The reconstruction of the Tree of Life has been a primary goal in biology since Darwin coined the expression, the “great Tree of Life” in On the Origin of Species: “The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species…. As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications” (Darwin 1859: pp. 129–130). Ernst Haeckel was the first biologist who attempted to reconstruct the Darwinian Tree of Life. However, he could not reach his goal because his method of tree reconstruction was deeply anchored in the pre-Darwinian scala naturae (Dayrat 2003). A segment of the Darwinian Tree of Life is illustrated in the unique figure published in On the Origin of Species. This figure, which Darwin referred to as a “branching diagram,” represents ancestor-descendant relationships (ADR).

Consideration of the ways in which ontogenetic development may be modified to give morphological novelty provides a conceptual framework that can greatly assist in formulating and testing hypotheses of patterns and constraints in evolution. Previous attempts to identify distinct modes of ontogenetic modification have been inconsistent or ambiguous in definition, and incomprehensive in description of interspecific morphological differences. This has resulted in a situation whereby almost all morphological evolution is attributed to heterochrony, and the remainder is commonly either assigned to vague or potentially overly inclusive alternative classes, or overlooked altogether.

The present paper recognizes six distinct modes of ontogenetic change, each a unique modification to morphological development: (1) rate modification, (2) timing modification, (3) heterotopy, (4) heterotypy, (5) heterometry, and (6) allometric repatterning. Heterochrony, modeled in terms of shape /time /size ontogenetic parameters, relates to parallelism between ontogenetic and phylogenetic shape change and results from a rate or timing modification to the ancestral trajectory of ontogenetic shape change. Loss of a particular morphological feature may be described in terms of timing modification (extreme postdisplacement) or heterometry, depending on the temporal development of the feature in the ancestor. Testing hypotheses of the operation of each mode entails examining the morphological development of the ancestor and descendant by using trajectory-based studies of ontogenetically dynamic features and non-trajectory-based studies of ontogenetically static features.

The modes identified here unite cases based on commonalities of observed modification to the process of morphological development at the structural scale. They may be heterogeneous or partially overlapping with regard to changes to genetic and cellular processes guiding development, which therefore require separate treatment and terminology. Consideration of the modes outlined here will provide a balanced framework within which questions of evolutionary change and constraint within phylogenetic lineages can be addressed more meaningfully.

Mononykus olecranus, a theropod dinosaur from the Upper Cretaceous of Mongolia, exhibits reduced forelimbs with a single functional digit. These bizarre forelimbs have aroused great curiosity as to the behavior of the animal, but until now no functional study on the forelimbs of Mononykus has been undertaken. Here I show that the orientation and range of motion in the forelimb elements of Mononykus are such that the humeri sprawl laterally, the antebrachia are held subvertically, the palms face ventrally, and intramanual movement is restricted to subparasagittal motion. This is a radical departure from the typical theropod condition, in which the palms face medially and intramanual movement is transverse. The results of this study confirm that the forelimbs of Mononykus could not have been used to grasp prey or dig burrows, but were well suited for scratch-digging or hook-and-pull movements such as are used by extant anteaters and pangolins to open tough insect nests. Mononykus likely occupied a niche equivalent to that of an anteater or pangolin, an unusual niche for a dinosaur.

Flying birds flap their wings to generate aerodynamic forces large enough to overcome weight and drag. During this behavior, the forelimbs are displaced and deformed in a complex, coordinated sequence of movements collectively known as the “flight stroke.” Despite an influx of relevant fossil material and new functional insights from extant birds, the historical origin of the avian flight stroke remains poorly resolved. Potential behavioral precursors have been identified primarily on the basis of kinematic resemblance—similarity of movement irrespective of underlying mechanisms. We discuss fundamental issues of motion analysis that are frequently overlooked by paleontologists, and conclude that a purely kinematic approach is insufficient. Consideration of kinetics, the forces responsible for motion, offers a more complete picture of flight stroke evolution. We introduce six kinetic components that interact to determine a limb's trajectory. Phylogenetic mapping reveals that forelimb loading patterns have undergone at least two major transitions on the line from basal archosaur to modern bird. Using this kinematic and kinetic perspective, we offer four specific criteria to help constrain and evaluate competing scenarios for the origin of the avian flight stroke.

Fossil vertebrate distributions are typically based on body fossils, which are often poorly sampled at the margins of their true temporal and spatial ranges. Because vertebrate ichnofossils can be preserved in great abundance and in different environments than vertebrate body fossils, inclusion of ichnofossil data may improve sampled ranges. However, if ichnofossils are to serve as an independent source of distributional data, then their attribution to a body fossil group (i.e., trackmaker identification) cannot rely on temporal and spatial coincidence. Ichnofossils identified by synapomorphies can act as an independent source of distributional data that can modify spatial, temporal, and character distributions, which in turn may influence hypotheses of locomotor evolution.

In this paper I evaluate the spatial, temporal, and character distributions of early sauropod dinosaurs by using a combined ichnofossil and body fossil data set. Sauropod ichnofossils supplement the spatiotemporal distributions of early sauropods and provide important information on early sauropod foot posture that is rarely preserved or can only be inferred from body fossils. The presence of derived features in early-appearing ichnofossils challenges previous hypotheses of character transformation, implying either parallelism, reversal, or ghost lineages.

Stratocladistics can be used to resolve conflicting character and temporal distributions from body fossils and ichnofossils. Stratocladistic analysis of a combined ichnofossil and body fossil data set suggests a richer, more widely distributed diversity of early sauropods than currently recognized in body fossils and suggests that several locomotor characters originated much earlier than implied by body fossils.

Batches of freshly fallen Metasequoia glyptostroboides litter were subjected to one of 12 degradation regimes varying in temperature, pH, and oxygen availability for a three-month decay period. The regimes were intended to simulate possible conditions prevailing during the first winter following the autumnal leaf fall for the Metasequoia dominated forests of Axel Heiberg Island ca. 45 Ma. The decayed leaves were examined by transmission electron microscopy to quantify the extent and quality of chloroplast preservation. The best preservation of chloroplast membranes was observed at pH 8.5 and at 10°C, although it was found that rapidly freezing samples also reliably preserved ultrastructural chloroplast features with a high degree of fidelity to the living state. The results from this study suggest that the ambient water chemistry of the depositional environment in the Eocene floodplain forests of Axel Heiberg Island could have been basic, and maintained by a natural carbonate buffering system, but they also demonstrate that the preservation of chloroplast features can occur under varying environmental conditions.

Quantitative analysis of growth rings in pre-Quaternary fossil woods is commonly used as a paleoclimatic indicator. In this paper, a global analysis of the relationship between climate and growth ring parameters in modern trees is presented that, in part, invalidates the use of fossil woods in this way. Data reprocessed from the International Tree-Ring Data Bank are used to analyze three parameters, mean ring width, mean sensitivity, and percentage latewood, from 727 sites across a global climatic range. Results allow the complex relationship between climate and growth ring parameters to be quantified at the global scale for the first time. They reveal the enormous variability in tree response to climate-forcing, which is influenced by disparate factors such as taxonomy, ontogeny, ecology, and environment. Quantitative analysis of fossil growth ring data in light of the modern results indicates that even the largest and most detailed fossil studies conducted to date are probably inadequate in distinguishing a paleoclimate signal from the background noise of variability. The validity of using quantitative growth ring parameters as indicators of Pre-Quaternary climates is therefore questionable. Only in well-constrained studies where paleoclimatic, ontogenetic, and taxonomic sources of variability can be controlled, and data sets are very large, may fossil growth ring analysis provide useful paleoecological data. The findings of this paper do not invalidate in any way the use of growth rings in fossil woods as qualitative paleoclimatic indicators.

Previous studies have shown that secular variation in the Mg/Ca ratio of seawater throughout the Phanerozoic would have subjected the aragonite-producing codiacean algae to at least three transitions between the low-Mg calcite (molar Mg/Ca <2) and aragonite + high-Mg calcite (molar Mg/Ca >2) nucleation fields in the oceans, since their origin in the Ordovician. These studies have asserted that major sediment production by codiacean algae in Recent tropical seas is permitted by the Mg/Ca ratio of modern seawater (molar Mg/Ca ∼5.2) remaining within the aragonitic/high-Mg calcite nucleation field (molar Mg/Ca >2). Here I present the results of experiments conducted to determine the effects of ambient Mg/Ca on the mineralogy, growth rate, primary productivity, calcification rate, and biomechanics of the codiacean alga Penicillus capitatus.

P. capitatus specimens were grown in three artificial seawater treatments that mimic ancient seawater of differing Mg/Ca ratios, corresponding to the low-Mg calcite nucleation field (molar Mg/Ca ∼1.0), a “boundary field” (molar Mg/Ca ∼2.5), and the aragonite + high-Mg calcite nucleation field (molar Mg/Ca ∼5.2). Significantly, P. capitatus specimens maintained a mostly aragonitic mineralogy in all three seawater treatments. However, linear growth rates, primary productivity, calcification, and thallus stiffness decreased with reductions in ambient Mg/Ca. That P. capitatus precipitates approximately three-quarters of its CaCO3 as aragonite in the seawater treatment that favors the inorganic precipitation of low-Mg calcite suggests that the alga dictates the precipitation of that polymorph, either by pumping cations to create an internal aragonite nucleation field (molar Mg/Ca >2) or by employing organic templates that specify the nucleation of the aragonite polymorph (Borowitzka 1984). However, the alga's precipitation of one-quarter of its CaCO3 as low-Mg calcite suggests that its mineralogical control is limited and can be partially overridden by the Mg/Ca ratio of ambient seawater. The reduced calcification of P. capitatus specimens grown in the low-Mg calcite and boundary nucleation fields is probably due to the inherent difficulty of precipitating aragonite from seawater which does not naturally support its nucleation. The decreased rates of linear growth and primary production are probably caused by reductions in CO2 available for photosynthesis due to the reduction in calcification (Borowitzka and Larkum 1977). The observed decrease in thallus stiffness is probably due to the reductions in calcification and primary productivity observed in P. capitatus specimens grown in the low-Mg calcite and boundary nucleation fields.

The present study suggests that aragonitic algae would have been handicapped in oceans characterized by Mg/Ca ratios that did not support their inherent mineralogy. Producing aragonite in seawater outside of the aragonite + high-Mg calcite nucleation field would probably have reduced the competitiveness of these algae, made them more susceptible to predation, and reduced their contribution to carbonate sedimentation. These findings support earlier assertions that the dominant ecological and sedimentological roles of codiacean algae in Recent tropical seas is permitted by a Mg/Ca ratio of seawater that supports the algae's aragonitic mineralogy during this time.

The Mesozoic–Cenozoic transition is generally seen as a pivotal time in the evolution of benthic marine assemblages but the details of the timing and drivers of these changes are poorly known. The Atlantic and Gulf Coastal Plains of the United States contain assemblages preserved as original aragonitic and calcitic material in unconsolidated sediments. This makes coastal plain assemblages ideally suited to paleoecological analyses. Data derived from bulk samples of the Coffee Formation (lower/middle Campanian: Mississippi) as well as published faunal lists from comparable samples of the Severn (Maastrichtian: Maryland), Providence (Maastrichtian: Georgia and Alabama), Stone City (Eocene: Texas), and Gosport (Eocene: Alabama) Formations are used to assess changes in taxonomic diversity and ecomorphological group (life habit and trophic group) composition through this time interval.

These analyses find a significant decrease in rarefied-sample species richness from the Campanian through the Eocene, but no change in evenness. With the notable exception of the Stone City Formation, increases in carnivore (neogastropod) richness and abundance occur before the Campanian. Epifaunal suspension-feeding species are a smaller proportion of the sample richness in Eocene samples than in Cretaceous samples. Decreased relative epifaunal suspension-feeder biomass but unchanged relative numbers of epifaunal suspension-feeder individuals suggests a relative decrease in epifaunal suspension-feeder size. Infaunal suspension feeders increase in richness and abundance through the interval. The proportion of drilled bivalves and gastropods does not change through the interval. Changes found in the structure of local shallow-shelf benthic assemblages from the Campanian through the Eocene are generally small relative to the variability between samples. Formation-level variation between assemblages is high relative to the magnitude of the temporal signal, emphasizing the need for investigators to include multiple formations per interval in tests of temporal trends.

Relative abundance data are of primary importance in paleoecology, but it is not always obvious how they should be interpreted. Because relative abundance is expressed as a proportion of the total sample, change in the abundance of one group necessarily changes the relative abundance of all groups in the sample. There are two possible interpretations for a trend in the relative abundance of a taxon: an “active” scenario in which the trend reflects change in the population density of the group itself, or a “passive” scenario in which the change is driven by population changes in other taxa. To discriminate between these scenarios it is necessary to collect absolute abundance data (abundance expressed as a function of sample area or volume).

We examine both absolute and relative abundance trends through a major paleoecological transition: the shift from trilobite-dominated to brachiopod-dominated paleocommunities in shallow marine carbonates spanning the Lower/Middle Ordovician boundary in western Utah and eastern Nevada. We sampled 61 carbonate mudstone and wackestone beds from the upper Ibex Series (Lower Ordovician) and lower Whiterock Series (Middle Ordovician) at three sections that span the boundary. All samples come from the shallow subtidal Bathyurid trilobite biofacies. Samples were broken into small pieces, and all skeletal fragments >2 mm were identified to the finest possible taxonomic level. Consistent with previous work on this interval, the relative abundance of trilobites declines sharply across the boundary, while the relative abundance of brachiopods increases. Absolute abundance data indicate that the decline in trilobite abundance is genuine and not an artifact of normalization. The trend is not easily explained by sampling bias, facies distribution, taphonomic regime, or sedimentation style.

The dramatic shift in abundance contrasts with relatively minor changes in relative genus richness across the boundary. This is partly ascribable to differences in the relative abundance structure of trilobite faunas. Though comparable numbers of trilobite and brachiopod genera occur above and below the boundary, the trilobite fauna from the upper Ibex Series has lower evenness then the lower Whiterock Series fauna. Hence sampled trilobite richness is high in the lower Whiterock despite the small number of specimens. This highlights the importance of collecting abundance data. Although these data suggest that in at least some cases richness and abundance patterns are not closely coupled, more robust richness data are necessary to confirm this conclusion.

All interpretable trace fossils from the Ediacarian–Cambrian transition strata of northern Siberia, Ukraine, and elsewhere represent shelters of infaunal animals feeding from the sediment surface. There is a gradation of forms ranging from (1) makers of horizontal galleries in soft sand with bilobed lower surface and proboscis extended to the surface, through (2) linear or zigzag series of short, widely U-shaped burrows in firm clay with bilobed or three-lobed lower surface, to (3) series of cylindrical chambers dug completely inside the sediment but opening to its surface. At the same time, protective skeleton originated in animals living above the sediment surface. Apparently, the diversification of predators in the earliest Cambrian forced other animals to invest energy either in digging or in a protective armor (“the Verdun Syndrome”). True mud-eaters appeared later, as documented by the late Tommotian horizontal spreite structures from central Siberia. Most, if not all, of those infaunal traces of activity were produced probably by relatives of priapulid worms. It appears that body cavities and segmentation in the Metazoa (diverse already in the Ediacarian) evolved independently of, and prior to, hydraulic burrowing.

The emergence of shell forms in the growth of foraminifera is an essential problem in the morphogenesis of these microorganisms. We present a model of foraminiferal shells that applies a moving-reference system. Previous models have referred to fixed-reference axes and have neglected apertures. Our model focuses on real morphologic characteristics and follows stepwise natural biological processes. It introduces apertures based on minimization of the local communication path and applies three parameters, which are either predetermined or selected at random from given ranges. Expression of stochastic parameters mimics phenotypic variability of a shell. We also present a detailed description of the method with examples of simulated shells and the first step toward analyses of the theoretical morphospace. The morphospace is divided into certain regions (phases) separated by transitional planes (phase transitions). Further prospects for foraminiferal modeling, which should focus on more in-depth models based on realistic intracellular dynamics, are also presented.

Much of what is known about the long-term history of biodiversity and rates of taxonomic evolution in the fossil record derives from literature-based compilations of fossil stratigraphic ranges. It has been suggested that taxonomic and stratigraphic errors in these compilations are randomly distributed and, therefore, introduce no significant bias to macroevolutionary patterns. Here we compare a new, comprehensive global database of Ordovician and Early Silurian crinoids to Sepkoski's global genus compendium.

Approximately 44% of the crinoid genera resolved to substage in Sepkoski's compendium are taxonomically inaccurate (i.e., invalid, nomina dubia, or column genera) or have incorrect first and/or last occurrences. Errors in Sepkoski's compendium result from incomplete coverage of existing taxonomic work and incorrect stratigraphic correlations that, in some cases, are propagated throughout the taxonomic literature. Stratigraphic range errors are nonrandomly distributed among substages in Sepkoski's compendium. The result is underestimated richness in the Early Silurian and significantly overestimated rates of extinction in the Late Ordovician. There is no similar bias in Sepkoski's substage origination rates for crinoids.

At the stage-level of temporal resolution, Sepkoski's crinoid data are more accurate. In this case, only 32% of the compendium's crinoid genera contain some stratigraphic or taxonomic inaccuracy. However, errors still result in incorrect macroevolutionary patterns, particularly with respect to rate of origination in the Ashgill, which is significantly underestimated in Sepkoski's compendium. Genera described since the completion of Sepkoski's compendium have had relatively little effect on estimated rates of evolution at both stage and substage resolution.

These results suggest that macroevolutionary patterns among some taxa in Sepkoski's compilation may be significantly influenced by nonrandomly distributed taxonomic inaccuracies and stratigraphic range errors. In the case of the apparent end-Ordovician mass extinction among crinoids, the revised history reveals a dramatically reduced role for extinction at the substage-level of temporal resolution. At the stage level, Sepkoski's original compilation strongly exaggerates the excess of extinction over origination in the Ashgill. Although biases inherent in the stratigraphic record remain unaccounted for, removing taxonomic and stratigraphic errors in Sepkoski's compendium substantially changes our understanding of the nature of large-scale biotic change for an important Paleozoic taxon during the end-Ordovician.