex = "W2603991543"
}

A fossil record of lampreys has previously been unknown. A new genus demonstrates the presence of this group in the Pennsylvanian. The body outline, parts of the head skeleton, rasping tongue mechanism, gill basket, and other internal organs are preserved. The fossils are very similar in structure to modern forms. The absence of hagfish characters in the fossil supports the view that the common ancestor of lampreys and hagfishes lived prior to the Pennsylvanian.

@article{doi101126science16238591265,
    author = "Bardack, David and Zangerl, Rainer",
    title = "First Fossil Lamprey: A Record from the Pennsylvanian of Illinois",
    year = "1968",
    journal = "Science",
    abstract = "A fossil record of lampreys has previously been unknown. A new genus demonstrates the presence of this group in the Pennsylvanian. The body outline, parts of the head skeleton, rasping tongue mechanism, gill basket, and other internal organs are preserved. The fossils are very similar in structure to modern forms. The absence of hagfish characters in the fossil supports the view that the common ancestor of lampreys and hagfishes lived prior to the Pennsylvanian.",
    url = "https://doi.org/10.1126/science.162.3859.1265",
    doi = "10.1126/science.162.3859.1265",
    openalex = "W1980643034",
    references = "doi101086627194, doi101093bioscience1610752a, doi101111j146363951948tb00030x, doi101126science1593814526, doi105281zenodo16034360"
}

@article{doi101130001676061968791315tailif20co2,
    author = "Lawrence, David R.",
    title = "Taphonomy and Information Losses in Fossil Communities",
    year = "1968",
    journal = "Geological Society of America Bulletin",
    url = "https://doi.org/10.1130/0016-7606(1968)79[1315:tailif]2.0.co;2",
    doi = "10.1130/0016-7606(1968)79[1315:tailif]2.0.co;2",
    openalex = "W2134383609"
}

@book{openalexw1549886310,
    author = "Rudwick, Martin J. S.",
    title = "Living and fossil brachiopods",
    year = "1970",
    openalex = "W1549886310"
}

The theory of plate tectonics implies greatly different continental geographies in the past which can be reconstructed from a variety of geophysical, structural, petrologic, and stratigraphic evidence. Platetectonic processes affect relative sizes, the relative emergence, and the latitudinal and longitudinal patterns of continents. These factors affect the patterns of trophic-resource regimes in shallow marine water and also determine the patterns of provinciality of the shallow-water biota, and these patterns are probably chiefly responsible for the regulation of species diversity in shallow waters. The diversity patterns are partially the products of the adaptive strategies followed by populations in different resource regimes; high diversities correlate with stable regimes and low diversities with fluctuating regimes. The proportions of feeding types vary among types of regime also, resulting in qualitative differences in the faunas. Precam-brian and Cambrian radiations from which the higher invertebrate phyla developed may have been primarily adaptive responses to changes in trophic-resource regimes, brought about by changing land-sea natterns.

@article{doi101086627723,
    author = "Valentine, James W. and Moores, Eldridge M.",
    title = "Global Tectonics and the Fossil Record",
    year = "1972",
    journal = "The Journal of Geology",
    abstract = "The theory of plate tectonics implies greatly different continental geographies in the past which can be reconstructed from a variety of geophysical, structural, petrologic, and stratigraphic evidence. Platetectonic processes affect relative sizes, the relative emergence, and the latitudinal and longitudinal patterns of continents. These factors affect the patterns of trophic-resource regimes in shallow marine water and also determine the patterns of provinciality of the shallow-water biota, and these patterns are probably chiefly responsible for the regulation of species diversity in shallow waters. The diversity patterns are partially the products of the adaptive strategies followed by populations in different resource regimes; high diversities correlate with stable regimes and low diversities with fluctuating regimes. The proportions of feeding types vary among types of regime also, resulting in qualitative differences in the faunas. Precam-brian and Cambrian radiations from which the higher invertebrate phyla developed may have been primarily adaptive responses to changes in trophic-resource regimes, brought about by changing land-sea natterns.",
    url = "https://doi.org/10.1086/627723",
    doi = "10.1086/627723",
    openalex = "W1994293426",
    references = "doi10100703064746897, doi101029jb073i012p03661, doi101029jb075i014p02625, doi101086282398, doi101086282541, doi101126science166390172, doi1015159781400881376, doi1023072258471, doi1023072405671, doi104159harvard9780674865327"
}

@article{doi1010160034666775900056,
    author = "Schopf, James M.",
    title = "Modes of fossil preservation",
    year = "1975",
    journal = "Review of Palaeobotany and Palynology",
    url = "https://doi.org/10.1016/0034-6667(75)90005-6",
    doi = "10.1016/0034-6667(75)90005-6",
    openalex = "W2132959526",
    references = "doi101093oxfordjournalsaoba083546, doi101098rstb19360008, doi101126science16238591265, doi101126science16338721157, doi101126science17440151229, doi1023071795148, doi105962bhltitle7199, openalexw2326083785, openalexw603784498"
}

@article{doi101016s0016787876800077,
    author = "Ager, D.V.",
    title = "The nature of the fossil record",
    year = "1976",
    journal = "Proceedings of the Geologists Association",
    url = "https://doi.org/10.1016/s0016-7878(76)80007-7",
    doi = "10.1016/s0016-7878(76)80007-7",
    openalex = "W1990851360",
    references = "doi1010160031018265900118, doi101038207270a0, doi101038212339a0, doi101038242032a0, doi101086627723, doi101111j1469185x1973tb00979x, doi101111j150239311968tb01724x, doi101111j155856461968tb03995x, doi101130spe89p63, doi1023071484577, doi105281zenodo16298542, openalexw2171088317, openalexw2761886851, openalexw3135630760"
}

The fossil record of echinoids is poor because soon after death they break apart into isolated plates. In the present seas regular echinoid species outnumber irregular species; whereas, in the Tertiary only 20% of the known echinoid species are regular. This suggests that regular echinoids are less likely to be preserved than irregular echinoids. The tests of regular echinoids are exposed to scavengers and currents upon their death, but irregular echinoids generally live buried in the sediment and are protected from these destructive forces. Furthermore, the tests of the regular echinoids lack the calcareous supports found in some irregular echinoids. The gut is not filled with sediment and its apical system is generally larger and more fragile. Finally, many regular echinoids live in environments less likely to be preserved in the sedimentary record. Although the irregular echinoid is more likely to be fossilized, its record is poor during some periods in the past. Although 1,014 irregular echinoid species are known from the Eocene, only 83 species are known from the Paleocene and only 343 are known from the Oligocene. Is this reduction because fewer species lived then or because they have not been preserved?

@article{doi101017s0094837300005248,
    author = "Kier, Porter M.",
    title = "The poor fossil record of the regular echinoid",
    year = "1977",
    journal = "Paleobiology",
    abstract = "The fossil record of echinoids is poor because soon after death they break apart into isolated plates. In the present seas regular echinoid species outnumber irregular species; whereas, in the Tertiary only 20\% of the known echinoid species are regular. This suggests that regular echinoids are less likely to be preserved than irregular echinoids. The tests of regular echinoids are exposed to scavengers and currents upon their death, but irregular echinoids generally live buried in the sediment and are protected from these destructive forces. Furthermore, the tests of the regular echinoids lack the calcareous supports found in some irregular echinoids. The gut is not filled with sediment and its apical system is generally larger and more fragile. Finally, many regular echinoids live in environments less likely to be preserved in the sedimentary record. Although the irregular echinoid is more likely to be fossilized, its record is poor during some periods in the past. Although 1,014 irregular echinoid species are known from the Eocene, only 83 species are known from the Paleocene and only 343 are known from the Oligocene. Is this reduction because fewer species lived then or because they have not been preserved?",
    url = "https://doi.org/10.1017/s0094837300005248",
    doi = "10.1017/s0094837300005248",
    openalex = "W2212209098",
    references = "doi101017s0094837300002232, doi101111j150239311972tb00852x, doi10113000167606197586243eosbca20co2, doi10130683d923e816c711d78645000102c1865d, doi10130683d923ed16c711d78645000102c1865d, doi105479si00810282206, openalexw2603991543, openalexw2800093945, openalexw2995010560"
}

How much of a living marine fauna would be reflected in the fossil record? In order to answer this, I investigated the probable fate of 169 megascopic genera of the intertidal fauna of the Friday Harbor, Washington region. Three methods were used and these give very similar results. (I) From morphologic examination, 30% of the mud fauna, 32% of the sand fauna, and 29% of the rock fauna are predicted to yield many identifiable fossils; 38% of the mud fauna, 42% of the sand fauna, and 41% of the rock fauna are predicted to yield few identifiable fossils; and the remainder are predicted to yield no fossils. (II) In actual fact, 44% of the mud fauna, 32% of the sand fauna, and 39% of the rock fauna have a fossil record (data from Treatise on Invertebrate Paleontology). (III) The 16 sediment samples which were examined yielded 29% of the total fauna. I conclude (1) that the fossilization potential for the Friday Harbor intertidal fauna is largely independent of habitat, and (2) that 40% of the present megascopic fauna would be (and has been!) preserved in the fossil record. The fossil record would accurately (and preferentially) include the herbivore and filter feeding genera. The reason which I postulate for this is based on the suitability of heavily calcified exoskeletons to an essentially sessile mode of life, and the lack of suitability of such skeletons for readily mobile forms. 67% of the genera which essentially rest in one place are known as fossils. In contrast, only 16 to 27% of the burrowing detritus eaters (e.g., polychaetes) and roving carnivores (e.g., sea stars and crabs) are known as fossils. The percentage of herbivore and filter feeding genera in rocky environments is 39%, in sand 16% and in mud 34%. In the fossil record, deposits which were originally mud are likely to be most fossiliferous because (1) that environment has a high proportion of essentially sessile genera, (2) essentially sessile genera are far more likely to have a heavily calcified skeleton, and (3) few rock intertidal regions are buried.

@article{schopf1978fossilization,
    author = "Schopf, Thomas J. M.",
    title = "Fossilization potential of an intertidal fauna: Friday Harbor, Washington",
    year = "1978",
    journal = "Paleobiology",
    abstract = "How much of a living marine fauna would be reflected in the fossil record? In order to answer this, I investigated the probable fate of 169 megascopic genera of the intertidal fauna of the Friday Harbor, Washington region. Three methods were used and these give very similar results. (I) From morphologic examination, 30\% of the mud fauna, 32\% of the sand fauna, and 29\% of the rock fauna are predicted to yield many identifiable fossils; 38\% of the mud fauna, 42\% of the sand fauna, and 41\% of the rock fauna are predicted to yield few identifiable fossils; and the remainder are predicted to yield no fossils. (II) In actual fact, 44\% of the mud fauna, 32\% of the sand fauna, and 39\% of the rock fauna have a fossil record (data from Treatise on Invertebrate Paleontology). (III) The 16 sediment samples which were examined yielded 29\% of the total fauna. I conclude (1) that the fossilization potential for the Friday Harbor intertidal fauna is largely independent of habitat, and (2) that 40\% of the present megascopic fauna would be (and has been!) preserved in the fossil record. The fossil record would accurately (and preferentially) include the herbivore and filter feeding genera. The reason which I postulate for this is based on the suitability of heavily calcified exoskeletons to an essentially sessile mode of life, and the lack of suitability of such skeletons for readily mobile forms. 67\% of the genera which essentially rest in one place are known as fossils. In contrast, only 16 to 27\% of the burrowing detritus eaters (e.g., polychaetes) and roving carnivores (e.g., sea stars and crabs) are known as fossils. The percentage of herbivore and filter feeding genera in rocky environments is 39\%, in sand 16\% and in mud 34\%. In the fossil record, deposits which were originally mud are likely to be most fossiliferous because (1) that environment has a high proportion of essentially sessile genera, (2) essentially sessile genera are far more likely to have a heavily calcified skeleton, and (3) few rock intertidal regions are buried.",
    url = "https://doi.org/10.1017/s0094837300005996",
    doi = "10.1017/s0094837300005996",
    number = "3",
    openalex = "W2505387446",
    pages = "261-270",
    volume = "4",
    references = "doi101016s0016787876800077, doi101017s0094837300005236, doi101017s0094837300005248, doi101086282400, doi101111j143904691975tb00509x, doi101126science1924238461, doi1023071935526, doi1023071942565, openalexw1549886310, openalexw574363047"
}

@misc{schopf1978fossilization2,
    author = "Schopf, T. J. M",
    title = "Fossilization potential of an intertidal fauna",
    year = "1978",
    howpublished = "Friday Harbor, Washington: Paleobiology, v. 4, p. 261-270",
    note = "talkorigins\_source = {true}; raw\_reference = {Schopf, T. J. M., 1978, Fossilization potential of an intertidal fauna: Friday Harbor, Washington: Paleobiology, v. 4, p. 261-270.}"
}

Data on numbers of marine families within 91 metazoan classes known from the Phanerozoic fossil record are analyzed. The distribution of the 2800 fossil families among the classes is very uneven, with most belonging to a small minority of classes. Similarly, the stratigraphic distribution of the classes is very uneven, with most first appearing early in the Paleozoic and with many of the smaller classes becoming extinct before the end of that era. However, despite this unevenness, a Q -mode factor analysis indicates that the structure of these data is rather simple. Only three factors are needed to account for more than 90% of the data. These factors are interpreted as reflecting the three great “evolutionary faunas” of the Phanerozoic marine record: a trilobite-dominated Cambrian fauna, a brachiopod-dominated later Paleozoic fauna, and a mollusc-dominated Mesozoic-Cenozoic, or “modern,” fauna. Lesser factors relate to slow taxonomic turnover within the major faunas through time and to unique aspects of particular taxa and times. Each of the three major faunas seems to have its own characteristic diversity so that its expansion or contraction appears as being intimately associated with a particular phase in the history of total marine diversity. The Cambrian fauna expands rapidly during the Early Cambrian radiations and maintains dominance during the Middle to Late Cambrian “equilibrium.” The Paleozoic fauna then ascends to dominance during the Ordovician radiations, which increase diversity dramatically; this new fauna then maintains dominance throughout the long interval of apparent equilibrium that lasts until the end of the Paleozoic Era. The modern fauna, which slowly increases in importance during the Paleozoic Era, quickly rises to dominance with the Late Permian extinctions and maintains that status during the general rise in diversity to the apparent maximum in the Neogene. The increase in diversity associated with the expansion of each new fauna appears to coincide with an approximately exponential decline of the previously dominant fauna, suggesting possible displacement of each evolutionary fauna by its successor.

@article{doi101017s0094837300003778,
    author = "Sepkoski, J. John",
    title = "A factor analytic description of the Phanerozoic marine fossil record",
    year = "1981",
    journal = "Paleobiology",
    abstract = "Data on numbers of marine families within 91 metazoan classes known from the Phanerozoic fossil record are analyzed. The distribution of the 2800 fossil families among the classes is very uneven, with most belonging to a small minority of classes. Similarly, the stratigraphic distribution of the classes is very uneven, with most first appearing early in the Paleozoic and with many of the smaller classes becoming extinct before the end of that era. However, despite this unevenness, a Q -mode factor analysis indicates that the structure of these data is rather simple. Only three factors are needed to account for more than 90\% of the data. These factors are interpreted as reflecting the three great “evolutionary faunas” of the Phanerozoic marine record: a trilobite-dominated Cambrian fauna, a brachiopod-dominated later Paleozoic fauna, and a mollusc-dominated Mesozoic-Cenozoic, or “modern,” fauna. Lesser factors relate to slow taxonomic turnover within the major faunas through time and to unique aspects of particular taxa and times. Each of the three major faunas seems to have its own characteristic diversity so that its expansion or contraction appears as being intimately associated with a particular phase in the history of total marine diversity. The Cambrian fauna expands rapidly during the Early Cambrian radiations and maintains dominance during the Middle to Late Cambrian “equilibrium.” The Paleozoic fauna then ascends to dominance during the Ordovician radiations, which increase diversity dramatically; this new fauna then maintains dominance throughout the long interval of apparent equilibrium that lasts until the end of the Paleozoic Era. The modern fauna, which slowly increases in importance during the Paleozoic Era, quickly rises to dominance with the Late Permian extinctions and maintains that status during the general rise in diversity to the apparent maximum in the Neogene. The increase in diversity associated with the expansion of each new fauna appears to coincide with an approximately exponential decline of the previously dominant fauna, suggesting possible displacement of each evolutionary fauna by its successor.",
    url = "https://doi.org/10.1017/s0094837300003778",
    doi = "10.1017/s0094837300003778",
    openalex = "W2505144080",
    references = "doi10100797814613088367, doi1010160012825272900724, doi101017s0094837300004917, doi101017s009483730000508x, doi101017s0094837300005236, doi101017s0094837300005352, doi101017s0094837300005649, doi101017s0094837300005972, doi101017s0094837300012549, doi101126science17740541065, doi101126science2064415217, doi101130spe89p63, doi1023071483846, doi1023071796560, doi1023072405671, doi1023072412725, doi1023072412728, doi1023072806339, doi107312simp93764, openalexw1504049102, openalexw645218623"
}

@article{doi101038293435a0,
    author = "Sepkoski, J. John and Bambach, Richard K. and Raup, David M. and Valentine, James W.",
    title = "Phanerozoic marine diversity and the fossil record",
    year = "1981",
    journal = "Nature",
    url = "https://doi.org/10.1038/293435a0",
    doi = "10.1038/293435a0",
    openalex = "W2002352667",
    references = "doi101017s0094837300003778, doi101017s0094837300004917, doi101017s0094837300004929, doi101017s0094837300004930, doi101017s0094837300005236, doi101017s0094837300005972, doi101017s0094837300006539, doi101111j150239311980tb00632x, doi101126science17740541065, doi1023071441916, doi1023072341482, openalexw645218623"
}

A new compilation of fossil data on invertebrate and vertebrate families indicates that four mass extinctions in the marine realm are statistically distinct from background extinction levels. These four occurred late in the Ordovician, Permian, Triassic, and Cretaceous periods. A fifth extinction event in the Devonian stands out from the background but is not statistically significant in these data. Background extinction rates appear to have declined since Cambrian time, which is consistent with the prediction that optimization of fitness should increase through evolutionary time.

@article{doi101126science21545391501,
    author = "Raup, David M. and Sepkoski, J. John",
    title = "Mass Extinctions in the Marine Fossil Record",
    year = "1982",
    journal = "Science",
    abstract = "A new compilation of fossil data on invertebrate and vertebrate families indicates that four mass extinctions in the marine realm are statistically distinct from background extinction levels. These four occurred late in the Ordovician, Permian, Triassic, and Cretaceous periods. A fifth extinction event in the Devonian stands out from the background but is not statistically significant in these data. Background extinction rates appear to have declined since Cambrian time, which is consistent with the prediction that optimization of fitness should increase through evolutionary time.",
    url = "https://doi.org/10.1126/science.215.4539.1501",
    doi = "10.1126/science.215.4539.1501",
    openalex = "W1976721572",
    references = "doi101017s009483730000511x, doi101017s0094837300006539, doi101130spe89p63, doi105281zenodo16226412, openalexw2335729143, openalexw2591197405, openalexw2596207362"
}

Catastrophic hypotheses for mass extinctions are commonly criticized because many taxa gradually disappear from the fossil record prior to the extinction. Presumably, a geologically instantaneous catastrophe would not cause a reduction in diversity or a series of minor extinctions before the actual mass extinction. Two types of sampling effects, however, could cause taxa to appear to decline before their actual biotic extinction. The first of these is reduced sample size provided in the sedimentary record and the second, which we examine in greater detail, is artificial range truncation. The fossil record is discontinuous in time and the recorded ranges of species or of higher taxa can only extend to their last known occurrence in the fossil record. If the distribution of last occurrences is random with respect to actual biotic extinction, then apparent extinctions will begin well before a mass extinction and will gradually increase in frequency until the mass extinction event, thus giving the appearance of a gradual extinction. Other factors, such as regressions, can exacerbate the bias toward gradual disappearance of taxa from the fossil record. Hence, gradual extinction patterns prior to a mass extinction do not necessarily eliminate catastrophic extinction hypotheses. The recorded ranges of fossils, especially of uncommon taxa or taxa in habitats not represented by a continuous record, may be inadequate to test either gradual or catastrophic hypotheses.

@incollection{doi101130spe190p291,
    author = "Signor, Philip W. and Lipps, Jere H.",
    title = "Sampling bias, gradual extinction patterns and catastrophes in the fossil record",
    year = "1982",
    booktitle = "Geological Society of America eBooks",
    abstract = "Catastrophic hypotheses for mass extinctions are commonly criticized because many taxa gradually disappear from the fossil record prior to the extinction. Presumably, a geologically instantaneous catastrophe would not cause a reduction in diversity or a series of minor extinctions before the actual mass extinction. Two types of sampling effects, however, could cause taxa to appear to decline before their actual biotic extinction. The first of these is reduced sample size provided in the sedimentary record and the second, which we examine in greater detail, is artificial range truncation. The fossil record is discontinuous in time and the recorded ranges of species or of higher taxa can only extend to their last known occurrence in the fossil record. If the distribution of last occurrences is random with respect to actual biotic extinction, then apparent extinctions will begin well before a mass extinction and will gradually increase in frequency until the mass extinction event, thus giving the appearance of a gradual extinction. Other factors, such as regressions, can exacerbate the bias toward gradual disappearance of taxa from the fossil record. Hence, gradual extinction patterns prior to a mass extinction do not necessarily eliminate catastrophic extinction hypotheses. The recorded ranges of fossils, especially of uncommon taxa or taxa in habitats not represented by a continuous record, may be inadequate to test either gradual or catastrophic hypotheses.",
    url = "https://doi.org/10.1130/spe190-p291",
    doi = "10.1130/spe190-p291",
    openalex = "W2414724882"
}

Because of fundamental differences between trace fossils and body fossils, ichnologic nomenclature is beset with difficulties. Foremost is inconsistent treatment by the International Commission on Zoological Nomenclature (lack of sanction for post-1930 names, confusion over the rule of priority) and inadequate curation of type specimens. However, ichnologists have contributed their own problems via inadequate diagnoses and descriptions, misconceptions of ichnologic and taxonomic principles, proliferation of names and failure to engage in true monographic revisions. All these difficulties are illustrated in a thorough reevaluation of the ichnogenera Planolites Nicholson and Palaeophycus Hall. Contrary to a popular but ill-founded scheme in which these ichnogenera are differentiated simply on the presence or absence of branches, Planolites is an unlined burrow infilled with sediments having textural and fabricational characters unlike those of the host rock, whereas Palaeophycus is a lined burrow filled with sediments typically identical to those of the surrounding matrix. Planolites represents active backfilling of sediment in an ephemeral burrow constructed by a mobile deposit feeder and Palaeophycus represents passive sedimentation within an open dwelling burrow constructed by a predaceous or suspension-feeding animal. In addition to ichnological nomenclature and ethology, the ramifications are important in paleoecology, sedimentology and diagenetic studies. Currently recognized ichnospecies of Planolites include P. montanus Richter, P. beverleyensis (Billings) and P. annularis Walcott. Those of Palaeophycus include P. heberti (Saporta), P. tubularis Hall, P. striatus Hall, P. sulcatus (Miller and Dyer) and P. alternatus n. ichnosp.

@article{openalexw2344228935,
    author = "Pemberton, S. George and Frey, Robert W.",
    title = "Trace fossil nomenclature and the Planolites-Palaeophycus dilemma",
    year = "1982",
    journal = "Journal of Paleontology",
    abstract = "Because of fundamental differences between trace fossils and body fossils, ichnologic nomenclature is beset with difficulties. Foremost is inconsistent treatment by the International Commission on Zoological Nomenclature (lack of sanction for post-1930 names, confusion over the rule of priority) and inadequate curation of type specimens. However, ichnologists have contributed their own problems via inadequate diagnoses and descriptions, misconceptions of ichnologic and taxonomic principles, proliferation of names and failure to engage in true monographic revisions. All these difficulties are illustrated in a thorough reevaluation of the ichnogenera Planolites Nicholson and Palaeophycus Hall. Contrary to a popular but ill-founded scheme in which these ichnogenera are differentiated simply on the presence or absence of branches, Planolites is an unlined burrow infilled with sediments having textural and fabricational characters unlike those of the host rock, whereas Palaeophycus is a lined burrow filled with sediments typically identical to those of the surrounding matrix. Planolites represents active backfilling of sediment in an ephemeral burrow constructed by a mobile deposit feeder and Palaeophycus represents passive sedimentation within an open dwelling burrow constructed by a predaceous or suspension-feeding animal. In addition to ichnological nomenclature and ethology, the ramifications are important in paleoecology, sedimentology and diagenetic studies. Currently recognized ichnospecies of Planolites include P. montanus Richter, P. beverleyensis (Billings) and P. annularis Walcott. Those of Palaeophycus include P. heberti (Saporta), P. tubularis Hall, P. striatus Hall, P. sulcatus (Miller and Dyer) and P. alternatus n. ichnosp.",
    openalex = "W2344228935",
    references = "doi1010079783642659232, doi101111j150239311980tb00632x, doi101130gsab10199, doi1023071485443, openalexw3127114020, openalexw574363047"
}

@book{doi1010079781475707403,
    author = "Tevesz, Michael J. S. and McCall, Peter L.",
    title = "Biotic Interactions in Recent and Fossil Benthic Communities",
    year = "1983",
    booktitle = "Topics in geobiology",
    url = "https://doi.org/10.1007/978-1-4757-0740-3",
    doi = "10.1007/978-1-4757-0740-3",
    openalex = "W1993827688",
    references = "doi1010029783527809080cataz15836, doi101126science3095734532o"
}

@article{doi1010160278416583900089,
    author = "Shipman, Pat and Rose, Jennie J.",
    title = "Early hominid hunting, butchering, and carcass-processing behaviors: Approaches to the fossil record",
    year = "1983",
    journal = "Journal of Anthropological Archaeology",
    url = "https://doi.org/10.1016/0278-4165(83)90008-9",
    doi = "10.1016/0278-4165(83)90008-9",
    openalex = "W2002557964",
    references = "doi101016b9780120031047500132, doi101017s0094837300005820, doi101038scientificamerican096062, doi102113gsrocky8specialpaper11, doi1023072798801, doi105962bhlpart22969, openalexw1974359478"
}

Soft-bodied and lightly sclerotized Burgess shale fossils have been found at more than a dozen new localities in an area extending for 20 kilometers along the front of the Cathedral Escarpment in the Middle Cambrian Stephen Formation of the Canadian Rockies. Five different fossil assemblages from four stratigraphic levels have been recognized. These assemblages represent distinct penecontemporaneous marine communities that together make up a normal fore-reef faunal complex.

@article{doi101126science2224620163,
    author = "Collins, Desmond and Briggs, Derek E. G. and Morris, Simon Conway",
    title = "New Burgess Shale Fossil Sites Reveal Middle Cambrian Faunal Complex",
    year = "1983",
    journal = "Science",
    abstract = "Soft-bodied and lightly sclerotized Burgess shale fossils have been found at more than a dozen new localities in an area extending for 20 kilometers along the front of the Cathedral Escarpment in the Middle Cambrian Stephen Formation of the Canadian Rockies. Five different fossil assemblages from four stratigraphic levels have been recognized. These assemblages represent distinct penecontemporaneous marine communities that together make up a normal fore-reef faunal complex.",
    url = "https://doi.org/10.1126/science.222.4620.163",
    doi = "10.1126/science.222.4620.163",
    openalex = "W1994380053",
    references = "doi101017s0094837300006539, doi101038scientificamerican0779122, doi101098rstb19810033, doi101130gsab51731, doi105281zenodo15932730, doi105281zenodo16490103, openalexw2600671946, openalexw2608196808, openalexw614215761"
}

@article{doi1010160278416584900047,
    author = "Lyman, R. Lee",
    title = "Bone density and differential survivorship of fossil classes",
    year = "1984",
    journal = "Journal of Anthropological Archaeology",
    url = "https://doi.org/10.1016/0278-4165(84)90004-7",
    doi = "10.1016/0278-4165(84)90004-7",
    openalex = "W1996561641",
    references = "doi101016030544038590072x, doi102113gsrocky8specialpaper11, doi102307281081, doi105962bhlpart22969, openalexw2167869521"
}

The trace fossil Chondrites, a highly branched burrow system of unknown endobenthic deposit feeders, occurs in all types of sediment, including those deposited under anaerobic conditions. In some cases, such as the Jurassic Posidonienschiefer Formation of Germany, Chondrites occurs in black, laminated, carbonaceous sediment that was deposited in chemically reducing conditions. In other cases, such as numerous oxic clastic and carbonate units throughout the geologic column, Chondrites typically represents the last trace fossil in a biotutbation sequence. This indicates that the burrow system was produced deep within the sediment in the anaerobic zone below the surficial oxidized zone that was characterized by freely circulating and oxidizing pore waters.

@article{doi101126science2244651872,
    author = "Bromley, Richard G. and Ekdale, A. A.",
    title = "Chondrites: A Trace Fossil Indicator of Anoxia in Sediments",
    year = "1984",
    journal = "Science",
    abstract = "The trace fossil Chondrites, a highly branched burrow system of unknown endobenthic deposit feeders, occurs in all types of sediment, including those deposited under anaerobic conditions. In some cases, such as the Jurassic Posidonienschiefer Formation of Germany, Chondrites occurs in black, laminated, carbonaceous sediment that was deposited in chemically reducing conditions. In other cases, such as numerous oxic clastic and carbonate units throughout the geologic column, Chondrites typically represents the last trace fossil in a biotutbation sequence. This indicates that the burrow system was produced deep within the sediment in the anaerobic zone below the surficial oxidized zone that was characterized by freely circulating and oxidizing pore waters.",
    url = "https://doi.org/10.1126/science.224.4651.872",
    doi = "10.1126/science.224.4651.872",
    openalex = "W2165117122",
    references = "doi1010079783642659232, doi1010160025322767900515"
}

Abstract Preservation of non-mineralized structures (including plants) and of articulated skeletons results from extraordinary hydrographic, sedimentational and early diagenetic conditions. The corresponding chief causative effects (stagnation, obrution and bacterial sealing) define a conceptual continuum into which individual occurrences may be mapped. A more pragmatic, typological classification of conservation deposits, using a standard questionnaire, reveals ecological replacements, as well as trends related to the evolution of the biosphere, through geological time.

@article{doi101098rstb19850134,
    author = "Seilacher, Adolf and Reif, Wolf‐Ernst and Westphal, Florian",
    title = "Sedimentological, ecological and temporal patterns of fossil Lagerstätten",
    year = "1985",
    journal = "Philosophical transactions of the Royal Society of London. Series B, Biological sciences",
    abstract = "Abstract Preservation of non-mineralized structures (including plants) and of articulated skeletons results from extraordinary hydrographic, sedimentational and early diagenetic conditions. The corresponding chief causative effects (stagnation, obrution and bacterial sealing) define a conceptual continuum into which individual occurrences may be mapped. A more pragmatic, typological classification of conservation deposits, using a standard questionnaire, reveals ecological replacements, as well as trends related to the evolution of the biosphere, through geological time.",
    url = "https://doi.org/10.1098/rstb.1985.0134",
    doi = "10.1098/rstb.1985.0134",
    openalex = "W2111944730",
    references = "doi101007978364269317510, doi1010079783642758294, doi101007bfb0009832, doi101111j136530911982tb00072x, doi101111j150239311985tb00688x, doi101126science2224620163, doi101126science2244651872, doi101127njgpa1591980324, doi101306ad4616f116f711d78645000102c1865d"
}

Four basic types of skeletal concentrations are modeled in terms of changes in sedimentation rate alone. The model categorizes fossil concentrations on the relatively objective basis of their bed contacts, and uses this criterion to infer directional shifts in net sedimentation. This radical simplification of accumulation histories, in which hardpart input is held constant, yields a surprisingly powerful model capable of predicting a broad spectrum of taphonomic and paleobiologic phenomena. Type I concentrations grade from less fossiliferous sediments and terminate in omission surfaces; if hardpart supply is held constant, they record a slowdown from positive to zero net sedimentation. Type II concentrations are the same as Type I but terminate in erosion surfaces (slowdown to negative net sedimentation), and Type III and IV concentrations are characterized by basal erosion or omission surfaces, respectively, grade upward into less fossiliferous sediments, and record increases in net sedimentation from negative or zero rates to positive rates. According to the model, samples collected from successive horizons within any of these shell beds will differ in the degree and type of post-mortem bias owing to differing histories of hardpart exposure at the depositional interface. Moreover, because rates of sediment accumulation govern the abundance of hardparts at the depositional interface and thus many of the physical characteristics of the benthic habitat, the dynamics of fossil accumulation have direct consequences for the structure of benthic communities (taphonomic feedback) and for ecologically controlled species morphometry. The model is highly robust to fluctuations in hardpart input, as judged by its ability to correctly infer modes of formation of concentrations in synthetic stratigraphic sections. In addition, field examples of Type I–IV concentrations show independent evidence of formation during intervals of reduced net sedimentation, and many exhibit trends in taphonomic and paleobiologic features expected from the postulated changes in net sedimentation. The model thus provides a testable working hypothesis for the accumulation of fossil material in a wide range of environments, and should be applicable to concentrations of any taxonomic composition, state of preservation, or geologic age. The power and robustness of this heuristic model in fact argue that fossil-rich and fossil-poor strata provide fundamentally different records of past conditions, and that sedimentation rather than hardpart input is the primary control on the nature of the fossil record.

@article{doi101017s0094837300002943,
    author = "Kidwell, Susan M.",
    title = "Models for fossil concentrations: paleobiologic implications",
    year = "1986",
    journal = "Paleobiology",
    abstract = "Four basic types of skeletal concentrations are modeled in terms of changes in sedimentation rate alone. The model categorizes fossil concentrations on the relatively objective basis of their bed contacts, and uses this criterion to infer directional shifts in net sedimentation. This radical simplification of accumulation histories, in which hardpart input is held constant, yields a surprisingly powerful model capable of predicting a broad spectrum of taphonomic and paleobiologic phenomena. Type I concentrations grade from less fossiliferous sediments and terminate in omission surfaces; if hardpart supply is held constant, they record a slowdown from positive to zero net sedimentation. Type II concentrations are the same as Type I but terminate in erosion surfaces (slowdown to negative net sedimentation), and Type III and IV concentrations are characterized by basal erosion or omission surfaces, respectively, grade upward into less fossiliferous sediments, and record increases in net sedimentation from negative or zero rates to positive rates. According to the model, samples collected from successive horizons within any of these shell beds will differ in the degree and type of post-mortem bias owing to differing histories of hardpart exposure at the depositional interface. Moreover, because rates of sediment accumulation govern the abundance of hardparts at the depositional interface and thus many of the physical characteristics of the benthic habitat, the dynamics of fossil accumulation have direct consequences for the structure of benthic communities (taphonomic feedback) and for ecologically controlled species morphometry. The model is highly robust to fluctuations in hardpart input, as judged by its ability to correctly infer modes of formation of concentrations in synthetic stratigraphic sections. In addition, field examples of Type I–IV concentrations show independent evidence of formation during intervals of reduced net sedimentation, and many exhibit trends in taphonomic and paleobiologic features expected from the postulated changes in net sedimentation. The model thus provides a testable working hypothesis for the accumulation of fossil material in a wide range of environments, and should be applicable to concentrations of any taxonomic composition, state of preservation, or geologic age. The power and robustness of this heuristic model in fact argue that fossil-rich and fossil-poor strata provide fundamentally different records of past conditions, and that sedimentation rather than hardpart input is the primary control on the nature of the fossil record.",
    url = "https://doi.org/10.1017/s0094837300002943",
    doi = "10.1017/s0094837300002943",
    openalex = "W1810485278",
    references = "doi101007978364265923211, openalexw574363047"
}

@article{doi1023073514686,
    author = "Brett, Carlton E. and Baird, Gordon C.",
    title = "Comparative Taphonomy: A Key to Paleoenvironmental Interpretation Based on Fossil Preservation",
    year = "1986",
    journal = "Palaios",
    url = "https://doi.org/10.2307/3514686",
    doi = "10.2307/3514686",
    openalex = "W1974521733",
    references = "doi102110pec8535"
}

Densely fossiliferous deposits are receiving increasing attention for their yield of paleobiologic data and their usefulness in sedimentology and stratigraphy. This trend has created a pressing need for standardized descriptive terminology and a genetic classification based on a coherent conceptual framework. The descriptive procedure outlined here for skeletal concentrations stresses four features -taxonomic composition, bioclastic fabric, geometry, and internal structure-that can be described readily in the field by nonspecialists. The genetic classification scheme is based on three end members, representing biologic, sedimentologic, and diagenetic factors in skeletal concentration. Concentrations created through the simultaneous or sequential action of two or more factors are classified as mixed types. As a conceptual framework for comparative biostratinomic analysis, the broad categories of this ternary classification scheme should facilitate recognition of large-scale temporal and spatial patterns in skeletal accumulation. The usefulness of this approach is suggested by the good agreement between biostratinomic patterns observed in ancient onshore-offshore facies tracts and those predicted across paleobathymetric transects based on modern processes of skeletal concentration.

@article{doi1023073514687,
    author = "Kidwell, Susan M. and Fürsich, Franz T. and Aigner, Thomas",
    title = "Conceptual Framework for the Analysis and Classification of Fossil Concentrations",
    year = "1986",
    journal = "Palaios",
    abstract = "Densely fossiliferous deposits are receiving increasing attention for their yield of paleobiologic data and their usefulness in sedimentology and stratigraphy. This trend has created a pressing need for standardized descriptive terminology and a genetic classification based on a coherent conceptual framework. The descriptive procedure outlined here for skeletal concentrations stresses four features -taxonomic composition, bioclastic fabric, geometry, and internal structure-that can be described readily in the field by nonspecialists. The genetic classification scheme is based on three end members, representing biologic, sedimentologic, and diagenetic factors in skeletal concentration. Concentrations created through the simultaneous or sequential action of two or more factors are classified as mixed types. As a conceptual framework for comparative biostratinomic analysis, the broad categories of this ternary classification scheme should facilitate recognition of large-scale temporal and spatial patterns in skeletal accumulation. The usefulness of this approach is suggested by the good agreement between biostratinomic patterns observed in ancient onshore-offshore facies tracts and those predicted across paleobathymetric transects based on modern processes of skeletal concentration.",
    url = "https://doi.org/10.2307/3514687",
    doi = "10.2307/3514687",
    openalex = "W2021838482",
    references = "doi1010079783662010204, doi10108011035898709454746, doi101086628652, doi101098rstb19850134, doi101111j150239311970tb00830x, doi101130001676061964751197fciptr20co2, doi101130001676061968791315tailif20co2, doi101306212f77662b2411d78648000102c1865d, doi1023072258940, openalexw1533729466"
}

@article{doi1010160031018287900642,
    author = "Krantz, David E. and Williams, Douglas F. and Jones, D. S.",
    title = "Ecological and paleoenvironmental information using stable isotope profiles from living and fossil molluscs",
    year = "1987",
    journal = "Palaeogeography Palaeoclimatology Palaeoecology",
    url = "https://doi.org/10.1016/0031-0182(87)90064-2",
    doi = "10.1016/0031-0182(87)90064-2",
    openalex = "W2077924960",
    references = "doi1010160016703765901183"
}

Chapter 1 has outlined the extent to which many endemic Mascarene Island birds have become extinct, probably during the last 300 years since man arrived on the islands. Thirty extinct species are recognised today (Cowles in press), but of these only five are known from skins preserved in museums and institutions throughout the world. Four of these species, the Mauritian Blue Pigeon Alectroenas nitidissima, the Mascarene Parrot from Réunion Mascarinus mascarinus, the Rodrigues Parakeet Psittacula exsul and the contentious Leguat's Starling Necropsar (Orphanopsar) leguati of unknown locality, are represented by a total of only eight skins. The Reunion Crested Starling Fregilupus varius was better represented by 24-25 skins, all documented by Hachisuka (1953), although fewer survive today (Chapter 1). The remaining 25 extinct species are known only from fossil bones discovered in caverns and deposits on the three islands. In number these range to well over 200 elements for the better known Solitaire of Rodrigues Pezophaps solitaria and perhaps the Mauritius Dodo Raphus cucullatus, but the remaining species are unfortunately known from very few bones or bone fragments.

@incollection{doi101017cbo9780511735769004,
    author = "Cowles, G. S.",
    title = "The fossil record",
    year = "1987",
    booktitle = "Cambridge University Press eBooks",
    abstract = "Chapter 1 has outlined the extent to which many endemic Mascarene Island birds have become extinct, probably during the last 300 years since man arrived on the islands. Thirty extinct species are recognised today (Cowles in press), but of these only five are known from skins preserved in museums and institutions throughout the world. Four of these species, the Mauritian Blue Pigeon Alectroenas nitidissima, the Mascarene Parrot from Réunion Mascarinus mascarinus, the Rodrigues Parakeet Psittacula exsul and the contentious Leguat's Starling Necropsar (Orphanopsar) leguati of unknown locality, are represented by a total of only eight skins. The Reunion Crested Starling Fregilupus varius was better represented by 24-25 skins, all documented by Hachisuka (1953), although fewer survive today (Chapter 1). The remaining 25 extinct species are known only from fossil bones discovered in caverns and deposits on the three islands. In number these range to well over 200 elements for the better known Solitaire of Rodrigues Pezophaps solitaria and perhaps the Mauritius Dodo Raphus cucullatus, but the remaining species are unfortunately known from very few bones or bone fragments.",
    url = "https://doi.org/10.1017/cbo9780511735769.004",
    doi = "10.1017/cbo9780511735769.004",
    openalex = "W2496925084"
}

Actualistic experiments have quantified rate of anaerobic decay and associated mineralization around proteinaceous macro-organisms. Carcasses of the polychaete worm Nereis and the eumalacostracans Nephrops and Palaemon were buried in airtight glass jars filled with sediment and water from marine, brackish, and lacustrine environments. Over a period of 25 weeks the contents were examined to determine the state of decay and were chemically analyzed to monitor early diagenetic mineralization (two methods for such analysis are reviewed). Decay processes were active in the experimental conditions despite anoxia and had virtually destroyed the carcasses within 25 weeks. However, decay-rate in the sulfate-reducing marine system was greater than in the methanogenic freshwater environments. Petrological and geochemical analyses of the organic remains identified discrete layers of authigenic iron monosulfide (a pyrite precursor) on the surface of the decaying Nephrops cuticle within weeks of initiating the experiment. Chemical analysis of decomposing flesh showed a marked increase in pore-water calcium content with time. The results clearly show that anoxia is ineffective as a long-term conservation medium in the preservation of soft-bodied fossils. However, decay-induced mineralization can be very rapid so that even a slight reduction in decay rate can lead to improved levels of fossil preservation. Traditionally, stagnation and rapid burial are considered to be the main prerequisites for the preservation of soft-bodied fossils and the formation of Konservat-Lagerstätten. Clearly these factors are only important in that they promote early diagenetic mineralization. This is the only way to halt information loss through decay.

@article{allison1988the,
    author = "Allison, Peter A.",
    title = "The role of anoxia in the decay and mineralization of proteinaceous macro-fossils",
    year = "1988",
    journal = "Paleobiology",
    abstract = "Actualistic experiments have quantified rate of anaerobic decay and associated mineralization around proteinaceous macro-organisms. Carcasses of the polychaete worm Nereis and the eumalacostracans Nephrops and Palaemon were buried in airtight glass jars filled with sediment and water from marine, brackish, and lacustrine environments. Over a period of 25 weeks the contents were examined to determine the state of decay and were chemically analyzed to monitor early diagenetic mineralization (two methods for such analysis are reviewed). Decay processes were active in the experimental conditions despite anoxia and had virtually destroyed the carcasses within 25 weeks. However, decay-rate in the sulfate-reducing marine system was greater than in the methanogenic freshwater environments. Petrological and geochemical analyses of the organic remains identified discrete layers of authigenic iron monosulfide (a pyrite precursor) on the surface of the decaying Nephrops cuticle within weeks of initiating the experiment. Chemical analysis of decomposing flesh showed a marked increase in pore-water calcium content with time. The results clearly show that anoxia is ineffective as a long-term conservation medium in the preservation of soft-bodied fossils. However, decay-induced mineralization can be very rapid so that even a slight reduction in decay rate can lead to improved levels of fossil preservation. Traditionally, stagnation and rapid burial are considered to be the main prerequisites for the preservation of soft-bodied fossils and the formation of Konservat-Lagerstätten. Clearly these factors are only important in that they promote early diagenetic mineralization. This is the only way to halt information loss through decay.",
    url = "https://doi.org/10.1017/s009483730001188x",
    doi = "10.1017/s009483730001188x",
    number = "2",
    openalex = "W2487864689",
    pages = "139-154",
    volume = "14",
    references = "doi1010160016703784900899, doi101017s0094837300005996, doi101017s009483730000676x, doi101098rstb19850134, doi101130001676061968791315tailif20co2, doi1015159780691209401, doi102475ajs26811, doi104319lo19842920236, doi105962bhlpart22969, doi105962bhltitle7199, openalexw2754161204, openalexw599354073, schopf1978fossilization"
}

@misc{allison1988the1,
    author = "Allison, P. A",
    title = "The role of anoxia in the decay and mineralization of proteinaceous macro-fossils",
    year = "1988",
    howpublished = "Paleobiology, v. 14, p. 139-154",
    note = "talkorigins\_source = {true}; raw\_reference = {Allison, P. A., 1988, The role of anoxia in the decay and mineralization of proteinaceous macro-fossils: Paleobiology, v. 14, p. 139-154.}"
}

Laboratory experiments on regular echinoids indicate that low water temperatures retard organic decomposition far more effectively than anoxia, and that the primary role of anoxia in the preservation of articulated multi-element calcareous skeletons may be in excluding scavenging organisms. When tumbled at 20 rpm, specimens that were first allowed to decay for two days in warm seawater (30°C) disintegrated more than six times faster than specimens treated at room temperature (23°C) and more than an order of magnitude faster than specimens treated in cool water (11°C). In contrast, the effects of aerobic versus anerobic decay on disintegration rates were insignificant. The longer the period that specimens were allowed to decay before tumbling, the greater the rate at which specimens disintegrated, until a threshold time that appears to mark the decomposition of collagenous ligaments. This required a few days at 30°C, about two weeks at 23°C, and more than 4 weeks at 11°C for Strongylocentrotus. Up until this threshold, coronas disintegrate by a combination of cross-plate fractures and separation along plate sutures; cross-plate fractures thus can be taphonomic in origin and are not necessarily related to predation. Specimens decayed for longer-than-threshold periods of time disintegrate virtually instantaneously upon tumbling by sutural separation only. Undisturbed coronas can remain intact for months, sufficient time for epibiont occupation. Rates of disintegration were documented semi-quantitatively by recognizing seven stages of test disarticulation, and quantitatively by tensometer measures of test strength and toughness. The effects of temperature and oxygen on decay and the existence of a decay threshold in disintegration should apply at least in a qualitative sense to many other animals whose skeletons consist of multiple, collagen-bound elements. Regular echinoids should still be perceived as taphonomically fragile organisms, but our results suggest the potential for latitudinal as well as bathymetric gradients in the preservation of fossil echinoid faunas. Echinoid preservation under any given set of conditions should also be a function of taxonomic differences in test construction (particularly stereom interlocking along plate sutures) as suggested by previous workers, although our experiments indicate that these effects should only be significant among post-threshold specimens. A survey of regular echinoids from Upper Cretaceous white chalk facies of Britain substantiates the basic experimental patterns, yielding examples of all disarticulation stages and significant taxonomic differences in quality of preservation. A diverse array of borers and encrusters on fossil coronas also corroborates the post-mortem persistence of some tests on mid-latitude seafloors.

@article{doi101017s0094837300009982,
    author = "Kidwell, Susan M. and Baumiller, Tomasz K.",
    title = "Experimental disintegration of regular echinoids: roles of temperature, oxygen, and decay thresholds",
    year = "1990",
    journal = "Paleobiology",
    abstract = "Laboratory experiments on regular echinoids indicate that low water temperatures retard organic decomposition far more effectively than anoxia, and that the primary role of anoxia in the preservation of articulated multi-element calcareous skeletons may be in excluding scavenging organisms. When tumbled at 20 rpm, specimens that were first allowed to decay for two days in warm seawater (30°C) disintegrated more than six times faster than specimens treated at room temperature (23°C) and more than an order of magnitude faster than specimens treated in cool water (11°C). In contrast, the effects of aerobic versus anerobic decay on disintegration rates were insignificant. The longer the period that specimens were allowed to decay before tumbling, the greater the rate at which specimens disintegrated, until a threshold time that appears to mark the decomposition of collagenous ligaments. This required a few days at 30°C, about two weeks at 23°C, and more than 4 weeks at 11°C for Strongylocentrotus. Up until this threshold, coronas disintegrate by a combination of cross-plate fractures and separation along plate sutures; cross-plate fractures thus can be taphonomic in origin and are not necessarily related to predation. Specimens decayed for longer-than-threshold periods of time disintegrate virtually instantaneously upon tumbling by sutural separation only. Undisturbed coronas can remain intact for months, sufficient time for epibiont occupation. Rates of disintegration were documented semi-quantitatively by recognizing seven stages of test disarticulation, and quantitatively by tensometer measures of test strength and toughness. The effects of temperature and oxygen on decay and the existence of a decay threshold in disintegration should apply at least in a qualitative sense to many other animals whose skeletons consist of multiple, collagen-bound elements. Regular echinoids should still be perceived as taphonomically fragile organisms, but our results suggest the potential for latitudinal as well as bathymetric gradients in the preservation of fossil echinoid faunas. Echinoid preservation under any given set of conditions should also be a function of taxonomic differences in test construction (particularly stereom interlocking along plate sutures) as suggested by previous workers, although our experiments indicate that these effects should only be significant among post-threshold specimens. A survey of regular echinoids from Upper Cretaceous white chalk facies of Britain substantiates the basic experimental patterns, yielding examples of all disarticulation stages and significant taxonomic differences in quality of preservation. A diverse array of borers and encrusters on fossil coronas also corroborates the post-mortem persistence of some tests on mid-latitude seafloors.",
    url = "https://doi.org/10.1017/s0094837300009982",
    doi = "10.1017/s0094837300009982",
    openalex = "W2493502125",
    references = "doi101017s0094837300005248"
}

@incollection{doi10100797814899503457,
    author = "Canfield, Donald E. and Raiswell, R.",
    title = "Pyrite Formation and Fossil Preservation",
    year = "1991",
    booktitle = "Topics in geobiology",
    url = "https://doi.org/10.1007/978-1-4899-5034-5\_7",
    doi = "10.1007/978-1-4899-5034-5\_7",
    openalex = "W2483523994",
    references = "doi101017s0094837300012082, doi1023073514686"
}

@article{doi105860choice300309,
    author = "Allison, PA and Briggs, DEG",
    title = "Taphonomy: releasing the data locked in the fossil record",
    year = "1992",
    journal = "Choice Reviews Online",
    url = "https://doi.org/10.5860/choice.30-0309",
    doi = "10.5860/choice.30-0309",
    openalex = "W1587340106"
}

@incollection{doi101007978940173622048,
    author = "Flower, Roger J.",
    title = "Diatom preservation: experiments and observations on dissolution and breakage in modern and fossil material",
    year = "1993",
    url = "https://doi.org/10.1007/978-94-017-3622-0\_48",
    doi = "10.1007/978-94-017-3622-0\_48",
    openalex = "W2062608412",
    references = "doi101017s009483730001143x"
}

A series of experiments was carried out to investigate the nature and controls (oxygen, microbial populations, agitation) on the degradation of soft tissues. Decay was monitored in terms of morphological change, weight loss, and change in chemical composition in the polychaete Nereis virens. Polychaetes include a range of tissue types of differing chemical composition and preservation potential: muscle, cuticle, setae, and jaws. Regardless of conditions, all the muscle had broken down and fluid loss through the ruptured cuticle had reduced the carcass to two dimensions within 8 days at 20°C. In most cases some cuticle, in addition to the jaws and setae, remained after 30 days. Where oxygen was completely eliminated, the rate of decay of the more volatile issues was significantly reduced. The degree of both osmotic uptake of water by the carcass and changes in water pH differed depending on whether the system was open or closed to oxygen diffusion. Autolytic and chemical processes are not sufficient to fully degrade the carcass in the absence of bacteria. Where internal bacteria are present, the presence or absence of water column bacteria made little difference to decay rate. Initial degradation (in the first 3 days) affects mainly the lipid fraction and the collagen of the cuticle. Later decay reduces the nonsoluble protein and increases the relative proportion of refractory structural components (tanned chitin and collagen) to more than 95% by day 30. Thus, only the sclerotized tissues are likely to survive beyond 30 days in the absence of early diagenetic mineralization. The sequence of degradation predicted from the relative decay resistance of macromolecules in the sedimentary record (protein → carbohydrate → lipid) is not, therefore, a consistent indicator of the preservation potential of structural tissues which incorporate them. The experiments reveal five stages in the decay of polychaete carcasses; whole/shriveled, flaccid, unsupported gut, cuticle sac, jaws and setae. All are represented in the fossil record. This allows an estimation of how far decay proceeded before it was halted by the fossilization process. The most complete preservations occur in the Cambrian where the Burgess Shale preserves evidence of muscle tissues. Traces of the gut and cuticle are more widely preserved, as at Mazon Creek, Grès à Voltzia, Solnhofen, and Hakel. Preservation varies within Konservat-Lagerstätten. The most common whole body preservation includes only the more recalcitrant tissues, jaws (where present) and setae, with an impression of the body outline. The stage of decay can be used as a taphonomic threshold, to provide an indication of how significantly the diversity of an exceptionally preserved biota is likely to have been reduced by taphonomic loss.

@article{doi101017s0094837300012343,
    author = "Briggs, Derek E. G. and Kear, Amanda J.",
    title = "Decay and preservation of polychaetes: taphonomic thresholds in soft-bodied organisms",
    year = "1993",
    journal = "Paleobiology",
    abstract = "A series of experiments was carried out to investigate the nature and controls (oxygen, microbial populations, agitation) on the degradation of soft tissues. Decay was monitored in terms of morphological change, weight loss, and change in chemical composition in the polychaete Nereis virens. Polychaetes include a range of tissue types of differing chemical composition and preservation potential: muscle, cuticle, setae, and jaws. Regardless of conditions, all the muscle had broken down and fluid loss through the ruptured cuticle had reduced the carcass to two dimensions within 8 days at 20°C. In most cases some cuticle, in addition to the jaws and setae, remained after 30 days. Where oxygen was completely eliminated, the rate of decay of the more volatile issues was significantly reduced. The degree of both osmotic uptake of water by the carcass and changes in water pH differed depending on whether the system was open or closed to oxygen diffusion. Autolytic and chemical processes are not sufficient to fully degrade the carcass in the absence of bacteria. Where internal bacteria are present, the presence or absence of water column bacteria made little difference to decay rate. Initial degradation (in the first 3 days) affects mainly the lipid fraction and the collagen of the cuticle. Later decay reduces the nonsoluble protein and increases the relative proportion of refractory structural components (tanned chitin and collagen) to more than 95\% by day 30. Thus, only the sclerotized tissues are likely to survive beyond 30 days in the absence of early diagenetic mineralization. The sequence of degradation predicted from the relative decay resistance of macromolecules in the sedimentary record (protein → carbohydrate → lipid) is not, therefore, a consistent indicator of the preservation potential of structural tissues which incorporate them. The experiments reveal five stages in the decay of polychaete carcasses; whole/shriveled, flaccid, unsupported gut, cuticle sac, jaws and setae. All are represented in the fossil record. This allows an estimation of how far decay proceeded before it was halted by the fossilization process. The most complete preservations occur in the Cambrian where the Burgess Shale preserves evidence of muscle tissues. Traces of the gut and cuticle are more widely preserved, as at Mazon Creek, Grès à Voltzia, Solnhofen, and Hakel. Preservation varies within Konservat-Lagerstätten. The most common whole body preservation includes only the more recalcitrant tissues, jaws (where present) and setae, with an impression of the body outline. The stage of decay can be used as a taphonomic threshold, to provide an indication of how significantly the diversity of an exceptionally preserved biota is likely to have been reduced by taphonomic loss.",
    url = "https://doi.org/10.1017/s0094837300012343",
    doi = "10.1017/s0094837300012343",
    openalex = "W1959245684",
    references = "doi101016003101829390065q, doi101038345802a0, doi10108003115517908565437, doi101144gsjgs14940631, doi105860choice295135"
}

Since their inception in 1978, the annual short courses sponsored by the Paleontological Society have aimed to broaden and to enhance the professional education of paleontologists, including students new to the field. The 1993 short course continues in that tradition, but differs from many previous courses in focussing not on a taxonomic group but on a broader aspect of the fossil record, namely the time resolution of fossil assemblages. This seemed an especially good topic for a short course because questions of absolute and relative time – how old? how fast? how synchronously? – pervade paleontology and historical geology in general.

@article{doi101017s2475263000001021,
    author = "Kidwell, Susan M. and Behrensmeyer, Anna K.",
    title = "Taphonomic approaches to time resolution in fossil assemblages: Introduction",
    year = "1993",
    journal = "Short Courses in Paleontology",
    abstract = "Since their inception in 1978, the annual short courses sponsored by the Paleontological Society have aimed to broaden and to enhance the professional education of paleontologists, including students new to the field. The 1993 short course continues in that tradition, but differs from many previous courses in focussing not on a taxonomic group but on a broader aspect of the fossil record, namely the time resolution of fossil assemblages. This seemed an especially good topic for a short course because questions of absolute and relative time – how old? how fast? how synchronously? – pervade paleontology and historical geology in general.",
    url = "https://doi.org/10.1017/s2475263000001021",
    doi = "10.1017/s2475263000001021",
    openalex = "W3194457679",
    references = "doi1010079781489950345, doi101017s0094837300004917, doi101017s009483730000974x, doi101038293435a0, doi101098rstb19850134, doi101130001676061960711075mamfao20co2, doi101144gsjgs15010169, doi1023073514686, doi1023073514978, doi105860choice295135, doi105860choice300309"
}

Some of the most remarkable fossils preserve cellular details of soft tissues. In many of these, the tissues have been replaced by calcium phosphate. This process has been assumed to require elevated concentrations of phosphate in sediment pore waters. In decay experiments modern shrimps became partially mineralized in amorphous calcium phosphate, preserving cellular details of muscle tissue, particularly in a system closed to oxygen. The source for the formation of calcium phosphate was the shrimp itself. Mineralization, which was accompanied by a drop in pH, commenced within 2 weeks and increased in extent for at least 4 to 8 weeks. This mechanism halts the normal loss of detail of soft-tissue morphology before fossilization. Similar closed conditions would prevail where organisms are rapidly overgrown by microbial mats.

@article{doi101126science25951001439,
    author = "Briggs, Derek E. G. and Kear, Amanda J.",
    title = "Fossilization of Soft Tissue in the Laboratory",
    year = "1993",
    journal = "Science",
    abstract = "Some of the most remarkable fossils preserve cellular details of soft tissues. In many of these, the tissues have been replaced by calcium phosphate. This process has been assumed to require elevated concentrations of phosphate in sediment pore waters. In decay experiments modern shrimps became partially mineralized in amorphous calcium phosphate, preserving cellular details of muscle tissue, particularly in a system closed to oxygen. The source for the formation of calcium phosphate was the shrimp itself. Mineralization, which was accompanied by a drop in pH, commenced within 2 weeks and increased in extent for at least 4 to 8 weeks. This mechanism halts the normal loss of detail of soft-tissue morphology before fossilization. Similar closed conditions would prevail where organisms are rapidly overgrown by microbial mats.",
    url = "https://doi.org/10.1126/science.259.5100.1439",
    doi = "10.1126/science.259.5100.1439",
    openalex = "W2052326945",
    references = "allison1988the, doi1010160025322788900928, doi101017s009483730001188x, doi101017s0094837300012343, doi101038340138a0, doi101038346171a0, doi101099002212871351175, doi101126science1593811195, doi101306d42676db2b2611d78648000102c1865d, doi10310910520298309066811, openalexw114633828"
}

Introduction. Basal Groups. Monera (bacteria blue-green algae). Fungi.Algae. Animals: Invertebrates. Protozoa. Porifera. Coelenterata. Mollusca: Amphineura and Monoplacophora. Mollusca: Gastropoda. Mollusca: Cephalopoda (Nautiloidea). Mollusca: Cephalopoda (Pre-Jurassic Ammonoidea). Mollusca: Cephalopoda (Ammonoidea: Phylloceratina, Lytoceratina, Ammonitina, Ancyloceratina). Mollusca: Cephalopoda (Coleoidea). Mollusca: Rostroconchia, Scaphopoda, and Bivalvia. Mollusca: incertae sedis. Annelida. Arthropoda (Trilobita). Arthropoda (Aglaspidida, Chelicerata, Pycnogonida). Arthropoda (Crustacea, excluding Ostracoda). Arthropoda (Crustacea: Ostracoda). Arthropoda (Euthycarcinoidea and Myriapoda). Arthropoda (Hexapoda: Insecta). Brachiopoda. Phoronida. Bryozoa. Echinodermata. Basal deuterostomes (chaetognaths, hemichordates, calcichordates, cephalochordates, and tunicates). Graptolithina. Problematica. Miscellania. Animals: Vertebrates. Conodonta. Agnatha. Placodermi. Acanthodii. Chondrichthyes. Osteichthyes: basal actinopterygians. Osteichthyes: Teleostei. Osteichthyes: Sarcopterygii. Amphibian-grade Tetrapoda. Reptilia. Aves. Mammalia. Plants. Bryophyta. Pteridophyta. Gymnospermophyta. Magnoliophyta (Angiospermae). Index.

@book{openalexw1599677799,
    author = "Benton, Michael J.",
    title = "The fossil record 2",
    year = "1993",
    abstract = "Introduction. Basal Groups. Monera (bacteria blue-green algae). Fungi.Algae. Animals: Invertebrates. Protozoa. Porifera. Coelenterata. Mollusca: Amphineura and Monoplacophora. Mollusca: Gastropoda. Mollusca: Cephalopoda (Nautiloidea). Mollusca: Cephalopoda (Pre-Jurassic Ammonoidea). Mollusca: Cephalopoda (Ammonoidea: Phylloceratina, Lytoceratina, Ammonitina, Ancyloceratina). Mollusca: Cephalopoda (Coleoidea). Mollusca: Rostroconchia, Scaphopoda, and Bivalvia. Mollusca: incertae sedis. Annelida. Arthropoda (Trilobita). Arthropoda (Aglaspidida, Chelicerata, Pycnogonida). Arthropoda (Crustacea, excluding Ostracoda). Arthropoda (Crustacea: Ostracoda). Arthropoda (Euthycarcinoidea and Myriapoda). Arthropoda (Hexapoda: Insecta). Brachiopoda. Phoronida. Bryozoa. Echinodermata. Basal deuterostomes (chaetognaths, hemichordates, calcichordates, cephalochordates, and tunicates). Graptolithina. Problematica. Miscellania. Animals: Vertebrates. Conodonta. Agnatha. Placodermi. Acanthodii. Chondrichthyes. Osteichthyes: basal actinopterygians. Osteichthyes: Teleostei. Osteichthyes: Sarcopterygii. Amphibian-grade Tetrapoda. Reptilia. Aves. Mammalia. Plants. Bryophyta. Pteridophyta. Gymnospermophyta. Magnoliophyta (Angiospermae). Index.",
    openalex = "W1599677799"
}

@book{doi1010029781444313918,
    author = "Smith, Andrew B.",
    title = "Systematics and the Fossil Record",
    year = "1994",
    url = "https://doi.org/10.1002/9781444313918",
    doi = "10.1002/9781444313918",
    openalex = "W4244814634"
}

Ediacaran fossils are taphonomically similar to impressions of fossil plants common in quartz sandstones, and the relief of the fossils suggests that they were as resistant to compaction during burial as some kinds of Pennsylvanian tree trunks. Fossils of jellyfish are known from siderite nodules and fine-grained limestone, and even in these compaction-resistant media were more compressed during burial than were the Vendobionta. Vendobionta were constructed of materials that responded to burial compaction in a way intermediate between conifer and lycopsid logs. This comparative taphonomic study thus falsifies the concept of Vendobionta as thin soft-bodied creatures such as worms and jellyfish. Lichens, with their structural chitin, present a viable model for the observed preservational style of Vendobionta, as well as for a variety of other features that now can be reassessed from this new perspective. The diversity of Ediacaran body plans can be compared with the variety of form in fungi, algae, and lichens. The large size (ca. 1 m) of some Ediacaran fossils is reasonable for sessile photosynthetic symbioses, and much bigger than associated burrows of metazoans not preserved. Microscopic tubular structures and darkly pigmented cells in permineralized late Precambrian fossils from Namibia and China are also compatible with interpretation as lichens. The presumed marine habitat of Ediacaran fossils is not crucial to interpretation as lichens, because fungi and lichens live in the sea as well as on land.

@article{doi101017s0094837300012975,
    author = "Retallack, Gregory J.",
    title = "Were the Ediacaran fossils lichens?",
    year = "1994",
    journal = "Paleobiology",
    abstract = "Ediacaran fossils are taphonomically similar to impressions of fossil plants common in quartz sandstones, and the relief of the fossils suggests that they were as resistant to compaction during burial as some kinds of Pennsylvanian tree trunks. Fossils of jellyfish are known from siderite nodules and fine-grained limestone, and even in these compaction-resistant media were more compressed during burial than were the Vendobionta. Vendobionta were constructed of materials that responded to burial compaction in a way intermediate between conifer and lycopsid logs. This comparative taphonomic study thus falsifies the concept of Vendobionta as thin soft-bodied creatures such as worms and jellyfish. Lichens, with their structural chitin, present a viable model for the observed preservational style of Vendobionta, as well as for a variety of other features that now can be reassessed from this new perspective. The diversity of Ediacaran body plans can be compared with the variety of form in fungi, algae, and lichens. The large size (ca. 1 m) of some Ediacaran fossils is reasonable for sessile photosynthetic symbioses, and much bigger than associated burrows of metazoans not preserved. Microscopic tubular structures and darkly pigmented cells in permineralized late Precambrian fossils from Namibia and China are also compatible with interpretation as lichens. The presumed marine habitat of Ediacaran fossils is not crucial to interpretation as lichens, because fungi and lichens live in the sea as well as on land.",
    url = "https://doi.org/10.1017/s0094837300012975",
    doi = "10.1017/s0094837300012975",
    openalex = "W2115571905",
    references = "doi1010160034666775900056, doi101017s0094837300008022, doi101144pygs313211, openalexw2603635224"
}

Authigenic minerals play an important role in the preservation of most soft-bodied fossils. The greatest detail is preserved in apatite (calcium phosphate) but its precipitation is usually inhibited by the high concentrations of HCO 3 - in aqueous settings. Nonetheless, investigations of soft-bodied biotas have revealed very early authigenic calcite crystal bundles in close association with phosphatized soft-tissues. This demonstrates that the geochemical controls on soft-tissue mineralization are dynamic and act on a very local scale. Direct comparisons with experimental results permit the conditions of fossilization to be inferred.

@article{briggs1996the,
    author = "BRIGGS, DEREK E. G. and WILBY, PHILIP R.",
    title = "The role of the calcium carbonate-calcium phosphate switch in the mineralization of soft-bodied fossils",
    year = "1996",
    journal = "Journal of the Geological Society",
    abstract = "Authigenic minerals play an important role in the preservation of most soft-bodied fossils. The greatest detail is preserved in apatite (calcium phosphate) but its precipitation is usually inhibited by the high concentrations of HCO 3 - in aqueous settings. Nonetheless, investigations of soft-bodied biotas have revealed very early authigenic calcite crystal bundles in close association with phosphatized soft-tissues. This demonstrates that the geochemical controls on soft-tissue mineralization are dynamic and act on a very local scale. Direct comparisons with experimental results permit the conditions of fossilization to be inferred.",
    url = "https://doi.org/10.1144/gsjgs.153.5.0665",
    doi = "10.1144/gsjgs.153.5.0665",
    number = "5",
    openalex = "W2053600018",
    pages = "665-668",
    volume = "153",
    references = "briggs1994decay, doi101016001670379090374t, doi1010160016703793903816, doi101017s0094837300012082, doi101038269209a0, doi101098rstb19850134, doi101126science25951001439, doi1011300091761319960240787rommit23co2, doi101306d42676db2b2611d78648000102c1865d, doi1023073514973"
}

The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy. Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased.(3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of fossiliferous rock more than failure of species to enter the fossil record in the first place.

@article{doi101017s0094837300016134,
    author = "Foote, Mike and Raup, David M.",
    title = "Fossil preservation and the stratigraphic ranges of taxa",
    year = "1996",
    journal = "Paleobiology",
    abstract = "The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy. Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased.(3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60\% to 90\%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of fossiliferous rock more than failure of species to enter the fossil record in the first place.",
    url = "https://doi.org/10.1017/s0094837300016134",
    doi = "10.1017/s0094837300016134",
    openalex = "W1936619567",
    references = "doi1010029781444313918, doi101007bf00897326, doi101017s0094837300004929, doi101017s0094837300005996, doi101017s009483730001263x, doi10106314822961, doi101126science11539488, doi1023072405671, doi107312simp93764, openalexw1522518756, openalexw2145250129, openalexw3135630760, schopf1978fossilization"
}

Three homogeneous models of species origination and extinction are used to assess the probability that ancestor-descendant pairs are preserved in the fossil record. In the model of cladogenetic budding, a species can persist after it branches and can therefore have multiple direct descendants. In the bifurcation model, a species branches to give rise to two distinct direct descendants, itself terminating in the process. In the model of phyletic transformation, a species gives rise to a single direct descendant without branching, itself terminating in the process. Assuming homogeneous preservation, even under pessimistic assumptions regarding the completeness of the fossil record, the probability of finding fossil ancestor-descendant pairs is not negligible. Even if all species of Phanerozoic marine invertebrates in the paleontologically important taxa had the same probability of preservation, on the order of 1%-10% or more of the known fossil species would be directly ancestral to other known fossil species. However, this is likely to be an underestimate, since the probability of finding ancestor-descendant pairs is enhanced by taxonomic, temporal, and spatial heterogeneities in preservation probability. Moreover, indirect genealogical relationships substantially increase the probability of finding ancestor-descendant pairs. The model of budding, the only one in which an ancestor can persist after a branching event, predicts that half or more of extant species have ancestors that are also extant. Thus, the question of how to recognize ancestor-descendant pairs must be carefully considered.

@article{doi101017s0094837300016146,
    author = "Foote, Mike",
    title = "On the probability of ancestors in the fossil record",
    year = "1996",
    journal = "Paleobiology",
    abstract = "Three homogeneous models of species origination and extinction are used to assess the probability that ancestor-descendant pairs are preserved in the fossil record. In the model of cladogenetic budding, a species can persist after it branches and can therefore have multiple direct descendants. In the bifurcation model, a species branches to give rise to two distinct direct descendants, itself terminating in the process. In the model of phyletic transformation, a species gives rise to a single direct descendant without branching, itself terminating in the process. Assuming homogeneous preservation, even under pessimistic assumptions regarding the completeness of the fossil record, the probability of finding fossil ancestor-descendant pairs is not negligible. Even if all species of Phanerozoic marine invertebrates in the paleontologically important taxa had the same probability of preservation, on the order of 1\%-10\% or more of the known fossil species would be directly ancestral to other known fossil species. However, this is likely to be an underestimate, since the probability of finding ancestor-descendant pairs is enhanced by taxonomic, temporal, and spatial heterogeneities in preservation probability. Moreover, indirect genealogical relationships substantially increase the probability of finding ancestor-descendant pairs. The model of budding, the only one in which an ancestor can persist after a branching event, predicts that half or more of extant species have ancestors that are also extant. Thus, the question of how to recognize ancestor-descendant pairs must be carefully considered.",
    url = "https://doi.org/10.1017/s0094837300016146",
    doi = "10.1017/s0094837300016146",
    openalex = "W2482356112"
}

▪ Abstract Paleontologists have always been concerned about the documentary quality of the fossil record, and this has also become an important issue for biologists, who increasingly look to accumulations of bones, shells, and plant material as possible ways to extend the time-frame of observation on species and community behaviors. Quantitative data on the postmortem behavior of organic remains in modern environments are providing new insights into death and fossil assemblages as sources of biological information. Important findings include: 1. With the exception of a few circumstances, usually recognizable by independent criteria, transport out of the original life habitat affects few individuals. 2. Most species with preservable hardparts are in fact represented in the local death assemblage, commonly in correct rank importance. Molluscs are the most durable of modern aquatic groups studied so far, and they show highest fidelity to the original community. 3. Time-averaging of remains from successive generations and communities often prevents the detection of short-term (seasons, years) variability but provides an excellent record of the natural range of community composition and structure over longer periods. Thus, although a complex array of processes and circumstances influences preservation, death assemblages of resistant skeletal elements are for many major groups good to excellent records of community composition, morphological variation, and environmental and geographic distribution of species, and such assemblages can record temporal dynamics at ecologically and evolutionarily meaningful scales.

@article{doi101146annurevearth241433,
    author = "Kidwell, Susan M. and Flessa, Karl W.",
    title = "THE QUALITY OF THE FOSSIL RECORD: Populations, Species, and Communities",
    year = "1996",
    journal = "Annual Review of Earth and Planetary Sciences",
    abstract = "▪ Abstract Paleontologists have always been concerned about the documentary quality of the fossil record, and this has also become an important issue for biologists, who increasingly look to accumulations of bones, shells, and plant material as possible ways to extend the time-frame of observation on species and community behaviors. Quantitative data on the postmortem behavior of organic remains in modern environments are providing new insights into death and fossil assemblages as sources of biological information. Important findings include: 1. With the exception of a few circumstances, usually recognizable by independent criteria, transport out of the original life habitat affects few individuals. 2. Most species with preservable hardparts are in fact represented in the local death assemblage, commonly in correct rank importance. Molluscs are the most durable of modern aquatic groups studied so far, and they show highest fidelity to the original community. 3. Time-averaging of remains from successive generations and communities often prevents the detection of short-term (seasons, years) variability but provides an excellent record of the natural range of community composition and structure over longer periods. Thus, although a complex array of processes and circumstances influences preservation, death assemblages of resistant skeletal elements are for many major groups good to excellent records of community composition, morphological variation, and environmental and geographic distribution of species, and such assemblages can record temporal dynamics at ecologically and evolutionarily meaningful scales.",
    url = "https://doi.org/10.1146/annurev.earth.24.1.433",
    doi = "10.1146/annurev.earth.24.1.433",
    openalex = "W2062946655",
    references = "doi101017s2475263000001021, rigby1987dinosaurs"
}

We used radiocarbon ages on dead Holocene shells of the venerid bivalve Chione spp. to investigate how time-averaging and taphonomy in shallow marine benthic assemblages vary with sedimentary and tectonic setting. We compared shells collected from the sediment surface in five depositional environments from two regions of the Gulf of California, Mexico: Bahía Concepción, a young faulted rift basin with high rates of terrigenous and carbonate sedimentation; and Bahía la Choya, an intertidal system along a sediment-starved shelf. Frequency distributions of shell ages in all environments form a hollow curve, with a mode at young ages and a long tail toward older ages. This pattern suggests that shells are added to the taphonomically active zone (TAZ) at roughly constant rates (via continuous shell deaths), and removed from the TAZ at random, either through destruction or by achieving final burial. Shell half-lives (the amount of time to remove half the shells from the TAZ) provide a comparative measure of time-averaging. Time-averaging varies with sedimentary and tectonic setting. The lowest amounts of time-averaging (shell half-lives of 90 to 165 years) occur in Bahía Concepción, where rapid rates of terrigenous sedimentation (on fan-deltas) and carbonate sedimentation (in pocket bays) bury shells rapidly. Time-averaging is higher in the sediment-starved environments of Bahía la Choya (shell half-lives of 285 to 550 years). The highest amounts of time-averaging occur the inner tidal flats of Bahía la Choya (shell half-life of 550 years). Here the conjunction of low sedimentation rates with low rates of shell destruction (due to periodic tidal emergence) permits shells to persist in the TAZ for very long time spans. There is no systematic relationship between a shell's age and its taphonomic condition (taphonomic grade) in any environment, probably because of the complex and random nature of burial-exhumation in the TAZ. Age variance tends to increase with increasing taphonomic alteration: highly altered shells range in age from young to several thousand years old, while less altered shells are mostly young. The correspondence between time-averaging and the taphonomic condition of entire shell assemblages is also weak, but might be resolved with further study. These results provide quantitative data on time-averaging in benthic assemblages as a function of sedimentary and tectonic setting, and suggest some guidelines for facies appropriate for particular studies. Shallow marine rift basins like Bahía Concepción can potentially contain within-horizon fossil assemblages representing time spans of only a few hundred years—time resolution often beyond reach in paleontology. In contrast, sediment-starved shelf habitats like Bahía la Choya are unlikely to yield assemblages with time resolution finer than several thousands of years.

@article{doi101017s0094837300016791,
    author = "Meldahl, Keith Heyer and Flessa, Karl W. and Cutler, Alan H.",
    title = "Time-averaging and postmortem skeletal survival in benthic fossil assemblages: quantitative comparisons among Holocene environments",
    year = "1997",
    journal = "Paleobiology",
    abstract = "We used radiocarbon ages on dead Holocene shells of the venerid bivalve Chione spp. to investigate how time-averaging and taphonomy in shallow marine benthic assemblages vary with sedimentary and tectonic setting. We compared shells collected from the sediment surface in five depositional environments from two regions of the Gulf of California, Mexico: Bahía Concepción, a young faulted rift basin with high rates of terrigenous and carbonate sedimentation; and Bahía la Choya, an intertidal system along a sediment-starved shelf. Frequency distributions of shell ages in all environments form a hollow curve, with a mode at young ages and a long tail toward older ages. This pattern suggests that shells are added to the taphonomically active zone (TAZ) at roughly constant rates (via continuous shell deaths), and removed from the TAZ at random, either through destruction or by achieving final burial. Shell half-lives (the amount of time to remove half the shells from the TAZ) provide a comparative measure of time-averaging. Time-averaging varies with sedimentary and tectonic setting. The lowest amounts of time-averaging (shell half-lives of 90 to 165 years) occur in Bahía Concepción, where rapid rates of terrigenous sedimentation (on fan-deltas) and carbonate sedimentation (in pocket bays) bury shells rapidly. Time-averaging is higher in the sediment-starved environments of Bahía la Choya (shell half-lives of 285 to 550 years). The highest amounts of time-averaging occur the inner tidal flats of Bahía la Choya (shell half-life of 550 years). Here the conjunction of low sedimentation rates with low rates of shell destruction (due to periodic tidal emergence) permits shells to persist in the TAZ for very long time spans. There is no systematic relationship between a shell's age and its taphonomic condition (taphonomic grade) in any environment, probably because of the complex and random nature of burial-exhumation in the TAZ. Age variance tends to increase with increasing taphonomic alteration: highly altered shells range in age from young to several thousand years old, while less altered shells are mostly young. The correspondence between time-averaging and the taphonomic condition of entire shell assemblages is also weak, but might be resolved with further study. These results provide quantitative data on time-averaging in benthic assemblages as a function of sedimentary and tectonic setting, and suggest some guidelines for facies appropriate for particular studies. Shallow marine rift basins like Bahía Concepción can potentially contain within-horizon fossil assemblages representing time spans of only a few hundred years—time resolution often beyond reach in paleontology. In contrast, sediment-starved shelf habitats like Bahía la Choya are unlikely to yield assemblages with time resolution finer than several thousands of years.",
    url = "https://doi.org/10.1017/s0094837300016791",
    doi = "10.1017/s0094837300016791",
    openalex = "W2489898519",
    references = "doi10100797814899503456, doi101016s0037073896000048, doi101017s0033822200013874, doi101017s0033822200060264, doi101017s0094837300006941, doi101017s0094837300015918, doi101017s2475263000001021, doi101144gslsp19870280111, doi1023073514978, doi104319lo19661110092, doi105860choice300309, openalexw2152529191"
}

@article{doi101016s0031018297001089,
    author = "Markwick, Paul",
    title = "Fossil crocodilians as indicators of Late Cretaceous and Cenozoic climates: implications for using palaeontological data in reconstructing palaeoclimate",
    year = "1998",
    journal = "Palaeogeography Palaeoclimatology Palaeoecology",
    url = "https://doi.org/10.1016/s0031-0182(97)00108-9",
    doi = "10.1016/s0031-0182(97)00108-9",
    openalex = "W2092060384",
    references = "doi10100797814899503456, doi10100797894011125435, doi1010160031018265900131, doi101016003101829290096n, doi101016003192018990263x, doi1010160195667191900155, doi101017s0094837300006060, doi101029pa002i001p00001, doi1010719781486309702, doi101098rstb19930109, doi101126science19142321131, doi101126science24148691043, doi10113000917613198614535scaia20co2, doi101146annurevph57030195000441, doi102110pec88010071, doi1023071444927, doi1023071563593, doi1023073514444, doi1023073514548, doi1023073669094, doi102973odpprocsr1192001991, openalexw2983381470, openalexw575222456, spotila1973a"
}

Data from palaeontology and biodiversity suggest that the global biota should produce an average of three new species per year. However, the fossil record shows large variation around this mean. Rates of origination have declined through the Phanerozoic. This appears to have been largely a function of sorting among higher taxa (especially classes), which exhibit characteristic rates of speciation (and extinction) that differ among them by nearly an order of magnitude. Secular decline of origination rates is hardly constant, however; many positive deviations reflect accelerated speciation during rebounds from mass extinctions. There has also been general decline in rates of speciation within major taxa through their histories, although rates have tended to remain higher among members in tropical regions. Finally, pulses of speciation appear sometimes to be associated with climate change, although moderate oscillations of climate do not necessarily promote speciation despite forcing changes in species' geographical ranges.

@article{doi101098rstb19980212,
    author = "Sepkoski, J. John",
    title = "Rates of speciation in the fossil record",
    year = "1998",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "Data from palaeontology and biodiversity suggest that the global biota should produce an average of three new species per year. However, the fossil record shows large variation around this mean. Rates of origination have declined through the Phanerozoic. This appears to have been largely a function of sorting among higher taxa (especially classes), which exhibit characteristic rates of speciation (and extinction) that differ among them by nearly an order of magnitude. Secular decline of origination rates is hardly constant, however; many positive deviations reflect accelerated speciation during rebounds from mass extinctions. There has also been general decline in rates of speciation within major taxa through their histories, although rates have tended to remain higher among members in tropical regions. Finally, pulses of speciation appear sometimes to be associated with climate change, although moderate oscillations of climate do not necessarily promote speciation despite forcing changes in species' geographical ranges.",
    url = "https://doi.org/10.1098/rstb.1998.0212",
    doi = "10.1098/rstb.1998.0212",
    openalex = "W2146368901",
    references = "doi101007bfb0011143, doi101016s0031018296000855, doi105860choice321548, openalexw658437845"
}

Body mass estimates for 1534 North American fossil mammal species show that new species are on average 9.1% larger than older species in the same genera. This within-lineage effect is not a sampling bias. It persists throughout the Cenozoic, accounting for the gradual overall increase in average mass (Cope's rule). The effect is stronger for larger mammals, being near zero for small mammals. This variation partially explains the unwavering lower size limit and the gradually expanding mid-sized gap, but not the sudden large increase in the upper size limit, at the Cretaceous-Tertiary boundary.

@article{doi101126science2805364731,
    author = "Alroy, John",
    title = "Cope's Rule and the Dynamics of Body Mass Evolution in North American Fossil Mammals",
    year = "1998",
    journal = "Science",
    abstract = "Body mass estimates for 1534 North American fossil mammal species show that new species are on average 9.1\% larger than older species in the same genera. This within-lineage effect is not a sampling bias. It persists throughout the Cenozoic, accounting for the gradual overall increase in average mass (Cope's rule). The effect is stronger for larger mammals, being near zero for small mammals. This variation partially explains the unwavering lower size limit and the gradually expanding mid-sized gap, but not the sudden large increase in the upper size limit, at the Cretaceous-Tertiary boundary.",
    url = "https://doi.org/10.1126/science.280.5364.731",
    doi = "10.1126/science.280.5364.731",
    openalex = "W2053649449",
    references = "doi101017s0022336000059126, doi101017s0094837300016134, doi101038365748a0, doi101111j155856461949tb00010x, doi101111j155856461973tb05912x, doi105860choice290302"
}

Introduction - adequacy versus incompleteness, Stephen K. Donovan and Christopher R.C. Paul adequacy, completeness and the fossil record, Christopher R.C. Paul determining stratugraphics ranges, Charles R. Marshall resolution of the fossil record - the fidelity of preservation, David M. Martill the completeness of the Pleistocene fossil record - implications for stratigraphic adequacy, Benjamin J. Greenstein et al an overview of the completeness of the fossil record, Christopher R.C. Paul and Stephen K. Donovan fossil solids and completeness of the rock and fossil records, Gregory J. Retallack phylogenetic analyses and the quality of the fossil record, Peter J. Wagner taxonomic barriers and other distortions within the fossil record, Carl F. Koch patterns of occurrence of benthic Foraminifera in time and space, Stephen J. Culver and Martin A. Buzas the fossil record of cheilostome bryozoa in the Neogene and Quaternay of tropical America - adequacy for phylogenetic and evolutionary studies, Alan H. Cheetham and Jeremy B.C. Jackson the fossil record of bivalue molluscs, Elizabeth M. Harper the quality of the fossil record of the vertebrates, Michael J. Benton.

@book{openalexw1522518756,
    author = "Donovan, Stephen K. and Paul, C. R. C.",
    title = "The adequacy of the fossil record",
    year = "1998",
    booktitle = "J. Wiley eBooks",
    abstract = "Introduction - adequacy versus incompleteness, Stephen K. Donovan and Christopher R.C. Paul adequacy, completeness and the fossil record, Christopher R.C. Paul determining stratugraphics ranges, Charles R. Marshall resolution of the fossil record - the fidelity of preservation, David M. Martill the completeness of the Pleistocene fossil record - implications for stratigraphic adequacy, Benjamin J. Greenstein et al an overview of the completeness of the fossil record, Christopher R.C. Paul and Stephen K. Donovan fossil solids and completeness of the rock and fossil records, Gregory J. Retallack phylogenetic analyses and the quality of the fossil record, Peter J. Wagner taxonomic barriers and other distortions within the fossil record, Carl F. Koch patterns of occurrence of benthic Foraminifera in time and space, Stephen J. Culver and Martin A. Buzas the fossil record of cheilostome bryozoa in the Neogene and Quaternay of tropical America - adequacy for phylogenetic and evolutionary studies, Alan H. Cheetham and Jeremy B.C. Jackson the fossil record of bivalue molluscs, Elizabeth M. Harper the quality of the fossil record of the vertebrates, Michael J. Benton.",
    openalex = "W1522518756"
}

@article{doi10103818872,
    author = "Foote, Mike and Sepkoski, J. John",
    title = "Absolute measures of the completeness of the fossil record",
    year = "1999",
    journal = "Nature",
    url = "https://doi.org/10.1038/18872",
    doi = "10.1038/18872",
    openalex = "W1614214072",
    references = "doi10100797836427963404, doi1010160305197885900559, doi101017cbo9780511735769004, doi101017s0022336000040026, doi101017s0094837300005996, doi101017s0094837300016134, doi101017s0094837300016146, doi101098rstb19980212, doi101130spe190p291, doi1023071220820, doi1023072413454, schopf1978fossilization"
}

Molecular fossils of biological lipids are preserved in 2700-million-year-old shales from the Pilbara Craton, Australia. Sequential extraction of adjacent samples shows that these hydrocarbon biomarkers are indigenous and syngenetic to the Archean shales, greatly extending the known geological range of such molecules. The presence of abundant 2α-methylhopanes, which are characteristic of cyanobacteria, indicates that oxygenic photosynthesis evolved well before the atmosphere became oxidizing. The presence of steranes, particularly cholestane and its 28- to 30-carbon analogs, provides persuasive evidence for the existence of eukaryotes 500 million to 1 billion years before the extant fossil record indicates that the lineage arose.

@article{doi101126science28554301033,
    author = "Brocks, Jochen J. and Logan, Graham A. and Buick, Roger and Summons, Roger E.",
    title = "Archean Molecular Fossils and the Early Rise of Eukaryotes",
    year = "1999",
    journal = "Science",
    abstract = "Molecular fossils of biological lipids are preserved in 2700-million-year-old shales from the Pilbara Craton, Australia. Sequential extraction of adjacent samples shows that these hydrocarbon biomarkers are indigenous and syngenetic to the Archean shales, greatly extending the known geological range of such molecules. The presence of abundant 2α-methylhopanes, which are characteristic of cyanobacteria, indicates that oxygenic photosynthesis evolved well before the atmosphere became oxidizing. The presence of steranes, particularly cholestane and its 28- to 30-carbon analogs, provides persuasive evidence for the existence of eukaryotes 500 million to 1 billion years before the extant fossil record indicates that the lineage arose.",
    url = "https://doi.org/10.1126/science.285.5430.1033",
    doi = "10.1126/science.285.5430.1033",
    openalex = "W2032247127",
    references = "doi101038362834a0, doi101038376053a0, doi101038384055a0, doi101126science11539686, doi101126science1585174, doi101126science1603829729, doi101126science1631544, doi101126science2605108640, doi101146annurevmi41100187001505, doi102113gsecongeo6871135"
}

It has long been assumed that the extant bilaterian phyla generally have their origin in the Cambrian explosion, when they appear in an essentially modern form. Both these assumptions are questionable. A strict application of stem- and crown-group concepts to phyla shows that although the branching points of many clades may have occurred in the Early Cambrian or before, the appearance of the modern body plans was in most cases later: very few bilaterian phyla sensu stricto have demonstrable representatives in the earliest Cambrian. Given that the early branching points of major clades is an inevitable result of the geometry of clade diversi®cation, the alleged phenomenon of phyla appearing early and remaining morphologically static is seen not to require particular explanation. Confusion in the de®nition of a phylum has thus led to attempts to explain (especially from a developmental perspective) a feature that is partly inevitable, partly illusory. We critically discuss models for Proterozoic diversi®cation based on small body size, limited developmental capacity and poor preservation and cryptic habits, and show that the prospect of lineage diversi®cation occurring early in the Proterozoic can be seen to be unlikely on grounds of both parsimonyand functional morphology. Indeed, the combination of the body and trace fossil record demonstrates a progressive diversi®cation through the end of the Proterozoic well into the Cambrian and beyond, a picture consistent with body plans being assembled during this time. Body-plan characters are likely to have been acquired monophyletically in the history of the bilaterians, and a model explaining the diversity in just oneof them, the coelom, is presented. This analysis points to the requirement for a careful application of systematic methodology before explanations are sought for alleged patterns of constraint and ¯fexibility.

@article{doi101017s000632310000548x,
    author = "Budd, Graham E. and Jensen, Sören",
    title = "A critical reappraisal of the fossil record of the bilaterian phyla",
    year = "2000",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "It has long been assumed that the extant bilaterian phyla generally have their origin in the Cambrian explosion, when they appear in an essentially modern form. Both these assumptions are questionable. A strict application of stem- and crown-group concepts to phyla shows that although the branching points of many clades may have occurred in the Early Cambrian or before, the appearance of the modern body plans was in most cases later: very few bilaterian phyla sensu stricto have demonstrable representatives in the earliest Cambrian. Given that the early branching points of major clades is an inevitable result of the geometry of clade diversi®cation, the alleged phenomenon of phyla appearing early and remaining morphologically static is seen not to require particular explanation. Confusion in the de®nition of a phylum has thus led to attempts to explain (especially from a developmental perspective) a feature that is partly inevitable, partly illusory. We critically discuss models for Proterozoic diversi®cation based on small body size, limited developmental capacity and poor preservation and cryptic habits, and show that the prospect of lineage diversi®cation occurring early in the Proterozoic can be seen to be unlikely on grounds of both parsimonyand functional morphology. Indeed, the combination of the body and trace fossil record demonstrates a progressive diversi®cation through the end of the Proterozoic well into the Cambrian and beyond, a picture consistent with body plans being assembled during this time. Body-plan characters are likely to have been acquired monophyletically in the history of the bilaterians, and a model explaining the diversity in just oneof them, the coelom, is presented. This analysis points to the requirement for a careful application of systematic methodology before explanations are sought for alleged patterns of constraint and ¯fexibility.",
    url = "https://doi.org/10.1017/s000632310000548x",
    doi = "10.1017/s000632310000548x",
    openalex = "W2148377177",
    references = "doi101002aja1002030302, doi101002jmor1050540103, doi101017s0022336000024963, doi101017s0094837300012793, doi101017s009483730001681x, doi10103835318, doi101038361490a0, doi101038377720a0, doi101038382127a0, doi101038387489a0, doi10103846965, doi101098rstb19780005, doi101098rstb19790006, doi101098rstb19950029, doi101111j109583121996tb01693x, doi101111j109600311991tb00045x, doi101111j146363951991tb00312x, doi101111j146363951995tb00988x, doi101111j146364091991tb00303x, doi101111j1469185x1988tb00631x, doi101111j150239311975tb01311x, doi101111j150239311990tb01373x, doi101111j150239311998tb00509x, doi101126science28354091919, doi101126science28454232129, doi101126science7886451, doi101139e87124, doi101508300037918, doi101826182003741571989, doi101826182003769311997, doi1023073515360, doi1023073515362, doi1023073515363, doi105281zenodo16238847, dzik1988the, openalexw2055967869, openalexw2598873191, openalexw2754161204"
}

The study of fossil preservation – taphonomy – reveals biases of the fossil record and also provides insights into depositional rates and processes.

@misc{brett2001fossils,
    author = "Brett, Carlton E",
    title = "Fossils and Fossilization",
    year = "2001",
    booktitle = "Encyclopedia of Life Sciences",
    abstract = "The study of fossil preservation – taphonomy – reveals biases of the fossil record and also provides insights into depositional rates and processes.",
    url = "https://doi.org/10.1038/npg.els.0001621",
    doi = "10.1038/npg.els.0001621",
    openalex = "W1515610845",
    references = "doi1010079781489950345, doi101017cbo9780511612381, doi101017s009483730001143x, doi101017s2475263000001021, doi1023073514686, doi1023073514687, doi105860choice284524, doi105860choice295135"
}

Patterns of origination, extinction and standing diversity through time have been inferred from tallies of taxa preserved in the fossil record. This approach assumes that sampling of the fossil record is effectively uniform over time. Although recent evidence suggests that our sampling of the available rock record has indeed been very thorough and effective, there is also overwhelming evidence that the rock record available for sampling is itself distorted by major systematic biases. Data on rock outcrop area compiled for post-Palaeozoic sediments from Western Europe at stage level are presented. These show a strongly cyclical pattern corresponding to first- and second-order sequence stratigraphical depositional cycles. Standing diversity increases over time and, at the coarsest scale, is decoupled from surface outcrop area. This increasing trend can therefore be considered a real pattern. Changes in standing diversity and origination rates over time-scales measured in tens of millions of years, however, are strongly correlated with surface outcrop area. Extinction peaks conform to a random-walk model, but larger peaks occur at just two positions with respect to second-order stratigraphical sequences, towards the culmination of stacked transgressive system tracts and close to system bases, precisely the positions where taxonomic last occurrences are predicted to cluster under a random distribution model. Many of the taxonomic patterns that have been described from the fossil record conform to a species-area effect. Whether this arises primarily from sampling bias, or from changing surface area of marine shelf seas through time and its effect on biodiversity, remains problematic.

@article{doi101098rstb20000768,
    author = "Smith, Andrew B.",
    title = "Large–scale heterogeneity of the fossil record: implications for Phanerozoic biodiversity studies",
    year = "2001",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "Patterns of origination, extinction and standing diversity through time have been inferred from tallies of taxa preserved in the fossil record. This approach assumes that sampling of the fossil record is effectively uniform over time. Although recent evidence suggests that our sampling of the available rock record has indeed been very thorough and effective, there is also overwhelming evidence that the rock record available for sampling is itself distorted by major systematic biases. Data on rock outcrop area compiled for post-Palaeozoic sediments from Western Europe at stage level are presented. These show a strongly cyclical pattern corresponding to first- and second-order sequence stratigraphical depositional cycles. Standing diversity increases over time and, at the coarsest scale, is decoupled from surface outcrop area. This increasing trend can therefore be considered a real pattern. Changes in standing diversity and origination rates over time-scales measured in tens of millions of years, however, are strongly correlated with surface outcrop area. Extinction peaks conform to a random-walk model, but larger peaks occur at just two positions with respect to second-order stratigraphical sequences, towards the culmination of stacked transgressive system tracts and close to system bases, precisely the positions where taxonomic last occurrences are predicted to cluster under a random distribution model. Many of the taxonomic patterns that have been described from the fossil record conform to a species-area effect. Whether this arises primarily from sampling bias, or from changing surface area of marine shelf seas through time and its effect on biodiversity, remains problematic.",
    url = "https://doi.org/10.1098/rstb.2000.0768",
    doi = "10.1098/rstb.2000.0768",
    openalex = "W1978097234",
    references = "doi10100797814615695961, doi101017s0094837300004930, doi10103818872, doi102110pec98020003, doi1023073515097"
}

@article{doi101038416726a,
    author = "Tavaré, Simon and Marshall, Charles R. and Will, Oliver and Soligo, Christophe and Martín, Robert D.",
    title = "Using the fossil record to estimate the age of the last common ancestor of extant primates",
    year = "2002",
    journal = "Nature",
    url = "https://doi.org/10.1038/416726a",
    doi = "10.1038/416726a",
    openalex = "W2051801987",
    references = "doi10103818872"
}

▪ Abstract Advances in taphonomy and stratigraphy over the past two decades have dramatically improved our understanding of the causes, effects, and remedies of incompleteness in the fossil record for the study of evolution. Taphonomic research has focused on quantifying probabilities of preservation across taxonomic groups, the temporal and spatial resolution of fossil deposits, and secular changes in preservation over the course of the Phanerozoic. Stratigraphic research has elucidated systematic trends in the formation of sedimentary gaps and permanent stratigraphic records, the quantitative consequences of environmental change and variable rock accumulation rates over short and long timescales, and has benefited from greatly improved methods of correlation and absolute age determination. We provide examples of how these advances are transforming paleontologic investigations of the tempo and mode of morphologic change, phylogenetic analysis, and the environmental and temporal analysis of macroevolutionary patterns.

@article{doi101146annurevecolsys33030602152151,
    author = "Kidwell, Susan M. and Holland, Steven M.",
    title = "The Quality of the Fossil Record: Implications for Evolutionary Analyses",
    year = "2002",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "▪ Abstract Advances in taphonomy and stratigraphy over the past two decades have dramatically improved our understanding of the causes, effects, and remedies of incompleteness in the fossil record for the study of evolution. Taphonomic research has focused on quantifying probabilities of preservation across taxonomic groups, the temporal and spatial resolution of fossil deposits, and secular changes in preservation over the course of the Phanerozoic. Stratigraphic research has elucidated systematic trends in the formation of sedimentary gaps and permanent stratigraphic records, the quantitative consequences of environmental change and variable rock accumulation rates over short and long timescales, and has benefited from greatly improved methods of correlation and absolute age determination. We provide examples of how these advances are transforming paleontologic investigations of the tempo and mode of morphologic change, phylogenetic analysis, and the environmental and temporal analysis of macroevolutionary patterns.",
    url = "https://doi.org/10.1146/annurev.ecolsys.33.030602.152151",
    doi = "10.1146/annurev.ecolsys.33.030602.152151",
    openalex = "W2101107494",
    references = "doi1010079781489950345, doi101017s0094837300005996, doi101017s0094837300008186, doi101017s0094837300016791, doi101017s0094837300026907, doi101017s2475263000001021, doi10103831927, doi101086628623, doi101126science1061457, doi101126science1067179, doi101126science21545391501, doi101126science28954821139b, doi101146annurevearth281419, doi10166600948373200026103tap20co2, doi102110pec95040129, doi1023073515097, doi1023073515233, doi105860choice300309, doi105860choice333929, schopf1978fossilization"
}

▪ Abstract Fossil deposits that preserve soft-bodied organisms provide critical evidence of the history of life. Usually, only more decay resistant materials, e.g., cuticles, survive as organic remains as a result of selective preservation and subsequent diagenesis to more resistant biopolymers. Permineralization, the permeation of tissues by mineralizing fluids, may preserve remarkable detail, particularly of plants. However, evidence of more labile tissues, e.g., muscle, normally requires the replication of their morphology by rapid in situ growth of minerals, i.e., authigenic mineralization. This process relies on the steep geochemical gradients generated by decay microbes. The minerals involved, and the level of detail preserved (which may be subcellular), depend on a number of factors, including the nature of microbial activity and amount of decay, availability of ions, and the type of organism that is fossilized. Understanding these controls is essential to determining the conditions that favor exceptional preservation.

@article{briggs2003the,
    author = "Briggs, Derek E.G.",
    title = "The Role of Decay and Mineralization in the Preservation of Soft-Bodied Fossils",
    year = "2003",
    journal = "Annual Review of Earth and Planetary Sciences",
    abstract = "▪ Abstract Fossil deposits that preserve soft-bodied organisms provide critical evidence of the history of life. Usually, only more decay resistant materials, e.g., cuticles, survive as organic remains as a result of selective preservation and subsequent diagenesis to more resistant biopolymers. Permineralization, the permeation of tissues by mineralizing fluids, may preserve remarkable detail, particularly of plants. However, evidence of more labile tissues, e.g., muscle, normally requires the replication of their morphology by rapid in situ growth of minerals, i.e., authigenic mineralization. This process relies on the steep geochemical gradients generated by decay microbes. The minerals involved, and the level of detail preserved (which may be subcellular), depend on a number of factors, including the nature of microbial activity and amount of decay, availability of ions, and the type of organism that is fossilized. Understanding these controls is essential to determining the conditions that favor exceptional preservation.",
    url = "https://doi.org/10.1146/annurev.earth.31.100901.144746",
    doi = "10.1146/annurev.earth.31.100901.144746",
    number = "1",
    openalex = "W2125375419",
    pages = "275-301",
    volume = "31",
    references = "allison1988the, briggs1994decay, briggs1996the, doi1010160016703789901919, doi1010160016703794902984, doi101016002532279390147n, doi1010160034666775900056, doi101017s0006323199005472, doi101017s0022336000040026, doi101017s0094837300009994, doi101017s009483730001188x, doi101017s0094837300012082, doi101098rstb19790006, doi101098rstb19850134, doi101098rstb19930082, doi101111j150239311983tb01993x, doi101126science25951001439, doi101126science28153801173, doi1011300091761319880160149mibbbs23co2, doi1015159781501509247, doi1016660094837320020280155lgatio20co2, doi1023071222284, doi1023073515360, doi1023073515363, doi105860choice284524, doi107208chicago97802261597130010001, openalexw2754161204"
}

Exceptionally preserved, non-biomineralizing fossils contribute importantly to resolving details of the Cambrian explosion, but little to its overall patterns. Six distinct "types" of exceptional preservation are identified for the terminal Proterozoic-Cambrian interval, each of which is dependent on particular taphonomic circumstances, typically restricted both in space and time. Taphonomic pathways yielding exceptional preservation were particularly variable through the Proterozoic-Cambrian transition, at least in part a consequence of contemporaneous evolutionary innovations. Combined with the reasonably continuous record of "Doushantuo-type preservation," and the fundamentally more robust records of shelly fossils, phytoplankton cysts and trace fossils, these taphonomic perturbations contribute to the documentation of major evolutionary and biogeochemical shifts through the terminal Proterozoic and early Cambrian.Appreciation of the relationship between taphonomic pathway and fossil expression serves as a useful tool for interpreting exceptionally preserved, often problematic, early Cambrian fossils. In shale facies, for example, flattened non-biomineralizing structures typically represent the remains of degradation-resistant acellular and extracellular "tissues" such as chaetae and cuticles, whereas three-dimensional preservation represents labile cellular tissues with a propensity for attracting and precipitating early diagenetic minerals. Such distinction helps to identify the acuticular integument of hyolithids, the chaetae-like nature of Wiwaxia sclerites, the chaetognath-like integument of Amiskwia, the midgut glands of various Burgess Shale arthropods, and the misidentification of deposit-feeding arthropods in the Chengjiang biota. By the same reasoning, putative lobopods in the Sirius Passet biota and putative deuterostomes in the Chengiang biota are better interpreted as arthropods.

@article{doi101093icb431166,
    author = "Butterfield, Nicholas J.",
    title = "Exceptional Fossil Preservation and the Cambrian Explosion",
    year = "2003",
    journal = "Integrative and Comparative Biology",
    abstract = {Exceptionally preserved, non-biomineralizing fossils contribute importantly to resolving details of the Cambrian explosion, but little to its overall patterns. Six distinct "types" of exceptional preservation are identified for the terminal Proterozoic-Cambrian interval, each of which is dependent on particular taphonomic circumstances, typically restricted both in space and time. Taphonomic pathways yielding exceptional preservation were particularly variable through the Proterozoic-Cambrian transition, at least in part a consequence of contemporaneous evolutionary innovations. Combined with the reasonably continuous record of "Doushantuo-type preservation," and the fundamentally more robust records of shelly fossils, phytoplankton cysts and trace fossils, these taphonomic perturbations contribute to the documentation of major evolutionary and biogeochemical shifts through the terminal Proterozoic and early Cambrian.Appreciation of the relationship between taphonomic pathway and fossil expression serves as a useful tool for interpreting exceptionally preserved, often problematic, early Cambrian fossils. In shale facies, for example, flattened non-biomineralizing structures typically represent the remains of degradation-resistant acellular and extracellular "tissues" such as chaetae and cuticles, whereas three-dimensional preservation represents labile cellular tissues with a propensity for attracting and precipitating early diagenetic minerals. Such distinction helps to identify the acuticular integument of hyolithids, the chaetae-like nature of Wiwaxia sclerites, the chaetognath-like integument of Amiskwia, the midgut glands of various Burgess Shale arthropods, and the misidentification of deposit-feeding arthropods in the Chengjiang biota. By the same reasoning, putative lobopods in the Sirius Passet biota and putative deuterostomes in the Chengiang biota are better interpreted as arthropods.},
    url = "https://doi.org/10.1093/icb/43.1.166",
    doi = "10.1093/icb/43.1.166",
    openalex = "W2181027699",
    references = "doi1010160016703789901919, doi101017s000632310000548x, doi101017s0094837300009994, doi101017s0094837300012082, doi10103834391, doi10103835318, doi101098rstb19790006, doi101098rstb19850005, doi101111j1469185x1999tb00046x, doi101111j150239311975tb01311x, doi101111j150239311994tb01558x, doi101111j150239311995tb01587x, doi101111j150239311995tb01591x, doi101126science1066611, doi101126science28153801173, doi1016660094837320000260386bpngns20co2, doi1016660094837320020280155lgatio20co2, doi1023073514743, doi1023073515360, openalexw2326083785, openalexw2754161204, openalexw3127114020, openalexw659399033"
}

Laser-Raman imagery is a non-intrusive, non-destructive analytical technique, recently introduced to Precambrian paleobiology, that can be used to demonstrate a one-to-one spatial correlation between the optically discernible morphology and kerogenous composition of permineralized fossil microorganisms. Made possible by the submicron-scale resolution of the technique and its high sensitivity to the Raman signal of carbonaceous matter, such analyses can be used to determine the chemical-structural characteristics of organic-walled microfossils and associated sapropelic carbonaceous matter in acid-resistant residues and petrographic thin sections. Here we use this technique to analyze kerogenous microscopic fossils and associated carbonaceous sapropel permineralized in 22 unmetamorphosed or little-metamorphosed fine-grained chert units ranging from approximately 400 to approximately 2,100 Ma old. The lineshapes of the Raman spectra acquired vary systematically with five indices of organic geochemical maturation: (1) the mineral-based metamorphic grade of the fossil-bearing units; (2) the fidelity of preservation of the fossils studied; (3) the color of the organic matter analyzed; and both the (4) H/C and (5) N/C ratios measured in particulate kerogens isolated from bulk samples of the fossil-bearing cherts. Deconvolution of relevant spectra shows that those of relatively well-preserved permineralized kerogens analyzed in situ exhibit a distinctive set of Raman bands that are identifiable also in hydrated organic-walled microfossils and particulate carbonaceous matter freed from the cherts by acid maceration. These distinctive Raman bands, however, become indeterminate upon dehydration of such specimens. To compare quantitatively the variations observed among the spectra measured, we introduce the Raman Index of Preservation, an approximate measure of the geochemical maturity of the kerogens studied that is consistent both with the five indices of organic geochemical alteration and with spectra acquired from fossils experimentally heated under controlled laboratory conditions. The results reported provide new insight into the chemical-structural characteristics of ancient carbonaceous matter, the physicochemical changes that accompany organic geochemical maturation, and a new criterion to be added to the suite of evidence by which to evaluate the origin of minute fossil-like objects of possible but uncertain biogenicity.

@article{doi101089ast20055333,
    author = "Schopf, J. William and Kudryavtsev, Anatoliy B. and Agresti, D. G. and Czaja, Andrew D. and Wdowiak, Thomas J.",
    title = "Raman Imagery: A New Approach to Assess the Geochemical Maturity and Biogenicity of Permineralized Precambrian Fossils",
    year = "2005",
    journal = "Astrobiology",
    abstract = "Laser-Raman imagery is a non-intrusive, non-destructive analytical technique, recently introduced to Precambrian paleobiology, that can be used to demonstrate a one-to-one spatial correlation between the optically discernible morphology and kerogenous composition of permineralized fossil microorganisms. Made possible by the submicron-scale resolution of the technique and its high sensitivity to the Raman signal of carbonaceous matter, such analyses can be used to determine the chemical-structural characteristics of organic-walled microfossils and associated sapropelic carbonaceous matter in acid-resistant residues and petrographic thin sections. Here we use this technique to analyze kerogenous microscopic fossils and associated carbonaceous sapropel permineralized in 22 unmetamorphosed or little-metamorphosed fine-grained chert units ranging from approximately 400 to approximately 2,100 Ma old. The lineshapes of the Raman spectra acquired vary systematically with five indices of organic geochemical maturation: (1) the mineral-based metamorphic grade of the fossil-bearing units; (2) the fidelity of preservation of the fossils studied; (3) the color of the organic matter analyzed; and both the (4) H/C and (5) N/C ratios measured in particulate kerogens isolated from bulk samples of the fossil-bearing cherts. Deconvolution of relevant spectra shows that those of relatively well-preserved permineralized kerogens analyzed in situ exhibit a distinctive set of Raman bands that are identifiable also in hydrated organic-walled microfossils and particulate carbonaceous matter freed from the cherts by acid maceration. These distinctive Raman bands, however, become indeterminate upon dehydration of such specimens. To compare quantitatively the variations observed among the spectra measured, we introduce the Raman Index of Preservation, an approximate measure of the geochemical maturity of the kerogens studied that is consistent both with the five indices of organic geochemical alteration and with spectra acquired from fossils experimentally heated under controlled laboratory conditions. The results reported provide new insight into the chemical-structural characteristics of ancient carbonaceous matter, the physicochemical changes that accompany organic geochemical maturation, and a new criterion to be added to the suite of evidence by which to evaluate the origin of minute fossil-like objects of possible but uncertain biogenicity.",
    url = "https://doi.org/10.1089/ast.2005.5.333",
    doi = "10.1089/ast.2005.5.333",
    openalex = "W2088266853",
    references = "doi1010079783642964466, doi1010160034666775900056, doi1010160301926877900262, doi1010160301926888900058, doi101016s014663809900145x, doi101038nature02260, doi101046j15251314200200408x, doi10106311674108, doi101103physrevb20392, doi101126science2605108640, doi101126science2735277924, doi101557jmr19890385, doi105860choice295702, openalexw1558677347"
}

@article{doi101038nature04890,
    author = "Donoghue, Philip C. J. and Bengtson, Stefan and Dong, Xi-ping and Gostling, Neil J. and Huldtgren, Therese and Cunningham, John A. and Yin, Chongyu and Zhao, Yue and Peng, Fan and Stampanoni, Marco",
    title = "Synchrotron X-ray tomographic microscopy of fossil embryos",
    year = "2006",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature04890",
    doi = "10.1038/nature04890",
    openalex = "W2099181563",
    references = "briggs2003the, doi101006dbio20020714, doi101016jgeobios200308001, doi101016jtoxlet200611011, doi10103835318, doi101073pnas250491697, doi101073pnas9794457, doi101111j150239311989tb01679x, doi101126science1099213, doi101126science27753321645, doi102517prpsj771"
}

Fossiliferous deposits of the Greenhorn Limestone (Upper Cretaceous) are found on the Comanche National Grassland in southeastern Colorado. The lowest portion of the Greenhorn Limestone, the base of the Lincoln Limestone Member, contains calcarenite beds rich in disarticulated remains of marine vertebrates. We examined the composition of the vertebrate paleofauna from one particular location (Tobe locality) through surface collecting and acid solution of rocks. The paleofauna is taxonomically diverse, consisting of 22 chondrichthyans, at least 15 osteichthyan fishes, and six aquatic reptiles. Molluscan taxa indicate that the basal Lincoln Limestone in southeastern Colorado was deposited sometime between middle Middle Cenomanian (ca. 95 Ma) and late Middle Cenomanian (ca. 94.7 Ma), and the composition of the vertebrate fauna (primarily chondrichthyan taxa) agrees with this interpretation. The Tobe locality was situated far from the shorelines of the Western Interior Seaway, with relatively high-energy waves impinging upon the seafloor, concentrating biogenic remains. Fossil remains within the calcarenite appear to have undergone minor time-averaging, based upon erosional rounding and breakage present in numerous specimens. Nevertheless, the deposit contains one of the best representative Middle Cenomanian vertebrate communities so far described from the Western Interior Seaway of North America. Considering that the paleofauna consists of taxa diverse in size, morphology, and inferred ecology, the trophic structure of the paleocommunity was probably complex.

@article{doi101666002233602006801fmvftl20co2,
    author = "Shimada, Kenshu and Schumacher, Bruce A. and PARKIN, JENNIFER A. and PALERMO, JACLYN M.",
    title = "FOSSIL MARINE VERTEBRATES FROM THE LOWERMOST GREENHORN LIMESTONE (UPPER CRETACEOUS: MIDDLE CENOMANIAN) IN SOUTHEASTERN COLORADO",
    year = "2006",
    journal = "Journal of Paleontology",
    abstract = "Fossiliferous deposits of the Greenhorn Limestone (Upper Cretaceous) are found on the Comanche National Grassland in southeastern Colorado. The lowest portion of the Greenhorn Limestone, the base of the Lincoln Limestone Member, contains calcarenite beds rich in disarticulated remains of marine vertebrates. We examined the composition of the vertebrate paleofauna from one particular location (Tobe locality) through surface collecting and acid solution of rocks. The paleofauna is taxonomically diverse, consisting of 22 chondrichthyans, at least 15 osteichthyan fishes, and six aquatic reptiles. Molluscan taxa indicate that the basal Lincoln Limestone in southeastern Colorado was deposited sometime between middle Middle Cenomanian (ca. 95 Ma) and late Middle Cenomanian (ca. 94.7 Ma), and the composition of the vertebrate fauna (primarily chondrichthyan taxa) agrees with this interpretation. The Tobe locality was situated far from the shorelines of the Western Interior Seaway, with relatively high-energy waves impinging upon the seafloor, concentrating biogenic remains. Fossil remains within the calcarenite appear to have undergone minor time-averaging, based upon erosional rounding and breakage present in numerous specimens. Nevertheless, the deposit contains one of the best representative Middle Cenomanian vertebrate communities so far described from the Western Interior Seaway of North America. Considering that the paleofauna consists of taxa diverse in size, morphology, and inferred ecology, the trophic structure of the paleocommunity was probably complex.",
    url = "https://doi.org/10.1666/0022-3360(2006)80[1:fmvftl]2.0.co;2",
    doi = "10.1666/0022-3360(2006)80[1:fmvftl]2.0.co;2",
    openalex = "W2175522597",
    references = "andgray1851list, doi101002jmor1073, doi101017s2475263000001021, doi101130spe190p291, doi10130683d923ed16c711d78645000102c1865d, doi1023071437499, doi1023071442263, doi1023071447582, doi105962bhltitle4275, doi105962bhltitle4911, doi105962bhltitle61854, forey1996interrelationships, openalexw1599677799, openalexw570265017"
}

Death assemblages from contemporary marginal marine settings carved into ancient shell deposits are composed of fossil shells exhumed by currents or tides and shells derived from living populations. A better understanding of the bias produced by such a mixing process is of interest for studies that use modern death assemblages as analogues of similar past habitats. In order to evaluate the magnitude of reworking and redeposition of fossil shells in modern environments, a taxonomic (composition, abundance, and richness) and taphonomic (taphofacies) study was carried out in the Mar Chiquita coastal lagoon, Argentina (37°40′S, 57°20′W). The nature and extent of reworking was explored along a gradient in tidal energy from the outer to the inner reaches of the coastal lagoon. Results indicate that modern death assemblages in the lagoon are composed mostly of fossil (late Holocene) reworked shells and that reworking varies along a gradient in tidal energy, being higher in the outer reaches of the coastal lagoon, where tidal action is more significant. Temporal mixing in the coastal lagoon appears to be associated with condensation (remanié) rather than with a subtle mixing of shells, as occurs in time-averaged deposits. This reworking process leads to an abundance of old shells in modern death assemblages, which has negative consequences for their utilization as modern analogues of past lagoons. Multidisciplinary studies involving various biological indicators need to take this type of bias into consideration in order to avoid erroneous inferences on the Quaternary evolution of coastal lagoons.

@article{doi102110palo2006p06124r,
    author = "Francesco, Claudio G. De and Hassan, Gabriela S.",
    title = "DOMINANCE OF REWORKED FOSSIL SHELLS IN MODERN ESTUARINE ENVIRONMENTS: IMPLICATIONS FOR PALEOENVIRONMENTAL RECONSTRUCTIONS BASED ON BIOLOGICAL REMAINS",
    year = "2008",
    journal = "Palaios",
    abstract = "Death assemblages from contemporary marginal marine settings carved into ancient shell deposits are composed of fossil shells exhumed by currents or tides and shells derived from living populations. A better understanding of the bias produced by such a mixing process is of interest for studies that use modern death assemblages as analogues of similar past habitats. In order to evaluate the magnitude of reworking and redeposition of fossil shells in modern environments, a taxonomic (composition, abundance, and richness) and taphonomic (taphofacies) study was carried out in the Mar Chiquita coastal lagoon, Argentina (37°40′S, 57°20′W). The nature and extent of reworking was explored along a gradient in tidal energy from the outer to the inner reaches of the coastal lagoon. Results indicate that modern death assemblages in the lagoon are composed mostly of fossil (late Holocene) reworked shells and that reworking varies along a gradient in tidal energy, being higher in the outer reaches of the coastal lagoon, where tidal action is more significant. Temporal mixing in the coastal lagoon appears to be associated with condensation (remanié) rather than with a subtle mixing of shells, as occurs in time-averaged deposits. This reworking process leads to an abundance of old shells in modern death assemblages, which has negative consequences for their utilization as modern analogues of past lagoons. Multidisciplinary studies involving various biological indicators need to take this type of bias into consideration in order to avoid erroneous inferences on the Quaternary evolution of coastal lagoons.",
    url = "https://doi.org/10.2110/palo.2006.p06-124r",
    doi = "10.2110/palo.2006.p06-124r",
    openalex = "W2145345219",
    references = "doi101016001669959180043y, doi101016s001282520300014x"
}

This study concerns the formation, taphonomy, and preservation of human footprints in microbial mats of present-day tidal-flat environments. Due to differences in water content and nature of the microbial mats and the underlying sediment, a wide range of footprint morphologies was produced by the same trackmaker. Most true tracks are subjected to modification due to taphonomic processes, leading to modified true tracks. In addition to formation of biolaminites, microbial mats play a major role in the preservation of footprints on tidal flats. A footprint may be consolidated by desiccation or lithification of the mat, or by ongoing growth of the mat. The latter process may lead to the formation of overtracks. Among consolidated or (partially) lithified footprints found on present-day tidal flats, poorly defined true tracks, modified true tracks, and overtracks were most frequently encountered while unmodified and well-defined true tracks are rather rare. We suggest that modified true tracks and overtracks make up an important percentage of fossil footprints and that they may be as common as undertracks. However, making unambiguous distinctions between poorly defined true tracks, modified true tracks, undertracks, and overtracks in the fossil record will remain a difficult task, which necessitates systematic excavation of footprints combined with careful analysis of the encasing sediment.

@article{doi10108010420940802471027,
    author = "Marty, Daniel and Strasser, André and Meyer, Christian A.",
    title = "Formation and Taphonomy of Human Footprints in Microbial Mats of Present-Day Tidal-flat Environments: Implications for the Study of Fossil Footprints",
    year = "2009",
    journal = "Ichnos/Ichnos : an international journal for plant and animal traces",
    abstract = "This study concerns the formation, taphonomy, and preservation of human footprints in microbial mats of present-day tidal-flat environments. Due to differences in water content and nature of the microbial mats and the underlying sediment, a wide range of footprint morphologies was produced by the same trackmaker. Most true tracks are subjected to modification due to taphonomic processes, leading to modified true tracks. In addition to formation of biolaminites, microbial mats play a major role in the preservation of footprints on tidal flats. A footprint may be consolidated by desiccation or lithification of the mat, or by ongoing growth of the mat. The latter process may lead to the formation of overtracks. Among consolidated or (partially) lithified footprints found on present-day tidal flats, poorly defined true tracks, modified true tracks, and overtracks were most frequently encountered while unmodified and well-defined true tracks are rather rare. We suggest that modified true tracks and overtracks make up an important percentage of fossil footprints and that they may be as common as undertracks. However, making unambiguous distinctions between poorly defined true tracks, modified true tracks, undertracks, and overtracks in the fossil record will remain a difficult task, which necessitates systematic excavation of footprints combined with careful analysis of the encasing sediment.",
    url = "https://doi.org/10.1080/10420940802471027",
    doi = "10.1080/10420940802471027",
    openalex = "W2103008101",
    references = "doi1010079789400904095, doi101016jtim200507008, doi10103820167, doi101046j13653091200000284x, doi101111j13653091200400649x, doi101144gslsp20042280106, doi1023073514674, doi1023073514964, doi1023073514973, doi105860choice273305, doi105860choice295709, doi105860choice332752, doi105860choice393984, doi107312lock90868, openalexw114509570, openalexw39955589, openalexw603337959"
}

@article{doi101016jtree201005002,
    author = "Quental, Tiago B. and Marshall, Charles R.",
    title = "Diversity dynamics: molecular phylogenies need the fossil record",
    year = "2010",
    journal = "Trends in Ecology \& Evolution",
    url = "https://doi.org/10.1016/j.tree.2010.05.002",
    doi = "10.1016/j.tree.2010.05.002",
    openalex = "W2157452947",
    references = "doi101017s0094837300016134, doi101073pnas111144698, doi101111j14754983200600612x"
}

@article{doi101038nature08745,
    author = "Sansom, Robert S. and Gabbott, Sarah E. and Purnell, Mark A.",
    title = "Non-random decay of chordate characters causes bias in fossil interpretation",
    year = "2010",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature08745",
    doi = "10.1038/nature08745",
    openalex = "W1980460712",
    references = "briggs2003the, doi101016jtree200504008, doi101016s0016703799000873, doi101017s0094837300009994, doi101038nature04336, doi101093icb431166, doi1010970000044619570500000033, doi101098rstb20072246, doi101111j146364091997tb00412x, doi101130g24961a1, doi101666061301"
}

@article{doi101038ngeo934,
    author = "Maloof, Adam C. and Rose, Catherine and Beach, Robert and Samuels, Bradley M. and Calmet, Claire and Erwin, Douglas H. and Poirier, Gerald and Yao, Nan and Simons, Frederik J.",
    title = "Possible animal-body fossils in pre-Marinoan limestones from South Australia",
    year = "2010",
    journal = "Nature Geoscience",
    url = "https://doi.org/10.1038/ngeo934",
    doi = "10.1038/ngeo934",
    openalex = "W2105844326",
    references = "briggs2003the, doi10103835318, doi101038nature07673, doi101046j13653091200000003x, doi101126science1107765, doi101128jb17320655865671991, doi101130b256301, doi101130g205191, openalexw2183707334, openalexw2912219260"
}

We present a complete phylogeny of macroperforate planktonic foraminifer species of the Cenozoic Era (∼65 million years ago to present). The phylogeny is developed from a large body of palaeontological work that details the evolutionary relationships and stratigraphic (time) distributions of species-level taxa identified from morphology ('morphospecies'). Morphospecies are assigned to morphogroups and ecogroups depending on test morphology and inferred habitat, respectively. Because gradual evolution is well documented in this clade, we have identified many instances of morphospecies intergrading over time, allowing us to eliminate 'pseudospeciation' and 'pseudoextinction' from the record and thereby permit the construction of a more natural phylogeny based on inferred biological lineages. Each cladogenetic event is determined as either budding or bifurcating depending on the pattern of morphological change at the time of branching. This lineage phylogeny provides palaeontologically calibrated ages for each divergence that are entirely independent of molecular data. The tree provides a model system for macroevolutionary studies in the fossil record addressing questions of speciation, extinction, and rates and patterns of evolution.

@article{doi101111j1469185x201100178x,
    author = "Aze, Tracy and Ezard, Thomas H. G. and Purvis, Andy and Coxall, Helen K. and Stewart, Duncan R. M. and Wade, Bridget S. and Pearson, Paul N.",
    title = "A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data",
    year = "2011",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "We present a complete phylogeny of macroperforate planktonic foraminifer species of the Cenozoic Era (∼65 million years ago to present). The phylogeny is developed from a large body of palaeontological work that details the evolutionary relationships and stratigraphic (time) distributions of species-level taxa identified from morphology ('morphospecies'). Morphospecies are assigned to morphogroups and ecogroups depending on test morphology and inferred habitat, respectively. Because gradual evolution is well documented in this clade, we have identified many instances of morphospecies intergrading over time, allowing us to eliminate 'pseudospeciation' and 'pseudoextinction' from the record and thereby permit the construction of a more natural phylogeny based on inferred biological lineages. Each cladogenetic event is determined as either budding or bifurcating depending on the pattern of morphological change at the time of branching. This lineage phylogeny provides palaeontologically calibrated ages for each divergence that are entirely independent of molecular data. The tree provides a model system for macroevolutionary studies in the fossil record addressing questions of speciation, extinction, and rates and patterns of evolution.",
    url = "https://doi.org/10.1111/j.1469-185x.2011.00178.x",
    doi = "10.1111/j.1469-185x.2011.00178.x",
    openalex = "W1989146507",
    references = "doi101016037783988790020x, doi101016jearscirev201009003, doi101016jmarmicro200801009, doi101017s0094837300004000, doi101017s0094837300012094, doi101017s0094837300016638, doi101038nature05634, doi101038nature06588, doi10108010635150600852011, doi101093sysbio463523, doi101111j1474919x1955tb01923x, doi101126science1059412, doi101146annurevecolsys33030602152151, doi101722611310, doi102110pec95040129, doi1023071485586, doi102307jctvjsf433, doi102687999013, doi105860choice295135, doi105860choice396411, doi107312simp92414, smith2007marine"
}

@book{openalexw2727239071,
    author = "Smith, James Perrin",
    title = "Marine Fossils from the Coal Measures of Arkansas",
    year = "2012",
    booktitle = "Biodiversity Heritage Library (Smithsonian Institution)",
    openalex = "W2727239071"
}

Authigenic pyrite preserves non-biomineralized tissues in the fossil record under exceptional circumstances. Diagenetic models and taphonomic experiments demonstrate that active, localized sulfate reduction in iron-rich pore waters results in a strong concentration gradient, which confines pyrite precipitation to decaying organic matter. The locus and timing of pyrite precipitation is also influenced by the original composition of the organic matter. In recent decades, new sites with three-dimensional pyritized soft tissues have been discovered, although the Hunsrück Slate (Devonian) and Beecher's Trilobite Bed (Ordovician), known since the late 1800s, remain the primary examples in terms of diversity, abundance, and quality of preservation. Sedimentological and geochemical analyses at these sites have shown that rapid burial in fine-grained, reworked sediments sets up the high iron, low organic carbon conditions necessary for soft-tissue pyritization. Soft-tissue pyritization may also occur in association with other taphonomic modes, in particular with Burgess Shale-type preservation and carbonaceous preservation in lakes, although many of these specimens are now weathered. Continued comparison among sites and between specimens with variable degrees of preservation could help clarify the limits to soft-tissue pyritization and its distribution in ancient sediments.

@article{doi101017s1089332600002795,
    author = "Farrell, Úna C.",
    title = "Pyritization of Soft Tissues in the Fossil Record: An Overview",
    year = "2014",
    journal = "The Paleontological Society Papers",
    abstract = "Authigenic pyrite preserves non-biomineralized tissues in the fossil record under exceptional circumstances. Diagenetic models and taphonomic experiments demonstrate that active, localized sulfate reduction in iron-rich pore waters results in a strong concentration gradient, which confines pyrite precipitation to decaying organic matter. The locus and timing of pyrite precipitation is also influenced by the original composition of the organic matter. In recent decades, new sites with three-dimensional pyritized soft tissues have been discovered, although the Hunsrück Slate (Devonian) and Beecher's Trilobite Bed (Ordovician), known since the late 1800s, remain the primary examples in terms of diversity, abundance, and quality of preservation. Sedimentological and geochemical analyses at these sites have shown that rapid burial in fine-grained, reworked sediments sets up the high iron, low organic carbon conditions necessary for soft-tissue pyritization. Soft-tissue pyritization may also occur in association with other taphonomic modes, in particular with Burgess Shale-type preservation and carbonaceous preservation in lakes, although many of these specimens are now weathered. Continued comparison among sites and between specimens with variable degrees of preservation could help clarify the limits to soft-tissue pyritization and its distribution in ancient sediments.",
    url = "https://doi.org/10.1017/s1089332600002795",
    doi = "10.1017/s1089332600002795",
    openalex = "W3112572013",
    references = "doi1010079781489950345, doi1010160016703779900954, doi1010160016703784900899, doi1010160016703789900057, doi1010160016703796002098, doi101016jchemgeo200409003, doi101021cr0503658, doi101139e06012, doi1015159780691209401, doi102475ajs26811, doi104319lo19842920236"
}

Climate refugia, locations where taxa survive periods of regionally adverse climate, are thought to be critical for maintaining biodiversity through the glacial-interglacial climate changes of the Quaternary. A critical research need is to better integrate and reconcile the three major lines of evidence used to infer the existence of past refugia - fossil records, species distribution models and phylogeographic surveys - in order to characterize the complex spatiotemporal trajectories of species and populations in and out of refugia. Here we review the complementary strengths, limitations and new advances for these three approaches. We provide case studies to illustrate their combined application, and point the way towards new opportunities for synthesizing these disparate lines of evidence. Case studies with European beech, Qinghai spruce and Douglas-fir illustrate how the combination of these three approaches successfully resolves complex species histories not attainable from any one approach. Promising new statistical techniques can capitalize on the strengths of each method and provide a robust quantitative reconstruction of species history. Studying past refugia can help identify contemporary refugia and clarify their conservation significance, in particular by elucidating the fine-scale processes and the particular geographic locations that buffer species against rapidly changing climate.

@article{doi101111nph12929,
    author = "Gavin, Daniel G. and Fitzpatrick, Matthew C. and Gugger, Paul F. and Heath, Katy D. and Rodríguez‐Sánchez, Francisco and Dobrowski, Solomon Z. and Hampe, Arndt and Hu, Feng Sheng and Ashcroft, Michael B. and Bartlein, Patrick J. and Blois, Jessica L. and Carstens, Bryan C. and Davis, Edward and de Lafontaine, Guillaume and Edwards, Mary E. and Fernandez, Matias and Henne, Paul D. and Herring, Erin M. and Holden, Zachary A. and Kong, Woo‐Seok and Liu, Jianquan and Magri, Donatella and Matzke, Nicholas J. and McGlone, Matt S. and Saltré, Frédérik and Stigall, Alycia L. and Tsai, Yi‐Hsin Erica and Williams, John W.",
    title = "Climate refugia: joint inference from fossil records, species distribution models and phylogeography",
    year = "2014",
    journal = "New Phytologist",
    abstract = "Climate refugia, locations where taxa survive periods of regionally adverse climate, are thought to be critical for maintaining biodiversity through the glacial-interglacial climate changes of the Quaternary. A critical research need is to better integrate and reconcile the three major lines of evidence used to infer the existence of past refugia - fossil records, species distribution models and phylogeographic surveys - in order to characterize the complex spatiotemporal trajectories of species and populations in and out of refugia. Here we review the complementary strengths, limitations and new advances for these three approaches. We provide case studies to illustrate their combined application, and point the way towards new opportunities for synthesizing these disparate lines of evidence. Case studies with European beech, Qinghai spruce and Douglas-fir illustrate how the combination of these three approaches successfully resolves complex species histories not attainable from any one approach. Promising new statistical techniques can capitalize on the strengths of each method and provide a robust quantitative reconstruction of species history. Studying past refugia can help identify contemporary refugia and clarify their conservation significance, in particular by elucidating the fine-scale processes and the particular geographic locations that buffer species against rapidly changing climate.",
    url = "https://doi.org/10.1111/nph.12929",
    doi = "10.1111/nph.12929",
    openalex = "W2122476379",
    references = "doi101016jpalaeo201107021, doi101016jtree201009010, doi101016jympev200909016, doi101017s0094837300026907, doi101098rspb20091272, doi101111j14668238201100686x, doi101111j14724642201000658x, doi101111j14754754200800394x, doi101130001676061949601315botp20co2, doi10166600948373200026103tap20co2"
}

@incollection{crossref2015fossils,
    title = "Fossils and fossilization",
    year = "2015",
    booktitle = "Fossil Primates",
    url = "https://doi.org/10.1017/cbo9780511793844.004",
    doi = "10.1017/cbo9780511793844.004",
    openalex = "W2494514411",
    pages = "36-58"
}

Progressive biomineralization of a skeleton occurs during ontogeny in most animals. In fishes, larvae are poorly mineralized, whereas juveniles and adults display a progressively more biomineralized skeleton. Fossil remains primarily consist of adult specimens because the fossilization of poorly-mineralized larvae and juveniles necessitates exceptional conditions. The Miguasha Fossil-Lagerstätte is renowned for its Late Devonian vertebrate fauna, revealing the exceptional preservation of fossilized ontogenies for 14 of the 20 fish species from this locality. The mineralization of anatomical structures of the acanthodian Triazeugacanthus affinis from Miguasha are compared among larval, juvenile and adult specimens using Energy Dispersive X-ray Spectrometry. Chemical composition of anatomical structures of Triazeugacanthus reveals differences between cartilage and bone. Although the histology and anatomy is well-preserved, Fourier transform infrared spectrometry shows that the original chemical composition of bone is altered by diagenesis; the mineral phase of the bone (i.e., hydroxyapatite) is modified chemically to form more stable carbonate-fluorapatite. Fluorination occurring in mineralized skeletal structures of adult Triazeugacanthus is indicative of exchanges between groundwater and skeleton at burial, whereas the preservation of larval soft tissues is likely owing to a rapid burial under anoxic conditions. The exceptional state of preservation of a fossilized ontogeny allowed us to characterize chemically the progressive mineralization of the skeleton in a Devonian early vertebrate.

@article{doi103390min6010001,
    author = "Chevrinais, Marion and Balan, Etienne and Cloutier, Richard",
    title = "New Insights in the Ontogeny and Taphonomy of the Devonian Acanthodian Triazeugacanthus affinis From the Miguasha Fossil-Lagerstätte, Eastern Canada",
    year = "2015",
    journal = "Minerals",
    abstract = "Progressive biomineralization of a skeleton occurs during ontogeny in most animals. In fishes, larvae are poorly mineralized, whereas juveniles and adults display a progressively more biomineralized skeleton. Fossil remains primarily consist of adult specimens because the fossilization of poorly-mineralized larvae and juveniles necessitates exceptional conditions. The Miguasha Fossil-Lagerstätte is renowned for its Late Devonian vertebrate fauna, revealing the exceptional preservation of fossilized ontogenies for 14 of the 20 fish species from this locality. The mineralization of anatomical structures of the acanthodian Triazeugacanthus affinis from Miguasha are compared among larval, juvenile and adult specimens using Energy Dispersive X-ray Spectrometry. Chemical composition of anatomical structures of Triazeugacanthus reveals differences between cartilage and bone. Although the histology and anatomy is well-preserved, Fourier transform infrared spectrometry shows that the original chemical composition of bone is altered by diagenesis; the mineral phase of the bone (i.e., hydroxyapatite) is modified chemically to form more stable carbonate-fluorapatite. Fluorination occurring in mineralized skeletal structures of adult Triazeugacanthus is indicative of exchanges between groundwater and skeleton at burial, whereas the preservation of larval soft tissues is likely owing to a rapid burial under anoxic conditions. The exceptional state of preservation of a fossilized ontogeny allowed us to characterize chemically the progressive mineralization of the skeleton in a Devonian early vertebrate.",
    url = "https://doi.org/10.3390/min6010001",
    doi = "10.3390/min6010001",
    openalex = "W2220426136",
    references = "doi1010079781489950345, doi101111j1469185x201200220x"
}

The fossil record provides the primary source of data for calibrating the origin of clades. Although minimum ages of clades are given by the oldest preserved fossil, these underestimate the true age, which must be bracketed by probabilistic methods based on multiple fossil occurrences. Although most of these methods assume uniform preservation rates, this assumption is unsupported over geological timescales. On geologically long timescales (more than 10 Myr), the origin and cessation of sedimentary basins, and long-term variations in tectonic subsidence, eustatic sea level and sedimentation rate control the availability of depositional facies that preserve the environments in which species lived. The loss of doomed sediments, those with a low probability of preservation, imparts a secular trend to fossil preservation. As a result, the fossil record is spatially and temporally non-uniform. Models of fossil preservation should reflect this non-uniformity by using empirical estimates of fossil preservation that are spatially and temporally partitioned, or by using indirect proxies of fossil preservation. Geologically, realistic models of preservation will provide substantially more reliable estimates of the origination of clades.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

@article{doi101098rstb20150130,
    author = "Holland, Steven M.",
    title = "The non-uniformity of fossil preservation",
    year = "2016",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "The fossil record provides the primary source of data for calibrating the origin of clades. Although minimum ages of clades are given by the oldest preserved fossil, these underestimate the true age, which must be bracketed by probabilistic methods based on multiple fossil occurrences. Although most of these methods assume uniform preservation rates, this assumption is unsupported over geological timescales. On geologically long timescales (more than 10 Myr), the origin and cessation of sedimentary basins, and long-term variations in tectonic subsidence, eustatic sea level and sedimentation rate control the availability of depositional facies that preserve the environments in which species lived. The loss of doomed sediments, those with a low probability of preservation, imparts a secular trend to fossil preservation. As a result, the fossil record is spatially and temporally non-uniform. Models of fossil preservation should reflect this non-uniformity by using empirical estimates of fossil preservation that are spatially and temporally partitioned, or by using indirect proxies of fossil preservation. Geologically, realistic models of preservation will provide substantially more reliable estimates of the origination of clades.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.",
    url = "https://doi.org/10.1098/rstb.2015.0130",
    doi = "10.1098/rstb.2015.0130",
    openalex = "W2467321918",
    references = "doi10100797890481864337, doi101086501220, doi101098rspb20142245, doi101111pala12042"
}

Les foraminiferes sont des organismes unicellulaires ubiquistes des habitats marins. Les foraminiferes benthiques modernes ont des caracteristiques specifiques (comme par exemple une abondance et une diversite elevees, une excellente preservation) qui en font un excellent outil pour mettre en evidence des changements environnementaux globaux et locaux. Dans un proche passe, les estuaires de la region des Hauts-de-France ont subi des influences humaines. Les objectifs principaux de ce travail sont 1) decrire les distributions des foraminiferes benthiques, et 2) investiguer leurs reponses aux variations a court-terme (a l’echelle des saisons) et a long-terme (centaines d’annees) dans les zones naturelles contaminees et non contaminees de la region. L’analyse des microfaunes est associee aux analyses sedimentologiques et geochimiques, pour mieux comprendre le controle qu'ont les parametres environnementaux sur les variations spatiales et temporales des foraminiferes benthiques. Dans le milieu intertidal, differentes associations de foraminiferes vivants sont distinguees en relation avec les principaux parametres guides identifies dans la region des Hauts-de-France. Les observations sur le long-terme ont permis de distinguer des transformations naturelles et anthropiques, a travers la surveillance des variations des foraminiferes benthiques. L’etude demontre le potentiel des foraminiferes comme bioindicateurs pour des applications dans la surveillance environnementale.

@phdthesis{doi1013140rg222087221761,
    author = "Francescangeli, Fabio",
    title = "Spatio-temporal distribution of benthic foraminifera in intertidal areas of hauts-de-france: environmental applications and implications",
    year = "2017",
    booktitle = "theses.fr (ABES)",
    abstract = "Les foraminiferes sont des organismes unicellulaires ubiquistes des habitats marins. Les foraminiferes benthiques modernes ont des caracteristiques specifiques (comme par exemple une abondance et une diversite elevees, une excellente preservation) qui en font un excellent outil pour mettre en evidence des changements environnementaux globaux et locaux. Dans un proche passe, les estuaires de la region des Hauts-de-France ont subi des influences humaines. Les objectifs principaux de ce travail sont 1) decrire les distributions des foraminiferes benthiques, et 2) investiguer leurs reponses aux variations a court-terme (a l’echelle des saisons) et a long-terme (centaines d’annees) dans les zones naturelles contaminees et non contaminees de la region. L’analyse des microfaunes est associee aux analyses sedimentologiques et geochimiques, pour mieux comprendre le controle qu'ont les parametres environnementaux sur les variations spatiales et temporales des foraminiferes benthiques. Dans le milieu intertidal, differentes associations de foraminiferes vivants sont distinguees en relation avec les principaux parametres guides identifies dans la region des Hauts-de-France. Les observations sur le long-terme ont permis de distinguer des transformations naturelles et anthropiques, a travers la surveillance des variations des foraminiferes benthiques. L’etude demontre le potentiel des foraminiferes comme bioindicateurs pour des applications dans la surveillance environnementale.",
    url = "https://doi.org/10.13140/rg.2.2.20872.21761",
    doi = "10.13140/rg.2.2.20872.21761",
    openalex = "W2690998659"
}

@article{doi101016jearscirev201902020,
    author = "Klompmaker, Adiël A. and Kelley, Patricia H. and Chattopadhyay, Devapriya and Clements, Jeff C. and Huntley, John Warren and Kowalewski, Michał",
    title = "Predation in the marine fossil record: Studies, data, recognition, environmental factors, and behavior",
    year = "2019",
    journal = "Earth-Science Reviews",
    url = "https://doi.org/10.1016/j.earscirev.2019.02.020",
    doi = "10.1016/j.earscirev.2019.02.020",
    openalex = "W2917611271",
    references = "doi101016001669959180043y, doi1010160195667182900416, doi101016jpalaeo200909010, doi101016jpalwor201104001, doi101016s001282520300014x, doi101080027246342011601714, doi101111j150239312002tb00062x, doi101111pala12042, doi101111pala12254, doi101146annureves10110179001551, doi101371journalpone0052200, morris1979the"
}

@article{doi101016jearscirev201904008,
    author = "Marchetti, Lorenzo and Belvedere, Matteo and Voigt, Sebastian and Klein, Hendrik and Castanera, Diego and Díaz‐Martínez, Ignacio and Marty, Daniel and Xing, Lida and Feola, Silverio and Melchor, Ricardo N. and Farlow, James O.",
    title = "Defining the morphological quality of fossil footprints. Problems and principles of preservation in tetrapod ichnology with examples from the Palaeozoic to the present",
    year = "2019",
    journal = "Earth-Science Reviews",
    url = "https://doi.org/10.1016/j.earscirev.2019.04.008",
    doi = "10.1016/j.earscirev.2019.04.008",
    openalex = "W2937229098",
    references = "doi1010079783540472261, doi1010160025322767900515, doi101016jearscirev201608009, doi101016s0012821x0100588x, doi101016s0031018296001423, doi101016s0031018297852005, doi101017cbo9780511975622, doi101017s0025315400028198, doi101017s0025315400028575, doi101017s009483730001143x, doi101017s0094837300026907, doi10103820167, doi101073pnas1416252111, doi10108000241160600787890, doi10108002724634199510011271, doi1010800272463420171314298, doi10108008912960903503345, doi1010801042094020171350856, doi10108010420940802471027, doi101098rstb19920051, doi101111jzo12110, doi101144pygs543185, doi101371journalpone0004591, doi101371journalpone0180289, doi10166600948373200026103tap20co2, doi1023073514457, doi1023073514964, doi105860choice273305, doi105860choice435907, doi105860choice456807, doi107312lock90868, openalexw2149387945, openalexw2619609965, openalexw39955589, openalexw560158229"
}

Present knowledge of Late Triassic tetrapod evolution, including the rise of dinosaurs, relies heavily on the fossil-rich continental deposits of South America, their precise depositional histories and correlations. We report on an extended succession of the Ischigualasto Formation exposed in the Hoyada del Cerro Las Lajas (La Rioja, Argentina), where more than 100 tetrapod fossils were newly collected, augmented by historical finds such as the ornithosuchid Venaticosuchus rusconii and the putative ornithischian Pisanosaurus mertii. Detailed lithostratigraphy combined with high-precision U-Pb geochronology from three intercalated tuffs are used to construct a robust Bayesian age model for the formation, constraining its deposition between 230.2 ± 1.9 Ma and 221.4 ± 1.2 Ma, and its fossil-bearing interval to 229.20 + 0.11/- 0.15-226.85 + 1.45/- 2.01 Ma. The latter is divided into a lower Hyperodapedon and an upper Teyumbaita biozones, based on the ranges of the eponymous rhynchosaurs, allowing biostratigraphic correlations to elsewhere in the Ischigualasto-Villa Unión Basin, as well as to the Paraná Basin in Brazil. The temporally calibrated Ischigualasto biostratigraphy suggests the persistence of rhynchosaur-dominated faunas into the earliest Norian. Our ca. 229 Ma age assignment to Pi. mertii partially fills the ghost lineage between younger ornithischian records and the oldest known saurischians at ca. 233 Ma.

@article{doi101038s41598020678541,
    author = "Desojo, Julia B. and Fiorelli, Lucas E. and Ezcurra, Martín D. and Martinelli, Agustín G. and Ramezani, Jahandar and da Rosa, Átila Augusto Stock and von Baczko, M. Belén and Trotteyn, M. Jimena and Montefeltro, Felipe C. and Ezpeleta, Miguel and Langer, Max C.",
    title = "The Late Triassic Ischigualasto Formation at Cerro Las Lajas (La Rioja, Argentina): fossil tetrapods, high-resolution chronostratigraphy, and faunal correlations",
    year = "2020",
    journal = "Scientific Reports",
    abstract = "Present knowledge of Late Triassic tetrapod evolution, including the rise of dinosaurs, relies heavily on the fossil-rich continental deposits of South America, their precise depositional histories and correlations. We report on an extended succession of the Ischigualasto Formation exposed in the Hoyada del Cerro Las Lajas (La Rioja, Argentina), where more than 100 tetrapod fossils were newly collected, augmented by historical finds such as the ornithosuchid Venaticosuchus rusconii and the putative ornithischian Pisanosaurus mertii. Detailed lithostratigraphy combined with high-precision U-Pb geochronology from three intercalated tuffs are used to construct a robust Bayesian age model for the formation, constraining its deposition between 230.2 ± 1.9 Ma and 221.4 ± 1.2 Ma, and its fossil-bearing interval to 229.20 + 0.11/- 0.15-226.85 + 1.45/- 2.01 Ma. The latter is divided into a lower Hyperodapedon and an upper Teyumbaita biozones, based on the ranges of the eponymous rhynchosaurs, allowing biostratigraphic correlations to elsewhere in the Ischigualasto-Villa Unión Basin, as well as to the Paraná Basin in Brazil. The temporally calibrated Ischigualasto biostratigraphy suggests the persistence of rhynchosaur-dominated faunas into the earliest Norian. Our ca. 229 Ma age assignment to Pi. mertii partially fills the ghost lineage between younger ornithischian records and the oldest known saurischians at ca. 233 Ma.",
    url = "https://doi.org/10.1038/s41598-020-67854-1",
    doi = "10.1038/s41598-020-67854-1",
    openalex = "W3045879460",
    references = "doi101016c20090644421, doi101016jgr201801005, doi101016jquascirev200807009, doi101016s0753396900800026, doi101017cbo9780511612381, doi101017s1755691013000431, doi101038nature22037, doi101073pnas1402369111, doi101080027246342013818546, doi101080027246342013820113, doi101080031155182015994114, doi101098rstb19740001, doi101111j109600311988tb00514x, doi101111j10963642200900631x, doi101111j14679876200800623x, doi101126science1198467, doi101144sp37916, doi1012063521, doi1018814epiiugs2013v36i3002, doi1023071005355, doi1023072413376, doi107717peerj1778"
}

Abstract Spatiotemporal changes in fossil specimen completeness can bias our understanding of a group's evolutionary history. The quality of the sauropodomorph fossil record was assessed a decade ago, but the number of valid species has since increased by 60%, and 17% of the taxa from that study have since undergone taxonomic revision. Here, we assess how 10 years of additional research has changed our outlook on the group's fossil record. We quantified the completeness of all 307 sauropodomorph species currently considered valid using the skeletal completeness metric, which calculates the proportion of a complete skeleton preserved for each taxon. Taxonomic and stratigraphic age revisions, rather than new species, are the drivers of the most significant differences between the current results and those of the previous assessment. No statistical differences appeared when we use our new dataset to generate temporal completeness curves based solely on taxa known in 2009 or 1999. We now observe a severe drop in mean completeness values across the Jurassic–Cretaceous boundary that never recovers to pre‐Cretaceous levels. Explaining this pattern is difficult, as we find no convincing evidence that it is related to environmental preferences or body size changes. Instead, it might result from: (1) reduction of terrestrial fossil preservation space due to sea level rise; (2) ecological specificities and relatively high diagnosability of Cretaceous species; and/or (3) increased sampling of newly explored sites with many previously unknown taxa. Revisiting patterns in this manner allows us to test the longevity of conclusions made in previous quantitative studies.

@article{doi101111pala12496,
    author = "Cashmore, Daniel D. and Mannion, Philip D. and Upchurch, Paul and Butler, Richard J.",
    title = "Ten more years of discovery: revisiting the quality of the sauropodomorph dinosaur fossil record",
    year = "2020",
    journal = "Palaeontology",
    abstract = "Abstract Spatiotemporal changes in fossil specimen completeness can bias our understanding of a group's evolutionary history. The quality of the sauropodomorph fossil record was assessed a decade ago, but the number of valid species has since increased by 60\%, and 17\% of the taxa from that study have since undergone taxonomic revision. Here, we assess how 10 years of additional research has changed our outlook on the group's fossil record. We quantified the completeness of all 307 sauropodomorph species currently considered valid using the skeletal completeness metric, which calculates the proportion of a complete skeleton preserved for each taxon. Taxonomic and stratigraphic age revisions, rather than new species, are the drivers of the most significant differences between the current results and those of the previous assessment. No statistical differences appeared when we use our new dataset to generate temporal completeness curves based solely on taxa known in 2009 or 1999. We now observe a severe drop in mean completeness values across the Jurassic–Cretaceous boundary that never recovers to pre‐Cretaceous levels. Explaining this pattern is difficult, as we find no convincing evidence that it is related to environmental preferences or body size changes. Instead, it might result from: (1) reduction of terrestrial fossil preservation space due to sea level rise; (2) ecological specificities and relatively high diagnosability of Cretaceous species; and/or (3) increased sampling of newly explored sites with many previously unknown taxa. Revisiting patterns in this manner allows us to test the longevity of conclusions made in previous quantitative studies.",
    url = "https://doi.org/10.1111/pala.12496",
    doi = "10.1111/pala.12496",
    openalex = "W3017772092",
    references = "doi1010079780387981413, doi1010079783319242774, doi101016jjsames201411008, doi101016jpalaeo200901002, doi101016jpalaeo200906004, doi101016s0016787876800077, doi101038s41467018051281, doi101038s41467019089972, doi101046j14209101200200472x, doi101073pnas1521478113, doi10108008912969009386535, doi101093bioinformaticsbty633, doi101093zoolinneanzlx103, doi101093zoolinneanzly009, doi101093zoolinneanzly068, doi101098rsbl20180431, doi101098rspb20122526, doi101111brv12255, doi101111j2041210x201100169x, doi101111j2041210x201200196x, doi101111j251761611995tb02031x, doi101126science1105113, doi101126science23547931156, doi101371journalpone0078573, openalexw2611511275"
}

Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ 18 novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise the phylogeny and divergence times of echinoids, and place their history within the broader context of echinoderm evolution. We also introduce the concept of a chronospace - a multidimensional representation of node ages - and use it to explore methodological decisions involved in time calibrating phylogenies. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models and alternative node prior distributions show minimal effects. The choice of loci has an intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent with fossil evidence. Our results reveal that crown group echinoids originated in the Permian and diversified rapidly in the Triassic, despite the relative lack of fossil evidence for this early diversification. We also clarify the relationships between sand dollars and their close relatives and confidently date their origins to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.

@article{doi107554elife72460,
    author = "Koch, Nicolás Mongiardino and Thompson, Jeffrey R. and Hiley, Avery S. and McCowin, Marina F. and Armstrong, Anne Frances and Coppard, Simon E. and Aguilera, Felipe and Bronstein, Omri and Kroh, Andreas and Mooi, Rich and Rouse, Greg W.",
    title = "Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record",
    year = "2022",
    journal = "eLife",
    abstract = "Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ 18 novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise the phylogeny and divergence times of echinoids, and place their history within the broader context of echinoderm evolution. We also introduce the concept of a chronospace - a multidimensional representation of node ages - and use it to explore methodological decisions involved in time calibrating phylogenies. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models and alternative node prior distributions show minimal effects. The choice of loci has an intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent with fossil evidence. Our results reveal that crown group echinoids originated in the Permian and diversified rapidly in the Triassic, despite the relative lack of fossil evidence for this early diversification. We also clarify the relationships between sand dollars and their close relatives and confidently date their origins to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.",
    url = "https://doi.org/10.7554/elife.72460",
    doi = "10.7554/elife.72460",
    openalex = "W4225692575",
    references = "doi101017s0094837300005248"
}

@article{doi101016jearscirev2023104537,
    author = "Nanglu, Karma and Cullen, Thomas M.",
    title = "Across space and time: A review of sampling, preservational, analytical, and anthropogenic biases in fossil data across macroecological scales",
    year = "2023",
    journal = "Earth-Science Reviews",
    url = "https://doi.org/10.1016/j.earscirev.2023.104537",
    doi = "10.1016/j.earscirev.2023.104537",
    openalex = "W4385621646",
    references = "carrano2016vertebrate, connell1961effects, doi101007bf00345739, doi101007s003380000129, doi101016003101829090202i, doi101016jpalaeo201512015, doi101016jtree202009001, doi101017pab201637, doi101017pab201942, doi101017s2475263000001021, doi101038s41467021237540, doi101080027246342012717567, doi101093nsrnwt032, doi101098rsbl20180431, doi1011112041210x12666, doi101111j14610248200400608x, doi101111pala12591, doi101126science1156963, doi101126science1206375, doi101126science13134091292, doi101126science21545391501, doi101126scienceabd9220, doi101130g473991, doi101130g479071, doi101139cjes20120185, doi101144jgs2015017, doi101186s1289801601068, doi1016660094837336180, doi10166612056, doi1018900012965820020831771tuntob20co2, doi102110palo2014084, doi105962bhltitle115853, eberth1990stratigraphy, openalexw2561546966"
}

@misc{crossrefNonefossils,
    title = "Fossils and fossilization",
    year = "None",
    booktitle = "SpringerReference",
    url = "https://doi.org/10.1007/springerreference\_43497",
    doi = "10.1007/springerreference\_43497",
    openalex = "W4251942143"
}

@incollection{finksNonefossils,
    author = "Finks, Robert M.",
    title = "Fossils and fossilization",
    year = "None",
    booktitle = "Encyclopedia of Earth Science",
    url = "https://doi.org/10.1007/3-540-31078-9\_62",
    doi = "10.1007/3-540-31078-9\_62",
    openalex = "W1032096371",
    pages = "327-332",
    references = "doi1010160016703765901183, doi1010160034666775900056, doi101146annurevea03050175001151"
}