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).

Evolutionary trends seemingly abound throughout the history of life. Perhaps the best-known example is Cope's rule, the tendency for lineages to increase in size over time. Other examples include hypothesized trends toward increasing complexity and fitness. What kinds of mechanisms cause such large-scale trends—trends occurring in higher taxa over geological time spans—and how can we effectively visualize them?

The classification of fossils has long been controversial. Should traditional taxonomic concepts be expanded to encompass plesiomorphic extinct relatives that exhibit subsets of essential defining characters in so many shades of gray? Should rank taxa, established on extant taxa alone, and in a pre-Darwinian, pre-Hennigian framework, remain restricted to their living constituents and integral extinct relatives? Or should these taxonomic concepts be restricted to a membership exhibiting a defining suite of essential characters, regardless of whether they are extant or extinct?

For most people, the destruction of books has universally come to be thought of as a symbol of barbarity (e.g., Eco 1983). The burning of the library in Louvain, Belgium, by the German army in 1914 was, for example, seen around the world not only as an act of terror but also as an act against posterity (Tuchman 1962). Nazi book-burning is a virtual icon of anti-intellectualism and social malignancy (Rose 2001). The 1992 destruction of the main library in Sarajevo, the Vijecnica, during the Balkan war (which took place 78 years to the day after the destruction of the library in Louvain) was seen by many as one of that conflict's most tragic incidents (see Riedlmayer 1996; Zeco 1996; Basbanes 2003). Even if we justifiably bemoan the anti-intellectualism of much of modern society, Western culture at its best cherishes books and libraries as symbols of civilization, humanity, and intellectual freedom.

The pattern of variation in taxonomic turnover on short timescales is expected to leave detectable signals even when taxonomic data are compiled at coarser timescales. Global, stage-level data on first and last appearances of marine animal genera are analyzed to determine whether it is more likely that origination and extinction were spread throughout stages or that they were concentrated at a single episode per stage. The analysis takes incomplete and variable sampling of stratigraphic ranges into consideration, and it takes advantage of the fact that empirical sampling rates are within the range of values that allow the within-stage turnover models to be distinguished on the basis of stage-level data. The data strongly support the model of a single extinction pulse per stage over the alternative of continuous extinction within the stage. Pulsed origination is also supported over continuous origination, but the case is not as compelling as for extinction. Differential support for pulsed turnover is not confined to a few stages. Pulsed turnover therefore appears to be a general feature of the evolution of marine animals.

The application of molecular genetics, in particular comparative genomics, to the field of evolutionary biology is paving the way to an enhanced “New Synthesis.” Apart from their power to establish and refine phylogenies, understanding such genomic processes as the dynamics of change in genomes, even in hypothetical RNA-based genomes and the in vitro evolution of RNA molecules, helps to clarify evolutionary principles that are otherwise hidden among the nested hierarchies of evolutionary units. To this end, I outline the course of hereditary material and examine several issues including disparity, causation, or bookkeeping of genes, adaptation, and exaptation, as well as evolutionary contingency at the genomic level–issues at the heart of some of Stephen Jay Gould's intellectual battlegrounds. Interestingly, where relevant, the genomic perspective is consistent with Gould's agenda. Extensive documentation makes it particularly clear that exaptation plays a role in evolutionary processes that is at least as significant as–and perhaps more significant than–that played by adaptation.

The late Albian (Early Cretaceous) lineage of Actinoceramus sulcatus (Parkinson 1819) is a remarkable example of macro- and microevolution within the Bivalvia. Immediately following cladogenesis from ancestral A. concentricus, the lineage displays a conspicuous, short-term excursion through morphospace followed by a return to the ancestral form. This excursion is marked by the acquisition, and subsequent loss, of large radial folds affecting some part or all of the shell. The pattern is noteworthy because of the gross scale and rate of morphological evolution, the relatively short life span of an “extreme” morphology, an apparent evolutionary reversal, the presence of phenotypic clines through time, the extent of phenotypic variation within populations and abundance of morphological intermediates between disparate end-member types, the wide geographic distributions of phenotypic clines and variants, and the subtle asymmetry of morphological transitions bounding the evolutionary excursion.

From census and biometric analyses of stratigraphically constrained samples, we conclude that morphological change was not focused at speciation and the pattern of evolution does not conform to the classical paradigm of punctuated equilibrium. Instead, we infer that observed patterns are best explained by phyletic evolution, at widely varying rates, combined with ecophenotypic plasticity. Evolution targeted the potential to form radial folds; the expression of those in any individual was determined, in part at least, by environmental cues. Ecophenotypic plasticity in A. sulcatus was itself probably an evolutionary response favored by the presence of long-lived planktotrophic larvae and wide dispersal of the species. In A. sulcatus, there is a continuum of pattern between intrapopulational, ecophenotypic variation that can be observed on bedding planes, interregional variation, and phyletic change through time. We argue that this continuity of pattern is most easily explained by continuity of process: in the case of the visually striking radial folds in A. sulcatus, there is no reason to invoke distinct hierarchies of macro- and microevolution; instead, these seem to be parts of a continuum.

Although there is extraordinary interest in the quantitative measurement of species diversity, published statements on the behavior of the components of species diversity are contradictory and lead to opposite conclusions. In this paper, we demonstrate that the confusion is due to two key oversights: (1) whether or not biological sampling is carried out within or between communities; and (2) determination of the statistical distribution underlying a biological community, which is crucial for the evaluation of all of the components of diversity measurement.

The problem of sampling “within” a population or community is basically distinct from the equivalent integration of structure and diversity measurement “between” differing multispecies populations. “Within-community sampling” is defined as a set of biological samples from a statistical population that has a particular statistical distribution or a constant value for the associated parameter(s). As the number of individuals increases along with the number of species, for a log series distribution, the diversity measures of Shannon's H, log series or Fisher's α, and Simpson's Index 1/λ remain constant while the evenness measures of Buzas-Gibson's E and Pielou's J decrease. For a log-normal distribution, J will remain constant while E decreases and α, 1/λ, and H increase. No single measure of evenness remains constant over all statistical distributions, so if constancy as a type of independence is required, the appropriate distribution must first be determined. Each species ensemble is mathematically fixed by the applicable statistical distribution.

In contrast, “between-community sampling” is defined as a set of biological samples from different statistical distributions and/or the same distribution with differing parametric values. If sampling is between communities and S increases while the number of individuals remains constant, then all the other measures considered here increase. The exception is the broken stick, for which E remains constant while H, J, α, and 1/λ increase.

Herein we propose and justify the use of the log-series distribution (with regression on the information decomposition equation) as a null model for determination of community structure and demonstrate that the community structure of a Miocene bed at Calvert Cliffs, Maryland, is a log series by use of this new unified methodology.

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.

The concept of heterochrony has long had a central place in evolutionary theory. During their long history, heterochrony and several associated concepts such as paedomorphosis and neoteny have often been contentious and they continue to be criticized. Despite these criticisms, we review many examples showing that heterochrony and its associated concepts are increasingly cited and used in many areas of evolutionary study. Furthermore, major strides are being made in our understanding of the underlying genetic and developmental mechanisms of heterochrony, and in the methods used to describe heterochronic changes. A general theme of this accumulating research is that some of the simplistic notions of heterochrony, such as terminal addition, simple rate genes, and “pure” heterochronic categories are invalid. However, this research also shows that a more sophisticated view of the hierarchical nature of heterochrony provides many useful insights and improves our understanding of how ontogenetic changes are translated into phylogenetic changes.

Mass extinctions can play a role in shaping macroevolutionary trends through time, but the contribution of recoveries to this process has yet to be examined in detail. This study focuses on the effects of three extinction events, the end-Cretaceous (K/T), mid-Eocene (mid-E), and end-Eocene (E/O), on long-term patterns of body size in veneroid bivalves. Systematic data were collected for 719 species and 140 subgenera of veneroids from the Late Cretaceous through Oligocene of North America and Europe. Centroid size measures were calculated for 101 subgenera and global stratigraphic ranges were used to assess extinction selectivity and preferential recovery. Veneroids underwent a substantial extinction at the K/T boundary, although diversity recovered to pre-extinction levels by the early Eocene. The mid-E and E/O events were considerably smaller and their recovery intervals much shorter. None of these events were characterized by significant extinction selectivity according to body size at the subgenus level; however, all three recoveries were strongly size biased. The K/T recovery was biased toward smaller veneroids, whereas both the mid-E and E/O recoveries were biased toward larger ones. The decrease in veneroid size across the K/T recovery actually reinforced a Late Cretaceous trend toward smaller sizes, whereas the increase in size resulting from the Eocene recoveries was relatively short-lived. Early Cenozoic changes in predation, temperature, and/or productivity may explain these shifts.

Sutural perimeters of 301 Late Jurassic ammonites scale as the 3/8 power of phragmocone volume. This implies that septal surface grows as the ¾ power of body mass, the exponent of Kleiber's law (1932), one of the best-established empirical laws in biology, which is well known to be the scaling exponent of basal metabolic rate. Sutural complexity, as measured by fractal dimensions, emerges from the relationship between sutural perimeter and phragmocone volume, thus supporting the interpretations of septal folding as a mechanism for the increase in septal surface and as demanded by metabolic and physiologic processes (e.g., respiration or body chamber transport). The implications of these results strongly suggest that ammonite septa were involved in more than a simple structural support.

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.

The traditional “taxon counting” method of estimating ancient biodiversity is open to many criticisms, not least of which are the problem of inconsistency in the preservation of fossil organisms and the associated error on first and last appearance times of taxa. Construction of phylogenetic trees provides a way of correcting the first appearance of a taxon based on the origination time of its sister group. Workers have suggested that biodiversity studies include such phylogenetically implied range extensions. Potential problems with this method, in particular the bias inherent in altering origination—but not extinction—times, and the potential for incorrect addition of ghost ranges if the ancestor of a taxon is defined as its sister, are investigated by using a new computer simulation. The program creates a phylogeny, samples it and then adds ghost lineages, with diversity counts being made at all three stages. Results show that under certain conditions, such as in the case of a taxonomic group with many extant representatives, the phylogenetic method is superior to the taxic at capturing diversity pattern. However, there are also important conditions where the taxic approach provides an equal or superior estimate of diversity, such as if the group is extinct or has few extant lineages. Use of the phylogenetic method has the effect of magnifying the Signor-Lipps sampling effect seen before mass extinction events, and if ancestral species within a phylogeny are misdiagnosed as the sister species of their descendants, the phylogenetic method also consistently overestimates diversity magnitudes.

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.

Of all sessile filtrators, only some species of acorn barnacles managed to permanently settle on whales. Their key exaptation was probably a kind of biochemical cleaning process, which could be modified to penetrate into the host's dead cutis. Anchorage was further increased by coring prongs out of the whale skin (Coronula) or by transforming the wall into a cylindrical tube that added new rings at the base, while old ones flaked off at the surface in tandem with skin shedding (Tubicinella). Xenobalanus even everted its naked body into a stalked structure and reduced the wall plates to a minute, but highly efficient, anchor. Cryptolepas combines the strategies of Tubicinella and Coronula, but with a different structure of the radial folds. Because of a shared exaptational inventory, it is impossible to unravel phylogenetic relationships within the Coronulida from skeletal morphology alone.

Kelps and other fleshy macroalgae—dominant reef-inhabiting organisms in cool seas—may have radiated extensively following late Cenozoic polar cooling, thus triggering a chain of evolutionary change in the trophic ecology of nearshore temperate ecosystems. We explore this hypothesis through an analysis of body size in the abalones (Gastropoda; Haliotidae), a widely distributed group in modern oceans that displays a broad range of body sizes and contains fossil representatives from the late Cretaceous (60–75 Ma). Geographic analysis of maximum shell length in living abalones showed that small-bodied species, while most common in the Tropics, have a cosmopolitan distribution, whereas large-bodied species occur exclusively in cold-water ecosystems dominated by kelps and other macroalgae. The phylogeography of body size evolution in extant abalones was assessed by constructing a molecular phylogeny in a mix of large and small species obtained from different regions of the world. This analysis demonstrates that small body size is the plesiomorphic state and largeness has likely arisen at least twice. Finally, we compiled data on shell length from the fossil record to determine how (slowly or suddenly) and when large body size arose in the abalones. These data indicate that large body size appears suddenly at the Miocene/Pliocene boundary. Our findings support the view that fleshy-algal dominated ecosystems radiated rapidly in the coastal oceans with the onset of the most recent glacial age. We conclude with a discussion of the broader implications of this change.

Clymeniid ammonoids appeared during the Late Devonian (Mid-Famennian) and quickly radiated before becoming extinct at the Devonian/Carboniferous boundary. Outwardly indistinguishable from other ammonoids, clymeniids are distinguished internally by their dorsal siphuncle, contrasted to a ventral siphuncle in almost all other ammonoids. Comparisons of a sample of Clymeniida (n = 22 genera), Goniatitida (n = 33), Prolecanitida (n = 12), and Anarcestida (n = 13) indicate that clymeniids fall within the range of other ammonoids in terms of shell geometry and suture complexity, but their siphuncles average two to three times larger and clymeniid shells are approximately 33% thicker than those of other ammonoids. Although a dorsal siphuncle would be about 50% smaller in surface area and volume than if located in a ventral position, the enlarged clymeniid siphuncle partially and, in some cases, fully compensated for this loss. Hydrostatic simulations of 15 clymeniid genera indicate that their thicker (therefore heavier) shells would have resulted in relatively short body chambers (≈280°) and high aperture orientations (≈90°). In static life-position, these orientations would have placed the dorsal clymeniid siphuncle at or near the bottom of the most recently formed chambers, seemingly an ideal location for draining liquid from the chamber. Migration of the siphuncle to the dorsal side of the shell occurs suddenly during early ontogeny (within the first two or three chambers), and mutation of homeotic gene expression is offered as a possible explanation for the sudden shift. A dorsal siphuncle may have resulted in selection for enlarged siphuncles, but this may have incurred loss of strength against hydrostatic pressure (thereby reducing depth limits) and thus rendered the clade more susceptible to the multiple eustatic and anoxic events that marked the end of the Devonian.

The evolutionary history of a clade has traditionally been studied through phylogenetics, and taxonomic diversity has been used as a crude proxy for morphological diversity. However, morphological diversification—beyond counting taxa—can provide a very different view of a clade's evolutionary history and allows the investigation of patterns and timing of morphological evolution.

In this paper I use dentition to document the pattern of morphological and taxonomic diversification of Carnivoramorpha and mammalian meat eaters in North America. Using the dentition permits ecological inferences to be made, because teeth and diet are closely related. I present a method developed to describe the entire dentition of the Carnivoramorpha and other mammalian meat eaters (Creodonta). Morphological diversification is measured by dental disparity, using the mean pairwise dissimilarity among species.

I test the following hypotheses: (1) Morphological diversification was suppressed relative to taxonomic diversification, early in the evolutionary history of Carnivoramorpha; and (2) once an efficient system for consuming meat evolved, the dental system remained relatively unchanged.

The first hypothesis is rejected. Taxonomic and morphological diversity increase together through the clade's early evolution. There is no evidence of a morphological release in the carnivoramorphans with the demise of creodonts. The second hypothesis is supported. The ecological group “mammalian meat eaters” rapidly diversified morphologically and reached its maximum disparity early in its history, after which the dental system remained relatively unchanged.