Paleobiology

Published by Paleontological Society
Online ISSN: 1938-5331
Publications
Article
With Jack Sepkoski's sudden death from heart failure on May 1, 1999, paleontology lost one of its most important figures. In his 25–year career, Jack published more than 70 research articles, 15 of them in this journal, and an equal number of reviews, commentaries, and abstracts. He co-edited Paleobiology (1983–86), received the Schuchert Award (1983), and served as President of the Paleontological Society (1995–96). In 1997, he was elected to the Polish Academy of Sciences and in the same year received the Medal of the University of Helsinki. Further recognition would surely have followed but for his untimely death.
 
Article
Global taxonomic richness is affected by variation in three components: within-community, or alpha, diversity, between-community, or beta, diversity; and between-region, or gamma, diversity. A data set consisting of 505 faunal lists distributed among 40 stratigraphic intervals and six environmental zones was used to investigate how variation of alpha and beta diversity influenced global diversity through the Paleozoic, and especially during the Ordovician radiations. As first shown by Bambach (1977), alpha diversity increased by 50 to 70 percent in offshore marine environments during the Ordovician and then remained essentially constant of the remainder of the Paleozoic. The increase is insufficient, however, to account for the 300 percent rise observed in global generic diversity. It is shown that beta diversity among level, soft-bottom communities also increased significantly during the early Paleozoic. This change is related to enhanced habitat selection, and presumably increased overall specialization, among diversifying taxa during the Ordovician radiations. Combined with alpha diversity, the measured change in beta diversity still accounts for only about half of the increase in global diversity. Other sources of increase are probably not related to variation in gamma diversity but rather to appearance and/or expansion of organic reefs, hardground communities, bryozoan thickets, and crinoid gardens during the Ordovician.
 
Article
The global diversification of the class Bivalvia has historically received two conflicting interpretations. One is that a major upturn in diversification was associated with, and a consequence of, the Lake Permian mass extinction. The other is that mass extinctions have had little influence and that bivalves have experienced slow but nearly steady exponential diversification through most of their history, unaffected by interactions with other clades. We find that the most likely explanation lies between these two interpretations. Through most of the Phanerozoic, the diversity of bivalves did indeed exhibit slow growth, which was not substantially altered by mass extinctions. However, the presence of "hyperexponential bursts" in diversification during the initial Ordovician radiation and following the Late Permian and Late Cretaceous mass extinctions suggests a more complex history in which a higher characteristic diversification rate was dampened through most of the Phanerozoic. The observed pattern can be accounted for with a two-phase coupled (i.e., interactive) logistic model, where one phase is treated as the "bivalves" and the other phase is treated as a hypothetical group of clades with which the "bivalves" might have interacted. Results of this analysis suggest that interactions with other taxa have substantially affected bivalve global diversity through the Phanerozoic.
 
Article
Encrusting bryozoans provide one of the few systems in the fossil record in which ecological competition can be observed directly at local scales. The macroevolutionary history of diversity of cyclostome and cheilostome bryozoans is consistent with a coupled-logistic model of clade displacement predicated on species within clades interacting competitively. The model matches observed diversity history if the model is perturbed by a mass extinction with a position and magnitude analogous to the Cretaceous/Tertiary boundary event, Although it is difficult to measure all parameters in the model from fossil data, critical factors are intrinsic rates of extinction, which can be measured. Cyclostomes maintained a rather low rate of extinction, and the model solutions predict that they would lose diversity only slowly as competitively superior species of cheilostomes diversified into their environment. Thus, the microecological record of preserved competitive interactions between cyclostome and cheilostome bryozoans and the macroevolutionary record of global diversity are consistent in regard to competition as a significant influence on diversity histories of post-Paleozoic bryozoans.
 
Article
It has long been suspected that trends in global marine biodiversity calibrated for the Phanerozoic may be affected by sampling problems. However, this possibility has not been evaluated definitively, and raw diversity trends are generally accepted at face value in macroevolutionary investigations. Here, we analyze a global-scale sample of fossil occurrences that allows us to determine directly the effects of sample size on the calibration of what is generally thought to be among the most significant global biodiversity increases in the history of life: the Ordovician Radiation. Utilizing a composite database that includes trilobites, brachiopods, and three classes of molluscs, we conduct rarefaction analyses to demonstrate that the diversification trajectory for the Radiation was considerably different than suggested by raw diversity time-series. Our analyses suggest that a substantial portion of the increase recognized in raw diversity depictions for the last three Ordovician epochs (the Llandeilian, Caradocian, and Ashgillian) is a consequence of increased sample size of the preserved and catalogued fossil record. We also use biometric data for a global sample of Ordovician trilobites, along with methods of measuring morphological diversity that are not biased by sample size, to show that morphological diversification in this major clade had leveled off by the Llanvirnian. The discordance between raw diversity depictions and more robust taxonomic and morphological diversity metrics suggests that sampling effects may strongly influence our perception of biodiversity trends throughout the Phanerozoic.
 
Article
A comparison is made between compilations of times of origination and extinction of fossil marine animal families published in 1982 and 1992. As a result of ten years of library research, half of the information in the compendia has changed: families have been added and deleted, low-resolution stratigraphic data been improved, and intervals of origination and extinction have been altered. Despite these changes, apparent macroevolutionary patterns for the entire marine fauna have remained constant. Diversity curves compiled from the two data bases are very similar, with a goodness-of-fit of 99%; the principal difference is that the 1992 curve averages 13% higher than the older curve. Both numbers and percentages of origination and extinction also match well, with fits ranging from 83% to 95%. All major events of radiation and extinction are identical. Therefore, errors in large paleontological data bases and arbitrariness of included taxa are not necessarily impediments to the analysis of pattern in the fossil record, so long as the data are sufficiently numerous.
 
Article
A kill curve for Phanerozoic species is developed from an analysis of the stratigraphic ranges of 17,621 genera, as compiled by Sepkoski. The kill curve shows that a typical species' risk of extinction varies greatly, with most time intervals being characterized by very low risk. The mean extinction rate of 0.25/m.y. is thus a mixture of long periods of negligible extinction and occasional pulses of much higher rate. Because the kill curve is merely a description of the fossil record, it does not speak directly to the causes of extinction. The kill curve may be useful, however, to li¿mit choices of extinction mechanisms.
 
Article
Truth, goes an old proverb, is the daughter of time. Fifty years ago, G. G. Simpson (1944) brought paleontology into the Neodarwinian fold, arguing that evolutionary tempo can be documented in the geological record and used to inform debate about evolutionary mode. Today, increasingly sophisticated paleontological investigations of rate—be it diversification, extinction, migration, morphological change, or divergence in macromolecular sequence—require calibration of the geological time scale with a precision far greater than Simpson could have anticipated. Expanding research on the relationships between environmental history and evolution also requires unprecedented resolution in correlation and geochronometry.
 
Article
Onshore-offshore patterns of faunal change occurred at many taxonomic scales during the Paleozoic Era, ranging from replacement of the Cambrian evolutionary fauna by the Paleozoic fauna to the environmental expansion of many orders and classes. A simple mathematical model is constructed to investigate such change. The environmental gradient across the marine shelf-slope is treated as a linear array of discrete habitats, each of which holds a set number of species, as observed in the fossil record. During any interval of time, some portion of the species in each habitat becomes extinct by background processes, with rates of extinction varying among both clades and habitats, as also observed in the record. After extinction, species are replaced from within the habitat and from immediately adjacent habitats, with proportions dependent on surviving species. This model leads to the prediction that extinction-resistant clades will always diversify at the expense of extinction-prone clades. But if extinction intensity is highest in nearshore habitats, extinction-resistant clades will expand preferentially in the onshore direction, build up diversity there, and then diversify outward toward the offshore. Thus, onshore-offshore patterns of diversification may be the expectation for faunal change quite independently of whether or not clades originate onshore. When the model is parameterized for Paleozoic trilobites and brachiopods, numerical solutions exhibit both a pattern of faunal change and a time span for diversification similar to that seen in the fossil record. They also generate structure similar to that seen in global diversification, including logistic patterns of growth, declining origination but constant extinction within clades through time, and declining overall extinction across clades through time.
 
Article
Although available paleobiological data indicate that the geographic ranges of marine species are maintained throughout their entire observable durations, other evidence suggests, by contrast, that the ranges of higher taxa expand as they age, perhaps in association with increased species richness. Here, I utilize a database of Ordovician genus occurrences collected from the literature for several paleocontinents to demonstrate that a significant aging of the global biota during the Ordovician Radiation was accompanied by a geographic and environmental expansion of genus ranges. The proportion of genera occurring in two or more paleocontinents in the database, and two or more environmental zones within a six-zone onshore-offshore framework, increased significantly in the Caradocian and Ashgillian. Moreover, widespread genera tended to be significantly older than their endemic counterparts, suggesting a direct link between their ages and their environmental and geographic extents. Expansion in association with aging was corroborated further by demonstrating this pattern directly among genera that ranged from the Tremadocian through the Ashgillian. Taken together, these results are significant not only for what they reveal about the kinetics of a major, global-scale diversification, but also for what they suggest about the interpretation of relationships between diversity trends at the alpha (within-community) and beta (between-community) levels.
 
Article
Analysis of the stratigraphic records of 19,897 fossil genera indicates that most classes and orders show largely congruent rises and falls in extinction intensity throughout the Phanerozoic. Even an ecologically homogeneous sample of reef genera shows the same basic extinction profile. The most likely explanation for the congruence is that extinction is physically rather than biologically driven and that it is dominated by the effects of geographically widespread environmental perturbations influencing most habitats. Significant departures from the congruence are uncommon but important because they indicate physiological or habitat selectivity. The similarity of the extinction records of reef organisms and the marine biota as a whole confirms that reefs and other faunas are responding to the same history of environmental stress.
 
Article
The kill curve for Phanerozoic marine species is used to investigate large-body impact as a cause of species extinction. Current estimates of Phanerozoic impact rates are combined with the kill curve to produce an impact-kill curve, which predicts extinction levels from crater diameter, on the working assumption that impacts are responsible for all "pulsed" extinctions. By definition, pulsed extinction includes the approximately 60% of Phanerozoic extinctions that occurred in short-lived events having extinction rates greater than 5%. The resulting impact-kill curve is credible, thus justifying more thorough testing of the impact-extinction hypothesis. Such testing is possible but requires an exhaustive analysis of radiometric dating of Phanerozoic impact events.
 
Article
The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy. Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased.(3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of fossiliferous rock more than failure of species to enter the fossil record in the first place.
 
Article
The problem of how accurately paraphyletic taxa versus monophyletic (i.e., holophyletic) groups (clades) capture underlying species patterns of diversity and extinction is explored with Monte Carlo simulations. Phylogenies are modeled as stochastic trees. Paraphyletic taxa are defined in an arbitrary manner by randomly choosing progenitors and clustering all descendants not belonging to other taxa. These taxa are then examined to determine which are clades, and the remaining paraphyletic groups are dissected to discover monophyletic subgroups. Comparisons of diversity patterns and extinction rates between modeled taxa and lineages indicate that paraphyletic groups can adequately capture lineage information under a variety of conditions of diversification and mass extinction. This suggests that these groups constitute more than mere "taxonomic noise" in this context. But, strictly monophyletic groups perform somewhat better, especially with regard to mass extinctions. However, when low levels of paleontologic sampling are simulated, the veracity of clades deteriorates, especially with respect to diversity, and modeled paraphyletic taxa often capture more information about underlying lineages. Thus, for studies of diversity and taxic evolution in the fossil record, traditional paleontologic genera and families need not be rejected in favor of cladistically-defined taxa.
 
Article
Analysis of two independent data sets with increased taxonomic resolution (genera rather than families) using the revised 2012 time scale reveals that an extinction periodicity first detected by Raup and Sepkoski (1984) for only the post-Paleozoic actually runs through the entire Phanerozoic. Although there is not a local peak of extinction every 27 million years, an excess of the fraction of genus extinction by interval follows a 27 million year timing interval and differs from a random distribution at the p ~ 0.02 level. A 27 million year periodicity in the spectrum of interval lengths no longer appears, removing the question of a possible artifact arising from it. Using a method originally developed in Bambach (2006) we identify 19 intervals of marked extinction intensity, including mass extinctions, spanning the last 470 million years (and with another six present in the Cambrian) and find that 10 of the 19 lie within 3 Myr of the maxima in the spacing of the 27 Myr periodicity, which differs from a random distribution at the p = 0.004 level. These 19 intervals of marked extinction intensity also preferentially occur during decreasing diversity phases of a well-known 62 Myr periodicity in diversity (16 of 19, p = 0.002). Both periodicities appear to enhance the likelihood of increased severity of extinction, but the cause of neither periodicity is known. Variations in the strength of the many suggested causes of extinction coupled to the variation in combined effect of the two different periodicities as they shift in and out of phase is surely one of the reasons that definitive comparative study of the causes of major extinction events is so elusive.
 
Article
We use Fourier analysis and related techniques to investigate the question of periodicities in fossil biodiversity. These techniques are able to identify cycles superimposed on the long-term trends of the Phanerozoic. We review prior results and analyze data previously reduced and published. Joint time-series analysis of various reductions of the Sepkoski Data, Paleobiology Database, and Fossil Record 2 indicate the same periodicity in biodiversity of marine animals at 62 Myr. We have not found this periodicity in the terrestrial fossil record. We have found that the signal strength decreases with time because of the accumulation of apparently "resistant" long-lived genera. The existence of a 62-Myr periodicity despite very different treatment of systematic error, particularly sampling-strength biases, in all three major databases strongly argues for its reality in the fossil record. Comment: 56 pages. In press at Paleobiology. Submitted to conform with copyedited version
 
Article
A 62 Myr periodicity is superimposed on other longer-term trends in fossil biodiversity. This cycle can be discerned in marine data based on the Sepkoski compendium, the Paleobiology Database, and the Fossil Record 2. The signal also exists in changes in sea level/sediment, but is much weaker than in biodiversity itself. A significant excess of 19 previously identified Phanerozoic mass extinctions occur on the declining phase of the 62 Myr cycle. appearance of the signal in sampling-standardized biodiversity data, it is likely not to be a sampling artifact, but either a consequence of sea-level changes or an additional effect of some common cause for them both. In either case, it is intriguing why both changes would have a regular pattern. Comment: Summry of comments presented at the North American Paleontological Convention, June 25, 2009
 
Article
We investigate evolutionary dynamics related to periodicity fossil biodiversity. Coherent periodic fluctuation in origination/extinction of marine genera that survive <45 million years is the source of an observed ~62 million year periodicity analyzed in Paper I. We also show that the evolutionary dynamics of "long-lived" genera (those that survive >45 million years) do not participate in the periodic fluctuation in diversity and differ from those of "short-lived" genera. The difference between the evolutionary dynamics of these 2 genera classes indicates that the periodic pattern is not an artifact of variation in quality of the geologic record. The interplay of these two previously undifferentiated systems, together with the secular increase in abundance of "long-lived" genera, is probably the source of heretofore unexplained differences in evolutionary dynamics between the Paleozoic and post-Paleozoic as reported by others. Testing for cycles similar to the 62 Myr cycle in fossil biodiversity superimposed on the long-term trends of the Phanerozoic as described in Paper I, we find a significant (but weaker) signal in sedimentary rock packages, particularly carbonates, which suggests a connection. The presence of a periodic pattern in evolutionary dynamics of the vulnerable "short-lived" component of marine fauna demonstrates that a long-term periodic fluctuation in environmental conditions capable of affecting evolution in the marine realm characterizes our planet. Coincidence in timing is more consistent with a common cause than sampling bias. A previously identified set of mass extinctions preferentially occur during the declining phase of the 62 Myr periodicity, supporting the idea that the periodicity relates to variation in biotically important stresses. Further work should focus on finding links to physical phenomena that might reveal the causal system or systems.
 
Article
The morphological diversity of life has captivated systematists in the construction of classifications, embryologists in the study of development, and evolutionists in the formulation of theories of organic change. In a century marked by the advances of molecular biology, has the discipline of morphology produced anything...new? Yes. The solidification of paleontology and systematics and the emergence of macroevolution as a legitimate field owe much to an increased rigor in the analysis of morphological data. The discipline of morphology has also achieved an unprecedented sophistication through another development, the very expression of its maturity: theoretical morphology. Theoretical morphology forms the subject of McGhee's landmark book, an elegant combination of compendium and manifesto. Its richness and scope provide fodder for a critical appraisal of the discipline of morphology, particularly quantitative and developmental morphology.
 
Computer simulations compared with data. The diamonds with (2σ) error bars represent sampling-standardized extinction intensities from Krug and Patzkowsky (2007), right hand axis. The lines represent maximum relative DNA damage intensities as in the grayscale of Figure 1. The lines correspond to bursts at latitude 0 degrees (short dash),-45 (dot-dash),-60 (long dash), and over the South Pole-90 (solid line). The south polar burst fits quite well, and a line corresponding to-75 degrees (not shown) cannot quite fit between the error bars of the data. Therefore, given our criteria, a burst south of-75 degrees latitude would fit the extinction data.
Article
Based on the intensity and rates of various kinds of intense ionizing radiation events such as supernovae and gamma-ray bursts, it is likely that the Earth has been subjected to one or extinction level events during the Phanerozoic. These induce changes in atmospheric chemistry so that the level of Solar ultraviolet-B radiation reaching the surface and near-surface waters may be doubled for up to a decade. This UVB level is known from experiment to be more than enough to kill off many kinds of organisms, particularly phytoplankton. It could easily induce a crash of the photosynthetic-based food chain in the oceans. Regularities in the latitudinal distribution of damage are apparent in simulations of the atmospheric changes. We previously proposed that the late Ordovician extinction is a plausible candidate for a contribution from an ionizing radiation event, based on environmental selectivity in trilobites. To test a null hypothesis based on this proposal, we confront latitudinal differential extinction rates predicted from the simulations with data from a published analysis of latitudinal gradients in the Ordovician extinction. The pattern of UVB damage always shows a strong maximum at some latitude, with substantially lower intensity to the north and south of this maximum. We find that the pattern of damage predicted from our simulations is consistent with the data assuming a burst approximately over the South Pole, and no further north than -75 degrees. We predict that any land mass (such as parts of north China, Laurentia, and New Guinea) which then lay north of the equator should be a refuge from UVB effects, and show a different pattern of extinction in the first strike of the end-Ordovician extinction, if induced by such a radiation event. Comment: Accepted for publication in Paleobiology. 16 pages, 2 figures
 
Article
The identification of randomness and nonrandomness is a perennial problem in evolutionary research. Stochastic thinking in evolutionary biology and paleobiology has solidified the use of a statistical notion of chance, but the idea of chance in evolutionary studies goes beyond statistics. A duality arises from the use of a statistical meaning, on the one hand, and a more strictly evolutionary meaning, on the other. The former implies a combination of indiscriminate sampling and unpredictability due to multiple causes; the latter codifies independence from adaptation and the directionality imposed by natural selection. Often these meanings are kept separate in evolutionary research, used in isolation according to the empirical situation or the goal of the investigator (recognition of pattern versus process). I argue that evolutionary studies in general and paleobiological studies in particular can benefit from the simultaneous application of statistical and evolutionary notions of chance. Following some background on the notion of chance and its use, I discuss a series of examples in which insight can be gained by explicit consideration of both meanings. Thus, typologies of extinction become clearer when phenomena like wanton extinction are made explicit; exaptive radiations are exposed as an alternative to adaptive radiations; the possible nonadaptive nature of deterministic chaos becomes sensible; the nonrandomness of community-assembly is put into question; parallel taxonomies of sorting rooted in different notions of nonrandomness are suggested as a means of facilitating understanding of relationships across the hierarchy; developmental constraints and self-organization are more easily distinguished from selective constraints; and a new term, �incidentals�, is suggested to refer to both exaptations and nonaptations. Finally, I point to ways in which the dichotomy between chance and necessity can be approached in evolutionary theory, by showing that the dual nat
 
Main figure: the cumulative extinction intensity as a function of time during the Phanerozoic on linear-log scales. The straight line is the best logarithmic fit to the data. Inset: the same data on log-log scales.
Article
We show that the decline in the extinction rate during the Phanerozoic can be accurately parameterized by a logarithmic t to the cumulative total extinction. This implies that extinction intensity is falling o approximately as the reciprocal of time. We demonstrate that this observation alone is suÆcient to explain the existence of the proposed power-law forms in the distribution of the sizes of extinction events and in the power spectrum of Phanerozoic extinction, results which previously have been explained by appealing to self-organized critical theories of evolutionary dynamics.
 
Plot of adjusted versus observed extinction rates (Table 1, Fig. 3). On a log-log scale, regression lines for each era (not shown for clarity) have slopes statistically indistinguishable from 1.0 but different intercepts. The regression line for Cenozoic substages has the highest intercept, indicating that extinction rates for these stages are adjusted upward when controlling for taxonomic susceptibility. The regression line for Paleozoic substages has the lowest intercept, indicating that extinction rates for these stages are adjusted downward when controlling for taxonomic susceptibility. See also Figure 3 caption.  
Plot of adjusted versus observed extinction rates (Table 1, Fig. 3). On a log-log scale, regression lines for each era (not shown for clarity) have slopes statistically indistinguishable from 1.0 but different intercepts. The regression line for Cenozoic substages has the highest intercept, indicating that extinction rates for these stages are adjusted upward when controlling for taxonomic susceptibility. The regression line for Paleozoic substages has the lowest intercept, indicating that extinction rates for these stages are adjusted downward when controlling for taxonomic susceptibility. See also Figure 3 caption.  
Relationships between evenness of genera within classes and extinction rate. A, Proportional genus diversity of classes in Sepkoski's compilation. To reduce noise, values are smoothed with a five-bin running average, except across the marked mass extinctions. Classes are ordered and grouped according to their stage or substage of maximum proportional diversity. B, Adjusted extinction rate versus evenness, here measured as 1/(1 PIE). Adjusted extinction rates are inversely correlated with evenness (r 0.49 for all substages; r 0.64 when the cluster of mass extinction intervals [pink region in upper right] is excluded). The negative correlation holds when the Paleozoic (r 0.78) and Mesozoic (r 0.55) are considered separately, but not in the Cenozoic (r 0.41).  
Article
Studies of extinction in the fossil record commonly involve comparisons of taxonomic extinction rates, often expressed as the percentage of taxa (e.g., families or genera) going extinct in a time interval. Such extinction rates may be influenced by factors that do not reflect the intrinsic severity of an extinction trigger. Two identical triggering events (e.g., bolide impacts, sea level changes, volcanic eruptions) could lead to different taxonomic extinction rates depending on fac- tors specific to the time interval in which they occur, such as the susceptibility of the fauna or flora to extinction, the stability of food webs, the positions of the continents, and so on. Thus, it is pos- sible for an extinction event with a higher taxonomic extinction rate to be caused by an intrinsically less severe trigger, compared to an event with a lower taxonomic extinction rate. Here, we isolate the effects of taxonomic susceptibility on extinction rates. Specifically, we quan- tify the extent to which the taxonomic extinction rate in a substage is elevated or depressed by the vulnerability to extinction of classes extant in that substage. Using a logistic regression model, we estimate that the taxonomic susceptibility of marine fauna to extinction has generally declined through the Phanerozoic, and we adjust the observed extinction rate in each substage to estimate the intrinsic extinction severity more accurately. We find that mass extinctions do not generally occur during intervals of unusually high susceptibility, although susceptibility sometimes increas- es in post-extinction recovery intervals. Furthermore, the susceptibility of specific animal classes to extinction is generally similar in times of background and mass extinction, providing no evi- dence for differing regimes of extinction selectivity. Finally, we find an inverse correlation between extinction rate within substages and the evenness of diversity of major taxonomic groups, but fur- ther analyses indicate that low evenness itself does not cause high rates of extinction.
 
Article
The vertebrae of sauropod dinosaurs are characterized by complex architecture involv- ing laminae, fossae, and internal chambers of various shapes and sizes. These structures are inter- preted as osteological correlates of a system of air sacs and pneumatic diverticula similar to that of birds. In extant birds, diverticula of the cervical air sacs pneumatize the cervical and anterior thoracic vertebrae. Diverticula of the abdominal air sacs pneumatize the posterior thoracic verte- brae and synsacrum later in ontogeny. This ontogenetic sequence in birds parallels the evolution of vertebral pneumaticity in sauropods. In basal sauropods, only the presacral vertebrae were pneumatized, presumably by diverticula of cervical air sacs similar to those of birds. The sacrum was also pneumatized in most neosauropods, and pneumatization of the proximal caudal vertebrae was achieved independently in Diplodocidae and Titanosauria. Pneumatization of the sacral and caudal vertebrae in neosauropods may indicate the presence of abdominal air sacs. Air sacs and skeletal pneumaticity probably facilitated the evolution of extremely long necks in some sauropod lineages by overcoming respiratory dead space and reducing mass. In addition, pulmonary air sacs may have conveyed to sauropods some of the respiratory and thermoregulatory advantages en- joyed by birds, a possibility that is consistent with the observed rapid growth rates of sauropods.
 
Initial conditions for hardpart-input rate regimes. 
Comparison of predicted alteration and shelliness for constant hardpart-input rates and varying sedi- mentation rates. 
Scheme showing the terms used in the models and in computing the age-frequency distribution of exposed dead shells (EAFD). The y-axis with number of shells in a cohort is logarithmic. The entire shaded area represents all the shells in the death assemblage plotted against their ''exposed'' time since death. The light shaded area represents the number of shells that have not experienced any taphonomic alteration. 
Comparison of predicted alteration and shelliness for varying hardpart-input rates and constant sedi- mentation rates. 
Article
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.
 
Article
Avian skeletal remains occur in many fossil assemblages, and in spite of small sample sizes and incomplete preservation, they may be a source of valuable paleoecological information. In this paper, we examine the taphonomy of a modern avian bone assemblage and test the relationship between ecological data based on avifaunal skeletal remains and known ecological attributes of a living bird community. A total of 54 modern skeletal occurrences and a sample of 126 identifiable bones from Amboseli Park, Kenya, were analyzed for weathering features and skeletal part preservation in order to characterize preservation features and taphonomic biases. Avian remains, with the exception of ostrich, decay more rapidly than adult mammal bones and rarely reach advanced stages of weathering. Breakage and the percentage of anterior limb elements serve as indicators of taphonomic overprinting that may affect paleoecological signals. Using ecomorphic categories including body weight, diet, and habitat, we compared species in the bone assemblage with the living Amboseli avifauna. The documented bone sample is biased toward large body size, representation of open grassland habitats, and grazing or scavenging diets. In spite of this, multidimensional scaling analysis shows that the small faunal sample (16 out of 364 species) in the pre-fossil bone assemblage accurately represents general features of avian ecospace in Amboseli. This provides a measure of the potential fidelity of paleoecological reconstructions based on small samples of avian remains. In the Cenozoic, the utility of avian fossils is enhanced because bird ecomorphology is relatively well known and conservative through time, allowing back-extrapolations of habitat preferences, diet, etc. based on modern taxa.
 
Results of the autocorrelogram and nested ANOVA analyses used to evaluate the existence of phy- logenetic inertia on species body size and range. Values in bold: p 0.05; ns (nonsignificant): p 0.05.
Number of observed taxa surviving at different taxonomic level (black circles). Dotted lines shows the expected number of extinctions at each level (2.5 th and 97.5 th percentiles), based on 10,000 bootstrapped values. See ''Methods'' for details.
Selectivity patterns of the mass extinction according to several ecological and life-history traits. A, Life habit. B, Range. C, Original body size. D, Body size contrasts. See text for details. Error bars in A indicate the 95% confidence intervals based on binomial errors.
Article
We assessed selective extinction patterns in bivalves during a late Neogene mass extinction event observed along the temperate Pacific coast of South America. The analysis of 99 late Neogene and Quaternary fossil sites (recorded from 7 degrees S to 55 degrees S), yielding similar to 2800 occurrences and 118 species, revealed an abrupt decline in Lyellian percentages during the late Neogene-Pleistocene, suggesting the existence of a mass extinction that decimated similar to 66% of the original assemblage. Using the late Neogene data set (n - 59 species, 1346 occurrences), we tested whether the extinction was nonrandom according to taxonomic structure, life habit, geographic range, and body size. Our results showed that the number of higher taxa that went extinct was not different than expected by random. At first sight, extinction was selective only according to life habit and geographic range. i Nevertheless, when phylogenetic effects were accounted for, body size also showed significant selectivity. In general, epifaunal, small-sized (after phylogenetic correction), and short-ranged species tended to have increased probability of extinction. This is verified by strong interactions between the variables herein analyzed, suggesting the existence of nonlinear effects on extinction chances. In the heavily decimated epifaunal forms, survival was not enhanced by widespread ranges or larger body sizes. Conversely, the widespread and large-sized infaunal forms tended to have lower probability of extinction. Overall, the ultimate extinction of late Neogene bivalve species along the Pacific coast of South America seems to have been determined by a complex interplay of ecological and historical (phylogenetic) effects.
 
Article
Vase-shaped microfossils (VSMs) occur globally in Neoproterozoic rocks, but until now their biological relationships have remained problematic. Exceptionally preserved new populations from the uppermost Chuar Group, Grand Canyon, Arizona, display details of morphology and taphonomy that collectively point to affinities with the testate amoebae. The fossils are tear-shaped tests, ~20-300 µm long and ~10-200 µm wide, that are circular in transverse section, expand aborally toward a rounded or slightly pointed pole, and taper orally toward a "neck" that ends in a single aperture. Apertures may be circular, hexagonal, triangular, or crenulate, and may be rimmed by a distinct collar. Approximately 25% of the Chuar VSMs are curved, such that the oral and aboral poles do not lie opposite each other. Tests are preserved as mineralized casts and molds, commonly coated with organic debris or iron minerals, but they were originally composed of nonresistant organic matter. Approximately 1% have a "honeycomb-patterned" wall attributable to the original presence of mineralized scales whose bases were arranged regularly in the test wall. Scale-bearing restate amoebae, such as members of the Euglyphidae, are essentially identical to the honeycomb VSMs, and a close relationship between other Grand Canyon VSMs and additional testate amoebae, both lobose and filose, is likely. The VSM population therefore most likely represents a multispecies assemblage whose spatial association reflects a common habitat and/or taphonomic circumstances that favor test preservation. The assignment of these fossils to the testate amoebae strengthens the case for a major diversification of eukaryotic organisms by mid-Neoproterozoic times and, more significantly, provides the earliest morphological evidence for heterotrophic eukaryotes in marine ecosystems. Organismic and Evolutionary Biology Version of Record
 
Expected curves of taxonomic diversity (dashed line), adult morphological disparity (solid line), juvenile morphological disparity (dotted line), and allometric disparity (dot-dashed line; see up left insert) in a case of simple diffusion, expressed as percentage of their maximum (except for juvenile disparity, which is standardized in terms of adult maximum). All disparity estimates are measured as variance. Taxonomic rates, and magnitude and relative frequencies of occurring developmental changes are kept constant (origination rate p 5 0.32, extinction rate q 5 0.25, p(LT) 5 p(CS) 5 1/3, p(OS) 5 0). Diversity increases exponentially. Disparities increase linearly. 
Article
We devised a simple model for assessing the role of development in shaping the evolution of morphological disparity. Disparity of a clade at any given time is expressed in terms of the developmental dynamics that lead to the variety of adult morphotypes observed. We use assumed phenotypic manifestations of developmental processes, as they could be detected from allometric characterizations, to distinguish a few, nonexclusive types of evolutionary changes in ontogeny. On the basis of this formalization, we describe the diversification of hypothetical clades, using the standard curve of adult morphological disparity, the curve of juvenile disparity, and the curve of allometric disparity, the latter quantifying the diversification of clades in allometric space. Contrasts of these curves reflect the underlying developmental scheme that drives temporal changes in disparity. We then vary the parameters of the model to assess the expected signature of each metric under specific conditions: changes in the relative frequencies of the types of evolutionary developmental changes, changes in the transition magnitude attached to each of them, and effects of temporal variation in average adult size on disparity curves and patterns of morphospace occupation. Results emphasize the potential contribution of these proxies for developmental dynamics—juvenile morphological disparity, allometric disparity, and average adult size—in enriching the interpretation of standard disparity curves and the description of clade histories, with possible process-oriented inferences.
 
A, Light micrograph of Medullosa sp. tracheid; scale bar is approximately 130 m. B, Surface view of a torus-margo pit from Tsuga canadensis (Lancashire and Ennos 2002). C, Surface view of homogeneous pit membrane of Fraxinus (modified from Choat et al. 2006). D, Diagram of idealized water flow through tracheids, showing the location and simplified cross-sectional view of torus-margo and homogeneous pit membranes.  
Conductance normalized to cross-sectional wall thickness (K sp ) in Medullosa and Pinus tracheids versus diameter and length. Contours show lines of equal conductance (K sp ) in m 2 /MPa·s, and boxes outline size ranges possible in extant plants (for Pinus) or the fossil record (for Medullosa). Conductance in medullosan tracheids always exceeds that of pine tracheids.
Medullosa (thick line), Cordaites (dotted line), and Pinus (thin line) thickness-to-span ratios versus tracheid diameter. Ranges are based on tracheid diameters and thicknesses found in fossils and the literature (Bannan 1965; Greguss and Balkay 1972). The hashed zone is where given thickness-to-span ratios cause irrevers
Article
Medullosa stands apart from most Paleozoic seed plants in its combination of large leaf area, complex vascular structure, and extremely large water-conducting cells. To investigate the hydraulic consequences of these anatomical features and to compare them with other seed plants, we have adapted a model of water transport in xylem cells that accounts for resistance to flow from the lumen, pits, and pit membranes, and that can be used to compare extinct and extant plants in a quantitative way. Application of this model to Medullosa , the Paleozoic coniferophyte Cordaites , and the extant conifer Pinus shows that medullosan tracheids had the capacity to transport water at volume flow rates more comparable to those of angiosperm vessels than to those characteristic of ancient and modern coniferophyte tracheids. Tracheid structure in Medullosa , including the large pit membrane area per tracheid and the high ratio of tracheid diameter to wall thickness, suggests that its xylem cells operated at significant risk of embolism and implosion, making this plant unlikely to survive significant water stress These features further suggest that tracheids could not have furnished significant structural support, requiring either that other tissues supported these plants or that at least some medullosans were vines. In combination with high tracheid conductivity, distinctive anatomical characters of Medullosa such as the anomalous growth of vascular cambium and the large number of leaf traces that enter each petiole base suggest vascular adaptations to meet the evapotranspiration demands of its large leaves. The evolution of highly efficient conducting cells dictates a need to supply structural support via other tissues, both in tracheid-based stem seed plants and in vessel-bearing angiosperms. Organismic and Evolutionary Biology Version of Record
 
Transverse thin-sections of representative corallites of the three living species within the Montastraea ''annularis'' complex. Although corallites in the three species are similar in diameter and numbers of septa, distinct differences appear in wall structure. Corallites of M. annularis s.s. (A) have walls formed by septal thickening (septothecal), and well-developed extensions of costae beyond the wall. Corallites of M. faveolata (B) have very thin walls that are partially formed by dissepiments (parathecal); extensions of costae beyond the wall are reduced. Corallites of M. franksi (C) have thick septothecal walls, formed by coalesced costosepta. CL, ← columella; CN, coenosteum; PCS, primary costoseptum; TCS, tertiary costoseptum; W, wall. A, M. annularis s.s. (SUI 95206, a95-39); B, M. faveolata (SUI 95214, f95-16); C, M. franksi (SUI 95228, k97-1).
Summary of transects used in collecting samples and environmental and ecologic data. Statistical com- parisons among islands and environments were performed with the Kruskal-Wallis H-test. For environments, 1 reef crest, 2 patch reef, 3 forereef.
List of transverse and longitudinal characters analyzed. Shape coordinates (x1. . .x25, y11. . .y22) were selected, if they defined single morphologic structures and did not combine several different structures into one variable. Numbers for Tukey's test refer to Pleistocene Bahamian growth forms (1 columnar, 2 massive, 3 organ-pipe) and modern Panamanian members of the M. ''annularis'' complex (4 M. annularis s.s., 5 M. faveolata, 6 M. franksi). Species may belong to two groups ( homogeneous sets of means, in brackets) if there is partial overlap among groups. ns not significant.
Article
Recent molecular analyses indicate that many reef coral species belong to hybridizing species complexes or "syngameons." Such complexes consist of numerous genetically distinct-species or lineages, which periodically split and/or fuse as they extend through time. During splitting and fusion, morphologic intermediates form and species overlap. Here we focus on processes associated with lineage fusion, specifically introgressive hybridization, and the recognition of such hybridization in the fossil record. Our approach involves comparing patterns of ecologic and morphologic overlap in genetically characterized modern species with fossil representatives of the same or closely related species. We similarly consider the long-term consequences of past hybridization on the structure of modern-day species boundaries. Our study involves the species complex Montastraea annularis s.l. and is based in the Bahamas, where, unlike other Caribbean locations, two of the three members of the complex today are not genetically distinct. We measured and collected colonies along linear transects across Pleistocene reef terraces of last interglacial age (approximately 125 Ka) on the islands of San Salvador, Andros, and Great Inagua. We performed quantitative ecologic and morphologic analyses of the fossil data, and compared patterns of overlap among species with data from modern localities where species are and are not genetically distinct. Ecologic and morphologic analyses reveal "moderate" overlap (>10%, but statistically significant differences) and sometimes "high" overlap (no statistically significant differences) among Pleistocene growth forms (= "species"). Ecologic analyses show that three species (massive, column, organ-pipe) co-occurred. Although organ-pipes had higher abundances in patch reef environments, columnar and massive species exhibited broad, completely overlapping distributions and had abundances that were not related to reef environment. For morphometric analyses, we used multivariate discriminant analysis on landmark data and linear measurements. The results show that columnar species overlap "moderately" with organ-pipe and massive species. Comparisons with genetically characterized colonies from Panama show that the Pleistocene Bahamas species have intermediate morphologies, and that the observed "moderate" overlap differs from the morphologic separation among the three modern species. In contrast, massive and columnar species from the Pleistocene of the Dominican Republic comprise distinct morphologic clusters, similar to the modern species; organ-pipe species exhibit "low" overlap (<10%, only at species margins) with columnar and massive species. Assuming that "moderate" overlap implies hybridization and "high" overlap implies more complete lineage fusion, these results support the hypothesis of hybridization among species within the complex in the Bahamas during the Pleistocene. Hybridization involved introgression of three distinct evolutionary lineages, in association with Pleistocene sea level and temperature fluctuations, and appears to have been limited geographically primarily to the Bahamas and the northern Caribbean. Thus, not only does the structure of species boundaries within the complex vary geographically, but these geographic differences may have persisted since the Pleistocene.10%, but statistically significant differences) and sometimes "high" overlap (no statistically significant differences) among Pleistocene growth forms (= "species"). Ecologic analyses show that three species (massive, column, organ-pipe) co-occurred. Although organ-pipes had higher abundances in patch reef environments, columnar and massive species exhibited broad, completely overlapping distributions and had abundances that were not related to reef environment. For morphometric analyses, we used multivariate discriminant analysis on landmark data and linear measurements. The results show that columnar species overlap "moderately" with organ-pipe and massive species. Comparisons with genetically characterized colonies from Panama show that the Pleistocene Bahamas species have intermediate morphologies, and that the observed "moderate" overlap differs from the morphologic separation among the three modern species. In contrast, massive and columnar species from the Pleistocene of the Dominican Republic comprise distinct morphologic clusters, similar to the modern species; organ-pipe species exhibit "low" overlap (<10%, only at species margins) with columnar and massive species. Assuming that "moderate" overlap implies hybridization and "high" overlap implies more complete lineage fusion, these results support the hypothesis of hybridization among species within the complex in the Bahamas during the Pleistocene. Hybridization involved introgression of three distinct evolutionary lineages, in association with Pleistocene sea level and temperature fluctuations, and appears to have been limited geographically primarily to the Bahamas and the northern Caribbean. Thus, not only does the structure of species boundaries within the complex vary geographically, but these geographic differences may have persisted since the Pleistocene.');"
 
Article
A major goal of paleobiological research since the early 1960s has been the reconstruction in quantitative terms of the history of biological diversity. Spearheaded by Valentine (1969), Raup (1972, 1976a,b), and Sepkoski (1979, 1981, 1984, 1990, 1993), this effort has yielded estimates of global diversity through time, as well as calculations of global rates and magnitudes of extinction and diversification. A consensus emerging in the early 1980s (Sepkoski et al. 1981) indicated that global marine invertebrate diversity rose through the Cambrian and Ordovician periods to a plateau, which with brief extinction-related interruptions was maintained from the mid-Paleozoic to the mid-Mesozoic. Beginning in the Cretaceous, diversity rose again, reaching a peak in the late Neogene. The five mass extinctions of the Phanerozoic, and more or less distinct episodes of diversification, were identified and distinguished from many lesser events (Raup and Sepkoski 1982). Comparable studies, with varying results, were conducted on land vertebrates (Benton 1985, 1989), land plants (Knoll et al. 1979; Niklas et al. 1980, 1983; Tiffney 1981; Knoll 1984), early protistans (Knoll 1994), insects (Labandeira and Sepkoski 1993), and life as a whole (Van Valen 1984, 1985; Van Valen and Maiorana 1985; Signor 1990; Valentine et al. 1991; Benton 1995; Courtillot and Gaudemer 1996; Miller and Foote 1996). Recent analyses of diversity through time (Alroy et al. 2001), utilizing several different methodological protocols for handling sampling biases and taxon counting, have called some of the earlier work into question. Alroy and colleagues tentatively propose that global genus-level marine diversity reached plateaus of similar magnitude during the mid-Paleozoic and in the Cretaceous to Recent interval, with no detectable rise in diversity during the latter interval. Commenting on the new study, …
 
Eigenvectors from principal components analysis of crown height measurements of dp3's of LBB Teleoceras. Abbreviations: P protoconid, E entoco- nid, M metaconid, and H hypoconid.
Life table for Teleoceras proterum assemblage
Life table for Teleoceras proterum assemblage from LLB built from the most abundant deciduous- adult premolar pair (left dp3-p3). Abbreviations are as in Table 2.
Article
Among polygynous mammals, a heightened risk of mortality is linked to the intensity of intragender competition and life-history stages, such as sexual maturity, where inexperienced individuals are vulnerable to the aggressive behaviors of dominant individuals. In this respect, the age- and sex-specific mortality patterns found in fossil assemblages could be informative of soci- ality in extinct species. This possibility was explored by comparing the age- and sex-specific de- mography of attritional rhinoceros assemblages, Teleoceras proterum (n 5 2) and Aphelops malacor- hinus (n 5 1), from pond and fluvial sedimentary facies of the late Miocene of Florida, with modern skeletal assemblages of extant rhinos and other large mammals. Subadult and young adult males (between 15-40% of potential life span) numerically dominate the Teleoceras assemblages, indicating a disproportionately high frequency of localized young male mortality. The estimated age-specific mortality rates indicate elevated mortality risks among males at an age equivalent to the years encompassing male physiological and social maturity in modern rhinos, a pattern that suggests a high frequency of socially mediated mortality. Age-specific mor- tality rate curves of modern black rhino populations are essentially identical. A high frequency of intraspecific fight-related mortality characterizes modern rhinos and strongly suggests that ele- vated Teleoceras mortality was influenced by intragender competition. Although Teleoceras is widely believed to have been the analog of extant Hippopotamus, mortality rates of young males are not elevated in a modern Hippopotamus population. The Aphelops assemblage is not significantly male- biased and does not indicate elevated mortality rates of young males, suggesting that aspects of Aphelops sociality differed from modern rhinos. Although the nature of Aphelops sociality is not clear, aggression toward young males may have been less extreme or less frequent in Aphelops pop- ulations.
 
Article
Skeletal remains of Eocene Archaeoceti provide the only direct and unequivocal evidence of the evolutionary transition of whales from land to sea. Archaeocete skeletons complete enough to be informative about locomotion are rare (principally Rodhocetus and Dorudon), and these deserve to be studied in comparison to the full spectrum of semiaquatic mammals. A principal components analysis of 14 trunk and limb measurements for 50 species of living semiaquatic mammals reduces the observed variation to three informative axes. The first principal axis (PC-I) represents overall size (water mice and shrews have the lowest scores on this axis and the hippopotamus has the highest); the second axis (PC-II) represents a spectrum of aquatic adaptation (seals have the lowest scores and tapirs have the highest); and the third principal axis (PC-III) represents a spectrum ranging from hindlimb- to forelimb-dominated locomotion (sea otters have the lowest scores and the platypus the highest). Dorudon fits poorly into a morphospace defined solely by living semiaquatic mammals; thus a second 53-species set was analyzed, adding an anthracothere to represent an artiodactyl ancestral morphology and two species of archaeocetes to represent successive stages of early whale evolution. This addition has little effect on the first two principal axes but changes the third substantially. PC-III now represents a contrast of lumbus- (and presumably tail-) dominated versus hindlimb-dominated locomotion (Dorudon has the lowest score and Rodhocetus the highest, whereas the otter shrew has the lowest score among living mammals and the desman the highest). Mammals that are more aquatic have a shorter ilium and femur combined with longer manual and pedal phalanges, whereas the reverse is true for more terrestrial taxa. Lumbus- and tail-dominated swimmers tend to have a longer lumbus combined with shorter pedal elements, whereas the reverse is true for hindlimb-dominated swimmers. Trunk and limb proportions of early middle Eocene Rodhocetus are most similar to those of the living, highly aquatic, foot-powered desmans. Trunk and limb proportions of late middle Eocene Dorudon indicate that it was a lumbus-and-tail-powered swimmer specialized in the direction of modern whales. Thus it appears that the land-to-sea transition in whale evolution involved at least two distinct phases of locomotor specialization: (1) hindlimb domination for drag-based pelvic paddling in protocetids (Rodhocetus), with tail elongation for stability, followed by (2) lumbus domination for lift-based caudal undulation and oscillation in basilosaurids (Dorudon). Rates of evolution in both phases of this change of adaptive zone are about an order of magnitude higher than background rates for the timescale involved.
 
Article
Problems of taphonomy and sampling adequacy hinder direct evolutionary interpretations of pattern in the Precambrian paleontological record; however, molecular studies of microbial phylogeny and comparative physiological and ecological investigations of living microorganisms can be combined with geological research to establish patterns of early evolution. The Late Proterozoic record of planktonic algae resembles those of Phanerozoic plants, animals, and microplankton in its patterns of diversification and turnover, as well as in the importance of major extinction events in shaping the course of evolution. Late Proterozoic eukaryotes thus appear to be discussable in terms of the macroevolutionary issues that have become central to Phanerozoic paleobiology. In contrast, evolutionary patters in Precambrian prokaryotes appear to be different from those of plants and animals, a possible consequence of their differing systems of genetic organization and recombination. Organismic and Evolutionary Biology
 
Continued.
Morphospace of connections. The hips are represented in ventral view as in Figure 5. Framed and numbered graphs represent boundary patterns that are present in archosaurs.  
Article
Theoretical models of skeletal structures provide suitable frameworks to assess macroevolutionary patterns of form change. We discuss three theoretical approaches to account for morphological patterns of the pelvic girdle in archosaurs. Every approach targets a different level of organization within the concept of morphospace. First, we build a morphocline by applying a mathematical transformation to the outline of the hip of the theropod dinosaur Deinonychus antirrhopus, in order to look at theoretical paths of evolutionary change based on changes of proportion. Second, we analyze the variability of a sample of 86 hips within a theoretical construction that incorporates information about the spatial orientation of the three paired bones that build this skeletal compound. Finally, we look at boundary patterns within these hips as a basis for generating a formalism based on graph theory. Insights about the evolution and development of the archosaur triradiate pelvis and its morphological trends are suggested in the light of each theoretical approach, with a special focus on the convergent evolution of a retroverted pubis in ornithischians and birds.
 
Article
Movements of the pelvic girdle have recently been found to contribute to inspiratory airflow in both crocodilians and birds. Although the mechanisms are quite different in birds and crocodilians, participation of the pelvic girdle in the production of inspiration is rare among ver- tebrates. This raises the possibility that the pelvic musculoskeletal system may have played a role in the ventilation of basal archosaurs. Judging from the mechanism of pelvic aspiration in croco- dilians and the structure of gastralia in basal archosaurs, we suggest that an ischiotruncus muscle pulled the medial aspect of the gastralia caudally, and thereby helped to produce inspiration by increasing the volume of the abdominal cavity. From this basal mechanism, several archosaur lin- eages appear to have evolved specialized gastralia, pelvic kinesis, and/or pelvic mobility. Kinetic pubes appear to have evolved independently in at least two clades of Crocodylomorpha. This con- vergence suggests that a diaphragmatic muscle may be basal for Crocodylomorpha. The pelvis of pterosaurs was long, open ventrally, and had prepubic elements that resembled the pubic bones of Recent crocodilians. These characters suggest convergence on the pelvic aspiratory systems of both birds and crocodilians. The derived configuration of the pubis, ischium and gastralia of non-avian theropods appears to have enhanced the basal gastral breathing mechanism. Changes in structure of the pelvic musculoskeletal system that were present in both dromaeosaurs and basal birds may have set the stage for a gradual reduction in the importance of gastral breathing and for the evo- lution of the pelvic aspiration system of Recent birds. Lastly, the structure of the pelvis of some ornithischians appears to have been permissive of pubic and ischial kinesis. Large platelike pre- pubic processes evolved three times in Ornithischia. These plates are suggested to have been in- strumental in an active expansion of the lateral abdominal wall to produce inspiratory flow. Thus, many of the unique features found in the pelvic girdles of various archosaur groups may be related to the function of lung ventilation rather than to locomotion.
 
Original fossil bones (above) and 3-D computer bone image files (below) of Tyrannosaurus rex, from Museum of the Rockies specimen MOR 555. A, Right ilium in dorsolateral view. B, Pubes in right ventrolateral view. C, Right ischium in lateral view. D, Right femur in oblique caudomedial view. E, Right tibia (on left, cranial view)
Example sensitivity analysis for several key muscles in Tyrannosaurus rex, showing the effects of uncertainty about muscle paths for calculating muscle moment arms. See text for details. A, M. iliotibialis 3 (IT3) pelvic origin and knee extensor wrapping surface; hip (on left) and knee (on right) extensor moment arms plotted against hip or knee joint angle as in Figures 4A, 6A. ''cran'' and ''caud'' indicate the effects of moving the IT3 origin 0.10 m cranially
Pelvic and thigh muscles included in the Tyrannosaurus rex musculoskeletal model. For details on the methods and evidence used for these 22 main groups, see Carrano and Hutchinson 2002.
Lower limb muscles included in the Tyrannosaurus rex musculoskeletal model. For details on the methods and evidence used for these 11 muscle groups, see Carrano and Hutchinson 2002.
Article
Muscle moment arms are important determinants of muscle function; however, it is challenging to determine moment arms by inspecting bone specimens alone, as muscles have curvilinear paths that change as joints rotate. The goals of this study were to (1) develop a three-dimensional graphics-based model of the musculoskeletal system of the Cretaceous theropod dinosaur Tyrannosaurus rex that predicts muscle-tendon unit paths, lengths, and moment arms for a range of limb positions; (2) use the model to determine how the T. rex hindlimb muscle moment arms varied between crouched and upright poses; (3) compare the predicted moment arms with previous assessments of muscle function in dinosaurs; (4) evaluate how the magnitudes of these moment arms compare with those in other animals; and (5) integrate these findings with previous biomechanical studies to produce a revised appraisal of stance, gait, and speed in T. rex. The musculoskeletal model includes ten degrees of joint freedom (flexion/extension, ab/adduction, or medial/ lateral rotation) and 33 main muscle groups crossing the hip, knee, ankle, and toe joints of each hindlimb. The model was developed by acquiring and processing bone geometric data, defining joint rotation axes, justifying muscle attachment sites, and specifying muscle-tendon geometry and paths. Flexor and extensor muscle moment arms about all of the main limb joints were estimated, and limb orientation was statically varied to characterize how the muscle moment arms changed. We used sensitivity analysis of uncertain parameters, such as muscle origin and insertion centroids, to deterimine how much our conclusions depend on the muscle reconstruction we adopted. This shows that a specific amount of error in the reconstruction (e.g., position of muscle origins) can have a greater, lesser, similar, or no effect on the moment arms, depending on complex interactions between components of the musculoskeletal geometry. We found that more upright poses would have improved mechanical advantage of the muscles considerably. Our analysis shows that previously assumed moment arm values were generally conservatively high. Our results for muscle moment arms are generally lower than the values predicted by scaling data from extant taxa, suggesting that T. rex did not have the allometrically large muscle moment arms that might be expected in a proficient runner. The information provided by the model is important for determining how T. rex stood and walked, and how the muscles of a 4000–7000 kg biped might have worked in comparison with extant bipeds such as birds and humans. Our model thus strengthens the conclusion that T. rex was not an exceptionally fast runner, and supports the inference that more upright (although not completely columnar) poses are more plausible for T. rex. These results confirm general principles about the relationship between size, limb orientation, and locomotor mechanics: exceptionally big animals have a more limited range of locomotor abilities and tend to adopt more upright poses that improve extensor muscle effective mechanical advantage. This model builds on previous phylogenetically based muscle reconstructions and so moves closer to a fully dynamic, three-dimensional model of stance, gait, and speed in T. rex.
 
Article
The processes of fossilization have usually been perceived by paleontologists as destruc- tive ones, leading to consecutive (and in most cases irretrievable) losses of paleobiological infor- mation. However, recent developments of conceptual issues and methodological approaches have revealed that the decrease in paleobiological information runs parallel to the gain of taphonomic information. This taphonomic imprinting often makes it possible to decode the fraction of paleo- biological information that was lost during fossilization, and may also contribute new data for de- ciphering paleobiological information that was not originally preserved in the assemblage, such as paleoethology. A good example is the study of the macrovertebrate assemblage from the lower Pleistocene site at Venta Micena (Orce, southeastern Spain). Taphonomic analysis showed that the giant, short-faced hyenas (Pachycrocuta brevirostris) selectively transported ungulate carcasses and body parts to their maternity dens as a function of the mass of the ungulates scavenged. The frac- turing of major limb bones in the dens was also highly selective, correlating with marrow content and mineral density. Important differences in bone-cracking intensity were related to which species the bones came from, which in turn biased the composition of the bone assemblage. The analysis of mortality patterns deduced for ungulate species from juvenile/adult proportions revealed that most skeletal remains were scavenged by the hyenas from carcasses of animals hunted by hyper- carnivores, such as saber-tooths and wild dogs. Analytical study of the Venta Micena assemblage has unlocked paleobiological information that was lost during its taphonomic history, and has even provided paleobiological information that was not preserved in the original bone assemblage, such as the paleoethology of P. brevirostris, which differed substantially from modern hyenas in being a strict scavenger of the prey hunted by other carnivores.
 
Characteristics of fossil sites examined in this study.
Sample numbers, isotopic values, and sum- mary statistics for mammoth tooth enamel.
Article
Many late Pleistocene fossil localities contain the remains of multiple mammoths. Some of these sites have been interpreted as representing the mass death of an entire herd, or family group, of mammoths. These assemblages have been cited as evidence of intense human predation and used to reconstruct mammoth population dynamics. However, these interpretations remain controversial because the taphonomic settings of many sites are still debated. To reconstruct the taphonomic setting of each site and the movement patterns of mammoths among sites, I used analyses of carbon, oxygen, and strontium isotope ratios in mammoth tooth enamel. The carbon isotopes of fossils vary with diet and local vegetation, oxygen isotopes vary with local climate, and strontium isotopes vary with local soil chemistry. If Pleistocene mammoths traveled together in small family groups, then mammoths from sites that represent family groups should have lower isotopic variability than mammoths from sites containing unrelated individuals. I tested this conjecture by comparing the isotopic variability among mammoths from two sites—one that represents the mass death of a single herd (Waco, Texas) and one representing a time-averaged accumulation (Friesenhahn Cave, Texas)—and then used these analyses to examine mammoths from three Clovis sites: Blackwater Draw, New Mexico; Dent, Colorado; and Miami, Texas. Low levels of carbon isotope variability were found to be the most diagnostic signal of herd/family group association. Although the variability of oxygen and strontium isotope ratios proved less useful for identifying family group assemblages, these signals did provide information about the movement patterns of individuals among different sites. High levels of variability in each of the isotope systems at Clovis sites suggest that all of the sites examined represent time-averaged accumulations of unrelated individuals, rather than the mass deaths of family groups. In addition, analyses of the mean isotope values of Clovis mammoths show that although most mammoths from Blackwater and Miami had similar values, the values of Dent mammoths were significantly different. This demonstrates that the Dent mammoths belonged to a separate population and suggests that Clovis mammoths did not routinely undertake long distance (≥600 km) migrations.
 
Transect numbers, lengths (in m), and sampling intensities.
A. Slope, 95% confidence limits, r 2 values, and significance of log-transformed species-sampling curves. Higher slopes represent more diverse assemblages.
Taxon presence/absence. A. ANOSIM results.
Characteristic taxa for each group, taxon abundances. Characteristic taxa are those for which the ratio of average abundance to standard deviation of abundance is 1. Abundances are double square-root transformed counts.
Article
This paper assesses the reliability with which fossil reefs record the diversity and community structure of adjacent Recent reefs. The diversity and taxonomic composition of Holocene raised fossil reefs was compared with those of modern reef coral life and death assemblages in adjacent moderate and low-energy shallow reef habitats Of Madang Lagoon, Papua New Guinea. Species richness per sample area and Shannon-Wiener diversity (H') were highest in the fossil reefs, intermediate in the life assemblages, and lowest in the death assemblages. The taxonomic composition of the fossil reefs was most similar to the combination of the life and death assemblages from the modern reefs adjacent to the two fossil reefs. Depth zonation was recorded accurately in the fossil reefs. The Madang fossil reefs represent time-averaged composites of the combined life and death assemblages as they existed at the time the reef was uplifted. Because fossil reefs include overlapping cohorts from the life and death assemblages, lagoonal facies of fossil reefs are dominated by the dominant sediment-producing taxa, which are not necessarily the most abundant in the life assemblage. Rare or slow-growing taxa accumulate more slowly than the encasing sediments and are underrepresented in fossil reef lagoons. Time-averaging dilutes the contribution of rare taxa, rather than concentrating their contribution. Consequently, fidelity indices developed for mollusks in sediments yield low values in coral reef death and fossil assemblages. Branching corals dominate lagoonal facies of fossil reefs because they are abundant, they grow and produce sediment rapidly, and most of the sediment they produce is not exported. Fossil reefs distinguished kilometer-scale variations in community structure more clearly than did the modern life assemblages. This difference implies that fossil,reefs may provide a better long-term record of community structure than modern reefs. This difference also suggests that modern kilometer-scale variation in coral reef community structure may have been reduced by anthropogenic degradation, even in the relatively unimpacted reefs of Madang Lagoon. Holocene and Pleistocene fossil reefs provide a time-integrated historical record of community composition and may be used as long-term benchmarks for comparison with modern, degraded, nearshore reefs. Comparisons between fossil reefs and degraded modern reefs display gross changes in community structure more effectively than they demonstrate local extinction of rare taxa.
 
Article
In computational studies of the body mass and surface area of vertebrates, it is customary to assume that body cross-sections are approximately elliptical. However, a review of actual vertebrate cross-sections establishes that this assumption is not usually met. A new cross-sectional model using superellipses is therefore introduced, together with a scheme that allows estimates to be given with ranges. Tests of the new method, using geometrical shapes, miniature vertebrate models, and actual animals, show that the method has a high accuracy in body mass estimation. A new computer program to perform the computation is introduced. The application of the method to some Mesozoic marine reptiles suggests that the tuna-shaped ichthyosaur Stenopterygius probably had body masses comparable to those of average cetaceans of the same body length.
 
A, Number of barren marine units in each system/period (maps with rocks at outcrop in western Europe or Georef citations) per million years. B, Proportion of barren marine units per time interval. Georef sedimentary units citation survey (Peters 2007) and rock outcrop data for western Europe (this paper Table 1). Linear regression trend lines indicated with R 2 of 0.40 and 0.45 respectively. Abbreviations: Ca, Cambrian; Cb, Carboniferous; Cr, Cretaceous; D, Devonian; J, Jurassic; N, Neogene; O, Ordovician; Pe, Permian; Pg, Paleogene; S, Silurian; T, Triassic.  
Numbers of maps with fossiliferous and unfossiliferous marine sedimentary rocks for western Europe plotted against geological time (72 stage-level time intervals). A, Raw data. B, Proportional change of fossiliferous to unfossiliferous rock. 1 and 2 triangles indicate first-and second-order sequence stratigraphic bundles as derived from rock outcrop area counts (from Smith and McGowan 2007).  
Article
It has recently been argued that barren intervals of marine sedimentary rock are less common in the Cenozoic than in the Paleozoic, and that this arises as a direct consequence of widespread epeiric seas and the prevalence of dysaerobic conditions at such times. We show, using an independent and more direct measure of rock outcrop through time in western Europe, that barren marine sedimentary rocks do become less frequent toward the present, but that this is not linked to any epeiric-seas effect. The proportion of barren to fossiliferous rock outcrop correlates well with the inferred Phanerozoic marine diversity curve (although more so in the Paleozoic than in the post-Paleozoic), and shows no correlation or only a weak negative correlation with area over which the sediments have been deposited. We therefore concluded that the Phanerozoic trend in fossiliferousness most likely records the degree to which space is occupied in the shallow marine realm.
 
Article
This paper takes an alternative approach to the problem of inferring patterns of phenotypic evolution in the fossil record. Reconstructing temporal biological signal from noisy stratophenetic data is an inverse problem analogous to subsurface reconstructions in geophysics, and similar methods apply. To increase the information content of stratophenetic series, available geological data on sample ages and environments are included as prior knowledge, and all inferences are conditioned on the uncertainty in these geological variables. This uncertainty, as well as data error and the stochasticity of fossil preservation and evolution, prevents any unique solution to the stratophenetic inverse problem. Instead, the solution is defined as a distribution of model parameter values that explain the data to varying degrees. This distribution is obtained by direct Monte Carlo sampling of the parameter space, and evaluated with Bayesian integrals. The Bayesian inversion is illustrated with Miocene stratigraphic data from the ODP Leg 174AX Bethany Beach borehole. A sample of the benthic foraminifer Pseudononion pizarrensis is used to obtain a phenotypic covariance matrix for outline shape, which constrains a model of multivariate shape evolution. The forward model combines this evolutionary model and stochastic models of fossil occurrence with the empirical sedimentary record to generate predicted stratophenetic series. A synthetic data set is inverted, using the Neighbourhood Algorithm to sample the parameter space and characterize the posterior probability distribution. Despite small sample sizes and noisy shape data, most of the generating parameter values are well resolved, and the underlying pattern of phenotypic evolution can be reconstructed, with quantitative measures of uncertainty. Inversion of a stratigraphic series into a time series can significantly improve our perception and interpretation of an evolutionary pattern.
 
Trends in ecological, morphological, and mineralogical traits in Jurassic level-bottom communities based on the number of invertebrate species. Reference to figures showing the trends for occurrences are given in brackets. In C, left-hand scale refers to mean size and right hand scale refers to mean ornamentation. Abbreviations of time intervals: Het Hettangian; Sin Sinemurian; Plb Pliensbachian; Toa Toarcian; Aal–Baj Aalenian to Bajocian; Bth Bathonian; Clv Callovian; Oxf Oxfordian; Kim Kimmeridgian; Tth Tithonian. Timescale based on Gradstein and Ogg (2004). Error bars represent 95% confidence inter- vals.  
Mean size and mean ornamentation of epifaunal species throughout the Jurassic based on taxonomic occurrences. A, Mean size (based on geometric mean of shell length and shell height of largest known specimen of each species) of epifaunal bivalves. Total number of species 751. B, Mean ornamentation of epifaunal bivalves and gastropods. Total number of species 1435. For quantifying ornamentation see methods section . C, Mean ornamentation of epifaunal bivalves and gastropods from low latitudes. There is no significant trend in A (r s 0.12, p 0.75) or B (r s 0.53, p 0.12); mean ornamentation in low latitudes (C) shows a significant decrease (r s 0.68, p 0.03). Error bars represent 95% confidence intervals. For legend see Figure 1.  
Article
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.
 
Article
The association between mass extinction in the marine realm and eustatic sea-level change in the Mesozoic is well documented, but perplexing, because it seems implausible that sea- level change could actually cause a major extinction. However, large-scale cycles of sea-level change can and do alter the ratio of shallow to deep marine continental-shelf deposits preserved in the rock record both regionally and globally. This taphonomic megabias alone could be driving pat- terns of first and last occurrence and standing diversity because diversity and preservation poten- tial both change predictably with water depth. We show that the Cenomanian/Turonian faunal event in western Europe has all the predicted signatures expected if taphonomic megabias was the cause. Grade taxa terminating in pseudoextinction and Lazarus taxa are predominantly found in the onshore facies that disappear for extended periods from the rock record. Before other mass extinctions are taken at face value, a much more careful analysis of biases in the rock record needs to be carried out, and faunal disappearances need to be analyzed within a phylogenetic framework.
 
Article
When ambitious large-scale projects are proposed, like the Paleobiology Database (Alroy et al. 2001) and Panama Paleontology Projects (Jackson and Johnson 2001), there is inevitably a negative reaction from various quarters, which is quickly forgotten when the projects start to yield results. Given that, it may be useful to sing the praises of "big picture" science more generally and I will do so after briefly addressing this discussion starter in the context of my own research. Albeit a truism, it is also a profound truth that the kinds of patterns we observe and the kinds of explanations for these patterns are different at different scales (e.g., Willis and Whittaker 2002). A decade ago I studied the early evolution of the birds using a molecular phylogeny (Nee et al. 1992). In particular, we analyzed the rate of cladogenesis at the root of the phylogeny, the rate of diversification of those lineages that gave rise to all extant species-clearly a global measure of biodiversity dynamics. We wanted to see if the data fit an exponential model of radiation (they do not). This could be construed as "meaningless" by objecting that it is meaningless to talk of a "rate" when there is, inevitably, rate heterogeneity-not all lineages are the same and the devil is in the detail.
 
Article
For decades, paleobiologists have treated global diversity estimation as a straightforward problem (Miller 2000): count up the known higher taxa in each geological time interval, make a diversity curve, and go straight ahead to analyzing and interpreting the trends. However, global diversity curves recently have come under attack from all sides. Some researchers argue that although traditional curves are strongly affected by sampling biases (e.g., Smith 2001; Peters and Foote 2002), these biases can be corrected by assembling large, locality-level databases with detailed contextual information (Alroy et al. 2001). Others point to the large gap between true total global richness and the meager head counts the fossil record has to offer, and conclude that workers should focus exclusively on local and regional diversity (Jackson and Johnson 2001). Here I argue that although further fieldwork surely is needed, understanding global diversity in the short term remains a tractable goal—as long as we move quickly to build a discipline-wide, globally extensive paleontological database. Relative versus total diversity: Because the fossil record always is incomplete, we cannot directly determine true total diversity, i.e., a series of exact, direct counts of all the species that ever existed at each point in time (e.g., Jackson and Johnson 2001). However, demonstrating an adaptive radiation or diversity crash only requires showing in relative terms that diversity was higher or lower in one time interval than the next. The same is true of other important paleontological patterns: the replacement of one taxonomic group by another (e.g., McKinney et al. 1998), the contrast between taxonomic diversity and morphological disparity (Foote 1991), diversity differences among geographic regions (Miller 1997; Jablonski 1998), and the temporal dynamics of diversification (Sepkoski 1978). All of these things can be studied by quantifying relative diversity levels, instead of waiting for centuries to inventory …
 
Article
The claim that measures of global biodiversity dynamics are meaningless is based upon several methodological problems, including underrepresentation of tropical regions in “global” Phanerozoic data sets, inaccuracies in taxonomic data, non-equivalence of higher taxa among groups of organisms, and uneven sampling intensity across groups, environments, and time intervals. Some of these problems are inherent in the fossil record, whereas others lie in documentation and interpretation of the subject. But the subject of global biodiversity is perfectly legitimate, even if problems persist in evaluating its full history. Moreover, recognition of the methodological problems has resulted in notable improvements in the Phanerozoic diversity database (e.g., Adrain and Westrop 2000; Alroy et al. 2001). Here I offer three points: (1) The study of biodiversity is meaningful at many spatial and temporal scales, including the global scale. (2) Two major preservational biases limit the estimation of global biodiversity over the Phanerozoic, although estimates are still potentially meaningful. (3) Extrapolation of patterns and processes from a smaller scale to a larger one or from one clade to a more inclusive clade is inappropriate and justifies some criticisms of biodiversity studies at the largest scales. Below, I elaborate on these points from a perspective based in experience with vertebrates in terrestrial ecosystems. Significant patterns of biological diversity and the ecological and evolutionary processes that shape them occur at multiple spatial scales, including local, regional, continental, and global, and multiple temporal scales, including those of ecological and evolutionary processes. Biological diversity itself is a multi-scale concept, ranging from genetic diversity within local populations to ecosystem diversity across landscapes. Three sets of examples illustrate processes influencing biodiversity, including its protection, at different scales. (1) Global biodiversity is meaningful partly as the sum of biodiversity measures for smaller regions, but also because it is influenced by physical …
 
Top-cited authors
Niles Eldredge
  • American Museum of Natural History
David Wake
  • University of California, Berkeley
Gary Haynes
  • University of Nevada, Reno
Anna K. Behrensmeyer
  • Smithsonian Institution
Nicholas Butterfield
  • University of Cambridge