bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity changes in lycopsid and aquatic fern megaspores through geologic time
Authors: Kovach Warren L. , Batten David J.
Published: July 2016

Quantitative data on lycopsid and aquatic fern megaspore taxa recovered from Carboniferous, Mesozoic, and Tertiary strata have been compiled in order to analyze the changes in diversity of the two groups of fossil plants that produced them. Numbers of species of lycopsid megaspores are similar in the Carboniferous and Mesozoic, whereas the diversity of megafossils is much lower in post-Paleozoic deposits. Our data suggest that lycopsids were more diverse in the Mesozoic than previously thought and that there is a preservational bias against the megafossils, because the plants were probably mainly herbaceous. Heterosporous aquatic ferns first appeared in the Neocomian and gradually diversified until the early Late Cretaceous, after which their numbers remained relatively stable, whereas the variety of lycopsids declined dramatically during the Late Cretaceous. These changes occurred at a time of rapid angiosperm diversification. The reduced diversity of the lycopsids may have been caused by the invasion of their aquatic and damp forest-floor habitats by heterosporous ferns and by aquatic and herbaceous angiosperms. These diversity changes do not seem to be directly related to the global events at the Cretaceous-Tertiary boundary, but the relatively few samples available and the resulting range truncation would make detection of such correlations difficult.
A model for planktic foraminiferal shell growth
Authors: Signes Miguel , Bijma Jelle , Hemleben Christoph , Ott Rolf
Published: July 2016

In this paper we analyze the laws of growth that control planktic foraminiferal shell morphology. We assume that isometry is the key toward the understanding of their ontogeny. Hence, our null hypothesis is that these organisms construct isometric shells. To test this hypothesis, geometric models of their shells have been generated with a personal computer. It is demonstrated that early chambers in log-spirally coiled structures cannot follow a strict isometric arrangement. In the real world, the centers of juvenile chambers deviate from the logarithmic growth curve. Juvenile stages are generally more planispiral and contain more chambers per whorl than adult stages. These traits are shown to be essential in order to keep volumes of consecutive chambers in geometric progression. We are convinced that the neanic stage marks the constructional bridge from a juvenile set of growth parameters to an adult one. The adult stage can be strictly isometric, that is, the effective shape is constant and the increase in volume after a chamber addition is proportional to the preexisting volume of the shell.

The shell volume is related to the biomass, the ratio of outer shell surface area to shell volume is related to the respiration rate and the ratio of the total shell surface area to shell volume is related to the total calcification effort. The influence of the parameters of the model on these relationships is investigated. Only the initial radius and the rate of radius increase affect the relationships between shell volume and surface area. The other shape parameters merely provide a fine tune-up of these relationships. Size itself plays a major role during foraminiferal development.
Shell form in the biconvex articulate Brachiopoda: a geometric analysis
Authors: McGhee George R.
Published: July 2016

Using a geometric model of shell morphology, it is demonstrated that biconvex brachiopods occupy only a small region of the potential geometric space available to organisms with planispiral exoskeletons composed of two articulated valves. Measurements taken for a sample of 324 genera of the articulate orders Pentamerida, Rhynchonellida, Spiriferida, and Terebratulida were analyzed using a simple geometric model of shell form and ontogeny. The frequency distribution of brachiopod shell morphologies exhibited by the four orders represents the biological optimization of the spatial relationships between area and volume. Biconvex brachiopods develop shells which are designed to minimize shell surface area while maximizing internal shell volume. The means by which optimization is achieved is related directly to the effects of increase in absolute size during ontogeny. The boundaries upon shell geometries utilizable by biconvex brachiopods are determined by (1) limitations of articulation, and (2) limitations of surface and volume.
Disparity as an evolutionary index: a comparison of Cambrian and Recent arthropods
Authors: Wills Matthew A. , Briggs Derek E. G. , Fortey Richard A.
Published: July 2016

Disparity is a measure of the range or significance of morphology in a given sample of organisms, as opposed to diversity, which is expressed in terms of the number (and sometimes ranking) of taxa. At present there is no agreed definition of disparity, much less any consensus on how to measure it. Two possible categories of metric are considered here, one independent of any hypothesis of relationship (phenetics), the other constrained within an evolutionary framework (cladistics).

The Early Cambrian radiation was clearly a period of significant morphologic and taxonomic diversification. However, we question the interpretation of its first generation products as numerous body plans at the highest level. Four phenetic and two cladistic measures have been used to compare disparity among Cambrian arthropods with that in the living fauna. Phenetic methods assessing character-state variability and the amount of morphological attribute space occupied yield similar results for Cambrian and Recent arthropods. Assessments of disparity within a taxonomic framework rely on the identification of particular characters that delineate higher level body plans. This requires a phylogenetic interpretation, a cladistic investigation of hierarchical structure in the data. Both sets of arthropods fall within the same major clades, and within this cladistic framework the amount of character-state evolution in the two groups is comparable. None of these methods identifies markedly greater disparity among the Cambrian compared with the Recent taxa.

Although measures of disparity are applied here to a consideration of the Cambrian radiation, the metrics clearly have a much wider potential for estimating macroevolutionary trends independently from existing taxonomic frameworks. Geometric morphometry is ideal for measuring morphological variety at lower taxonomic levels, but it requires the recognition of homologous landmarks in all the forms under comparison, or the identification of entire homologous structures. Conventional phenetics has much wider application as it can operate on data coded as discrete homologous character states (this facility is also a requirement of cladistics), which are a more appropriate basis for comparing disparity in markedly dissimilar forms.
Hybrid crinoids in the fossil record (Early Mississippian, Phylum Echinodermata)
Authors: Ausich William I. , Meyer David L.
Published: July 2016

Potential hybrid fossil crinoids, Eretmocrinus magnificus x Eretmocrinus praegravis, are identified from the Lower Mississippian Fort Payne Formation of south-central Kentucky. These are the first fossil hybrid crinoids identified, and one of very few examples of hybrids recognized in the fossil record. Eretmocrinus magnificus x E. praegravis specimens have shapes and calyx plate sculpturing that are morphologically intermediate between well-defined, distinct parent species. Suspected hybrids occur at localities where parent species co-occur and where the parent species are the most abundant; the hybrids occur at what may have been the distributional margins of the parent species; and the mixture of characters on suspected hybrids seems to be morphogenetically partitioned. Parent species are derived from separate lineages within Eretmocrinus, and hybridization is the most probable explanation for these morphologically intermediate specimens. This example highlights the need to consider hybridization as a potential interpretation of intermediate morphologies among fossils and raises questions concerning the impact of hybridization for our interpretation of the fossil record and the role of hybridization in the evolutionary process.
Confidence intervals on stratigraphic ranges: partial relaxation of the assumption of randomly distributed fossil horizons
Authors: Marshall Charles R.
Published: July 2016

The equations for calculating classical confidence intervals on the end points of stratigraphic ranges are based on the restrictive assumption of randomly distributed fossil finds. Herein, a method is presented for calculating confidence intervals on the end-points of stratigraphic ranges that partially relaxes this assumption: the method will work for any continuous distribution of gap sizes, not just those generated by random processes. The price paid for the generality of the new approach is twofold: (1) there are uncertainties associated with the sizes of the confidence intervals, and (2) for large confidence values (e.g., 95%) a rich fossil record is required to place upper bounds on the corresponding confidence intervals. This new method is not universal; like the method for calculating classical confidence intervals it is based on the assumption that there is no correlation between gap size and stratigraphic position. The fossil record of the Neogene Caribbean bryozoan Metrarabdotos is analyzed with the new approach. The equations developed here, like those for classical confidence intervals, should not be applied to stratigraphic ranges based on discrete sampling regimes, such as those typically established from deep-sea drilling cores, though there are exceptions to this rule.
A task for Paleobiology at the threshold of majority
Authors: Gould Stephen Jay
Published: July 2016

When asked how he might sum up his long life, an aged Benjamin Franklin replied that he had, at least, been useful to his fellows. Paleobiology is still young, as our journal has just completed 20 years and now begins this season of its majority, while the vibrancy of our subject certainly proclaims a vigorous incipiency. But academic generations are short, a mere 5 years or so, and Paleobiology has therefore enjoyed adequate time to demand judgment by accomplished results, not simple promise. When, fifteen years ago (6, 1, 80), I wrote a similar piece to celebrate the completion of this journal's first five volumes, I spoke in my title about “the promise of paleobiology”; now I must refer to “the task of paleobiology” and delineate what has been accomplished, and how much we have yet to do.
Extinction selectivity and ecology of Neogene Caribbean reef corals
Authors: Johnson Kenneth G. , Budd Ann F. , Stemann Thomas A.
Published: July 2016

We analyze a new compilation of Neogene to Recent (22-0 Ma) Caribbean coral occurrences to determine how ecological and life history traits at the population level affect long-term evolutionary patterns. The compilation consists of occurrences of 175 species and 49 genera in one continuous (> 5 m.y.) sequence and 22 scattered sites across the Caribbean region. Previous study of evolutionary rates using these data has shown that both extinction and origination were accelerated between 4 and 1 Ma, resulting in large-scale faunal turnover. Categories for three morphological and two reproductive variables (colony size, colony shape, and corallite size; and sex, and mode of embryonic development; respectively) are assigned to each species in the compilation. Comparisons of the ecological variables with evolutionary rates using randomization procedures and modified analysis of variance show that only colony size was strongly related to rates of extinction and origination during either normal background times or times of accelerated extinction. Extinction rates were lower in species with large colonies, because species with small massive colonies tend to live in small, short-lived populations with highly fluctuating recruitment rates. During turnover, extinction rates increased disproportionately in species with small colonies. Origination rates are found to be less related to ecological variables, although species with small massive colonies originated at higher rates prior to turnover.

Accelerated turnover may have therefore involved an increase in local population extinction rates that caused increased rates of both species extinction and origination across the entire fauna. Since extinction rates accelerated disproportionately with respect to colony size, the overall result was a relative increase in species with large colonies. After severe disturbance, one might expect that populations of species with large colonies and high rates of fragmentation would be more likely to escape extinction, because of larger population sizes, longer generation times, and more constant rates of population increase. The modern Caribbean reef-coral fauna is therefore structured by large, long-lived colonies that are robust to regional environmental change. Many of the very taxa that allowed reef communities to escape collapse in the past are declining today in response to anthropogenic disturbances, suggesting that Caribbean reef communities may be less resilient in the future in response to ongoing environmental perturbations.
The stratigraphic distribution of fossils
Authors: Holland Steven M.
Published: July 2016

In several increasingly realistic steps, a model of the stratigraphic distribution of fossils is presented. The first and simplest step assumes that if a taxon was extant it will have been preserved. The second step admits that if a taxon was extant, there is some probability less than one that it will have been preserved. This step produces randomly distributed gaps, and fossil ranges that are somewhat shorter than the span of time in which a taxon actually lived. The third step assumes facies-controlled taxa and parasequence-style cyclicity. This produces randomly and nonrandomly distributed gaps, including the anomalously long gaps recognized in confidence limit studies. The final model incorporates depositional sequences and indicates that first and last occurrences will cluster at sequence boundaries and at flooding surfaces in the transgressive systems tract. Across-shelf gradients in diversity, taphonomy, or eurytopy can control the strength, but not the stratigraphic position of these peaks. Comparison of the model to data from the Upper Ordovician suggests that these modeled features are present in the fossil record. Many previously studied paleobiologic patterns may be, at least in part, an artifact of facies control and sequence architecture. Such patterns include gradual or stepwise mass extinction, punctuated morphologic and taxonomic change, iterative evolution, and the replacement of shallow water faunas by deeper water faunas at biomere boundaries.
Morphological diversification of Paleozoic crinoids
Authors: Foote Mike
Published: July 2016

Several metrics, including average difference among species, range of occupied morphological space, and number of character-state combinations, are used to investigate morphological diversification in Paleozoic crinoids. Despite several phases of taxonomic diversification, the maximal level of disparity reached in the Ordovician remained essentially unsurpassed. Although new regions in morphological space were occupied after the Devonian, these were not as extensive as those that had been evacuated prior to the Carboniferous. This discordance between extensive total morphological change and limited net change further supports previous arguments for the importance of morphological constraints in crinoid evolution. Major changes in the occupation of morphological space correspond with changes in taxonomic diversity within certain higher taxa. The extent to which advanced cladids (Poteriocrinina) appear to expand into new morphological space is exaggerated by the large number of very similar species in this group. If fewer species are sampled, by considering only those forms that differ from each other by at least some prescribed amount, poteriocrines appear to be less extreme morphologically. In contrast, other groups that seem to occupy unique regions in morphological space continue to do so even if fewer of them are sampled. Major crinoid clades—Camerata and Cladida+Flexibilia—do not show the same evolutionary pattern as Crinoidea, but instead exhibit a more gradual diversification of morphology. This observation provides additional support for the existence of qualitative differences among taxa of different rank.
Diversity patterns among early gastropods: contrasting taxonomic and phylogenetic descriptions
Authors: Wagner Peter J.
Published: July 2016

Paleobiologists have used taxonomic data for several types of diversity studies. Some systematists have charged that this practice obfuscates actual historical patterns of clades because many traditionally defined higher taxa are not monophyletic. Some have questioned whether ranked taxa ever represent comparable units, even when monophyletic. This study contrasts diversity patterns implied by phylogenetic estimates with those implied by ranked taxa. Early Paleozoic gastropods are useful as a test case because their generic taxonomy does not reflect the phylogenetic systematic philosophy, and fewer than one third of the genera represent monophyletic clades. Phylogenetic diversity is described in two ways: (1) numbers of lineages (i.e., observed plus phylogenetically implied “ghost lineages”), and (2) numbers of monophyla (i.e., clades whose sister taxa are other clades rather than species). “Monophyla” as tallied here are monophyletic relative to their contemporaries and older clades; however, they can be paraphyletic relative to “future” monophyla. Phylogenetic diversity is tallied with both maximum and minimum “ghost lineage” interpolations in order to reflect different possible speciation patterns and timings of speciation. Phylogenetic diversity as implied by a stricter cladistic criterion (i.e., taxa that are monophyletic relative to their contemporaries, older taxaandyounger taxa) is discussed also.

First differences between substage-to-substage standing diversities reveal significant congruence between generic data and both types of phylogenetic data. Taxonomic and phylogenetic data imply a major extinction event at the end of the Ordovician, although the phylogenetic data suggest greater extinction levels than do the taxonomic data. Both data sets also suggest diversity-dependent diversification reminiscent of logistic growth, which is the pattern predicted if one or a few major ecologic factors were constraining the diversification of gastropods. However, diversity described by strict Hennigian taxa is not highly congruent with diversity as described by either lineages or monophyla. Comparing subclade dynamics requires extensive redefinition of traditional orders, but lineages, monophyla and genera all suggest that the two major subclades had different logistic diversification patterns, with one (“murchisonioids”) having a higherKthan the other (“euomphaloids”). The concern that phylogenetic and taxonomic data might imply very different evolutionary histories is not borne out by gastropods, despite the nonphylogenetic nature of their traditional taxonomy.
A hierarchical branching model of evolutionary radiations
Authors: Patzkowsky Mark E.
Published: July 2016

A hierarchical branching model is presented that tracks diversity of lineages and paraclades simultaneously. It is based on three parameters: (1) lineage origination within a paraclade, (2) lineage origination that founds new paraclades, and (3) lineage extinction. The model assumes stochastic constancy of evolutionary rates and, therefore, exponential growth of diversity is the null expectation. The probabilistic model can be used to generate confidence intervals for exponential growth through Monte Carlo simulation. These confidence intervals can be compared to empirical curves to test the null hypothesis of exponential growth. The analytic solution for paraclade diversity gives the statistical expectation for the probabilistic model. It can be applied to empirical diversity curves of supraspecific taxa to estimate total speciation rate, the intrinsic rate of increase, and the proportion of speciation events that found new paraclades. Two factors were identified with the model that may cause diversity curves for higher taxa (e.g., genera, families) to deviate from simple exponential growth during initial phases of diversification: (1) stochastic fluctuation at low diversity, and (2) taxonomic structure (i.e., species/genus ratio). These sources of variability should be evaluated before macroevolutionary explanations for specific diversity trends are invoked. Two kinds of evolutionary radiations were investigated with this model: (1) prolonged periods of low diversity (macroevolutionary lag) in cheilostome bryozoans and mammals prior to their main phases of diversification, and (2) rapid bursts in diversity of bivalves following the late Permian and end-Cretaceous mass extinctions. In all cases these patterns were found to deviate significantly from the null expectation of exponential growth lending support to previous macroevolutionary explanations. Finally, rates of speciation during radiations were compared to rates of speciation during background times for articulate brachiopods, cheilostome bryozoans, bivalves, and mammals. Speciation events that found new paraclades tend to make up a larger proportion of total speciation events during radiations compared to background times indicating that the opportunity for new adaptive zones to be filled at higher taxonomic levels is proportionately higher during these periods of increased evolutionary activity, and is not simply a result of an increased frequency of speciation.
Taphonomy of mammalian fossil remains from Siwalik rocks of Pakistan
Authors: Badgley Catherine
Published: July 2016

Siwalik rocks of Pakistan are a virtually continuous, continental sedimentary sequence, extending in age from 18 to 1 ma b.p. This paper describes taphonomic features of late Miocene mammalian assemblages from a highly fossiliferous interval about 400 m thick, based on field documentation of sedimentary environments at 42 fossil localities and systematic fossil collection of 21 localities.

Within a broadly fluvial system, I recognize four sedimentary environments of bone accumulation, distinguished by lithology, unit-thickness, unit-geometry, contacts, sedimentary structures, and relationship to adjacent units. Each environment corresponds to an association of lithofacies. Facies Association I is interpreted as the persistent, major channel bodies of a meandering fluvial system; Facies Association II as coarse-grained flood deposits, such as crevasse splays, deposited beyond the main channels; Facies Association III as channel margins, including levees and swales; and Facies Association IV as predominantly subaerial floodplains.

Taphonomic features of bone assemblages from each facies association include skeletal-element composition, surface distribution of specimens, degree of articulation, hydraulic equivalence between organic and inorganic sedimentary particles, frequency of juvenile remains, size distribution of fauna, and an estimate of duration of accumulation of individual fossil localities. The distribution of these features among the four facies associations suggests that bone assemblages in Facies Associations I and II accumulated by the action of currents in river channels or floods, whereas bone assemblages in Facies Associations III and IV accumulated through concentration by biological agents and/or attrition at a repeatedly used site of predation.

Inclusion in fluvial accumulations depends on initial availability of skeletal remains and hydraulic characteristics of individual skeletal elements, but not taxonomic identity per se. For biological accumulations, however, taxonomic composition reflects the preferences of the individual agents of accumulation. The probability of preservation of taxa in fluvial accumulations is probably mainly a function of body size, as reflected in the sizes of isolated skeletal elements. Thus, in this Siwalik system, bone assemblages that experienced fluvial transport are better representations of original community composition than bone assemblages created by biological agents or passive accumulation.
Ecological causation of heterochrony: a test and implications for evolutionary theory
Authors: McKinney Michael L.
Published: July 2016

Biometric analyses of the ontogenies of 31 species of fossil echinoids support a hypothesized relationship between regulatory gene changes and environmental stability. In 15 of 17 pairs of related species, the larger species, undergoing slower (neotenic) and/or prolonged (hypermorphic) growth, apparently inhabited the stabler environment. If true, this relationship connects biological processes at a number of levels and explains or agrees with some important macroevolutionary observations, such as onshore evolutionary innovation and Cope's Rule.
Shape, Drag, and Power in Ammonoid Swimming
Authors: Jacobs David K.
Published: July 2016

This study assesses swimming potential in a variety of ammonoid shell shapes on the basis of coefficients of drag (Cd) and the power needed to maintain a constant velocity. Reynolds numbers (Re) relevant to swimming ammonoids, and lower than those previously studied, were examined. Power consumption was scaled to a range of sizes and swimming velocities. Estimates of power available derived from studies of oxygen consumption in modern cephalopods and fish were used to calculate maximum sustainable swimming velocities (MSV).

Laterally compressed, small thickness ratio (t. r.) ammonoids, previously assumed to be the most efficient swimmers, do not experience the lowest drag or power consumption at all sizes and velocities. At low values of size and velocity associated with Reynolds numbers below 104, less compressed forms have smaller drag coefficients and reduced power requirements. At hatching a roughly spherical shell shape would have minimized drag in ammonoids; with increasing size, hydrodynamic optima shift toward compressed morphologies.

The high energetic cost of ammonoid locomotion may have limited dispersal and excluded ammonoids from high current velocity environments.
Heterochronic Dimorphism of Loxoconcha Uranouchiensis (Ostracoda) and its Implication for Speciation
Authors: Kamiya Takahiro
Published: July 2016

Polymorphism is being actively investigated by ostracode specialists because the phenomenon is widespread and may be a key to understanding speciation patterns and evolutionary processes. However, the methods for recognizing the phenomenon and the cause or causes of polymorphism are still under debate. This study presents an example of genetically controlled ostracode dimorphism in which the relationship between the two forms can be explained in terms of heterochrony. The living males as well as the females of Loxoconcha uranouchiensis in Aburatsubo Cove, central Japan, are found to be dimorphic in size, shape, and surface ornamentation of the carapace. The dimorphic forms appear concurrently in the same microhabitat, suggesting that the dimorphism is genetically rather than environmentally controlled. Although the large and the small forms are indistinguishable in their early stages, morphological differences gradually appear and become complete after the final molting, which is the seventh molting for both forms. The characters determined by the number of moltings, such as the numbers of reticules, bristles, and pores, are identical between adults of the two forms. In contrast, for characters affected by the growth condition of the epidermal-cell system, such as carapace shape and fine surface ornamentation, the small-form adult is similar to the penultimate instar of the large form. Taking the large form as a standard, the small form is paedomorphic. These two forms are reproductively isolated and should be considered different species.
Temperature and extinction in the sea: a physiologist's view
Authors: Clarke Andrew
Published: July 2016

Climatic change has long been regarded as an important factor in evolutionary history. In particular, periods of enhanced extinction in marine taxa (especially those from warmer waters) have frequently been linked to decreases in seawater temperature. Studies of the physiology of marine invertebrates and fish alive today have revealed well-developed abilities to cope with temperature change, and there would thus appear to be a dichotomy between the rates of temperature change associated with extinction in geological history and the very much faster rates (by several orders of magnitude) with which many marine organisms can cope today. Nevertheless, evidence from ecology and biogeography indicates that temperature, or some temperature-associated factor, does play a significant role in determining the limits to performance, and hence distribution. The resolution of the dichotomy between the evidence from paleontology and physiology may come through a consideration of the role of the previous evolutionary history of the fauna, the influence of sudden temperature events, or the impact of climatic change on individual competitive ability, community structure, and ecosystem functioning. Studies of the energetics of marine invertebrates in relation to temperature and the evolutionary history of polar faunas indicate that we should beware of anthropocentric judgements in attempting to understand the role of climatic change in evolutionary history, and be critical in distinguishing the role of temperature per se from temperature-associated ecological factors. Present evidence suggests that climatic change in the sea, at least at the rates currently believed to be typical, is unlikely to cause extinction by direct physiological impact. It is more likely that extinction is caused by ecological factors; temperature change is thus only one of several factors that may promote those ecological changes that are currently the best candidates for the proximate cause of extinction in the sea.
Daughter of time
Authors: Knoll Andrew H.
Published: July 2016

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.
On the probability of ancestors in the fossil record
Authors: Foote Mike
Published: July 2016

Three homogeneous models of species origination and extinction are used to assess the probability that ancestor-descendant pairs are preserved in the fossil record. In the model of cladogenetic budding, a species can persist after it branches and can therefore have multiple direct descendants. In the bifurcation model, a species branches to give rise to two distinct direct descendants, itself terminating in the process. In the model of phyletic transformation, a species gives rise to a single direct descendant without branching, itself terminating in the process. Assuming homogeneous preservation, even under pessimistic assumptions regarding the completeness of the fossil record, the probability of finding fossil ancestor-descendant pairs is not negligible. Even if all species of Phanerozoic marine invertebrates in the paleontologically important taxa had the same probability of preservation, on the order of 1%-10% or more of the known fossil species would be directly ancestral to other known fossil species. However, this is likely to be an underestimate, since the probability of finding ancestor-descendant pairs is enhanced by taxonomic, temporal, and spatial heterogeneities in preservation probability. Moreover, indirect genealogical relationships substantially increase the probability of finding ancestor-descendant pairs. The model of budding, the only one in which an ancestor can persist after a branching event, predicts that half or more of extant species have ancestors that are also extant. Thus, the question of how to recognize ancestor-descendant pairs must be carefully considered.
Calibrating the Ordovician Radiation of marine life: implications for Phanerozoic diversity trends
Authors: Miller Arnold I. , Foote Mike
Published: July 2016

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.
K/T redux
Authors: MacLeod Norman
Published: July 2016

“There are still many dinosaur people who will say that, ‘Yes, there was an impact, but there were hardly any dinosaurs left by then.’ It's possible, but my first class prejudice is not to accept coincidence on that scale” (S. Gould quoted in Glenn 1994: p. 266, referring to the K/T mass extinction).
Prey selection by terrestrial carnivores in a lower Pleistocene paleocommunity
Authors: Palmqvist Paul , Martínez-Navarro Bienvenido , Arribas Alfonso
Published: July 2016

We report quantitative paleoecologic data on the large mammal assemblage preserved in lower Pleistocene deposits at Venta Micena (Orce, Granada, southeastern Spain). Taphonomic studies show that bones were collected mainly by hyaenids, which transported and deposited them near shallow dens. Differential fragmentation of major long bones was produced by hyaenas as a function of their density and marrow content. Strong selection of prey by carnivores—which preferentially killed juveniles, females, and individuals with diminished locomotor capabilities among ungulate prey species of larger body size—is indicated by (1) the abundance of remains of juvenile ungulates in relation to the average weight of adult individuals in each species, (2) attritional mortality profiles for ungulate species deduced from crown height measurements, (3) the presence of many metapodials with different osteopathologies in their epiphyses, such as arthrosis, and (4) a biased intersexual ratio of large bovids. Comparison of the frequencies with which modern African carnivores kill and scavenge ungulates from various size classes with the abundance of these size categories in the assemblage suggests that the Venta Micena hyaena (Pachycrocuta brevirostris) was a bone-cracking scavenger that fed largely on carcasses of ungulates preyed upon and partially consumed by fresh meat-eating carnivores such us saber-toothed felids (Homotherium latidens and Megantereon whitei) and wild dogs (Canis falconeri).
Comparing the fit of stratigraphic and morphologic data in phylogenetic analysis
Authors: Clyde William C. , Fisher Daniel C.
Published: July 2016

Stratigraphic data are compared to morphologic data in terms of their fit to phylogenetic hypotheses for 29 data sets taken from the literature. Stratigraphic fit is measured using MacClade's stratigraphic character, which tracks the number of independent discrepancies between observed order and the order of occurrence that would be expected on the basis of a given phylogenetic hypothesis. Acceptance of a phylogenetic hypothesis despite such discrepancies requires ad hoc hypotheses concerning differential probabilities of preservation and recovery. These stratigraphic ad hoc hypotheses are treated as logically equivalent to morphologic ad hoc hypotheses of homoplasy. The retention index is used to compare the number of stratigraphic and morphologic ad hoc hypotheses required by given phylogenetic hypotheses. Each data set is subjected to five analyses, varying in the constraints imposed on the structure of the phylogenetic tree against which fit is measured. Analyses 1–4 compare the stratigraphic and morphologic retention indices using phylogenetic trees consistent with the morphologically most-parsimonious cladogram reported in the original study. Analysis 5 compares retention indices using the overall (stratigraphically and morphologically) most-parsimonious phylogenetic tree, which may be, but is not necessarily, consistent with the reported cladogram. Proceeding from Analysis 1 to Analysis 5, stratigraphic data are allowed greater influence in determining the structure of phylogenetic trees, with the trees in Analysis 1 derived without reference to the stratigraphic character and the trees in Analysis 5 derived from full interaction of stratigraphic and morphologic characters. Morphologic and stratigraphic retention indices for these 29 studies cannot be statistically distinguished in comparisons 3–5, suggesting very similar degrees of fit. The values of these retention indices are high, indicating a generally high level of congruence under these phylogenetic hypotheses. Significant gains (49%) in stratigraphic fit can be realized without significant loss (4%) in morphologic fit as the stratigraphic and morphologic evidence are both allowed to participate in constraining the structure of phylogenetic hypotheses. These results suggest that arguments based on alleged “noisiness” of stratigraphic data offer inadequate grounds for ignoring stratigraphic order in phylogenetic analysis. In terms of congruence, stratigraphic and morphologic data perform about equally well.
Congruence between parsimony and stratigraphy: comparisons of three indices
Authors: Hitchin Rebecca , Benton Michael J.
Published: July 2016

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

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

Echinoderms show the best stratigraphic consistency of nodes, while continental tetrapods have the best matching of stratigraphic age and cladistic node order. Fishes have the worst match of age and clade ranks, but they do have the most complete fossil record as measured by the RCI. They are followed by echinoderms, and then continental tetrapods, which have the least complete record. This seems to show that life in an aquatic environment leads, in general, to a more complete fossil record.
Effects of hypothetical developmental barriers and abrupt environmental changes on adaptive walks in a computer-generated domain for early vascular land plants
Authors: Niklas Karl J.
Published: July 2016

Computer-generated searches through hypothetical fitness landscapes for progressively more fit variants were used to assess the effects of developmental barriers (mimicked by barring specific types of morphological transformations) and abruptly shifting environmental conditions (mimicked by sudden shifts in how fitness was defined) on the number and accessibility of optimal phenotypes. Relative fitness was defined in terms of maximizing light interception, mechanical stability, or reproductive success, or minimizing surface area, or optimizing the performance of various combinations of these tasks. Developmentally obstructed and unobstructed walks located, on average, equivalent numbers of phenotypic optima. The number of optima identified by both kinds of walks increased in proportion to the number of simultaneously performed tasks used to measure fitness. Walks passing from more complex to less complex fitness landscapes located more optima than walks passing through unchanging, stable landscapes. The model thus suggests that there are no a priori reasons to assume that (1) the morphological options available to adaptive evolution become more restrictive as biological complexity increases, (2) “developmental barriers” necessarily restrain a lineage from evolving well-adapted morphologies, and (3) generalist organisms are less successful than specialists. Also, because the number and accessibility of fitness peaks were proportional to the complexity of fitness landscapes, the model predicts that the probability of cladogenesis will increase as landscape complexity increases, while anagenesis will be encouraged when fitness is defined in terms of performing one or a few tasks simultaneously.
Major patterns of visual brain organization in teleosts and their relation to prehistoric events and the paleontological record
Authors: Wullimann Mario F.
Published: July 2016

A cladistic analysis of the three recognized patterns of central nervous visual organization among teleosts reveals that there is a pattern of intermediate complexity representing the plesiomorphic condition for teleosts, and that there is a simple visual pattern in two unrelated teleost groups which can be concluded to be a secondarily reduced derived condition, as well as an elaborate pattern which is present only in acanthomorph teleosts, thus likely representing a synapomorphy for this taxon. The elaborate central nervous visual pattern, therefore, is one of many functional-anatomical advanced features characterizing the acanthomorphs. Furthermore, when neontological and paleontological data is compared with the paleoecological record of early acanthomorph history during the Late Cretaceous, it is consistent with a hypothesis that this acanthomorph synapomorphic functional-anatomical complex arose likely in ctenothrissiforms as an adaptation to the life in the reorganizing reefs of that geologic period.
Patterns of morphologic diversification among the Rostroconchia
Authors: Wagner Peter J.
Published: July 2016

Morphologic diversification among rostroconch molluscs is explored using multiple phylogenies derived from different methods. In addition to strict parsimony, phylogenetic estimates were derived using four different methods that employ stratigraphic data. The resultant phylogenies are generally very similar to one another and to the phylogeny proposed by Pojeta and Runnegar (1976). All estimates (including the Pojeta and Runnegar estimate) imply much lower morphologic separations among post-Ordovician rostroconchs (measured here as the frequency of character state change per branch) than among Cambro-Ordovician rostroconchs. However, the data do not suggest that morphologic evolution became more constrained among rostroconchs as a whole, but instead suggest a reduced characteristic rate of morphologic change in the clade that happened to survive the end-Ordovician extinction. Likelihood ratio tests provide strongest support for the hypothesis that morphologic evolution was more constrained within a derived subclade (corresponding to previous definitions of the Conocardioidea, minus the Eopteriidae) than it was in a broad paraphylum (corresponding to the Ribeirioidea + Eopteriidae). Estimates from each of the phylogenetic methods lead to the same conclusions. Various metrics indicate that the pattern is not due to poor sampling of Cambro-Ordovician species and thus merits a biological explanation. Nonphylogenetic analyses of morphologic disparity suggest a similar history of morphologic evolution, including the apparent difference in characteristic rates of morphologic evolution between paraclade and subclade.
Confidence intervals on stratigraphic ranges with nonrandom distributions of fossil horizons
Authors: Marshall Charles R.
Published: July 2016

A generalized method for calculating confidence intervals on the position of the true end point of a stratigraphic range when the distributions of fossil horizons is nonrandom is presented. The method requires a quantitative measure of collecting and/or preservation biases with stratigraphic position. This fossil recovery potential function may be based on (among other variables) bedding-plane surface areas, or, given a water depth curve, an a priori estimate of the preservation potential with water depth. The approach assumes that the observed distribution of fossil horizons is consistent with the distribution predicted by the fossil recovery potential function, an assumption that must be tested before the method is applied. Unlike previous methods for calculating confidence intervals on the end points of stratigraphic ranges, this method may be applied when the number of fossil horizons is correlated with stratigraphic position. The approach should only be applied to sections that have been sampled continuously, or approximately continuously. Its efficacy will depend on how accurately fossil recovery potentials can be determined. A method is also presented for estimating the probability that a species became extinct during a major hiatus in the rock record.
Sampling, taxonomic description, and our evolving knowledge of morphological diversity
Authors: Foote Mike
Published: July 2016

Morphological analysis of four higher taxa of fossil marine invertebrates shows that, over the history of paleontology, there is no general tendency for morphologically extreme or modal species and genera to be described preferentially early or late. Reconstructing the expected evolutionary sequences of morphological disparity that would have been estimated at various times during the past century and a half reveals features that are sensitive to sampling (for example, peak trilobite disparity in the Ordovician, peak of post-Paleozoic crinoid disparity in the Triassic, and peak blastoid disparity in the Permian), as well as more robust features (for example, increase in trilobite disparity from the Cambrian to the Ordovician, continued increase in trilobite disparity despite a drop in taxonomic diversity after the Early Ordovician, decrease in blastoid disparity from the Devonian to the Carboniferous, and increase in crinoid disparity from the Jurassic to the Cretaceous followed by decline during the Cretaceous). Although we still have much to learn about the evolution of form, in many respects our view of the history of biological diversity is mature.