Mammalian evolution

@inproceedings{huxley1880on3,
    author = "Huxley, T. H",
    title = "On the application of the laws of evolution to the arrangement of the Vertebrata, and more particularly of the Mammalia",
    year = "1880",
    booktitle = "Proceedings of the Zoological Society of London, v. 43, p. 649-661",
    note = "talkorigins\_source = {true}; raw\_reference = {Huxley, T. H., 1880, On the application of the laws of evolution to the arrangement of the Vertebrata, and more particularly of the Mammalia: Proceedings of the Zoological Society of London, v. 43, p. 649-661.}"
}

@misc{crompton1968the1,
    author = "Crompton, A. W",
    title = "The enigma of the evolution of mammals",
    year = "1968",
    howpublished = "Optima, v. 18, p. 137-151",
    note = "talkorigins\_source = {true}; raw\_reference = {Crompton, A. W., 1968, The enigma of the evolution of mammals: Optima, v. 18, p. 137-151.}"
}

Certain worm-like configurations on rocks are recognized as shrinkage-crack infillings. Some genuine Precambrian trace fossils are briefly described. The early Cambrian contains a richer assemblage, including some distinctive and widespread form genera. The study of early trace fossils leads to conclusions not only on facies, but also on the evolution of behaviour and functional morphology in soft-bodied organisms.

@article{doi101111j150239311969tb01258x,
    author = "Glaessner, Martin F.",
    title = "TRACE FOSSILS FROM THE PRECAMBRIAN AND BASAL CAMBRIAN",
    year = "1969",
    journal = "Lethaia",
    abstract = "Certain worm-like configurations on rocks are recognized as shrinkage-crack infillings. Some genuine Precambrian trace fossils are briefly described. The early Cambrian contains a richer assemblage, including some distinctive and widespread form genera. The study of early trace fossils leads to conclusions not only on facies, but also on the evolution of behaviour and functional morphology in soft-bodied organisms.",
    url = "https://doi.org/10.1111/j.1502-3931.1969.tb01258.x",
    doi = "10.1111/j.1502-3931.1969.tb01258.x",
    openalex = "W1975727583",
    references = "doi1010160031018266900113, doi101038scientificamerican036172, doi10108011035896509448903, doi101086626811, doi101111j1469185x1962tb01331x, doi101111j150239311968tb01740x, doi101126science1543750766, doi101130gsab481873, doi101144gsljgs1890046010439, openalexw2170541304, openalexw2586923183"
}

The structure and evolution of the mandible, suspensorium, and stapes of mammal-like reptiles and early mammals are examined in an attempt to determine how, why, and when in phylogeny the precursors of the mammalian tympanic bone, malleus, and incus (postdentary jaw elements and quadrate) came to function in the reception of air-borne sound. The following conclusions are reached: It is possible that at no stage in mammalian phylogeny was there a middle ear similar to that of "typical" living reptiles, with a postquadrate tympanic membrane contracted by an extrastapes. The aquamosal sulcus of cynodonts and other therapsids, usually thought to have housed a long external acoustic meatus, possibly held a depressor mandibulae muscle. In therapsids an air-filled chamber (recessus mandibularis of Westoll) extended deep to the reflected lamina and into the depression (external fossa) on the outer aspect of the angular element. A similar chamber was present in sphenacodontids but pterygoideus musculature occupied the small external fossa. The thin tissues superficial to the recessus mandibularis served as eardrum. Primitively, vibrations reached the stapes mainly via the anterior hyoid cornu, but in dicynodonts, therocephalians, and cynodants vibrations passed mainly or exclusively from mandible to quadrate to stapes and the reflected lamina was a component of the eardrum. In the therapsid phase of mammalian phylogeny, auditory adaptation was an important aspect of jaw evolution. Auditory efficiency, and sensitivity to higher sound frequencies were enhanced by diminution and loosening of the postdentary elements and quadrate, along with transference of musculature from postdentary elements to the dentary. These changes were made possible by associated modifications, including posterior expansion of the dentary. Establishment of a dentary-squamosal articulation permitted continuation of these trends, leading to the definitive mammalian condition, with no major change in auditory mechanism except that in most mammals (not monotremes) the angular, as tympanic, eventually bcame a non-vibrating structure.

@article{doi101002jmor1051470404,
    author = "Allin, Edgar F.",
    title = "Evolution of the mammalian middle ear",
    year = "1975",
    journal = "Journal of Morphology",
    abstract = {The structure and evolution of the mandible, suspensorium, and stapes of mammal-like reptiles and early mammals are examined in an attempt to determine how, why, and when in phylogeny the precursors of the mammalian tympanic bone, malleus, and incus (postdentary jaw elements and quadrate) came to function in the reception of air-borne sound. The following conclusions are reached: It is possible that at no stage in mammalian phylogeny was there a middle ear similar to that of "typical" living reptiles, with a postquadrate tympanic membrane contracted by an extrastapes. The aquamosal sulcus of cynodonts and other therapsids, usually thought to have housed a long external acoustic meatus, possibly held a depressor mandibulae muscle. In therapsids an air-filled chamber (recessus mandibularis of Westoll) extended deep to the reflected lamina and into the depression (external fossa) on the outer aspect of the angular element. A similar chamber was present in sphenacodontids but pterygoideus musculature occupied the small external fossa. The thin tissues superficial to the recessus mandibularis served as eardrum. Primitively, vibrations reached the stapes mainly via the anterior hyoid cornu, but in dicynodonts, therocephalians, and cynodants vibrations passed mainly or exclusively from mandible to quadrate to stapes and the reflected lamina was a component of the eardrum. In the therapsid phase of mammalian phylogeny, auditory adaptation was an important aspect of jaw evolution. Auditory efficiency, and sensitivity to higher sound frequencies were enhanced by diminution and loosening of the postdentary elements and quadrate, along with transference of musculature from postdentary elements to the dentary. These changes were made possible by associated modifications, including posterior expansion of the dentary. Establishment of a dentary-squamosal articulation permitted continuation of these trends, leading to the definitive mammalian condition, with no major change in auditory mechanism except that in most mammals (not monotremes) the angular, as tympanic, eventually bcame a non-vibrating structure.},
    url = "https://doi.org/10.1002/jmor.1051470404",
    doi = "10.1002/jmor.1051470404",
    openalex = "W2050505441",
    references = "doi101111j109636421973tb00786x"
}

@incollection{crossref1977chapter,
    title = "Chapter 2 General Patterns of Metazoan Evolution",
    year = "1977",
    booktitle = "Developments in Palaeontology and Stratigraphy",
    url = "https://doi.org/10.1016/s0920-5446(08)70322-4",
    doi = "10.1016/s0920-5446(08)70322-4",
    openalex = "W2144968695",
    pages = "27-57",
    references = "doi101086282398, doi101086406830, doi101093aesa383396, doi101111j150239311971tb01864x, doi101130spe89p63, doi1023072405671, openalexw1480175384, openalexw2145250129, openalexw2418669733, openalexw3126336940"
}

@book{crossref1977patterns,
    title = "Patterns of Evolution as Illustrated by the Fossil Record",
    year = "1977",
    booktitle = "Developments in Palaeontology and Stratigraphy",
    url = "https://doi.org/10.1016/s0920-5446(08)x7012-8",
    doi = "10.1016/s0920-5446(08)x7012-8",
    openalex = "W563635432"
}

@book{gingerich1977patterns2,
    author = "Gingerich, P. D",
    title = "Patterns of Evolution in the Mammalian Fossil Record, in Hallam, A., ed., Patterns of Evolution as Illustrated by the Fossil Record",
    year = "1977",
    publisher = "Amsterdam, Elsevier, p. 469-500",
    note = "talkorigins\_source = {true}; raw\_reference = {Gingerich, P. D., 1977, Patterns of Evolution in the Mammalian Fossil Record, in Hallam, A., ed., Patterns of Evolution as Illustrated by the Fossil Record: Amsterdam, Elsevier, p. 469-500.}"
}

@article{bretsky1978patterns,
    author = "Bretsky, Sara S.",
    title = "Patterns of Evolution as Illustrated by the Fossil Record. A. Hallam",
    year = "1978",
    journal = "The Quarterly Review of Biology",
    url = "https://doi.org/10.1086/410816",
    doi = "10.1086/410816",
    number = "4",
    openalex = "W2514820112",
    pages = "431-432",
    volume = "53"
}

@article{simpson1978patterns,
    author = "SIMPSON, G",
    title = "Patterns of evolution, as illustrated by the fossil record",
    year = "1978",
    journal = "Earth-Science Reviews",
    url = "https://doi.org/10.1016/0012-8252(78)90014-4",
    doi = "10.1016/0012-8252(78)90014-4",
    number = "2",
    openalex = "W3036197351",
    pages = "177-178",
    volume = "14"
}

@article{cowen1979patterns,
    author = "Cowen, R.",
    title = "Patterns of evolution as illustrated by the fossil record",
    year = "1979",
    journal = "Palaeogeography, Palaeoclimatology, Palaeoecology",
    url = "https://doi.org/10.1016/0031-0182(79)90127-5",
    doi = "10.1016/0031-0182(79)90127-5",
    openalex = "W2323803959",
    pages = "323-324",
    volume = "28"
}

@article{haugh1979patterns,
    author = "Haugh, Bruce N.",
    title = "Patterns of evolution as illustrated by the fossil record",
    year = "1979",
    journal = "Precambrian Research",
    url = "https://doi.org/10.1016/0301-9268(79)90046-9",
    doi = "10.1016/0301-9268(79)90046-9",
    number = "1-2",
    openalex = "W2612078796",
    pages = "147-148",
    volume = "8"
}

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"
}

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"
}

Surprisingly, there is a relationship between rates of sediment accumulation and the time spans for which they have been calculated. This relationship can be used to estimate expected rates for specific sedimentary environments and time spans. The most probable completeness of a given sedimentary section at a given short time span can be calculated by the ratio of the measured long-term rate of sediment accumulation to the expected short-term rate. Although the measured time span is usually based on radiometric and paleomagnetic data, the cumulative time of formation estimated from fossil soils in a sequence may also be used to calculate rates and may be useful in comparing the completeness and rate of accumulation of different sequences. By both kinds of estimates, terrestrial sedimentary successions are disappointingly incomplete. Some reasons for incompleteness are illustrated with a simple model of episodic flooding, exceeding a threshold for destruction and sedimentation over a particular kind of vegetation, and thus initiating a new cycle of soil formation. In such a model, rock record is lost to erosion during cutting and filling cycles, to overprinting of weakly developed soils by later, better-developed soils, and to continued development, near steady state, of the soils preserved. Because fossil soils are evidence of ancient environments and ecosystems independent of the fossil record, they may provide evidence of expected kinds of fossils, such as silica phytoliths, calcareous phytoliths, pollen, leaves, fruits, seeds, charcoal, land snails, coprolites, and bones. The degree to which the kinds of fossils actually found fail to meet these expectations is a crude measure of the completeness of representation of a former ecosystem in the fossil record. Some of the discrepancy between expected and actual occurrence of fossils can be related to the original Eh and pH of a fossil soil, as approximated by the oxidation state of iron in its minerals (for Eh) and by carbonate or zeolite content (for pH). Different kinds of fossils can be envisaged as having a characteristic Eh-pH stability field within which they can be expected to have been preserved if originally present. Even under ideal conditions of preservation, it takes some time for fossils to accumulate in soils to levels at which representative collections can be made. Estimates of this temporal control on preservation can be gained by comparing fossil occurrences with the degree of development of fossil soils. Neither these chemical nor temporal factors account fully for the degree of incompleteness observed because original abundance, trampling, predation and many other factors are also important determinants of fossil occurrence. These considerations can be used as guidelines for choosing stratigraphic sections appropriate for particular paleobiological and geological problems. For example, a study of speciation of terrestrial vertebrates would best be in a sequence of weakly developed, calcareous fossil soils (Entisols and Inceptisols), of near-uniform texture and yellow to brown color, formed under an extraordinarily high long-term rate of sediment accumulation. On the other hand, a study of coevolution of vertebrates and plants would best be based on a sequence of weakly to moderately developed, calcareous fossil soils of predominantly drab (gray, green, and blue) color, with interbedded carbonaceous shales.

@article{doi101017s0094837300008022,
    author = "Retallack, Greg",
    title = "Completeness of the rock and fossil record: some estimates using fossil soils",
    year = "1984",
    journal = "Paleobiology",
    abstract = "Surprisingly, there is a relationship between rates of sediment accumulation and the time spans for which they have been calculated. This relationship can be used to estimate expected rates for specific sedimentary environments and time spans. The most probable completeness of a given sedimentary section at a given short time span can be calculated by the ratio of the measured long-term rate of sediment accumulation to the expected short-term rate. Although the measured time span is usually based on radiometric and paleomagnetic data, the cumulative time of formation estimated from fossil soils in a sequence may also be used to calculate rates and may be useful in comparing the completeness and rate of accumulation of different sequences. By both kinds of estimates, terrestrial sedimentary successions are disappointingly incomplete. Some reasons for incompleteness are illustrated with a simple model of episodic flooding, exceeding a threshold for destruction and sedimentation over a particular kind of vegetation, and thus initiating a new cycle of soil formation. In such a model, rock record is lost to erosion during cutting and filling cycles, to overprinting of weakly developed soils by later, better-developed soils, and to continued development, near steady state, of the soils preserved. Because fossil soils are evidence of ancient environments and ecosystems independent of the fossil record, they may provide evidence of expected kinds of fossils, such as silica phytoliths, calcareous phytoliths, pollen, leaves, fruits, seeds, charcoal, land snails, coprolites, and bones. The degree to which the kinds of fossils actually found fail to meet these expectations is a crude measure of the completeness of representation of a former ecosystem in the fossil record. Some of the discrepancy between expected and actual occurrence of fossils can be related to the original Eh and pH of a fossil soil, as approximated by the oxidation state of iron in its minerals (for Eh) and by carbonate or zeolite content (for pH). Different kinds of fossils can be envisaged as having a characteristic Eh-pH stability field within which they can be expected to have been preserved if originally present. Even under ideal conditions of preservation, it takes some time for fossils to accumulate in soils to levels at which representative collections can be made. Estimates of this temporal control on preservation can be gained by comparing fossil occurrences with the degree of development of fossil soils. Neither these chemical nor temporal factors account fully for the degree of incompleteness observed because original abundance, trampling, predation and many other factors are also important determinants of fossil occurrence. These considerations can be used as guidelines for choosing stratigraphic sections appropriate for particular paleobiological and geological problems. For example, a study of speciation of terrestrial vertebrates would best be in a sequence of weakly developed, calcareous fossil soils (Entisols and Inceptisols), of near-uniform texture and yellow to brown color, formed under an extraordinarily high long-term rate of sediment accumulation. On the other hand, a study of coevolution of vertebrates and plants would best be based on a sequence of weakly to moderately developed, calcareous fossil soils of predominantly drab (gray, green, and blue) color, with interbedded carbonaceous shales.",
    url = "https://doi.org/10.1017/s0094837300008022",
    doi = "10.1017/s0094837300008022",
    openalex = "W1865803994",
    references = "crossref1977chapter, doi1010079781461261124, doi101016039055197790076x, doi101017s0094837300005820, doi101086626659, doi101086628623, doi1010970001069419650700000024, doi1010970001069419660500000001, doi102307141416, doi104324978020337108412, doi105860choice493882"
}

Abstract- Several prominent cladists have questioned the importance of fossils in phylogenctic inference, and it is becoming increasingly popular to simply fit extinct forms, if they are considered at all, to a cladogram of Recent taxa. Gardiner's (1982) and Løvtrup's (1985) study of amniote phylogeny exemplifies this differential treatment, and we focused on that group of organisms to test the proposition that fossils cannot overturn a theory of relationships based only on the Recent biota. Our parsimony analysis of amniote phylogeny, special knowledge contributed by fossils being scrupulously avoided, led to the following best fitting classification, which is similar to the novel hypothesis Gardiner published: (lepidosaurs (turtles (mammals (birds, crocodiles)))). However, adding fossils resulted in a markedly different most parsimonious cladogram of the extant taxa: (mammals (turtles (lepidosaurs (birds, crocodiles)))). That classification is like the traditional hypothesis, and it provides a better fit to the stratigraphic record. To isolate the extinct taxa responsible for the latter classification, the data were successively partitioned with each phylogenetic analysis, and we concluded that: (1) the ingroup, not the outgroup, fossils were important; (2) synapsid, not reptile, fossils were pivotal; (3) certain synapsid fossils, not the earliest or latest, were responsible. The critical nature of the synapsid fossils seemed to lie in the particular combination of primitive and derived character slates they exhibited. Classifying those fossils, along with mammals, as the sister group to the lineage consisting of birds and crocodiles resulted in a relatively poor fit to data; one involving a 2-4 fold increase in evolutionary reversals! Thus, the importance of the critical fossils, collectively or individually, seems to reside in their relative primitive-ness, and the simplest explanation for their more conservative nature is that they have had less time to evolve. While fossils may be important in phylogenetic inference only under certain conditions, there is no compelling reason to prejudge their contribution. We urge systematists to evaluate fairly all of the available evidence.

@article{doi101111j109600311988tb00514x,
    author = "Gauthier, Jacques and Kluge, Arnold G. and Rowe, Timothy",
    title = "AMNIOTE PHYLOGENY AND THE IMPORTANCE OF FOSSILS",
    year = "1988",
    journal = "Cladistics",
    abstract = "Abstract- Several prominent cladists have questioned the importance of fossils in phylogenctic inference, and it is becoming increasingly popular to simply fit extinct forms, if they are considered at all, to a cladogram of Recent taxa. Gardiner's (1982) and Løvtrup's (1985) study of amniote phylogeny exemplifies this differential treatment, and we focused on that group of organisms to test the proposition that fossils cannot overturn a theory of relationships based only on the Recent biota. Our parsimony analysis of amniote phylogeny, special knowledge contributed by fossils being scrupulously avoided, led to the following best fitting classification, which is similar to the novel hypothesis Gardiner published: (lepidosaurs (turtles (mammals (birds, crocodiles)))). However, adding fossils resulted in a markedly different most parsimonious cladogram of the extant taxa: (mammals (turtles (lepidosaurs (birds, crocodiles)))). That classification is like the traditional hypothesis, and it provides a better fit to the stratigraphic record. To isolate the extinct taxa responsible for the latter classification, the data were successively partitioned with each phylogenetic analysis, and we concluded that: (1) the ingroup, not the outgroup, fossils were important; (2) synapsid, not reptile, fossils were pivotal; (3) certain synapsid fossils, not the earliest or latest, were responsible. The critical nature of the synapsid fossils seemed to lie in the particular combination of primitive and derived character slates they exhibited. Classifying those fossils, along with mammals, as the sister group to the lineage consisting of birds and crocodiles resulted in a relatively poor fit to data; one involving a 2-4 fold increase in evolutionary reversals! Thus, the importance of the critical fossils, collectively or individually, seems to reside in their relative primitive-ness, and the simplest explanation for their more conservative nature is that they have had less time to evolve. While fossils may be important in phylogenetic inference only under certain conditions, there is no compelling reason to prejudge their contribution. We urge systematists to evaluate fairly all of the available evidence.",
    url = "https://doi.org/10.1111/j.1096-0031.1988.tb00514.x",
    doi = "10.1111/j.1096-0031.1988.tb00514.x",
    openalex = "W1978557909",
    references = "crossref1943the, currie1985cranial, doi101001jama194302840160064031, doi1010079781468488517, doi101007978146848851721, doi101016002555648290027x, doi1010160169534789901626, doi101016b9781483198279500198, doi101016b9781483231426500124, doi101017cbo9780511693281002, doi101038142004a0, doi10108002724634198810011708, doi101086628623, doi101093sysbio1811, doi101093sysbio33183, doi1010970000505319311100000026, doi101098rstb19830079, doi101111j109636421977tb01031x, doi101111j109636421985tb01796x, doi101146annureven10010165000525, doi1023071005355, doi1023071220820, doi1023071292217, doi1023071441916, doi1023072412407, doi1023072412685, doi1023072413134, doi1023072413259, doi1023072413454, doi1023072485224, doi105281zenodo16171435, doi10560219780801847806, doi105962bhltitle6408, doi105962bhltitle82144, openalexw1534787790, openalexw1534857865, openalexw2954279587, openalexw2983381470, openalexw3146596760, openalexw3184837389, openalexw575222456, roaf1943the"
}

1. Introduction J. Damuth and B. MacFadden Part I. The Biological Significance of Mammalian Body Size: 2. The physiological significance of body size B. K. McNab 3. The behavioral/ecological significance of body size J. F. Eisenberg 4. The functional anatomy of body weight T. Grand 5. Evolutionary strategies and body size in a guild of mammals V. C. Maiorana 6. The cotton rat model R. A. Martin Part II. The Estimation of Mammalian Body Mass: 7. Methods and problems in estimating body size in fossil primates W. Jungers 8. Structural allometry of the lower limb bones in the Anthropoidea C. Ruff 9. Skeletal and dental predictors of body weight in carnivores B. Van Valkenburgh 10. Estimates of body size for insular dwarf mammoths V. L. Roth 11. Skeletal dimensions of ungulates as predictors of body weight K. M. Scott 12. Correlation of body weight in ungulates with cranio-dental variables C. Janis 13. Problems with using tooth size to estimate the body size of fossil mammals M. Fortelius 14. Problems in estimating body masses of archaic fossil ungulates using dental measurements J. Damuth 15. Body-size estimates and size distribution of ungulates (Mammalia) from the Late Miocene Love Bone Bed, Florida B. J. MacFadden and R. C. Hulbert 16. Summary: discussion and recommendations for body-mass estimation J. Damuth and B. J. MacFadden Appendices: data and equations for body-mass estimation.

@article{doi105860choice290302,
    title = "Body size in mammalian paleobiology: estimation and biological implications",
    year = "1991",
    journal = "Choice Reviews Online",
    abstract = "1. Introduction J. Damuth and B. MacFadden Part I. The Biological Significance of Mammalian Body Size: 2. The physiological significance of body size B. K. McNab 3. The behavioral/ecological significance of body size J. F. Eisenberg 4. The functional anatomy of body weight T. Grand 5. Evolutionary strategies and body size in a guild of mammals V. C. Maiorana 6. The cotton rat model R. A. Martin Part II. The Estimation of Mammalian Body Mass: 7. Methods and problems in estimating body size in fossil primates W. Jungers 8. Structural allometry of the lower limb bones in the Anthropoidea C. Ruff 9. Skeletal and dental predictors of body weight in carnivores B. Van Valkenburgh 10. Estimates of body size for insular dwarf mammoths V. L. Roth 11. Skeletal dimensions of ungulates as predictors of body weight K. M. Scott 12. Correlation of body weight in ungulates with cranio-dental variables C. Janis 13. Problems with using tooth size to estimate the body size of fossil mammals M. Fortelius 14. Problems in estimating body masses of archaic fossil ungulates using dental measurements J. Damuth 15. Body-size estimates and size distribution of ungulates (Mammalia) from the Late Miocene Love Bone Bed, Florida B. J. MacFadden and R. C. Hulbert 16. Summary: discussion and recommendations for body-mass estimation J. Damuth and B. J. MacFadden Appendices: data and equations for body-mass estimation.",
    url = "https://doi.org/10.5860/choice.29-0302",
    doi = "10.5860/choice.29-0302",
    openalex = "W1524832411"
}

@article{doi101038361219a0,
    author = "Morris, Simon Conway",
    title = "The fossil record and the early evolution of the Metazoa",
    year = "1993",
    journal = "Nature",
    url = "https://doi.org/10.1038/361219a0",
    doi = "10.1038/361219a0",
    openalex = "W2143380472",
    references = "doi101016001670379290064p, doi1010160301926885900518, doi101016030192688590066x, doi101016s0959437x05801923, doi101017cbo9780511601064002, doi101038345802a0, doi101093oso97801985771880010001, doi101111j146364091991tb00303x, doi101111j150239311989tb01332x, doi101126science1585174, doi101126science1598573, doi101126science2464928339, doi101126science3277277, doi101144gsjgs14920171, doi101144gsjgs14940607, doi1023072992562, doi105860choice273873"
}

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"
}

Analysis of data collected on 131 species of primates, bats, and insectivores showed that the sizes of brain components, from medulla to forebrain, are highly predictable from absolute brain size by a nonlinear function. The order of neurogenesis was found to be highly conserved across a wide range of mammals and to correlate with the relative enlargement of structures as brain size increases, with disproportionately large growth occurring in late-generated structures. Because the order of neurogenesis is conserved, the most likely brain alteration resulting from selection for any behavioral ability may be a coordinated enlargement of the entire nonolfactory brain.

@article{doi101126science7777856,
    author = "Finlay, Barbara L. and Darlington, Richard B.",
    title = "Linked Regularities in the Development and Evolution of Mammalian Brains",
    year = "1995",
    journal = "Science",
    abstract = "Analysis of data collected on 131 species of primates, bats, and insectivores showed that the sizes of brain components, from medulla to forebrain, are highly predictable from absolute brain size by a nonlinear function. The order of neurogenesis was found to be highly conserved across a wide range of mammals and to correlate with the relative enlargement of structures as brain size increases, with disproportionately large growth occurring in late-generated structures. Because the order of neurogenesis is conserved, the most likely brain alteration resulting from selection for any behavioral ability may be a coordinated enlargement of the entire nonolfactory brain.",
    url = "https://doi.org/10.1126/science.7777856",
    doi = "10.1126/science.7777856",
    openalex = "W2040245119",
    references = "doi101016b9780123852502500183"
}

ABSTRACT The most commonly cited apomorphy of Archosauriformes is an opening in the snout known as the antorbital cavity. Despite the ubiquity and prominence of the antorbital cavity, its function and importance in craniofacial evolution have been problematic. Discovering the significance of the antorbital cavity is a two step process: first, establishing the function of the bony cavity (that is, its soft-tissue relations), and second, determining the biological role of the enclosed structure. The first step is the most fundamental, and hence is examined at length. Three hypotheses for the function of the antorbital cavity have been advanced, suggesting that it housed (1) a gland, (2) a muscle, or (3) a paranasal air sinus. Thus, resolution is correctly viewed as a “soft-tissue problem,” and is addressed within the context of the extant phylogenetic bracket (EPB) approach for reconstructing the unpreserved features of fossil organisms. The soft-anatomical relations of the antorbital cavity (or any bony structure) are important because (1) soft tissues generally have morphogenetic primacy over bony tissues and (2) inferences about soft tissues are the foundation for a cascading suite of paleobiological inferences. The EPB approach uses the shared causal associations between soft tissues and their osteological correlates (i.e., the signatures imparted to the bones by the soft tissues) that are observed in the extant outgroups of the fossil taxon of interest to infer the soft-anatomical attributes of the fossil; based on the assessment at the outgroup node, a hierarchy characterizing the strength of the inference can be constructed. This general approach is applied to the problem of the function of the antorbital cavity, taking each hypothesized soft-tissue candidate—gland, muscle, and air sac—in turn, (1) establishing the osteological correlates of each soft-tissue system in the EPB of any fossil archosaur (i.e., extant birds and crocodilians), (2) formulating a hypothesis of homology based on similarities in these causal associations between birds and crocodilians, (3) testing this hypothesis by surveying fossil archosaurs for the specified osteological correlates, and (4) accepting or rejecting the hypothesis based on its phylogenetic congruence. Using this approach, fossil archosaurs can be reliably reconstructed with a Glandula nasalis, M. pterygoideus, pars dorsalis, and Sinus antorbitalis that are homologous with those of extant archosaurs; however, the osteological correlates of only the antorbital paranasal air sinus involve the several structures associated with the antorbital cavity. Additional evidence for the pneumatic nature of the antorbital cavity comes from the presence of numerous accessory cavities (especially in theropod dinosaurs) surrounding the main antorbital cavity. To address the origin of the antorbital cavity, the EPB approach was applied to basal archosauriforms; the data are not as robust, but nevertheless suggest that the cavity appeared as a housing for a paranasal air sinus. The second step in discovering the evolutionary significance of the antorbital cavity is to assess the function of the enclosed paranasal air sac. In fact, the function of all pneumaticity is investigated here. Rather than the enclosed volume of air (i.e., the empty space) being functionally important, better explanations result by focusing on the pneumatic epithelial diverticulum itself. It is proposed here that the function of the epithelial air sac is simply to pneumatize bone in an opportunistic manner within the constraints of a particular biomechanical loading regime. Trends in facial evolution in three clades of archosaurs (crocodylomorphs, ornithopod dinosaurs, and theropod dinosaurs) were examined in light of this new perspective. Crocodylomorphs and ornithopods both show trends for reduction and enclosure of the antorbital cavity (but for different reasons), whereas theropods show a trend for relatively poorly constrained expansion. These findings are consistent with the view of air sacs as opportunistic pneumatizing machines, with weight reduction and design optimality as secondary effects.

@article{doi10108002724634199710011027,
    author = "Witmer, Lawrence M.",
    title = "The Evolution of the Antorbital Cavity of Archosaurs: A Study in Soft-Tissue Reconstruction in the Fossil Record with an Analysis of the Function of Pneumaticity",
    year = "1997",
    journal = "Journal of Vertebrate Paleontology",
    abstract = "ABSTRACT The most commonly cited apomorphy of Archosauriformes is an opening in the snout known as the antorbital cavity. Despite the ubiquity and prominence of the antorbital cavity, its function and importance in craniofacial evolution have been problematic. Discovering the significance of the antorbital cavity is a two step process: first, establishing the function of the bony cavity (that is, its soft-tissue relations), and second, determining the biological role of the enclosed structure. The first step is the most fundamental, and hence is examined at length. Three hypotheses for the function of the antorbital cavity have been advanced, suggesting that it housed (1) a gland, (2) a muscle, or (3) a paranasal air sinus. Thus, resolution is correctly viewed as a “soft-tissue problem,” and is addressed within the context of the extant phylogenetic bracket (EPB) approach for reconstructing the unpreserved features of fossil organisms. The soft-anatomical relations of the antorbital cavity (or any bony structure) are important because (1) soft tissues generally have morphogenetic primacy over bony tissues and (2) inferences about soft tissues are the foundation for a cascading suite of paleobiological inferences. The EPB approach uses the shared causal associations between soft tissues and their osteological correlates (i.e., the signatures imparted to the bones by the soft tissues) that are observed in the extant outgroups of the fossil taxon of interest to infer the soft-anatomical attributes of the fossil; based on the assessment at the outgroup node, a hierarchy characterizing the strength of the inference can be constructed. This general approach is applied to the problem of the function of the antorbital cavity, taking each hypothesized soft-tissue candidate—gland, muscle, and air sac—in turn, (1) establishing the osteological correlates of each soft-tissue system in the EPB of any fossil archosaur (i.e., extant birds and crocodilians), (2) formulating a hypothesis of homology based on similarities in these causal associations between birds and crocodilians, (3) testing this hypothesis by surveying fossil archosaurs for the specified osteological correlates, and (4) accepting or rejecting the hypothesis based on its phylogenetic congruence. Using this approach, fossil archosaurs can be reliably reconstructed with a Glandula nasalis, M. pterygoideus, pars dorsalis, and Sinus antorbitalis that are homologous with those of extant archosaurs; however, the osteological correlates of only the antorbital paranasal air sinus involve the several structures associated with the antorbital cavity. Additional evidence for the pneumatic nature of the antorbital cavity comes from the presence of numerous accessory cavities (especially in theropod dinosaurs) surrounding the main antorbital cavity. To address the origin of the antorbital cavity, the EPB approach was applied to basal archosauriforms; the data are not as robust, but nevertheless suggest that the cavity appeared as a housing for a paranasal air sinus. The second step in discovering the evolutionary significance of the antorbital cavity is to assess the function of the enclosed paranasal air sac. In fact, the function of all pneumaticity is investigated here. Rather than the enclosed volume of air (i.e., the empty space) being functionally important, better explanations result by focusing on the pneumatic epithelial diverticulum itself. It is proposed here that the function of the epithelial air sac is simply to pneumatize bone in an opportunistic manner within the constraints of a particular biomechanical loading regime. Trends in facial evolution in three clades of archosaurs (crocodylomorphs, ornithopod dinosaurs, and theropod dinosaurs) were examined in light of this new perspective. Crocodylomorphs and ornithopods both show trends for reduction and enclosure of the antorbital cavity (but for different reasons), whereas theropods show a trend for relatively poorly constrained expansion. These findings are consistent with the view of air sacs as opportunistic pneumatizing machines, with weight reduction and design optimality as secondary effects.",
    url = "https://doi.org/10.1080/02724634.1997.10011027",
    doi = "10.1080/02724634.1997.10011027",
    openalex = "W1973023986",
    references = "coria1995a, crossref1976allosaurus, currie1985cranial, doi10100797836426953391, doi1010160021929082902469, doi101016b9781483231426500124, doi101017s0022336000026706, doi101017s0022336000059126, doi101017s0094837300004310, doi101017s247526300000091x, doi101038019118a0, doi101038063003a0, doi101038114085a0, doi10108002724634199110011386, doi10108002724634199110011426, doi10108002724634199210011473, doi10108002724634199310011511, doi10108002724634199410011538, doi10108002724634199510011250, doi101098rstb19610007, doi101098rstb19650003, doi101098rstb19850092, doi101098rstb19910056, doi101098rstb19920117, doi101098rstb19950125, doi101111j109600311991tb00045x, doi101111j109636421978tb01049x, doi101111j146363951921tb00489x, doi101111j1469185x1990tb01427x, doi101111j146979981913tb06148x, doi101111j155856461965tb01720x, doi101111j174966321940tb57047x, doi101111j216409471940tb00068x, doi101126science11282807, doi101126science2665183267, doi101126science2725264986, doi101139e93179, doi10125900071285586941029, doi1015468p4gnhz, doi1015468yhxmzl, doi1023072406439, doi1023072413454, doi1023072421859, doi1023072992444, doi10230730135049, doi1023073514548, doi105281zenodo16171435, doi105281zenodo16673433, doi105479si03629236110i, doi105860choice326223, doi105962bhlpart22965, doi105962bhltitle54054, doi105962p226819, madsen1976a, openalexw1489366593, openalexw1534857865, openalexw193970361, openalexw2603028126, openalexw2788234611, openalexw3140893762, openalexw3184837389, openalexw607142922, openalexw616953834, rowe1989a, sues1978a, walker1964triassic"
}

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"
}

A fossil from the Early Jurassic (Sinemurian, approximately 195 million years ago) represents a new lineage of mammaliaforms, the extinct groups more closely related to the living mammals than to nonmammaliaform cynodonts. It has an enlarged cranial cavity, but no postdentary trough on the mandible, indicating separation of the middle ear bones from the mandible. This extends the earliest record of these crucial mammalian features by some 45 million years and suggests that separation of the middle ear bones from the mandible and the expanded brain vault could be correlated. It shows that several key mammalian evolutionary innovations in the ear region, the temporomandibular joint, and the brain vault evolved incrementally through mammaliaform evolution and long before the differentiation of the living mammal groups. With an estimated body weight of only 2 grams, its coexistence with other larger mammaliaforms with similar "triconodont-like" teeth for insectivory within the same fauna suggests a great trophic diversity within the mammaliaform insectivore feeding guild, as inferred from the range of body sizes.

@article{doi101126science1058476,
    author = "Luo, Zhe‐Xi and Crompton, A. W. and Sun, Ailin",
    title = "A New Mammaliaform from the Early Jurassic and Evolution of Mammalian Characteristics",
    year = "2001",
    journal = "Science",
    abstract = {A fossil from the Early Jurassic (Sinemurian, approximately 195 million years ago) represents a new lineage of mammaliaforms, the extinct groups more closely related to the living mammals than to nonmammaliaform cynodonts. It has an enlarged cranial cavity, but no postdentary trough on the mandible, indicating separation of the middle ear bones from the mandible. This extends the earliest record of these crucial mammalian features by some 45 million years and suggests that separation of the middle ear bones from the mandible and the expanded brain vault could be correlated. It shows that several key mammalian evolutionary innovations in the ear region, the temporomandibular joint, and the brain vault evolved incrementally through mammaliaform evolution and long before the differentiation of the living mammal groups. With an estimated body weight of only 2 grams, its coexistence with other larger mammaliaforms with similar "triconodont-like" teeth for insectivory within the same fauna suggests a great trophic diversity within the mammaliaform insectivore feeding guild, as inferred from the range of body sizes.},
    url = "https://doi.org/10.1126/science.1058476",
    doi = "10.1126/science.1058476",
    openalex = "W1980409596",
    references = "cifelli1998triconodont, doi101007978146122784737, doi10108002724634199810011048, doi101111j109636421973tb00786x, doi101111j109636421981tb01127x"
}

▪ 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"
}

@article{doi101016jpalaeo200309033,
    author = "Bobe, René",
    title = "The expansion of grassland ecosystems in Africa in relation to mammalian evolution and the origin of the genus Homo",
    year = "2004",
    journal = "Palaeogeography Palaeoclimatology Palaeoecology",
    url = "https://doi.org/10.1016/j.palaeo.2003.09.033",
    doi = "10.1016/j.palaeo.2003.09.033",
    openalex = "W2108676600",
    references = "doi10100797814899503456, doi101038202007a0, doi1043249780203792667, doi104324978131512740848"
}

@article{doi101038nature02426,
    author = "Gibbs, Richard A. and Weinstock, George M. and Metzker, Michael L. and Muzny, Donna M. and Sodergren, Erica and Scherer, Steven E. and Scott, Graham and Steffen, David L. and Worley, Kim C. and Burch, Paula E. and Okwuonu, Geoffrey and Hines, Sandra and Lewis, Lora and DeRamo, Christine and Delgado, Oliver and Dugan-Rocha, Shannon and Miner, George and Morgan, Margaret and Hawes, Alicia and Gill, Rachel and Holt, Celera Robert A. and Adams, Mark D. and Amanatides, Peter G. and Baden-Tillson, Holly and Barnstead, Mary and Chin, Soo H. and Evans, Cheryl and Ferriera, Steve and Fosler, Carl and Glodek, Anna and Gu, Zhiping and Jennings, D. E. and Kraft, Cheryl and Nguyen, Trixie and Pfannkoch, Cynthia and Sitter, Cynthia D. and Sutton, Granger and Venter, J. Craig and Woodage, Trevor and Therapeutics, Genome and Smith, Douglas and Lee, Hongmei and Gustafson, Erik and Cahill, Patrick and Kana, A. and Doucette‐Stamm, Lynn and Weinstock, Keith and Fechtel, Kim and Weiss, Robert B. and Dunn, Diane M. and NISC Comparative Sequencing Program, NHGRI and Green, Eric D. and Blakesley, Robert W. and Bouffard, Gerard G. and de Jong, Pieter J. and Osoegawa, Kazutoyo and Zhu, Baoli and Marra, Marco A. and Schein, Jacqueline E. and Bosdet, Ian and Fjell, Christopher D. and Jones, Steven J.M. and Krzywinski, Martin and Mathewson, Carrie and Siddiqui, Asim and Wye, Natasja and McPherson, John D. and end sequencing: TIGR, BAC and Zhao, Shaying and Fraser, Claire M. and Shetty, Jyoti and Shatsman, S. and Geer, Keita and Chen, Yixin and Abramzon, Sofyia and Nierman, William C. and Gibbs, Richard A. and Weinstock, George M. and Havlak, Paul and Chen, Rui and Durbin, K. James and Simons, R. and Ren, Yanru and Song, Xingzhi and Li, Bingshan and Liu, Yue and Qin, Xiang and Analysis and annotation: Affymetrix and Cawley, Simon and Weinstock, George M. and Worley, Kim C. and Cooney, Austin J. and Gibbs, Richard A. and D'Souza, Lisa M. and Martin, Kirt and Wu, Jia Qian and Gonzalez‐Garay, Manuel L. and Jackson, Andrew and Kalafus, Kenneth J. and McLeod, Michael P.",
    title = "Genome sequence of the Brown Norway rat yields insights into mammalian evolution",
    year = "2004",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature02426",
    doi = "10.1038/nature02426",
    openalex = "W2097040991",
    references = "doi101038nature01858, doi101073pnas0334222100, doi101126science1080049, doi101126science29054941151"
}

Bats make up more than 20% of extant mammals, yet their evolutionary history is largely unknown because of a limited fossil record and conflicting or incomplete phylogenies. Here, we present a highly resolved molecular phylogeny for all extant bat families. Our results support the hypothesis that megabats are nested among four major microbat lineages, which originated in the early Eocene [52 to 50 million years ago (Mya)], coincident with a significant global rise in temperature, increase in plant diversity and abundance, and the zenith of Tertiary insect diversity. Our data suggest that bats originated in Laurasia, possibly in North America, and that three of the major microbat lineages are Laurasian in origin, whereas the fourth is Gondwanan. Combining principles of ghost lineage analysis with molecular divergence dates, we estimate that the bat fossil record underestimates (unrepresented basal branch length, UBBL) first occurrences by, on average, 73% and that the sum of missing fossil history is 61%.

@article{doi101126science1105113,
    author = "Teeling, Emma C. and Springer, Mark S. and Madsen, Ole and Bates, Paul J. J. and O’Brien, Stephen J. and Murphy, William J.",
    title = "A Molecular Phylogeny for Bats Illuminates Biogeography and the Fossil Record",
    year = "2005",
    journal = "Science",
    abstract = "Bats make up more than 20\% of extant mammals, yet their evolutionary history is largely unknown because of a limited fossil record and conflicting or incomplete phylogenies. Here, we present a highly resolved molecular phylogeny for all extant bat families. Our results support the hypothesis that megabats are nested among four major microbat lineages, which originated in the early Eocene [52 to 50 million years ago (Mya)], coincident with a significant global rise in temperature, increase in plant diversity and abundance, and the zenith of Tertiary insect diversity. Our data suggest that bats originated in Laurasia, possibly in North America, and that three of the major microbat lineages are Laurasian in origin, whereas the fourth is Gondwanan. Combining principles of ghost lineage analysis with molecular divergence dates, we estimate that the bat fossil record underestimates (unrepresented basal branch length, UBBL) first occurrences by, on average, 73\% and that the sum of missing fossil history is 61\%.",
    url = "https://doi.org/10.1126/science.1105113",
    doi = "10.1126/science.1105113",
    openalex = "W1997655974",
    references = "doi101007bf01454359, doi101017cbo9780511529924, doi10103835003188, doi10103835055536, doi101073pnas0334222100, doi101073pnas111551998, doi101126science1067179, doi101126science11536548, doi101126science15437541333, doi101126science28454232153, doi1023071223169"
}

Finite element analysis (FEA) is a technique that reconstructs stress, strain, and deformation in a digital structure. Although commonplace in engineering and orthopedic science for more than 30 years, only recently has it begun to be adopted in the zoological and paleontological sciences to address questions of organismal morphology, function, and evolution. Current research tends to focus on either deductive studies that assume a close relationship between form and function or inductive studies that aim to test this relationship, although explicit hypothesis-testing bridges these two standpoints. Validation studies have shown congruence between in vivo or in vitro strain and FE-inferred strain. Future validation work on a broad range of taxa will assist in phylogenetically bracketing our extinct animal FE-models to increase confidence in our input parameters, although currently, FEA has much potential in addressing questions of form-function relationships, providing appropriate questions are asked of the existing data.

@article{doi101146annurevearth35031306140104,
    author = "Rayfield, Emily J.",
    title = "Finite Element Analysis and Understanding the Biomechanics and Evolution of Living and Fossil Organisms",
    year = "2007",
    journal = "Annual Review of Earth and Planetary Sciences",
    abstract = "Finite element analysis (FEA) is a technique that reconstructs stress, strain, and deformation in a digital structure. Although commonplace in engineering and orthopedic science for more than 30 years, only recently has it begun to be adopted in the zoological and paleontological sciences to address questions of organismal morphology, function, and evolution. Current research tends to focus on either deductive studies that assume a close relationship between form and function or inductive studies that aim to test this relationship, although explicit hypothesis-testing bridges these two standpoints. Validation studies have shown congruence between in vivo or in vitro strain and FE-inferred strain. Future validation work on a broad range of taxa will assist in phylogenetically bracketing our extinct animal FE-models to increase confidence in our input parameters, although currently, FEA has much potential in addressing questions of form-function relationships, providing appropriate questions are asked of the existing data.",
    url = "https://doi.org/10.1146/annurev.earth.35.031306.140104",
    doi = "10.1146/annurev.earth.35.031306.140104",
    openalex = "W2138656347",
    references = "doi10103835059070, doi101038nature04890, doi105860choice326223"
}

help resolve the phylogenetic relationships of conodonts and chordates, the analysis should be extended to include non-chordate taxa.

@article{doi1018814epiiugs2010v33i4002,
    author = "Blieck, Alain and Turner, Susan and Burrow, Carole J. and Schultze, Hans‐Peter and Rexroad, Carl B. and Bultynck, Pierre and Nowlan, Godfrey S.",
    title = "Fossils, histology, and phylogeny: Why conodonts are not vertebrates",
    year = "2010",
    journal = "Episodes",
    abstract = "help resolve the phylogenetic relationships of conodonts and chordates, the analysis should be extended to include non-chordate taxa.",
    url = "https://doi.org/10.18814/epiiugs/2010/v33i4/002",
    doi = "10.18814/epiiugs/2010/v33i4/002",
    openalex = "W2243536994"
}

Many hypotheses have been postulated regarding the early evolution of the mammalian brain. Here, x-ray tomography of the Early Jurassic mammaliaforms Morganucodon and Hadrocodium sheds light on this history. We found that relative brain size expanded to mammalian levels, with enlarged olfactory bulbs, neocortex, olfactory (pyriform) cortex, and cerebellum, in two evolutionary pulses. The initial pulse was probably driven by increased resolution in olfaction and improvements in tactile sensitivity (from body hair) and neuromuscular coordination. A second pulse of olfactory enhancement then enlarged the brain to mammalian levels. The origin of crown Mammalia saw a third pulse of olfactory enhancement, with ossified ethmoid turbinals supporting an expansive olfactory epithelium in the nasal cavity, allowing full expression of a huge odorant receptor genome.

@article{doi101126science1203117,
    author = "Rowe, Timothy B. and Macrini, Thomas E. and Luo, Zhe‐Xi",
    title = "Fossil Evidence on Origin of the Mammalian Brain",
    year = "2011",
    journal = "Science",
    abstract = "Many hypotheses have been postulated regarding the early evolution of the mammalian brain. Here, x-ray tomography of the Early Jurassic mammaliaforms Morganucodon and Hadrocodium sheds light on this history. We found that relative brain size expanded to mammalian levels, with enlarged olfactory bulbs, neocortex, olfactory (pyriform) cortex, and cerebellum, in two evolutionary pulses. The initial pulse was probably driven by increased resolution in olfaction and improvements in tactile sensitivity (from body hair) and neuromuscular coordination. A second pulse of olfactory enhancement then enlarged the brain to mammalian levels. The origin of crown Mammalia saw a third pulse of olfactory enhancement, with ossified ethmoid turbinals supporting an expansive olfactory epithelium in the nasal cavity, allowing full expression of a huge odorant receptor genome.",
    url = "https://doi.org/10.1126/science.1203117",
    doi = "10.1126/science.1203117",
    openalex = "W2071803223",
    references = "doi101038nature06277, doi101111j109636421973tb00786x, doi101111j109636421981tb01127x, doi107312kiel11918"
}

Although fossils have provided some of the most important evidence for evolution, the discipline of paleontology has not always had a central place in evolutionary biology. Beginning in Darwin's day, and for much of the twentieth century, paleontologists were often regarded as mere fossil collectors by many evolutionary biologists, their attempts to contribute to evolutionary theory ignored or regarded with scorn. In the 1950s, however, paleontologists began mounting a counter-movement that insisted on the valid, important, and original contribution of paleontology to evolutionary theory. This movement, called by its proponents, advocated for an approach to the fossil record that was theoretical, quantitative, and oriented towards explaining the broad patterns of evolution and extinction in the history of life. Rereading the Fossil Record provides, as never before, a historical account of the origin, rise, and importance of paleobiology, from the mid-nineteenth century to the late 1980s. Drawing on a wealth of archival material, David Sepkoski shows how the movement was conceived and promoted by a small but influential group of paleontologists - including Stephen Jay Gould and Niles Eldredge, among others - and examines the intellectual, disciplinary, and political dynamics involved in the ascendancy of paleobiology. By emphasizing the close relationship between paleobiology and other evolutionary disciplines, this book writes a new chapter in the history of evolutionary biology, while also offering insights into the dynamics of disciplinary change in modern science.

@article{doi105860choice500902,
    title = "Rereading the fossil record: the growth of paleobiology as an evolutionary discipline",
    year = "2012",
    journal = "Choice Reviews Online",
    abstract = "Although fossils have provided some of the most important evidence for evolution, the discipline of paleontology has not always had a central place in evolutionary biology. Beginning in Darwin's day, and for much of the twentieth century, paleontologists were often regarded as mere fossil collectors by many evolutionary biologists, their attempts to contribute to evolutionary theory ignored or regarded with scorn. In the 1950s, however, paleontologists began mounting a counter-movement that insisted on the valid, important, and original contribution of paleontology to evolutionary theory. This movement, called by its proponents, advocated for an approach to the fossil record that was theoretical, quantitative, and oriented towards explaining the broad patterns of evolution and extinction in the history of life. Rereading the Fossil Record provides, as never before, a historical account of the origin, rise, and importance of paleobiology, from the mid-nineteenth century to the late 1980s. Drawing on a wealth of archival material, David Sepkoski shows how the movement was conceived and promoted by a small but influential group of paleontologists - including Stephen Jay Gould and Niles Eldredge, among others - and examines the intellectual, disciplinary, and political dynamics involved in the ascendancy of paleobiology. By emphasizing the close relationship between paleobiology and other evolutionary disciplines, this book writes a new chapter in the history of evolutionary biology, while also offering insights into the dynamics of disciplinary change in modern science.",
    url = "https://doi.org/10.5860/choice.50-0902",
    doi = "10.5860/choice.50-0902",
    openalex = "W653308317"
}

The story of an unsolved paleontological puzzle

@misc{knell2012the,
    author = "Knell, Simon",
    title = "The Great Fossil Enigma",
    year = "2012",
    abstract = "The story of an unsolved paleontological puzzle",
    url = "https://doi.org/10.2979/6663.0",
    doi = "10.2979/6663.0",
    openalex = "W2340745648"
}

@article{cooper2014the,
    author = "Cooper, Barry",
    title = "The Great Fossil Enigma",
    year = "2014",
    journal = "Earth Sciences History",
    url = "https://doi.org/10.17704/eshi.33.1.40685h88736g3007",
    doi = "10.17704/eshi.33.1.40685h88736g3007",
    number = "1",
    openalex = "W2055626309",
    pages = "179-181",
    volume = "33",
    references = "doi1018814epiiugs2010v33i4002"
}

Large-scale analysis of the fossil record requires aggregation of palaeontological data from individual fossil localities. Prior to computers, these synoptic datasets were compiled by hand, a laborious undertaking that took years of effort and forced palaeontologists to make difficult choices about what types of data to tabulate. The advent of desktop computers ushered in palaeontology's first digital revolution-online literature-based databases, such as the Paleobiology Database (PBDB). However, the published literature represents only a small proportion of the palaeontological data housed in museum collections. Although this issue has long been appreciated, the magnitude, and thus potential significance, of these so-called 'dark data' has been difficult to determine. Here, in the early phases of a second digital revolution in palaeontology--the digitization of museum collections-we provide an estimate of the magnitude of palaeontology's dark data. Digitization of our nine institutions' holdings of Cenozoic marine invertebrate collections from California, Oregon and Washington in the USA reveals that they represent 23 times the number of unique localities than are currently available in the PBDB. These data, and the vast quantity of similarly untapped dark data in other museum collections, will, when digitally mobilized, enhance palaeontologists' ability to make inferences about the patterns and processes of past evolutionary and ecological changes.

@article{doi101098rsbl20180431,
    author = "Marshall, Charles R. and Finnegan, Seth and Clites, Erica C. and Holroyd, Patricia A. and Bonuso, N. and Cortez, Célia Martins and Davis, Edward and Dietl, Gregory P. and Druckenmiller, Patrick S. and Eng, Ronald and Garcia, Christine and Estes-Smargiassi, Kathryn and Hendy, Austin and Hollis, Kathy and Little, Holly and Nesbitt, Elizabeth A. and Roopnarine, Peter D. and Skibinski, L. and Vendetti, Jann E. and White, Lisa D.",
    title = "Quantifying the dark data in museum fossil collections as palaeontology undergoes a second digital revolution",
    year = "2018",
    journal = "Biology Letters",
    abstract = "Large-scale analysis of the fossil record requires aggregation of palaeontological data from individual fossil localities. Prior to computers, these synoptic datasets were compiled by hand, a laborious undertaking that took years of effort and forced palaeontologists to make difficult choices about what types of data to tabulate. The advent of desktop computers ushered in palaeontology's first digital revolution-online literature-based databases, such as the Paleobiology Database (PBDB). However, the published literature represents only a small proportion of the palaeontological data housed in museum collections. Although this issue has long been appreciated, the magnitude, and thus potential significance, of these so-called 'dark data' has been difficult to determine. Here, in the early phases of a second digital revolution in palaeontology--the digitization of museum collections-we provide an estimate of the magnitude of palaeontology's dark data. Digitization of our nine institutions' holdings of Cenozoic marine invertebrate collections from California, Oregon and Washington in the USA reveals that they represent 23 times the number of unique localities than are currently available in the PBDB. These data, and the vast quantity of similarly untapped dark data in other museum collections, will, when digitally mobilized, enhance palaeontologists' ability to make inferences about the patterns and processes of past evolutionary and ecological changes.",
    url = "https://doi.org/10.1098/rsbl.2018.0431",
    doi = "10.1098/rsbl.2018.0431",
    openalex = "W2890070252",
    references = "crossref1977patterns, doi101080027246342012716114, doi101093bioscibiv104, doi101126science3526287762, doi101126scienceaah4787, doi105860choice500902, doi105962bhltitle22153, openalexw1599677799, openalexw45809738, simpson1978patterns"
}

The fossil record of pinnipeds (seals, fur seals and walruses) is globally distributed, spanning from the late Oligocene to the Holocene. This record shows a complex evolutionary history that could not otherwise be inferred from their extant relatives, including multiple radiations and iterative ecomorphological specializations among different lineages, many of which are extinct. The fossil record of pinnipeds is not uniformly represented in space and time, however, leaving some gaps in our knowledge. We performed a historiographical investigation of the published fossil record of pinnipeds based on the information available in the Paleobiology Database, with the aim to broadly characterize and evaluate it from a taxonomic, geographical and temporal perspective. We identified major trends, strengths and weaknesses of the pinniped fossil record, including potential biases that may affect our interpretations. We found that 39% of the record corresponds to extant taxa, which are essentially from the Pleistocene and Holocene. There is a larger record from the Northern Hemisphere, suggesting biases in sampling and collection effort. The record is not strongly biased by sedimentary outcrop bias. Specifically, for extinct species, nearly half of them are represented by a single occurrence and a large proportion have type specimens consisting of single isolated postcranial elements. While the pinniped fossil record may have adequate temporal and taxonomic coverage, it has a strong geographical bias and its comparability is hindered by the incompleteness of type specimens. These results should be taken into account when addressing patterns of their past diversity, evolutionary history and paleoecology.

@article{doi101098rsos191394,
    author = "Valenzuela‐Toro, Ana M. and Pyenson, Nicholas D.",
    title = "What do we know about the fossil record of pinnipeds? A historiographical investigation",
    year = "2019",
    journal = "Royal Society Open Science",
    abstract = "The fossil record of pinnipeds (seals, fur seals and walruses) is globally distributed, spanning from the late Oligocene to the Holocene. This record shows a complex evolutionary history that could not otherwise be inferred from their extant relatives, including multiple radiations and iterative ecomorphological specializations among different lineages, many of which are extinct. The fossil record of pinnipeds is not uniformly represented in space and time, however, leaving some gaps in our knowledge. We performed a historiographical investigation of the published fossil record of pinnipeds based on the information available in the Paleobiology Database, with the aim to broadly characterize and evaluate it from a taxonomic, geographical and temporal perspective. We identified major trends, strengths and weaknesses of the pinniped fossil record, including potential biases that may affect our interpretations. We found that 39\% of the record corresponds to extant taxa, which are essentially from the Pleistocene and Holocene. There is a larger record from the Northern Hemisphere, suggesting biases in sampling and collection effort. The record is not strongly biased by sedimentary outcrop bias. Specifically, for extinct species, nearly half of them are represented by a single occurrence and a large proportion have type specimens consisting of single isolated postcranial elements. While the pinniped fossil record may have adequate temporal and taxonomic coverage, it has a strong geographical bias and its comparability is hindered by the incompleteness of type specimens. These results should be taken into account when addressing patterns of their past diversity, evolutionary history and paleoecology.",
    url = "https://doi.org/10.1098/rsos.191394",
    doi = "10.1098/rsos.191394",
    openalex = "W2990272826",
    references = "doi101017s0094837300006060, doi101098rsbl20180431"
}

The fossil and geologic records provide the primary data used to established absolute timescales for timetrees. For the paleontological evaluation of proposed timetree timescales, and for node-based methods for constructing timetrees, the fossil record is used to bracket divergence times. Minimum brackets (minimum ages) can be established robustly using well-dated fossils that can be reliably assigned to lineages based on positive morphological evidence. Maximum brackets are much harder to establish, largely because it is difficult to establish definitive evidence that the absence of a taxon in the fossil record is real and not just due to the incompleteness of the fossil and rock records. Five primary methods have been developed to estimate maximum age brackets, each of which is discussed. The fact that the fossilization potential of a group typically decreases the closer one approaches its time of origin increases the challenge of estimating maximum age brackets. Additional complications arise: 1) because fossil data actually bracket the time of origin of the first relevant fossilizable morphology (apomorphy), not the divergence time itself; 2) due to the phylogenetic uncertainty in the placement of fossils; 3) because of idiosyncratic temporal and geographic gaps in the rock and fossil records; and 4) if the preservation potential of a group changed significantly during its history. In contrast, uncertainties in the absolute ages of fossils are typically relatively unimportant, even though the vast majority of fossil cannot be dated directly. These issues and relevant quantitative methods are reviewed, and their relative magnitudes assessed, which typically correlate with the age of the group, its geographic range, and species richness.

@article{doi103389fgene201901049,
    author = "Marshall, Charles R.",
    title = "Using the Fossil Record to Evaluate Timetree Timescales",
    year = "2019",
    journal = "Frontiers in Genetics",
    abstract = "The fossil and geologic records provide the primary data used to established absolute timescales for timetrees. For the paleontological evaluation of proposed timetree timescales, and for node-based methods for constructing timetrees, the fossil record is used to bracket divergence times. Minimum brackets (minimum ages) can be established robustly using well-dated fossils that can be reliably assigned to lineages based on positive morphological evidence. Maximum brackets are much harder to establish, largely because it is difficult to establish definitive evidence that the absence of a taxon in the fossil record is real and not just due to the incompleteness of the fossil and rock records. Five primary methods have been developed to estimate maximum age brackets, each of which is discussed. The fact that the fossilization potential of a group typically decreases the closer one approaches its time of origin increases the challenge of estimating maximum age brackets. Additional complications arise: 1) because fossil data actually bracket the time of origin of the first relevant fossilizable morphology (apomorphy), not the divergence time itself; 2) due to the phylogenetic uncertainty in the placement of fossils; 3) because of idiosyncratic temporal and geographic gaps in the rock and fossil records; and 4) if the preservation potential of a group changed significantly during its history. In contrast, uncertainties in the absolute ages of fossils are typically relatively unimportant, even though the vast majority of fossil cannot be dated directly. These issues and relevant quantitative methods are reviewed, and their relative magnitudes assessed, which typically correlate with the age of the group, its geographic range, and species richness.",
    url = "https://doi.org/10.3389/fgene.2019.01049",
    doi = "10.3389/fgene.2019.01049",
    openalex = "W2983202100",
    references = "doi101016jympev201705008, doi101098rsbl20180431"
}

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"
}

Global diversity patterns in the fossil record comprise a mosaic of regional trends, underpinned by spatially non-random drivers and distorted by variation in sampling intensity through time and across space. Sampling-corrected diversity estimates from spatially-standardised fossil datasets retain their regional biogeographic nuances and avoid these biases, yet diversity-through-time arises from the interplay of origination and extinction, the processes that shape macroevolutionary history. Here we present a subsampling algorithm to eliminate spatial sampling bias, coupled with advanced probabilistic methods for estimating origination and extinction rates and a Bayesian method for estimating sampling-corrected diversity. We then re-examine the Late Permian to Early Jurassic marine fossil record, an interval spanning several global biotic upheavals that shaped the origins of the modern marine biosphere. We find that origination and extinction rates are regionally heterogenous even during events that manifested globally, highlighting the need for spatially explicit views of macroevolutionary processes through geological time.

@article{doi101038s41467022305070,
    author = "Flannery‐Sutherland, Joseph T. and Silvestro, Daniele and Benton, Michael J.",
    title = "Global diversity dynamics in the fossil record are regionally heterogeneous",
    year = "2022",
    journal = "Nature Communications",
    abstract = "Global diversity patterns in the fossil record comprise a mosaic of regional trends, underpinned by spatially non-random drivers and distorted by variation in sampling intensity through time and across space. Sampling-corrected diversity estimates from spatially-standardised fossil datasets retain their regional biogeographic nuances and avoid these biases, yet diversity-through-time arises from the interplay of origination and extinction, the processes that shape macroevolutionary history. Here we present a subsampling algorithm to eliminate spatial sampling bias, coupled with advanced probabilistic methods for estimating origination and extinction rates and a Bayesian method for estimating sampling-corrected diversity. We then re-examine the Late Permian to Early Jurassic marine fossil record, an interval spanning several global biotic upheavals that shaped the origins of the modern marine biosphere. We find that origination and extinction rates are regionally heterogenous even during events that manifested globally, highlighting the need for spatially explicit views of macroevolutionary processes through geological time.",
    url = "https://doi.org/10.1038/s41467-022-30507-0",
    doi = "10.1038/s41467-022-30507-0",
    openalex = "W4280565279",
    references = "doi101016jcub202107071, doi101016jearscirev2020103282, doi101038s41467021237540, doi101038s41559021016088, doi101073pnas2020778118, doi101093sysbiosyab045, doi101126sciadvaba0099, doi101130g479071"
}

The timing of the placental mammal radiation has been the focus of debate over the efficacy of competing methods for establishing evolutionary timescales. Molecular clock analyses estimate that placental mammals originated before the Cretaceous-Paleogene (K-Pg) mass extinction, anywhere from the Late Cretaceous to the Jurassic. However, the absence of definitive fossils of placentals before the K-Pg boundary is compatible with a post-Cretaceous origin. Nevertheless, lineage divergence must occur before it can be manifest phenotypically in descendent lineages. This, combined with the non-uniformity of the rock and fossil records, requires the fossil record to be interpreted rather than read literally. To achieve this, we introduce an extended Bayesian Brownian bridge model that estimates the age of origination and, where applicable, extinction through a probabilistic interpretation of the fossil record. The model estimates the origination of placentals in the Late Cretaceous, with ordinal crown groups originating at or after the K-Pg boundary. The results reduce the plausible interval for placental mammal origination to the younger range of molecular clock estimates. Our findings support both the Long Fuse and Soft Explosive models of placental mammal diversification, indicating that the placentals originated shortly prior to the K-Pg mass extinction. The origination of many modern mammal lineages overlapped with and followed the K-Pg mass extinction.

@article{doi101016jcub202306016,
    author = "Carlisle, Emily and Janis, Christine M. and Pisani, Davide and Donoghue, Philip C. J. and Silvestro, Daniele",
    title = "A timescale for placental mammal diversification based on Bayesian modeling of the fossil record",
    year = "2023",
    journal = "Current Biology",
    abstract = "The timing of the placental mammal radiation has been the focus of debate over the efficacy of competing methods for establishing evolutionary timescales. Molecular clock analyses estimate that placental mammals originated before the Cretaceous-Paleogene (K-Pg) mass extinction, anywhere from the Late Cretaceous to the Jurassic. However, the absence of definitive fossils of placentals before the K-Pg boundary is compatible with a post-Cretaceous origin. Nevertheless, lineage divergence must occur before it can be manifest phenotypically in descendent lineages. This, combined with the non-uniformity of the rock and fossil records, requires the fossil record to be interpreted rather than read literally. To achieve this, we introduce an extended Bayesian Brownian bridge model that estimates the age of origination and, where applicable, extinction through a probabilistic interpretation of the fossil record. The model estimates the origination of placentals in the Late Cretaceous, with ordinal crown groups originating at or after the K-Pg boundary. The results reduce the plausible interval for placental mammal origination to the younger range of molecular clock estimates. Our findings support both the Long Fuse and Soft Explosive models of placental mammal diversification, indicating that the placentals originated shortly prior to the K-Pg mass extinction. The origination of many modern mammal lineages overlapped with and followed the K-Pg mass extinction.",
    url = "https://doi.org/10.1016/j.cub.2023.06.016",
    doi = "10.1016/j.cub.2023.06.016",
    openalex = "W4382241650",
    references = "doi101017jpa2016141, doi103389fgene201901241, doi103389fgene2021521693"
}

@incollection{rowe2023evolution,
    author = "Rowe, Timothy B.",
    title = "Evolution of the Mammalian Neurosensory System: Fossil Evidence and Major Events",
    year = "2023",
    booktitle = "Paleoneurology of Amniotes",
    url = "https://doi.org/10.1007/978-3-031-13983-3\_10",
    doi = "10.1007/978-3-031-13983-3\_10",
    openalex = "W4309521433",
    pages = "365-422",
    references = "doi1010079783642182624, doi101016009286749190418x, doi101016jcub200812005, doi101038nn3917, doi101038nrn2719, doi101093jmammalgyx147, doi101126science3291116, doi1023071441916, doi105860choice326223, doi105860choice425260"
}

Last year, we challenged the view that large-bodied theropod dinosaurs such as Tyrannosaurus rex resembled primates in cognition and behavior, a proposition made by Herculano-Houzel in 2023. More recently, Jensen et al. have criticized our work on this topic, raising methodological and conceptual issues. Central to their argument is the assumption that tachymetabolic endotherms should be expected to converge in neurocognitive traits, which follows the recently proposed endothermic brain hypothesis. We here respond to their critique, address critical misconceptions, and argue that none of the points raised by Jensen et al. challenge the conclusions we have drawn. We show that the endothermic brain hypothesis lacks robust support from the fossil record. As of now, no compelling evidence suggests that endothermy coevolved with enlarged brains or elevated neuron densities in either the avian or mammalian lineage. Various fossil groups containing endothermic taxa retain plesiomorphic endocast traits and do not converge with birds and mammals in the relative size and proportions of their brains. Furthermore, we elaborate on our discussion on (forebrain) neuron counts as correlates of cognitive performance and highlight that neuron numbers evolve in tandem with body mass in birds and mammals, suggesting that comparatively high neuron number estimates for some Mesozoic dinosaurs do not require explanations that orbit around exceptional cognitive abilities. Despite these disagreements, we identify significant overlap in opinion between Jensen et al. and ourselves, including in the position that neuron count estimates for Mesozoic dinosaurs will remain unreliable and are unsuitable for inferring cognitive complexity.

@article{doi101002ar70113,
    author = "Caspar, Kai R. and Gutiérrez‐Ibáñez, Cristián and George, Hady and Holtz, Thomas R. and Naish, Darren and Hurlburt, Grant R.",
    title = "Endothermy, neuron counts, and other issues: Further remarks on neurocognitive evolution in fossil vertebrates",
    year = "2025",
    journal = "The Anatomical Record",
    abstract = "Last year, we challenged the view that large-bodied theropod dinosaurs such as Tyrannosaurus rex resembled primates in cognition and behavior, a proposition made by Herculano-Houzel in 2023. More recently, Jensen et al. have criticized our work on this topic, raising methodological and conceptual issues. Central to their argument is the assumption that tachymetabolic endotherms should be expected to converge in neurocognitive traits, which follows the recently proposed endothermic brain hypothesis. We here respond to their critique, address critical misconceptions, and argue that none of the points raised by Jensen et al. challenge the conclusions we have drawn. We show that the endothermic brain hypothesis lacks robust support from the fossil record. As of now, no compelling evidence suggests that endothermy coevolved with enlarged brains or elevated neuron densities in either the avian or mammalian lineage. Various fossil groups containing endothermic taxa retain plesiomorphic endocast traits and do not converge with birds and mammals in the relative size and proportions of their brains. Furthermore, we elaborate on our discussion on (forebrain) neuron counts as correlates of cognitive performance and highlight that neuron numbers evolve in tandem with body mass in birds and mammals, suggesting that comparatively high neuron number estimates for some Mesozoic dinosaurs do not require explanations that orbit around exceptional cognitive abilities. Despite these disagreements, we identify significant overlap in opinion between Jensen et al. and ourselves, including in the position that neuron count estimates for Mesozoic dinosaurs will remain unreliable and are unsuitable for inferring cognitive complexity.",
    url = "https://doi.org/10.1002/ar.70113",
    doi = "10.1002/ar.70113",
    openalex = "W4417503716",
    references = "chiarenza2024early, doi101002ar70074, doi101002cne70056, doi101016jtics202408002, doi101017jpa202510121"
}

Abstract Tritylodontidae are a cosmopolitan group of derived cynodonts that thrived during the Mesozoic Era. Among the tritylodontids, the genus Bienotheroides is distinguished by its short snout, reduced maxilla, and deep zygomatic arch. Here we describe the endocranial anatomy (brain endocast, inner ear, blood vessels and cranial nerves) of Bienotheroides sp. collected from the Middle Jurassic Lower Shaximiao Formation and Xintiangou Formation in the Yunyang area of Chongqing, China. The cranial endocast features enlarged olfactory bulbs and a slender hypophysis. It is long and horizontally oriented in the brain cavity. The unossified zone is moderately developed. The paraflocculus is less developed than in most known cynodonts. The brain cast of Bienotheroides is divided into two cerebral hemispheres by a median interhemispheric sulcus, which is present only in the anterior half of the forebrain. The posterior portion of the forebrain remains undifferentiated. This condition appears to be more derived than the completely undifferentiated forebrain found in basal cynodonts. However, it is primitive compared with the fully divided cerebral hemispheres observed in probainognathian cynodonts, as well as in mammaliaforms. The 11 pairs of cranial nerves (excluding CN VI) in Bienotheroides are arranged longitudinally along the brain endocast, and its inner ear labyrinth is characterized by an elongated, uncoiled cochlea. The estimated encephalization quotient of Bienotheroides is similar to that of basal probainognathians or traversodontids, but relatively lower compared with derived probainognathians and mammaliaforms.

@article{doi101002spp270021,
    author = "Ren, Jicheng and Wang, Ping and Wei, Zhaoying and Liu, Lu and Meng, Jin and Mao, Fangyuan",
    title = "The cranial endocast of tritylodontid Bienotheroides (Cynodontia, Mammaliamorpha) and its relevance to mammalian neurosensory evolution",
    year = "2025",
    journal = "Papers in Palaeontology",
    abstract = "Abstract Tritylodontidae are a cosmopolitan group of derived cynodonts that thrived during the Mesozoic Era. Among the tritylodontids, the genus Bienotheroides is distinguished by its short snout, reduced maxilla, and deep zygomatic arch. Here we describe the endocranial anatomy (brain endocast, inner ear, blood vessels and cranial nerves) of Bienotheroides sp. collected from the Middle Jurassic Lower Shaximiao Formation and Xintiangou Formation in the Yunyang area of Chongqing, China. The cranial endocast features enlarged olfactory bulbs and a slender hypophysis. It is long and horizontally oriented in the brain cavity. The unossified zone is moderately developed. The paraflocculus is less developed than in most known cynodonts. The brain cast of Bienotheroides is divided into two cerebral hemispheres by a median interhemispheric sulcus, which is present only in the anterior half of the forebrain. The posterior portion of the forebrain remains undifferentiated. This condition appears to be more derived than the completely undifferentiated forebrain found in basal cynodonts. However, it is primitive compared with the fully divided cerebral hemispheres observed in probainognathian cynodonts, as well as in mammaliaforms. The 11 pairs of cranial nerves (excluding CN VI) in Bienotheroides are arranged longitudinally along the brain endocast, and its inner ear labyrinth is characterized by an elongated, uncoiled cochlea. The estimated encephalization quotient of Bienotheroides is similar to that of basal probainognathians or traversodontids, but relatively lower compared with derived probainognathians and mammaliaforms.",
    url = "https://doi.org/10.1002/spp2.70021",
    doi = "10.1002/spp2.70021",
    openalex = "W4411283379",
    references = "doi1010079781489936479, doi101038nature03102, doi101093oso97801985076040010001, doi101126science1058476, doi101126science1123026, doi101126science1203117, doi1023072413376, doi105962bhltitle118972, doi105962p316087, rowe2023evolution"
}

Olfaction is a critical sense for tetrapods, playing a key role in survival and reproduction by aiding in food detection, predator avoidance, and social interactions. Olfactory performance has been experimentally tested in only a few taxa, so comparative analyses rely on anatomical and genomic proxies. Among anatomical proxies, the olfactory bulb endocast is widely used, particularly in extinct species, where it is often the only preserved proxy and can be reconstructed even in million-year-old fossils. While the functional significance of chemoreceptor genes has received attention, the extent to which the olfactory bulb endocast correlates with genomic proxies remains unclear. Using brain endocasts across all mammalian orders, we investigated the relationship between the absolute (absOB) and relative (relatOB) volumes of the olfactory bulb endocast and the number of intact chemoreceptor genes. While no clear correlations were found between absOB and the genomic proxies tested, we identified a significant correlation between relatOB and the total number of combined intact chemoreceptor genes (CombChemo), primarily driven by olfactory receptor genes (OR). Leveraging this correlation, and aiming to infer olfactory capabilities in taxa for which only the skull is available, we estimated OR numbers for three mammalian orders lacking genomic data, as well as for five extinct mammals. Building on studies that have established a link between intact OR and olfactory sensitivity and discrimination, we conclude that relatOB enables inference of olfactory capabilities in mammals. This provides a basis to investigate sensory evolution and opens perspectives for interpreting paleoecology and behavior of extinct mammals.

@article{doi101073pnas2510575122,
    author = "Martinez, Quentin and Molinier, Cécile and Barraza-Soltero, Ilse K. and Berger, Elena and Verger, Kévin Le and Fabre, Anne‐Claire and Billet, Guillaume and Fernández, Vincent and Ferreira, Gabriel S. and van de Kamp, Thomas and Hamann, Elias and Zubér, M. S. and Miguez, Roberto Portela and Hautier, Lionel and Amson, Eli",
    title = "The olfactory bulb endocast as a proxy for mammalian olfaction",
    year = "2025",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Olfaction is a critical sense for tetrapods, playing a key role in survival and reproduction by aiding in food detection, predator avoidance, and social interactions. Olfactory performance has been experimentally tested in only a few taxa, so comparative analyses rely on anatomical and genomic proxies. Among anatomical proxies, the olfactory bulb endocast is widely used, particularly in extinct species, where it is often the only preserved proxy and can be reconstructed even in million-year-old fossils. While the functional significance of chemoreceptor genes has received attention, the extent to which the olfactory bulb endocast correlates with genomic proxies remains unclear. Using brain endocasts across all mammalian orders, we investigated the relationship between the absolute (absOB) and relative (relatOB) volumes of the olfactory bulb endocast and the number of intact chemoreceptor genes. While no clear correlations were found between absOB and the genomic proxies tested, we identified a significant correlation between relatOB and the total number of combined intact chemoreceptor genes (CombChemo), primarily driven by olfactory receptor genes (OR). Leveraging this correlation, and aiming to infer olfactory capabilities in taxa for which only the skull is available, we estimated OR numbers for three mammalian orders lacking genomic data, as well as for five extinct mammals. Building on studies that have established a link between intact OR and olfactory sensitivity and discrimination, we conclude that relatOB enables inference of olfactory capabilities in mammals. This provides a basis to investigate sensory evolution and opens perspectives for interpreting paleoecology and behavior of extinct mammals.",
    url = "https://doi.org/10.1073/pnas.2510575122",
    doi = "10.1073/pnas.2510575122",
    openalex = "W4417134418",
    references = "doi10100797833192427749, doi101016009286749190418x, doi101038nature04338, doi101038nature05066, doi101093bioinformaticsbtg412, doi101111j2041210x201100169x, doi101126science1203117, doi101159000155963, doi101371journalpbio3000494, doi101890029003, rowe2023evolution"
}

ABSTRACT In non-mammalian synapsids, feeding and hearing are closely linked because some jaw bones are involved in both functions. The evolutionary decoupling of these two systems in early mammals likely catalyzed greater specialization of feeding and hearing. Although fossil osteological changes during this process are well documented, the corresponding evolutionary changes to soft tissue anatomy are less certain. The medial pterygoid muscle is a jaw adductor that is central to this evolutionary transition because in many fossil lineages it inserted near or possibly on jaw bones involved in both feeding and hearing. In therians (placentals and marsupials), the medial pterygoid muscle develops medial to Meckel’s cartilage and inserts on the mandibular angular process. Similarly, non-mammalian cynodonts are often reconstructed with a medial pterygoid muscle passing medial to the ossified Meckel’s cartilage, inserting on the dentary ‘angular’ (i.e., pseudangular) process. Thus, the traditional interpretation is that the medial pterygoid remained medial to Meckel’s cartilage through the evolutionary transitions from early cynodonts to therians. Here we highlight issues with that interpretation: the medial pterygoid muscle inserts lateral (not medial) to Meckel’s cartilage in monotremes and, presumably, early mammal groups (e.g., spalacotherioids) that lacked an angular process. This suggests at least two possible explanatory hypotheses: 1) the medial pterygoid muscle is evolutionarily labile, shifting in position relative to Meckel’s cartilage multiple times or 2) the medial pterygoid muscle did not insert on the pseudangular process of non-mammalian cynodonts and instead inserted on the mandibular medial ridge, dorsal to Meckel’s cartilage. We advocate for the latter hypothesis, proposed by Patterson (1956), which suggests that the medial pterygoid did not shift medial to Meckel’s cartilage until the complete separation of the ear and jaw in cladotherians (therians and close relatives), with the shift in position possibly triggering the evolution of the therian angular process as an insertion site. Patterson’s hypothesis is in line with a growing body of evidence that indicate concomitant evolutionary changes of muscles, ears, and jaws at the cladotherian node were important catalysts for the evolution of hearing and feeding specializations in extant mammals.

@misc{doi10110120250819671132,
    author = "Schultz, Julia A. and Weaver, Lucas N. and Jäger, Kai R. K. and Grossnickle, David M.",
    title = "Reexamining the evolutionary history of the mammalian medial pterygoid muscle",
    year = "2025",
    booktitle = "bioRxiv (Cold Spring Harbor Laboratory)",
    abstract = "ABSTRACT In non-mammalian synapsids, feeding and hearing are closely linked because some jaw bones are involved in both functions. The evolutionary decoupling of these two systems in early mammals likely catalyzed greater specialization of feeding and hearing. Although fossil osteological changes during this process are well documented, the corresponding evolutionary changes to soft tissue anatomy are less certain. The medial pterygoid muscle is a jaw adductor that is central to this evolutionary transition because in many fossil lineages it inserted near or possibly on jaw bones involved in both feeding and hearing. In therians (placentals and marsupials), the medial pterygoid muscle develops medial to Meckel’s cartilage and inserts on the mandibular angular process. Similarly, non-mammalian cynodonts are often reconstructed with a medial pterygoid muscle passing medial to the ossified Meckel’s cartilage, inserting on the dentary ‘angular’ (i.e., pseudangular) process. Thus, the traditional interpretation is that the medial pterygoid remained medial to Meckel’s cartilage through the evolutionary transitions from early cynodonts to therians. Here we highlight issues with that interpretation: the medial pterygoid muscle inserts lateral (not medial) to Meckel’s cartilage in monotremes and, presumably, early mammal groups (e.g., spalacotherioids) that lacked an angular process. This suggests at least two possible explanatory hypotheses: 1) the medial pterygoid muscle is evolutionarily labile, shifting in position relative to Meckel’s cartilage multiple times or 2) the medial pterygoid muscle did not insert on the pseudangular process of non-mammalian cynodonts and instead inserted on the mandibular medial ridge, dorsal to Meckel’s cartilage. We advocate for the latter hypothesis, proposed by Patterson (1956), which suggests that the medial pterygoid did not shift medial to Meckel’s cartilage until the complete separation of the ear and jaw in cladotherians (therians and close relatives), with the shift in position possibly triggering the evolution of the therian angular process as an insertion site. Patterson’s hypothesis is in line with a growing body of evidence that indicate concomitant evolutionary changes of muscles, ears, and jaws at the cladotherian node were important catalysts for the evolution of hearing and feeding specializations in extant mammals.",
    url = "https://doi.org/10.1101/2025.08.19.671132",
    doi = "10.1101/2025.08.19.671132",
    openalex = "W4413348795",
    references = "doi101002ar25652, doi101093zoolinneanzlad050"
}

Fossil sites with exceptional preservation (Lagerstätten) are instrumental in accurately reconstructing ancient ecosystems on Earth. Although Lagerstätten are typically approached from a body fossil perspective, trace fossils can also be associated with these assemblages and provide unique evidence of in situ past animal behaviours. In this study, we describe the trace fossils found with the Cabrières Biota, a recently discovered Lagerstätte from southern France. Trace fossils are reported from the mudstone-dominated Lower Ordovician Landeyran Formation and consist of simple horizontal trails (Helminthoidichnites tenuis, Helminthopsis granulata), passively filled horizontal burrows (Palaeophycus tubularis), actively filled burrows (Alcyonidiopsis longobardiae, Planolites montanus,?Torrowangea isp.), rare vertical burrows (Skolithos linearis), isolated faecal pellets (Coprulus oblongus), and indiscriminate meiofaunal burrows. Ichnological metrics (e.g. absent to low bioturbation intensity, low ichnodiversity) suggest fluctuations between anoxia and dysoxia in sediments of the shelf (i.e. below the mean storm wave base), which favoured the preservation of soft-bodied organisms. These organisms, such as algae or sponges that can have relatively simple morphologies, are differentiated from trace fossils based on five criteria that we review here, and which can be used by other researchers facing difficulties in identifying fossilized objects regardless of the age or location of the investigated Lagerstätte.

@article{doi1018261let5925,
    author = "Gougeon, Romain and Vaucher, Romain and Vidal, Muriel and Birolini, Enzo and Dupichaud, Christophe and Lefebvre, Bertrand and Saleh, Farid",
    title = "Ichnology of the Lower Ordovician Landeyran Formation, Montagne Noire, France and criteria for distinguishing simple trace fossils from body fossils",
    year = "2025",
    journal = "Lethaia",
    abstract = "Fossil sites with exceptional preservation (Lagerstätten) are instrumental in accurately reconstructing ancient ecosystems on Earth. Although Lagerstätten are typically approached from a body fossil perspective, trace fossils can also be associated with these assemblages and provide unique evidence of in situ past animal behaviours. In this study, we describe the trace fossils found with the Cabrières Biota, a recently discovered Lagerstätte from southern France. Trace fossils are reported from the mudstone-dominated Lower Ordovician Landeyran Formation and consist of simple horizontal trails (Helminthoidichnites tenuis, Helminthopsis granulata), passively filled horizontal burrows (Palaeophycus tubularis), actively filled burrows (Alcyonidiopsis longobardiae, Planolites montanus,?Torrowangea isp.), rare vertical burrows (Skolithos linearis), isolated faecal pellets (Coprulus oblongus), and indiscriminate meiofaunal burrows. Ichnological metrics (e.g. absent to low bioturbation intensity, low ichnodiversity) suggest fluctuations between anoxia and dysoxia in sediments of the shelf (i.e. below the mean storm wave base), which favoured the preservation of soft-bodied organisms. These organisms, such as algae or sponges that can have relatively simple morphologies, are differentiated from trace fossils based on five criteria that we review here, and which can be used by other researchers facing difficulties in identifying fossilized objects regardless of the age or location of the investigated Lagerstätte.",
    url = "https://doi.org/10.18261/let.59.2.5",
    doi = "10.18261/let.59.2.5",
    openalex = "W7151600699",
    references = "doi101144sp55620252, gaines2025fossil"
}

Over the last 50 years, paleobiology has made great strides in illuminating organisms and ecosystems in deep time through study of the often-curious nature of the fossil record itself. Among fossil deposits, none are as enigmatic or as important to our understanding of the history of life as Konservat-Lagerstätten, deposits that preserve soft-bodied fossils and thereby retain disproportionately large amounts of paleobiological information. While Konservat-Lagerstätten are often viewed as curiosities of the fossil record, decades of study have led to a better understanding of the environments and circumstances of exceptional fossilization.Whereas most types of exceptional preservation require very specific sets of conditions, which are rare but can occur at any time, Seilacher noted the problem of “anactualistic” modes of exceptional preservation, defined as modes of fossilization that are restricted in time and that no longer occur. Here, we focus on anactualistic preservation and the widely recognized overrepresentation of Konservat-Lagerstätten in the Ediacaran and early Paleozoic. While exceptional fossil deposits of Ediacaran, Cambrian, and Early Ordovician age encompass a number of modes of fossilization, the signal of exceptional preservation is driven by only two modes, Ediacara-type and Burgess Shale–type preservation. Both are “extinct” modes of fossilization that are no longer present in marine environments. We consider the controls that promoted widespread anactualistic preservation in the Ediacaran and early Paleozoic and their implications for the environmental conditions in which complex life first proliferated in the oceans.

@article{gaines2025fossil,
    author = "Gaines, Robert R. and Droser, Mary L.",
    title = "Fossil Lagerstätten and the enigma of anactualistic fossil preservation",
    year = "2025",
    journal = "Paleobiology",
    abstract = "Over the last 50 years, paleobiology has made great strides in illuminating organisms and ecosystems in deep time through study of the often-curious nature of the fossil record itself. Among fossil deposits, none are as enigmatic or as important to our understanding of the history of life as Konservat-Lagerstätten, deposits that preserve soft-bodied fossils and thereby retain disproportionately large amounts of paleobiological information. While Konservat-Lagerstätten are often viewed as curiosities of the fossil record, decades of study have led to a better understanding of the environments and circumstances of exceptional fossilization.Whereas most types of exceptional preservation require very specific sets of conditions, which are rare but can occur at any time, Seilacher noted the problem of “anactualistic” modes of exceptional preservation, defined as modes of fossilization that are restricted in time and that no longer occur. Here, we focus on anactualistic preservation and the widely recognized overrepresentation of Konservat-Lagerstätten in the Ediacaran and early Paleozoic. While exceptional fossil deposits of Ediacaran, Cambrian, and Early Ordovician age encompass a number of modes of fossilization, the signal of exceptional preservation is driven by only two modes, Ediacara-type and Burgess Shale–type preservation. Both are “extinct” modes of fossilization that are no longer present in marine environments. We consider the controls that promoted widespread anactualistic preservation in the Ediacaran and early Paleozoic and their implications for the environmental conditions in which complex life first proliferated in the oceans.",
    url = "https://doi.org/10.1017/pab.2024.38",
    doi = "10.1017/pab.2024.38",
    number = "1",
    openalex = "W4408332068",
    pages = "29-43",
    volume = "51",
    references = "briggs2003the, doi101016jearscirev201109004, doi101016jgca200511032, doi101016jprecamres200704021, doi101021cr0503613, doi101046j13653121200200408x, doi101126science1206375, doi10166600948373200026103tap20co2, doi1023073514686, doi1023073515360"
}

Abstract This paper reviews the morphological diversity of the anterior dentition (AD - incisors and canines) in fossil and extant mammals. The great diversity of the mammalian anterior dentition is due to mosaic evolution of different morphological features. The paper identifies twenty-one groups of genera that share specific features but are not phylogenetically related. These groups are referred to as clusters. Minor differences within the clusters are described as modifications that are found in the different mammalian orders. The clusters highlight convergent features as well as evolutionary trends that occur in different clusters, such as the reduction of antemolars, the formation of incisiform lower canines and of caniniform lower premolars. The different functions of the anterior teeth within these clusters are discussed. They suggest that adaptations for quite different functions have led to very similar structures. During evolution, the reduction of anterior teeth is rare in carnivores but common in herbivores. This illustrates the increasing importance of soft parts, such as lips, tongue and trunk for foraging. The setup of the clusters described here is not intended as an additional system to which taxa must be assigned, but as a framework for highlighting similarities in unrelated taxa.

@article{doi101007s12549025006901,
    author = "von Koenigswald, Wighart",
    title = "Diversity and function of the anterior dentitions in fossil and extant mammals",
    year = "2026",
    journal = "Palaeobiodiversity and Palaeoenvironments",
    abstract = "Abstract This paper reviews the morphological diversity of the anterior dentition (AD - incisors and canines) in fossil and extant mammals. The great diversity of the mammalian anterior dentition is due to mosaic evolution of different morphological features. The paper identifies twenty-one groups of genera that share specific features but are not phylogenetically related. These groups are referred to as clusters. Minor differences within the clusters are described as modifications that are found in the different mammalian orders. The clusters highlight convergent features as well as evolutionary trends that occur in different clusters, such as the reduction of antemolars, the formation of incisiform lower canines and of caniniform lower premolars. The different functions of the anterior teeth within these clusters are discussed. They suggest that adaptations for quite different functions have led to very similar structures. During evolution, the reduction of anterior teeth is rare in carnivores but common in herbivores. This illustrates the increasing importance of soft parts, such as lips, tongue and trunk for foraging. The setup of the clusters described here is not intended as an additional system to which taxa must be assigned, but as a framework for highlighting similarities in unrelated taxa.",
    url = "https://doi.org/10.1007/s12549-025-00690-1",
    doi = "10.1007/s12549-025-00690-1",
    openalex = "W7131360421",
    references = "doi101093zoolinneanzlad050"
}