Evidence that can be used to interpret the life habits of extinct organisms usually takes three forms: functional analysis, analogy with living organisms, and geological evidence. Independent quantitative tests for habit are rarely available. A theory of optimum eye design originally derived for living aquatic arthropods provides quantitative data that are used to test previous suppositions about the life habits of two Ordovician pelagic trilobites: that the telephinid trilobite Carolinites was epipelagic while the cyclopygid Pricyclopyge was mesopelagic. Optimum compound eye design theory uses measured lens diameters and interommatidial angles to determine the “eye parameter” (p), which can be used to gauge approximate optimum level of illumination for the eyes of these trilobites. The eye parameter provides an independent test for their relative paleobathymetry. Values of the eye parameter measured in the dorso-ventral direction across two eyes of Carolinites killaryensis utahensis were found to have medians of 2.13 and 3.24. Values measured in the antero-posterior direction have medians of 3.17 and 4.86 for the two eyes. Values measured in the dorso-ventral direction across two eyes of Pricyclopyge binodosa have medians of 4.23 and 4.98, while values measured in the antero-posterior direction have medians of 7.06 and 8.31. Eye parameters are higher in Pricyclopyge than in Carolinites, the difference statistically significant at p = 0.05. The eyes of Pricyclopyge are optimally designed for lower levels of illumination than are those of Carolinites. This accords with the previous interpretations of the former trilobite as mesopelagic and the latter as epipelagic.

Calliostoma ligatum shells inhabited by hermit crabs were weaker than shells inhabited by snails collected at the same locality. When shells of C. ligatum were loaded repetitively to 80% of their predicted failure load, hermit crab-inhabited shells showed an immediate drop in shell strength followed by a progressive further loss of shell strength over the next 18 days. Snailinhabited C. ligatum shells exhibited a decrease in strength after 9 days, but returned to initial values within 18 days of loading.

Hermit crabs thus bear shells significantly weaker than they were when borne by the gastropods that produced them. Reported similarities in vulnerability of gastropods and hermit crabs to shell-crushing predators may be artifacts of the metric (critical size) used to compare vulnerabilities. Hermit crabs probably were a significant factor in the diversification of durophagous predators in the Mesozoic, supplying a prey base identical in size and shape to gastropods but with significantly lower resistance to crushing. The unpredictability of strength in hermit-crab inhabited shells may maintain the apparently inefficient indiscriminate attacks common among durophagous predators.

Mammalian generic, familial, and ordinal diversities correlate significantly with continental area. The area effect is similar in form to that shown for true islands: S = kAz, where S is the diversity, A is the area, and k and z are fitted constants. For mammalian genera and continental area, z equals 0.33, for families, z equals 0.23, and for orders, z equals 0.13.

The area effect permits quantitative modeling of extinction due to biotic competition between previously isolated faunas. The Late Cenozoic extinction of North and South American mammalian faunas following the rise of the Panamanian land bridge is overestimated by seven families. The overestimate may result from assumptions of complete biotic interchange and universal competition. The role of plate tectonics in regulating diversity may be extensively modified by regional environmental conditions.

Studies of crinoid morphology have been pivotal in understanding the constraints on the range of morphology within a clade as well as the patterns of disparity throughout the Phanerozoic. Newly discovered and described faunas and recent study of early Paleozoic crinoid diversity provide an ideal opportunity to reanalyze Ordovician through Early Silurian crinoid disparity with more complete taxonomic coverage and finer stratigraphic resolution. Using the coarse stratigraphic binning of Foote (1999), the updated morphologic data set has a similar disparity pattern to those previously reported for the early Paleozoic. However, with the more resolved stratigraphic binning used by Peters and Ausich (2008), a significant difference exists between the original and current data sets. Both data sets have a pronounced disparity high during the late Middle Ordovician. However, the updated disparity curve has a much higher initial disparity during the Early Ordovician and a pronounced rise in disparity during the Silurian recovery. Examination of differential sampling, proportions of the crinoid orders through time, and methods of coding characters indicate these factors have little effect on the pattern of crinoid disparity. The Silurian morphospace expansion occurs primarily within disparids and coincides with the origination of the myelodactylids. These findings corroborate the rapid expansion of morphospace during the Ordovician. However, crinoid disparity did not remain static and, although less frequent than during the initial radiation, new body plans evolved following the Ordovician Extinction (e.g., the myelodactylids). These results are consistent with the hypothesis of ecology constraining the limits on morphologic disparity at the class level.

The preservation of compounds of biological origin (nucleic acids, proteins, carbohydrates, lipids, and resistant biopolymers) in terrigenous fossils and the chemical and structural changes that they undergo during fossilization are discussed over three critical stratigraphic levels or “time slices.” The youngest of these is the archeological record (e.g., <10 k.y. B.P.), when organic matter from living organisms undergoes the preliminary stages of fossilization (certain classes of biomolecule are selectively preserved while others undergo rapid degradation). The second time slice is the Tertiary. Well-preserved fossils of this age retain diagenetically modified biomarkers and biopolymers for which a product-precursor relationship with the original biological materials can still be identified. The final time slice is the Carboniferous. Organic material of this age has generally undergone such extensive diagenetic degradation that only the most resistant biopolymers remain and these have undergone substantial modification. Trends through time in the taphonomy and utility of ancient biomolecules in terrigenous fossils affect their potential for studies that involve chemosystematic and environmental data.

Seven endemic species of skates (Chondrichthyes: Rajidae) represent the only family of elasmobranchs currently known to live in Antarctic continental waters. Many previous authors believed skates colonized Antarctic waters from Patagonia during interglacial periods in the Quaternary. However, recent fossil material collected from the middle Eocene La Meseta Formation of Seymour Island, Antarctic Peninsula, indicates that they may have persisted in Antarctic waters since the Paleogene. Additionally, oceanographic barriers present in the Neogene and Quaternary would have prevented dispersal from southern continents to Antarctica. A revised dispersal scenario, based on skate fossils, biology, paleogeography, and present centers of skate diversity, suggests that skates evolved in the western Tethys and North Boreal seas of western Europe in the Late Cretaceous and early Paleogene and emigrated into Antarctica during the early to middle Eocene via a dispersal corridor along the continental margins of the western Atlantic Ocean. Skates probably populated the Pacific Basin by passing from this dispersal corridor through the Arctic Ocean. Vicariant events, such as opening of the Drake Passage, the development of the Circum-Antarctic Current, and formation of deep and wide basins around Antarctica in the late Paleogene, created barriers that isolated some species of skates in Antarctica and prevented movement of other species of skates into Antarctica from northern areas. Skates are the only group of fishes known to have survived the Oligocene cooling of Antarctica that killed or extirpated the Paleogene ichthyofauna; they persisted by a combination of cold-tolerance, generalized diet, and unspecialized bathymetric and habitat preferences.

The North African murine rodent Paraethomys evolved as an anagenetic lineage from the late Miocene until its extinction in the late—middle Pleistocene. A Fourier analysis of the outlines of the first upper and lower molars of this rodent was used to quantify the evolutionary patterns of this lineage and to compare evolutionary patterns to the climatic record. Morphological evolution and long-term environmental variations are strongly correlated. A change in molar shape, which may be related to the development of a more grass-eating diet, corresponds to the global cooling beginning around 3 Ma and the subsequent increase in aridity in North Africa. Concurrently, size increased, which may be related to increased masticatory efficiency or to metabolic adaptation to the cooler environmental conditions according to Bergmann's rule. This adaptive response to changing environmental conditions corresponds to an acceleration of evolutionary rates in the lineage. The modalities of the evolutionary response in size and shape are probably controlled by intrinsic factors such as different genetic determinisms for both characters.

“It's not all heterochrony.” Raff (1996)

“Heterochrony … explains everything.” McNamara (1997)

Few evolutionary topics have generated more confusion and controversy than heterochrony. Commonly defined as “evolution via change in rate or timing of development,” heterchrony has historically become associated with genocidal ideologies, simple-minded theories of evolution, and a bloated, baroque jargon describing patterns produced by largely unknown mechanisms. With a track record like that, perhaps the most surprising aspect of heterochrony is its continued, even rapid, growth as an area of productive scientific inquiry. For example, the number of papers devoted to heterochronic topics continues to increase in many evolutionary journals and books (reviews in Reilly et al. 1997; Klingenberg 1998), including those devoted to human development (Bogin 1997) and evolution (Vrba 1998; McKinney 1998; Parker and McKinney 1999).

Macerations of fragmented plant compressions of Silurian (Llandoverian) age yield sheets of organic material bearing ridges and depressions (interpreted as corresponding to surficial dimensions of cells), fragments of smooth walled tubular elements, and fragments of tubular elements with differentially thickened walls (“banded tubes”). A fragment of tissue (1.2 mm long), consisting of smooth walled tubes (17 ± 6.9 μm in diameter), surrounding 2–3 larger (18.8 ± 2.1 μm in diameter) banded tubes, was isolated from an irregularly shaped, relatively large (1 × 3 mm) compression. Comparisons between (1) fragments of tubular cell types, not organized into strands, isolated from 122 compressions, and (2) dispersed tubular cell types previously reported from the Massanutten Formation and other Silurian formations (Tuscarora and Clinton), reveal no significant morphologic differences. Comparisons between the organization of smooth-walled and banded tubular cell types found in the tissue strand and the organization of cell types in nematophytic plants (Nematothallus, Nematoplexus, Prototaxites) indicate a similarity in construction (tubular) but a lack of correspondence in organization. The strand of tissue is interpreted as representing part of the internal anatomy of a nonvascular land plant of unknown taxonomic affinity. On the basis of analogy with present-day embryophytes, the strand of tubular cell types is inferred to have functioned as a conductive tissue. The significance of “banded tubes” in Silurian strata is discussed, and it is concluded that, until more is known about the anatomy, morphology, and biochemistry of the parent plant(s), the habitat and systematic affinity of these organisms are conjectural.

Abundance is one of the primary factors believed to influence extinction yet little is known about its relationship to extinction rates over geologic time. Using data from the Paleobiology Database we show that abundance was an important factor in the extinction dynamics of marine bivalve genera over the post-Paleozoic. Contrary to expectations, our analyses reveal a nonlinear relationship between abundance and extinction rates, with rare and abundant genera exhibiting rates elevated over those of genera of moderate abundance. This U-shaped pattern is a persistent feature of the post-Paleozoic history of marine bivalves and provides one possible explanation for why we find strong support for heterogeneous extinction rates among genera grouped by similarity in abundance yet effectively no net relationship among these rates when using models of directional selection on abundance.

Fundamental to the interpretation of bone-bearing faunal deposits is an understanding of the taphonomic processes that have modified the once living fossil community. An often neglected source of bias is that of climate-averaging, which occurs when the duration of bone accumulation exceeds the duration of an individual climatic episode. Tropical and subtropical climate change is dominated by precessional cyclicity (~21,000 year cycle), which controls monsoon rainfall intensity and thus plant communities over time. Under a climate-averaging scenario, the paleoecological characteristics of a faunal deposit represent an amalgamation of more than one phase of the precessional cycle. We investigate the degree of climate-averaging in Plio-Pleistocene bone breccias from South Africa by comparing stable isotope measurements of fossil enamel with the evidence from high-resolution speleothem paleoclimate proxies. We conclude that each of the four faunal assemblages studied are climate-averaged, having formed over a time period in excess of one-third of a precessional cycle (~7000 years). This has implications for the reconstruction of hominin paleoenvironments and estimates of Plio-Pleistocene biodiversity. We hypothesize that climate-averaging may be a common feature of tropical terrestrial vertebrate assemblages throughout the Cenozoic and Mesozoic.

Use of quantitative statistical tests can show that there is generally good congruence between estimated cladistic hypotheses of relationship and observed stratigraphy. A data set of 376 cladograms of fishes, continental tetrapods, and echinoderms was tested using three metrics, Spearman Rank Correlation (SRC), Relative Completeness Index (RCI), and Stratigraphic Consistency Index (SCI), to explore the relationships between the indices and differences in results among the three groups of organisms.

There is a strong relationship between SCI and SRC, since both tests measure the same aspect of the fossil record. There is no relationship between RCI and either SCI or SRC. There is a highly significant relationship, as expected, between SRC coefficients and the number of taxa in a cladogram, but no such relationship for RCI or SCI (except in fishes). There is no significant relationship between any of the indices and either the number of internal nodes or tree balance.

Echinoderms show the best stratigraphic consistency of nodes, while continental tetrapods have the best matching of stratigraphic age and cladistic node order. Fishes have the worst match of age and clade ranks, but they do have the most complete fossil record as measured by the RCI. They are followed by echinoderms, and then continental tetrapods, which have the least complete record. This seems to show that life in an aquatic environment leads, in general, to a more complete fossil record.

The 2.0–1.8-billion-year-old Stirling Range Formation in southwestern Australia preserves the deposits of a siliciclastic shoreline formed under the influence of storms, longshore currents, and tidal currents. Sandstones contain a megascopic fossil biota represented by discoidal fossils similar to the Ediacaran Aspidella Billings, 1872, as well as ridge pairs preserved in positive hyporelief on the soles of channel-fill sandstones bounded by mud drapes. The ridges run parallel or nearly parallel for most of their length, meeting in a closed loop at one end and opening with a slight divergence at the opposite end. The ridges are interpreted as casts of sediment-laden mucus strings formed by the movement of multicellular or syncytial organisms along a muddy surface. The taxa Myxomitodes stirlingensis n. igen., n. isp., are introduced for these traces. The Stirling biota was roughly coeval with other presumed multicellular eukaryotes appearing after a long period of profound environmental changes involving a rise in ambient oxygen levels, similar to that which preceded the Cambrian explosion. The failure of multicellular life to diversify during most of the Proterozoic may be due to environmental constraints related to the comparatively low level of oxidation of the world oceans.

Evolutionary morphologists and paleontologists have long questioned whether there are general historical patterns to the distribution of morphological types. Few studies have rigorously addressed that question. This study tests the decoupling hypothesis, which predicts an increase in the number of morphological constraints with a reduction in the number of independent elements. Eight cases of historical transformation of the epicoracoid cartilages of frogs were selected for analysis. Similar morphological shape changes occurred across the independently derived historical transformations as determined by a triangle analysis of shape. These results support the decoupling hypothesis and indicate that there may be generalized historical pathways of structural change. This finding is important for the development of a predictive theory in evolutionary morphology.

During the latest Cretaceous and the Paleocene in western North America, disappearance rates for mammalian genera track appearance rates, both reaching their peak in the early Paleocene (Puercan) following the extinction of non-avian dinosaurs. Some of the disappearances during this time were pseudoextinctions that resulted when ancestral species disappeared during speciation.

Species-level cladistic analyses and a well-constrained biostratigraphic framework are required to study this form of pseudoextinction. Cladistic analyses show that monophyly cannot be established or rejected for some species because these species lack autapomorphies (uniquely derived character states) that unite their constituent members. Such taxa, termed metaspecies, are potential ancestors to species and higher clades with which they share a node in the cladogram.

A hypothetical species-level cladistic analysis coupled with three different hypothetical biostratigraphies shows how different models of speciation (bifurcation, budding, or anagenesis) result in very different patterns of true versus pseudoextinction. Depending on the speciation model, true extinction can be overestimated by as much as a factor of four, raising the specter of mass extinction. Species-level studies for three early Tertiary mammalian taxa—taeniodont eutherians, taeniolabidid multituberculates, and periptychid ungulates—use the same procedures. They show that almost 25% of disappearances during the early Paleocene (Puercan) for species in the analysis were pseudoextinctions of metaspecies. Budding and anagenetic-like peripatric speciation, but not bifurcation, are seen in the three examples.

Equating disappearance to true extinction can profoundly affect interpretations of faunal turnover, especially during mass extinctions or major faunal reorganizations. Some authors use pseudoextinction to describe the taxonomic rather than evolutionary disappearance of nonmonophyletic groups. Pseudoextinction, as used here refers only to the evolutionary disappearance of metaspecies via speciation. Both usages seem appropriate but should not be confounded.

Zooids of cheilostome bryozoans are on average substantially more robust than are zooids of cyclostome bryozoans. The differences include greater number, length, and cross-sectional area of tentacles, plus a more extensively developed funiculus. Median values for mouth size and cilia-generated feeding current velocity are greater for cheilostomes than for cyclostomes so that cheilostomes have the potential for greater intake of nutrient energy per unit time, which may explain their apparently higher growth rates. For unit area of substrate occupied, the Cheilostomata (Class Gymnolaemata; members of the post-Paleozoic fauna) contain greater biomass and apparently generate greater energy flow than do the Cyclostomata, which are the only extant order of the Class Stenolaemata (characteristic of the Paleozoic fauna).

Formulae are developed for the fraction of the population that must be eliminated by selection in each generation in order to account for a given rate of evolution in a metrical trait. A combination of directional and stabilizing selection is assumed. The effects of competition based on phenotypic value are also considered. The formulae are applied to data on evolutionary rates and their variances. It is concluded that most selective elimination is due to stabilizing selection, and that even very rapid evolutionary change in a single character usually involves low levels of additional elimination. It is suggested that long-sustained evolutionary trends are unlikely to be caused either by gradual change of the optimum under stabilizing selection or by the effects of competitive selection in favor of extreme individuals. It is possible that genetic correlations between traits under selection may limit the response of a single trait to directional selection and hence produce very gradual change.

The potential of the ichnofossil record for exploring the evolution of behavior has never been fully realized. Some of this is due to the nature of the trace fossil record itself. Equally responsible is the separation of ichnology from the relevant areas of modern behavioral biology. The two disciplines have virtually no concepts, methods, or literature in common. The study of animal behavior and its evolution is thus bereft of the rich data and insights of ichnologists.

One potential pathway forward is for ichnologists to adopt and adapt the movement ecology paradigm proposed several years ago by Ran Nathan and colleagues. This approach views movement as resulting from interactions of the organism's internal state, its movement abilities, and its sensory capabilities with each other and with the external environment. These interactions produce a movement path. The adoption of this paradigm would place trace fossil studies in a far wider common context for the study of movement, while providing the dimension of the evolution of movement behavior in deep time to neontological studies.

A second component of this integration would be for paleontologists to develop a taphonomy of behavior that places in a phylogenetic context the range of possible behaviors that organisms can carry out and assesses the potential of each of these behaviors in leaving a diagnostic trace. Parallel to other taphonomic concepts, this approach assesses the preservation potential of particular behaviors; behavioral fidelity is the extent to which trace fossils preserve these original behavioral signals.

Age-frequency distributions of dead skeletal material on the landscape or seabed—information on the time that has elapsed since the death of individuals—provide decadal- to millennial-scale perspectives both on the history of production and on the processes that lead to skeletal disintegration and burial. So far, however, models quantifying the dynamics of skeletal loss have assumed that skeletal production is constant during time-averaged accumulation. Here, to improve inferences in conservation paleobiology and historical ecology, we evaluate the joint effects of temporally variable production and skeletal loss on postmortem age-frequency distributions (AFDs) to determine how to detect fluctuations in production over the recent past from AFDs. We show that, relative to the true timing of past production pulses, the modes of AFDs will be shifted to younger age cohorts, causing the true age of past pulses to be underestimated. This shift in the apparent timing of a past pulse in production will be stronger where loss rates are high and/or the rate of decline in production is slow; also, a single pulse coupled with a declining loss rate can, under some circumstances, generate a bimodal distribution. We apply these models to death assemblages of the bivalve Nuculana taphria from the Southern California continental shelf, finding that: (1) an onshore-offshore gradient in time averaging is dominated by a gradient in the timing of production, reflecting the tracking of shallow-water habitats under a sea-level rise, rather than by a gradient in disintegration and sequestration rates, which remain constant with water depth; and (2) loss-corrected model-based estimates of the timing of past production are in good agreement with likely past changes in local production based on an independent sea-level curve.