Trace fossils in estuarine deposits of different ages have been compared to evaluate colonization history of brackish-water ecosystems and to calibrate trace-fossil, brackish-water models with respect to geologic time. This comparative analysis reveals that, although the colonization of marginal-marine, brackish-water environments was a long-term process that spanned most of the Phanerozoic, this process of invasion of fully marine organisms into restricted, marginal-marine habitats did not occur at a constant rate.

Five major colonization phases can be distinguished. The first phase (Ediacaran–Ordovician) represents a prelude to the major invasion that occurred during the rest of the Paleozoic. While Ediacaran–Cambrian ichnofaunas seem to be restricted to the outermost zones of marginal-marine depositional systems, Ordovician assemblages show some degree of landward expansion within brackish-water ecosystems. Intensity of bioturbation and ichnodiversity levels were relatively low during this phase. The second phase (Silurian–Carboniferous) is marked by the appearance of more varied morphologic patterns and behavioral strategies, resulting in a slight increase in ichnodiversity. While previous assemblages were arthropod dominated, brackish-water Silurian–Carboniferous ichnofaunas include structures produced by bivalves, ophiuroids, and polychaetes. Ichnofaunas from the third phase (Permian–Triassic) seem to be characterized by the presence of crustacean burrows, reflecting the late Paleozoic crustacean radiation and adaptation of some groups to brackish-water conditions. The fourth phase (Jurassic–Paleogene) is typified by a remarkable increase in ichnodiversity and intensity of bioturbation of estuarine facies. Colonization occurred not only in softgrounds and firmgrounds, but also in hardgrounds and xylic substrates. The fifth phase (Neogene–Recent) records the onset of modern brackish-water benthos. Although still impoverished with respect to their fully marine counterparts, brackish-water ichnofaunas may reach moderately high diversities, particularly in middle- and outer-estuarine regions, and degree of bioturbation may be high in certain estuarine subenvironments. Comparative analysis of brackish-water ichnofaunas through geologic time provides valuable evidence to understand colonization of marginal-marine environments through the Phanerozoic, and allows for calibration of ichnologic models that may aid in the recognition of estuarine valley-fill deposits in the stratigraphic record.

The Neoproterozoic Noonday Dolomite (Death Valley, USA), a post-glacial cap carbonate, contains closely packed, meter-long, cm-wide, tube-like structures that define the vertical accretion direction. Similar tubestones are known from post-glacial cap carbonates in Namibia and Brazil. In vertical cross section, the tubes average 2 cm in diameter, pinch and swell greatly along their length, may bifurcate and coalesce, and are filled with brown laminated micrite/microspar where best preserved. The tubes do not root or terminate in a particular layer and are randomly distributed where present. The laminated host rock is composed of an early lithified, microclotted fabric with framework void space filled with sparry dolomite cement. The contact between the tube fill and the host rock is diffuse and feathered; commonly, wisps of laminated host rock cross the tube fill and bridge between adjacent stromatolitic structures, compartmentalizing the tubes.

The tubes likely result from the contemporaneous interplay between microbialite growth and sedimentation/cementation, rather than fluid or gas escape, as demonstrated by the compartmentalization by bridging laminae. Vertical cross sections resemble inter-column depressions that form between columnar stromatolites. Bed-parallel sections, however, reveal that the tube structures represent isolated, sediment-filled depressions within a continuous layer of stromatolite. The genesis of this unusual stromatolite morphology is likely related to highly supersaturated seawater in the aftermath of low-latitude glaciation in Neoproterozoic time. Similar tube-forming microbialites are known from alkaline lake systems such as Lake Turkana, Pavilion Lake, and paleo-Lake Gosuite (Green River Formation). The tubestones are interpreted to represent a rarely attained end-member in stromatolite morphospace, likely associated with anomalously high carbonate supersaturation.

A comprehensive taphonomic analysis has yielded a novel interpretation for one of the most famous dinosaur quarries in the world. The Cleveland-Lloyd Dinosaur Quarry (CLDQ) traditionally has been interpreted as an attritional predator trap. This scenario is based largely on a remarkable 3:1 predator:prey ratio, dominated by the remains of the theropod Allosaurus fragilis. This study addresses the taphonomy of CLDQ by combining analyses of fossils and entombing sediments along with putative modern analogues.

Thousands of bones have been excavated from CLDQ, representing at least 70 individual dinosaurs from a minimum of nine genera. The fossils occur in a 1-m-thick fine-grained calcareous mudstone interpreted as a floodplain ephemeral-pond deposit. The bones show minimal carnivore modification and surface weathering, whereas approximately 1/3 of the elements studied possess pre-depositional fractures and evidence of abrasion. The vast majority of elements are found horizontal to subhorizontal, without a preferred long-axis orientation. The demographic profile of the CLDQ dinosaur assemblage appears to be highly skewed toward subadult individuals.

Numerous lines of evidence question the traditional predator-trap hypothesis. Of the alternatives, catastrophic drought appears to be most consistent with available data. Evidence includes a large assemblage of animals in a low-energy ephemeral-pond depositional setting and geologic and biologic evidence of desiccation. Additional support comes from modern drought analogues that frequently result in mass-death assemblages of large vertebrates. Climatic interpretations during Late Jurassic times are consistent with a semiarid environment characterized by periodic drought conditions.

The effects of acidification on the preservation of buried lacustrine microfossils were evaluated using experimental tanks to simulate pH, depth, duration of acidification, and buffering conditions below the sediment/water interface of a hypothetical acidified lake. The taphonomic data provided from these experiments suggest that buffering by the host catchment (i.e., the CaCO₃ content of the soils and outcrops that underlie the lake and drainage basin) is the primary factor promoting calcareous-fossil preservation under conditions of moderate and severe acidification.

Global acid-rain fallout was a likely environmental consequence of the Chicxulub impact event at the Cretaceous– Paleogene boundary, and may have been important at other times in Earth history. Fossil preservation at the K/Pg boundary may have been affected by acidic groundwater leaching. Whereas the duration and intensity of the acid-rain fallout is poorly constrained, acid rain would have had varying effects on the acidity of lacustrine and fluvial environments with different acid-buffering capacities. Variations in acid-buffering capacities of lacustrine and fluvial catchments also may be a factor in the apparent extinction selectivity of non-marine aquatic fauna at the K/Pg boundary. Last appearances of taxa can result from poor preservation conditions or extinction—both of which may result from acidification. Last appearances observed at the species level, but not in higher taxa, may be the result of regional heterogeneities in catchment geology. Understanding local buffering conditions may be important for interpreting the continental fossil record at the K/Pg boundary.

Fossil vertebrates commonly are preserved in paleosols that originally formed on the floodplains of ancient rivers. Laterally adjacent paleosols that differ in terms of their chemistry and morphology due to geological and environmental gradients on the ancient floodplain are called pedofacies. Vertebrate fossil assemblages from the Willwood Formation (Bighorn Basin, Wyoming) are investigated to determine if there is a relationship between faunal composition and pedofacies. This question is particularly important for the Willwood Formation because it records dramatic temporal changes in both faunal composition and pedofacies across the Paleocene–Eocene boundary—an interval marked by pronounced global warming. To understand the underlying causes of these temporal patterns, it is important to know the degree to which pedofacies and faunal composition are linked. Two separate analyses are conducted to investigate the relationship between pedofacies and faunal composition. Analysis 1 evaluates faunal compositions of established localities that are stratigraphically adjacent but characterized by different mean pedofacies. Results indicate that faunal compositions of these localities are not related to pedofacies but instead correspond to differences in the estimated body masses of the taxa. Results of Analysis 2, which evaluates new paleosol-specific collections from the same stratigraphic interval, indicate that different pedofacies are characterized by nearly identical faunas. The only exception is lizards, which are significantly more abundant in mature paleosols. Environmental gradients on the ancient floodplain seem to have exerted very little control on faunal composition at this spatial scale, but size sorting may have been an important taphonomic process in these Willwood collections.

The scarcity of fossil crabs compared to heavier calcified taxa implies either: (1) crab remains are rarely preserved (taphonomic hypothesis); (2) crab remains are frequently overlooked/misidentified (taxonomic hypothesis); or (3) crabs were less abundant in ancient ecosystems (ecological hypothesis). To evaluate the taphonomic hypothesis, the preservational potential of the yellow shore crab, Hemigrapsus oregonensis, was evaluated in a modern tidal pool of False Bay, San Juan Islands, Washington, USA. Crab remains were compared to molluscan taxa, which served as a taphonomic reference standard. The surface crab remains (4.2 parts per m²) displayed an anatomical bias: carapace and cheliped remains were more numerous than predicted, while leg remains were underrepresented. Crab remains often were disarticulated, but other alterations (bioerosion, dissolution, or encrustation) were virtually absent. This contrasts with non-crab material (bivalves, gastropods, and barnacles), which was abundant in the tidal pool (41 parts per m²), and dominated (94.7%) by highly taphonomic altered remains, suggesting long exposure at, or near, the surface. Ratios of non-crab to crab remains increased from 10: 1 at the surface to 154:1 in the subsurface. Low taphonomic alteration of crab remains, low density of surface crab material, an increase in non-crab to crab ratio in the subsurface, and a severe anatomical bias imply nearly complete loss of crab remains prior to burial. This suggests a low probability of preservation, especially when compared to co-occurring mollusks, providing quantitative support for the taphonomic hypothesis.