Where do species that become important players in ecosystems evolve? This simple yet crucial question must be answered if we want to understand how the biosphere is rejuvenated following a crisis. We cannot simply assume that the environments in which we find fossil remains of a given species, or living populations of a species, are the environments in which that species evolved. Take the most obvious example: Fossil human skeletons have been unearthed by the hundreds in North America, but all available evidence points to a human origin in Africa. We can often identify the general geographic origins of species and clades thanks to fossil occurrences and the application of phylogenetic techniques; but can we do likewise for more ecological aspects of the environment? Advances in population biology and in paleobiology now permit us to outline a hypothesis of the circumstances most favorable to the evolution of abundant, widespread, or ecologically powerful species, those with adaptations that are selectively advantageous across many environments, and large short-term and long-term effects in ecosystems.

Recent molecular phylogenetic and molecular clock data both suggest a pre-Mesozoic age for the divergence of the angiosperm lineage from other seed plants, greatly predating the confirmed fossil record of the angiosperm crown group. In addition, molecular phylogenetic studies have not supported the morphologically based conclusion that gnetophytes are the extant sister group to angiosperms. We examine these relationships and divergence ages by using a novel approach of examining the presence of oleanane. This includes the development of methods using zeolites to preferentially reduce hopanes that can co-elute with oleanane. The presence of this molecular fossil strongly correlates with angiosperm diversification; in its functionalized form, along with its triterpenoid precursors, it is found in many living angiosperms. Our data show that among non-angiosperm seed plants examined thus far, oleanane is found only in fossil Cretaceous Bennettitales and Permian Gigantopteridales, both of which share characteristics with angiosperms. Previous morphological phylogenetic results indicate Bennettitales could be a sister group to or member of the angiosperm stem lineage, and results of our preliminary phylogenetic analysis including the Gigantopteridales suggests the same. Our data, based on a new pyrolysis method to treat living species, support previous research indicating that oleanane and its precursors are absent in living gnetophytes. If oleanane originated once in seed plants then the angiosperm stem lineage would have diverged from other seed plant lineages by the late Paleozoic.

Stable isotope analysis of mammalian tooth enamel is a valuable method for examining resource partitioning in modern and ancient environments where there is a mixture of C3 and C4 plants. However, before 7 Ma North American ecosystems were composed predominantly of C3 plants, complicating isotopic assessment of resource partitioning. Study of modern African and North American ecosystems has shown that niche partitioning among mammals may be discerned in communities dominated by C3 plants, suggesting that a similar approach may work for ancient C3 ecosystems. Here, such analyses are applied to explore resource use and niche partitioning in two ancient C3-dominated communities, one from California and one from Florida. Each locality, Black Hawk Ranch (California) and the Love Bone Bed (Florida), occurs in Miocene deposits that accumulated prior to the rapid increase in C4 ecosystems 7 Myr ago. δ13C and δ18O values were obtained from the tooth enamel of eight species from Black Hawk Ranch, and 15 species from the Love Bone Bed. Results from the 197 bulk isotope samples showed significant differences in δ13C among taxa at the Love Bone Bed, but no significant differences were observed among taxa at Black Hawk Ranch. At both localities, equids generally have more positive δ13C values than co-occurring taxa, suggesting that equids occupied more open habitats, whereas antilocaprids, camelids, and proboscideans have more negative values, implying utilization of more closed communities. One result of note is the positive δ13C values of Pediomeryx (Yumaceras) hamiltoni from the Love Bone Bed, which suggests that P. (Y.) hamiltoni incorporated abundant fiber, possibly grass, in the diet similar to the horses from this locality. The lack of significant differences among taxa at Black Hawk Ranch may indicate a relatively homogeneous flora, or presence of abundant resources permitting niche overlap, whereas the opposite is implied by the presence of significantly different isotope values among taxa at the Love Bone Bed. The results from this study highlight the utility of isotopic techniques allowing discernment of resource partitioning in C3-dominated landscapes such as those that persisted for the millions of years before the rapid increase in C4 ecosystems that occurred during the late Miocene.

Spectral algorithms have been shown to work well in a wide range of situations that involve the task of ordering. When applied to the localities of a set of European Neogene land mammal taxa, spectral ordering relies almost entirely on the most common genera, depends on connectivity more than on length of taxon lists, and is robust to noise from rarer and less connected taxa. The spectral coefficients for localities are highly correlated with known geochronological ages. Although elementary compared with more sophisticated biochronological tools, spectral ordering allows a fast and standardized way to generate biochronological ordering of localities when other information than faunal lists is lacking. Compared with the conventional mammal Neogene (MN) units, spectral ordering of localities appears to lack distinct temporal boundaries in taxon content and render a much lower count of Lazarus events. If, as seems to be the case, biochronology depends mainly on the most common taxa and if evolutionary change is also most clearly reflected in them, then the main evolutionary patterns should be detectable at a modest level of sampling.

The Neoselachii are a monophyletic group including all of the extant sharks and rays. They underwent rapid diversification throughout the Jurassic and Cretaceous, going from low-diversity assemblages of members of extinct orders in the Late Triassic to diverse assemblages containing representatives of most extant clades by the end of the Cretaceous. The known fossil record of Mesozoic neoselachians is composed largely of isolated teeth, with articulated skeletal remains being known from a limited number of sites. The small tooth size of a large proportion of neoselachians, including almost all taxa in existence prior to the mid Cretaceous, led to very poor representation in older publications. Their state of knowledge has improved dramatically since 1970 with the increased use of bulk sampling for isolated dental remains. Despite this, the high proportion of Lazarus taxa from some stages suggests that the state of knowledge is still intermittent. Increase in assemblage diversity throughout the Jurassic and Cretaceous suggests that radiation events resulted in real and dramatic increases in diversity, and that the perceived diversification is not an artifact of poor knowledge. Cladogenesis inferred from the fossil record typically compares more favorably with divergence predicted from molecular analysis, where Batoidea form a discrete basal clade, than with divergence predicted from morphological analysis, where Batoidea are considered a derived crown group within the Squalea. The timing of diversification events is discussed in light of the known fossil record, cladistically generated divergence times, and the paleoenvironmental distribution of faunas.

The independent acquisition of high-crowned cheek teeth (hypsodonty) in several ungulate lineages (e.g., camels, equids, rhinoceroses) in the early to middle Miocene of North America has classically been used as an indication that savanna vegetation spread during this time. Implicit in this interpretation is the untested assumption that hypsodonty was an evolutionary response to feeding in open habitats, either due to a change in food source (from browse to graze) or to increased incorporation of airborne grit in the diet. I examined the adaptive explanation for hypsodonty in equids using criteria pertaining to process and pattern of adaptations set up in the comparative-methods literature. Specifically, I tested whether hypsodonty appeared coincident with or just after the spread of open, grass-dominated habitats in the Great Plains of North America.

Phytolith (plant opal) analysis of 99 phytolith assemblages extracted from sediment samples from Montana/Idaho, Nebraska/Wyoming, and Colorado were used to establish the first continuous record of middle Eocene-late Miocene vegetation change in the northern to Central Great Plains. This record was compared with the fossil record of equids from the same area in a phylogenetic framework.

The study showed that habitats dominated by C3 grasses were established in the Central Great Plains by early late Arikareean (≥21.9 Ma), at least 4 Myr prior to the emergence of hypsodont equids (Equinae). Nevertheless, the adaptive hypothesis for hypsodonty in equids could not be rejected, because the earliest savanna-woodlands roughly co-occurred with members of the grade constituting the closest outgroups to Equinae (“Parahippus”) showing mesodont dentition. Explanations for the slow evolution of full hypsodonty may include weak and changing selection pressures and/or phylogenetic inertia. These results suggest that care should be taken when using functional morphology alone to reconstruct habitat change.

Evaluating the relative importance of biotic versus abiotic factors in governing macroevolutionary patterns is a central question of paleobiology. Here, we analyzed patterns of changes in global relative abundances and diversity of ecological groups to infer the role of biological interactions as driving evolutionary forces in mid-Mesozoic macrobenthic marine ecosystems. Specifically, we tested the hypothesis of escalation, which states that macroevolutionary patterns were controlled by an increasing pressure exerted by enemies on their victims. Associated with evidence of increasing levels of predation and biogenic sediment reworking (bulldozing) is an increasing representation of predation- and disturbance-resistant groups in the fossil record. In particular, we observe increasing proportions of mobile organisms; a decline of vulnerable epifauna living freely on the substrate; and a trend toward infaunalization of the benthos. These trends were most pronounced in the paleotropics, i.e., the region where biological activity is thought to have been highest. The observation that these changes affected several biotic traits and occurred within independent clades argues against the overriding role of a single key adaptive innovation in causing shifts in ecological abundance. Also, changes in the abiotic environment cannot explain these faunal patterns because of lacking cross-correlations with physico-chemical parameters such as global sea level, climate, and seawater chemistry. We conclude that in marine benthic ecosystems of the mid Mesozoic, enemy-driven evolution, or escalation, was a plausible and important factor.

Distinguishing the differential roles of hardpart-input rates and burial rates in the formation of shell beds is important in paleobiologic and sedimentologic studies, because high shelliness can reflect either high population density of shell producers or lack of sediment. The modeling in this paper shows that differences in the relative importance of burial rates and hardpart-input rates lead to distinct patterns with respect to the degree of shelliness and taphonomic alteration in shell beds. Our approach substantially complements other models because it allows computation of both shelliness and assemblage-level alteration. To estimate shelliness, we dissected hardpart-input rates into dead-shell production and shell destruction rates. To estimate assemblage-level alteration, we computed an alteration rate that describes how rapidly shells accrue postmortem damage. Under decreasing burial rates but constant hardpart-input rates, a positive correlation between alteration and shelliness is expected (Kidwell's R-sediment model). In contrast, under decreased destruction rates and/or increased dead-shell production rates and constant burial rates (Kidwell's R-hardpart model), a negative correlation between shelliness and alteration is expected. The contrasting predictions thus provide a theoretical basis for distinguishing whether high shell density in shell beds reflects passive shell accumulation due to a lack of sediment dilution or whether it instead reflects high shell input from a life assemblage. This approach should be applicable for any fossil assemblages that vary in shell density and assemblage-level alteration. An example from the Lower Jurassic of Morocco, which has shell-rich samples less altered than shell-poor samples, suggests that the higher shelliness correlates with higher community-level abundance and lower proportion of juveniles of the main shell producer, supporting the driving role of hardpart-input rates in the origin of the shell-rich samples in this case. This is of significance in paleoecologic analyses because variations in shelliness can directly reflect fluctuations in population density of shell producers.

Attempts to use Fourier methods to quantify ammonoid suture shape have failed to yield robust, repeatable results because sutures are complex curves that violate the assumptions of Fourier mathematics. In particular, sampled sutures are artificially truncated such that the first and last sampled points are not equivalent, the folds are non-stationary, and a position along a horizontal reference axis may map to multiple amplitudes along the suture path. Here I introduce an alternative Fourier method—the windowed short-time Fourier transform (STFT)—that accommodates these characteristics of complex curves. For each suture, digitized landmarks were parameterized using a tangent angle function and then smoothed by convolving with an apodization function. Piece-wise Fourier transforms were then calculated and averaged, resulting in a robust, unique quantification of line morphology. STFT coefficients and estimated power spectra describing the relative weights of harmonics were generated for 576 Paleozoic-basal Triassic ammonoid genera, representative of the range of suture morphotypes. While insensitive to major episodes of taxonomic turnover (Frasnian/Famennian, end-Devonian, and Permian/Triassic extinctions), the summed power data support the previously observed trend toward increasing suture complexity through time. Moreover, partitioning the summed power statistic into harmonic ranges allows novel insight into Paleozoic suture evolution. In particular, the data show significant shifts in the dominant morphotypes during periods of rebound and radiation and suggest that basal Triassic ammonoids possessed unique suture morphotypes when compared with those of the Paleozoic.

Recent phylogenetic studies of Paleozoic gastropods show the classification provided by the Treatise on Invertebrate Paleontology to include numerous highly polyphyletic taxa. Here we test whether this classification reflects limits on the range of possible designs, general architectural constraints, or common functional solutions for Paleozoic gastropods. Our test evaluates whether superfamilial/subordinal level archetypes as defined by the Treatise evolved more frequently than expected among 626 Late Cambrian–Middle Devonian species. Using a previously established phylogeny and five general shell features (spire angle, exhalent current position, base angle, umbilical width, and apertural inclination) we show that there are fewer gastropod morphotypes than expected given the frequency of change in these features. This is true even after accounting for architectural constraints implied by the data. Moreover, the most common morphotypes include significantly more species and evolved significantly more times than expected. These results imply a set of architectural attractors for lower–middle Paleozoic gastropods, consistent with ecomorphological theory that particular morphotypes are best suited for particular lifestyles. Thus, the Treatise classifications likely reflect these ecomorphological patterns within subclades rather than phylogenetic patterns.