A submarine cave is a unique environment that is dark, food limited, semi-isolated from the outside, and sheltered from wave action. However, our knowledge of the long-term change in submarine-cave ecosystems remains limited. We document here the community-scale responses toward long-term change in a submarine cave, Daidokutsu in Okinawa in southern Japan. Using both metazoans (ostracods and bivalves) and protozoans (larger benthic foraminiferans) in two sediment cores obtained from the cave, we reconstruct the faunal and diversity changes of the past 7 Kyr. All taxonomic groups showed long-term, gradual linear change of faunal composition from predominantly open-water taxa to predominantly cave taxa, and ostracods showed short-term variability of species diversity. The long-term faunal trend probably reflects gradual isolation of the cave ecosystem due to coral reef development (i.e., development of the cave ceiling) during periods of the Holocene transgression and subsequent sea-level highstand. The short-term diversity changes show substantial similarity to centennial- to millennial-scale Holocene Asian monsoon variability. Ostracod species diversity peaks tend to correspond with periods of strong East Asian winter monsoons. The results indicate that limestone submarine-cave ecosystems, an important cryptic habitat, developed gradually during the Holocene and may be sensitive to rapid climate changes.

Clymeniid ammonoids appeared during the Late Devonian (Mid-Famennian) and quickly radiated before becoming extinct at the Devonian/Carboniferous boundary. Outwardly indistinguishable from other ammonoids, clymeniids are distinguished internally by their dorsal siphuncle, contrasted to a ventral siphuncle in almost all other ammonoids. Comparisons of a sample of Clymeniida (n = 22 genera), Goniatitida (n = 33), Prolecanitida (n = 12), and Anarcestida (n = 13) indicate that clymeniids fall within the range of other ammonoids in terms of shell geometry and suture complexity, but their siphuncles average two to three times larger and clymeniid shells are approximately 33% thicker than those of other ammonoids. Although a dorsal siphuncle would be about 50% smaller in surface area and volume than if located in a ventral position, the enlarged clymeniid siphuncle partially and, in some cases, fully compensated for this loss. Hydrostatic simulations of 15 clymeniid genera indicate that their thicker (therefore heavier) shells would have resulted in relatively short body chambers (≈280°) and high aperture orientations (≈90°). In static life-position, these orientations would have placed the dorsal clymeniid siphuncle at or near the bottom of the most recently formed chambers, seemingly an ideal location for draining liquid from the chamber. Migration of the siphuncle to the dorsal side of the shell occurs suddenly during early ontogeny (within the first two or three chambers), and mutation of homeotic gene expression is offered as a possible explanation for the sudden shift. A dorsal siphuncle may have resulted in selection for enlarged siphuncles, but this may have incurred loss of strength against hydrostatic pressure (thereby reducing depth limits) and thus rendered the clade more susceptible to the multiple eustatic and anoxic events that marked the end of the Devonian.

Farming is a behavior in which an organism promotes the growth and reproduction of other organisms in or on a substrate as a food source. A number of trace fossils have been suggested to record the occurrence of farming behavior. These include the deep-sea graphoglyptid trace fossils, proposed to be microbial farms on the seafloor, and terrestrial fossil social insect nests thought to represent fungicultural behavior. The presumed farming behavior of graphoglyptids is the basis of the ethological category agrichnia. Four criteria have been proposed as diagnostic of farming behavior, and these can be applied to both observed modern and proposed trace fossil examples of farming behavior. The evidence for farming behavior in the social insect trace record is strong but is much weaker in the case of graphoglyptids. The use of agrichnia as an ethological category should be limited to well-supported cases.

Relaxed clock models are fundamental in Bayesian clock dating, but a single distribution characterizing the clock variation is typically selected. Hence, I developed a new reversible-jump Markov chain Monte Carlo (rjMCMC) algorithm for drawing posterior samples between the independent lognormal (ILN) and independent gamma rates (IGR) clock models. The ability of the rjMCMC algorithm to infer the true model was verified through simulations. I then applied the algorithm to the Mesozoic bird data previously analyzed under the white noise (WN) clock model. In comparison, averaging over the ILN and IGR models provided more reliable estimates of the divergence times and evolutionary rates. The ILN model showed slightly better fit than the IGR model and much better fit than the autocorrelated lognormal (ALN) clock model. When the data were partitioned, different partitions showed heterogeneous model fit for ILN and IGR clocks. The implementation provides a general framework for selecting and averaging relaxed clock models in Bayesian dating analyses.

Biodiversity hotspots are increasingly recognized as areas of high taxonomic and functional diversity. These hotspots are dynamic and shift geographically over time in response to environmental change. To identify drivers of the origin, evolution, and persistence of diversity hotspots, we investigated the diversity patterns of reef-building corals (Scleractinia) in the Central Indo-Pacific, a marine biodiversity hotspot for the last 25 Myr. We used the scleractinian fossil record (based on literature and a newly acquired fossil collection) to examine the taxonomic and functional diversity of corals from the Eocene to Pliocene. Our data identify potential drivers of coral diversity through time (and space) in the Central Indo-Pacific by constraining the timing of taxonomic turnover events and correlating them with known environmental changes. Increases in taxonomic diversity, high origination rates, and changes in abundance of functional character states indicate that the origin of the Central Indo-Pacific hotspot occurred during the Oligocene, initially through proliferation of pre-existing taxa and then by origination of new taxa. In contrast to taxonomic diversity, overall functional diversity of Central Indo-Pacific reef-building corals remained constant from the Eocene to the Pliocene. Our results identify global sea level as a main driver of diversity increase that, together with local tectonics, regulates availability of suitable habitats. Moreover, marine biodiversity hotspots develop from both the accumulation of taxa from older biodiversity hotspots and origination of new taxa. Our study demonstrates the utility of a combined literature-based and new collection approach for gaining new insights into the timing, drivers, and development of tropical biodiversity hotspots.

Intrinsic features of organisms, such as morphology or DNA sequences, and the stratigraphic occurrence of fossils provide distinct evidence of the phylogenetic history of life. Because there is only one true history, we expect the historical signals preserved by these data sets to be similar, and several metrics have been developed to measure the fit of phylogenetic hypotheses to the fossil record. However, a variety of biases affect these metrics, and it is unclear whether they can provide more than an estimate of whether one tree fits the fossil record better than another when used on their own. Here we explore two novel applications of stratigraphic fit metrics when they are used with a combination of phylogeny reconstruction methods that do and do not directly include stratigraphic occurrence data (e.g., cladistics and stratocladistics). In particular, we are interested in whether differences in the stratigraphic fit of cladistic and stratocladistic trees can be used to identify cases in which the stratocladistic results are likely to be more accurate, as well as whether such differences can be used to identify potential problems in the underlying data sets.

Using 550 simulated data sets that were analyzed with cladistics and stratocladistics, we found that the absolute difference in fit to stratigraphy between the results of the two methods was strongly correlated with the probability of character state transition and the accuracy of the stratocladistic results relative to the cladistic results. Completeness of the fossil record and number of taxa included in the analysis were more weakly correlated with stratigraphic fit, and the statistical significance of the differences in fit between the two sets of results did not show a meaningful relationship with improvements in accuracy or potential data problems. These results suggest that measuring the difference in stratigraphic fit between cladistic and stratocladistic trees might be useful for qualitatively estimating whether the addition of stratigraphic data benefited a phylogenetic analysis, and for identifying data sets with high average rates of character state change.

In quantitative paleobiology, one common format for image-derived information is the closed two-dimensional outline curve. Before the end of the last century a great variety of morphometric tools were on offer to deal with this data type, including diverse analyses of distance from a central point, “eigenshape analysis” of a carefully normalized tangent angle function, and Procrustes analysis of configurations of sliding semilandmarks. For the special case of outline forms that are nominally bilaterally symmetric, this paper offers a hybrid approach that fuses the Procrustes toolkit with a variant of a much older method, analysis of radial distance according to angles out of a center. The synthesis represents each outline as a regularly resampled data set of radially aligned shape coordinates analogous to bilateral Procrustes shape coordinates. When the center is iteratively located in one particular way, this representation has the same Procrustes distance statistics as a conventional radial representation, while the formalism of shape coordinates permits symmetrization, localizability, and thin-plate spline visualizations. We explain the method and sketch some of its advantages and limitations in the course of an example involving 99 Baculites inornatus outlines spanning 90 m of deposits from a high-precision measured section in the Campanian-age Rosario Formation cropping out at Punta San Jose, Baja California. This sequence shows substantial changes of pole curvature over time, changes that may involve a punctuation event regarding hydrostatics, hydrodynamics, or defense against predators. A concluding comment deals with implications of the developments here for Baculites microevolution and for morphometrics.

Experiments show that diductor muscles of articulate brachiopods are normally relaxed, contracting only when the valves gape. Consequently, dead brachiopods rarely gape.

Paleoecological studies enhance our understanding of biotic responses to climate change because they consider long timescales not accessible through observational and experimental studies. Using predatory drillholes produced on fossil bivalve shells by carnivorous gastropods, we provide an example of how climate change affected predator–prey interactions. We quantitatively examine temporal changes in fossil molluscan assemblages and predation patterns from the Pleistocene Japan Sea, which experienced drastic environmental changes in relation to glacial–interglacial climate cycles. We found significant changes in predation patterns associated with a decline in the abundance of warm-water molluscan species. Climate-mediated fluctuations in the eustatic sea level and resultant weakening of the Tsushima Warm Current caused a decline in a warm-water shell-drilling predator, which moderated the predation pressure and size relationship between the predators and the bivalve prey. Our results indicate that climate-mediated range shifts of species in present-day and future marine ecosystems can likewise increase altered predator–prey interactions.

Feeding behaviors may differ between past and current predators due to differences in the environments inhabited by these species at different times. We provide an example of this behavioral variability in spotted hyena (Crocuta crocuta), for which our analysis of a late Pleistocene micromammal assemblage indicates that hyenas preyed upon small rodents, a feeding habit that is rarely observed today among hyenas.

The Bois Roche cave site is situated at the edge of a low bluff overlooking the floodplain of a small stream in Cherves-Richemont (Charente, France). The deposits are dated by electron spin resonance (ESR) to about 69.7 ± 4.1 Ka. Excavations at the site recovered fossil bones and teeth of large and small mammals, together with hyena coprolites. Water screening of the sediments produced large accumulations of rodent remains with low taxonomic diversity. Small mammal bones were recovered from hyena coprolites as well. Descriptions of small mammal bone modification, both from the sediments and coprolites, are reported here. The analysis yielded a distinct taphonomic pattern representative of large carnivores (over 30 kg), which differs from any other modern or fossil predator-accumulated microfaunal assemblage taphonomically analyzed to date. To our knowledge, previous studies of hyena diet have not recorded high concentrations of a single-rodent prey species. We conclude that the low species diversity of this small mammal assemblage most likely relates to a local abundance of the prey species due to an outbreak in the rodent population, rather than from specialist predator behavior and hunting technique.

To the student of evolution, Malmgren and Kennett's (1981) detailed study of the Globorotalia inflata lineage demonstrates the continuity of the stratigraphic record and the abundance of planktic microfossils in deep-sea sediments. Their work recalls the prediction (Prothero and Lazarus 1980) that planktic microfossils might serve as the laboratory animals of evolutionary studies and indicates the potential value of fossils in determining ancestry. However, for theorists to judge the evolutionary import of Malmgren and Kennett's high-resolution morphometric study, broader consideration of lineage relationships is needed. They portray the G. inflata lineage as a set of five successional taxa in simple ancestor-descendant relationship. Trends, established morphometrically and claimed to be “one of the clearest examples of gradualism in any group of fossils” (Malmgren and Kennett 1981, p. 236), are shown to progressively transform a compressed shell with peripheral keel (G. conoidea) into a globose shell (G. inflata) without a keel. While the succession of taxa given by Malmgren and Kennett has been supported in other studies of western South Pacific sequences (e.g., McInnes 1965; Walters 1965; Kennett 1966; 1973; Jenkins 1971; Scott 1979; Hornibrook 1982), it is not established that the order indicates simple phyletic transformation without branching, as Malmgren and Kennett imply. Crucial evidence concerns the history and status of keeled populations which resemble the ancestral G. conoidea but occur in the Pliocene, associated with advanced members of the G. inflata lineage. These populations are not mentioned by Malmgren and Kennett, yet, if they are also descendants of G. conoidea, their occurrence strongly suggests that lineage divergence occurred. I wish to review evidence in support of this view.

The Order Spiriferinida spanning the latest Ordovician to Early Jurassic is a small group of brachiopods overshadowed by other taxon-rich clades during the Paleozoic. It diversified significantly after the end-Permian extinction and became one of the four major clades of Triassic brachiopods. However, the phylogeny and recovery dynamics of this clade during the Triassic still remain unknown. Here, we present a higher-level parsimony-based phylogenetic analysis of Mesozoic spiriferinids to reveal their evolutionary relationships. Ecologically related characters are analyzed to indicate the variances in ecomorphospace occupation and disparity of spiriferinids through the Permian–Triassic (P-Tr) transition. For comparison with potential competitors of the spiriferinids, the pre-extinction spiriferids are also included in the analysis. Phylogenetic trees demonstrate that about half of the Mesozoic families appeared during the Anisian, indicating the greatest phylogenetic diversification at that time. Triassic spiriferinids reoccupied a large part of the ecomorphospace released by its competitor spiriferids during the end-Permian extinction; they also fully exploited the cyrtiniform region and developed novel lifestyles. Ecomorphologic disparity of the spiriferinids dropped greatly in the Early Triassic, but it rebounded rapidly and reached the level attained by the pre-extinction spiriferids in the Late Triassic. The replacement in ecomorphospace occupation between spiriferids and spiriferinids during the P-Tr transition clearly indicates that the empty ecomorphospace released by the extinction of Permian spiriferids was one of the important drivers for the diversification of the Triassic spiriferinids. The Spiriferinida took over the empty ecomorphospace and had the opportunity to flourish.

Accurate interpretation of origination and extinction of fossil species is crucial to answering a variety of questions in paleontology. Fossil datums, the observed age of first or last occurrences, are subject to sampling error as a result of preservation and low abundances near range endpoints. This sampling error can cause local range offset, an age difference between the observed first or last occurrence of a species and its true origination or extinction. Here, we develop and test a new technique, the Probable Datum Method (PDM), that can be used to assess the extent of local range offset for nannofossil species. The PDM estimates the original abundance of a taxon and its probable true age of first or last occurrence. The PDM uses a model in which original abundance is related to count abundance through preservation and the counting process. This model is empirically parameterized, including an experimental determination of false positive and error rates of a nannofossil count. The model is simulated then inverted to estimate likely original abundance and true datum age from count abundance data. We first test the PDM in a positive control experiment with known parameter values. This experiment shows that the PDM is robust and returns known values accurately. Next we apply the method to the origination of nannoplankton after the Cretaceous/Paleogene boundary to test whether first occurrences were synchronous between widely spaced locations. The PDM results suggest that observed diachrony of K/Pg originations cannot be explained by the effects of local range offset; rather, in some cases they indicate truly diachronous first occurrences between localities. Although the technique was developed to analyze nannoplankton ranges, the statistical nature of the PDM, its experimentally derived parameters, and its parsimonious nature should make it applicable to many micropaleontological studies that interpret patterns of origination and extinction.

Examination of the neanic apparatuses of known populations of Nephrolepidina praemarginata, N. morgani, and N. tournoueri reveals that the equatorial chamberlets are arranged in spirals, along the direction of connection of the oblique stolons, giving the optical effect of intersecting curves. In N. praemarginata commonly 34 left- and right-oriented primary spirals occur from the first annulus to the periphery, 21 secondary spirals from the third to fifth annulus, 13 ternary spirals from the fifth to eighth annulus, following the Fibonacci sequence.

The number of the spirals increases in larger specimens and in more embracing morphotypes, and especially in trybliolepidine specimens; the secondary and ternary spirals from the investigated N. praemarginata to N. tournoueri populations tend to start from more distal annuli. An interpretative model of the spiral growth of Nephrolepidina is attempted.

The angle formed by the basal annular stolon and distal oblique stolon in equatorial chamberlets ranges from 122° in N. praemarginata to mean values close to the golden angle (137.5°) in N. tournoueri.

The increase in the Fibonacci number of spirals during the evolution of the lineage, along with the disposition of the stolons between contiguous equatorial chamberlets, provides new evidence of evolutionary selection for specimens with optimally packed chamberlets.

Natural selection favors individuals with the most regular growth, which fills the equatorial space more efficiently, thus allowing these individuals to reach the adult stage faster. We refer to this new type of selection as “golden selection.”

The typical marine animal has increased in biovolume by more than two orders of magnitude since the beginning of the Cambrian, but the causes of this trend remain unknown. We test the hypothesis that the efficiency of intra-organism oxygen delivery is a major constraint on body-size evolution in marine animals. To test this hypothesis, we compiled a dataset comprising 13,723 marine animal genera spanning the Phanerozoic. We coded each genus according to its respiratory medium, circulatory anatomy, and feeding mode. In extant genera, we find that respiratory medium and circulatory anatomy explain more of the difference in size than feeding modes. Likewise, we find that most of the Phanerozoic increase in mean biovolume is accounted for by size increase in taxa that accomplish oxygen delivery through closed circulatory systems. During the Cambrian, water-breathing animals with closed circulatory systems were smaller, on average, than contemporaries with open circulatory systems. However, genera with closed circulatory systems superseded in size genera with open circulatory systems by the Middle Ordovician, as part of their Phanerozoic-long trend of increasing size. In a regression analysis, respiratory and circulatory anatomy explain far more size variation in the living fauna than do feeding modes, even after accounting for taxonomic affinity at the class level. These findings suggest that ecological and environmental drivers of the Phanerozoic increase in the mean size of marine animals operated within strong, anatomically determined constraints.

Insects in the fossil record are generally preserved in lacustrine shales or in amber. For those in lacustrine shales, preservation is usually via keroginization or mineralization. Given the extended period of microbial decay required to generate ions for mineralization, there is a predicted inherent bias toward lower preservation quality for this pathway by most taphonomic indices compared with keroginization. This study tests this hypothesis by comparing multiple measures of preservation quality between sites with similar sedimentology in the Eocene Green River Formation of Colorado. Here, insects are either mineralized in iron oxides (likely after pyrite) at the Paleoburn site or keroginized at the Anvil Points site.

Generally, the prediction that keroginization preserves soft-bodied fossils with higher preservational quality than mineralization is affirmed, but with some caveats. Beetles, known for their robust cuticles, are proportionately more abundant at the Paleoburn site, but eight of the nine orders recorded are shared between sites. As predicted, insects show lower preservation fidelity at the Paleoburn site, but they also show higher degrees of disarticulation. This second bias should be acquired primarily during the biostratinomy stage, and not early diagenesis. Nonetheless, higher-energy biostratinomic conditions may be compatible with taphonomic conditions that promote mineralization over keroginization.

Comparing the inherent taphonomic bias of different preservation pathways is often difficult, since fossil deposits may be preserved millions of years or thousands of kilometers apart. By studying two different preservation pathways of insects within the same formation, we can affirm that keroginization does indeed preserve recalcitrant organic matter with higher quality than pyritization or iron-oxide mineralization. Additionally, some guidelines can be proposed concerning the body parts and taxa that can be compared, and for what purpose, when contrasting mineralized and keroginized soft-bodied deposits.

One important and sometimes contentious challenge in paleobiology is discriminating between species, which is increasingly accomplished by comparing specimen shape. While lengths and proportions are needed to achieve this task, finer geometric information, such as concavity, convexity, and curvature, plays a crucial role in the undertaking. Nonetheless, standard morphometric methodologies such as landmark analysis are not able to capture in a quantitative way these features and other important fine-scale geometric notions.

Here we develop and implement state-of-the-art techniques from the emerging field of computational geometry to tackle this problem with the Mississippian blastoid Pentremites. We adapt a previously known computational framework to produce a measure of dissimilarity between shapes. More precisely, we compute “distances” between pairs of 3D surface scans of specimens by comparing a mix of global and fine-scale geometric measurements. This process uses the 3D scan of a specimen as a whole piece of data incorporating complete geometric information about the shape; as a result, scans used must accurately reflect the geometry of whole, undamaged, undeformed specimens. Using this information we are able to represent these data in clusters and ultimately reproduce and refine results obtained in previous work on species discrimination. Our methodology is landmark free, and therefore faster and less prone to human error than previous landmark-based methodologies.

Pteridinium simplex is an iconic erniettomorph taxon best known from late Ediacaran successions in South Australia, Russia, and Namibia. Despite nearly 100 years of study, there remain fundamental questions surrounding the paleobiology and paleoecology of this organism, including its life position relative to the sediment–water interface, and how it fed and functioned within benthic communities. Here, we combine a redescription of specimens housed at the Senckenberg Forschungsinstitut und Naturmuseum Frankfurt with field observations of fossiliferous surfaces, to constrain the life habit of Pteridinium and gain insights into the character of benthic ecosystems shortly before the beginning of the Cambrian. We present paleontological and sedimentological evidence suggesting that Pteridinium was semi-infaunal and lived gregariously in aggregated communities, preferentially adopting an orientation with the long axis perpendicular to the prevailing current direction. Using computational fluid dynamics simulations, we demonstrate that this life habit could plausibly have led to suspended food particles settling within the organism's central cavity. This supports interpretation of Pteridinium as a macroscopic suspension feeder that functioned similarly to the coeval erniettomorph Ernietta, emblematic of a broader paleoecological shift toward benthic suspension-feeding strategies over the course of the latest Ediacaran. Finally, we discuss how this new reconstruction of Pteridinium provides information concerning its potential relationships with extant animal groups and state a case for reconstructing Pteridinium as a colonial metazoan.

Discriminant function analysis is used to examine the role of within-species differentiation in macroevolution of four Miocene bivalve genera. According to the punctuational model, macroevolution is decoupled from microevolution; within-species trends may be unrelated to between-species differences. The reductionist alternative suggests that intraspecific (primarily geographic) differentiation is the basis of macroevolution. If macroevolution depends on within-species differentiation, discriminant function analysis should separate interspecific and intraspecific populations of a genus using the same set of characters.

Chesapecten macroevolution apparently involved within-species differentiation. Shell length, height, and posterior auricle length differentiate geographic populations within species as well as interspecific populations. Results for Astarte, Anadara, and Eucrassatella are more consistent with the punctuational model. Characters which readily separate species of a genus are much less successful at differentiating intraspecific populations. Rank correlation techniques indicate that, for all three genera, the order of importance of characters in interspecific discrimination is not significantly related to their order in intraspecific discrimination. Decoupling of macroevolution from microevolution is implied for these taxa.