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 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.

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.

One of the enduring puzzles to Stephen Jay Gould about life on Earth was the cause or causes of the fantastic diversity of animals that exploded in the fossil record starting around 530 Ma–the Cambrian explosion. In this contribution, we first review recent phylogenetic and molecular clock studies that estimate dates for high-level metazoan diversifications, in particular the origin of the major lineages of the bilaterally-symmetrical animals (Bilateria) including cnidarians. We next review possible “internal” triggers for the Cambrian explosion, and argue that pattern formation, those processes that delay the specification of cells and thereby allow for growth, was one major innovation that allowed for the evolution of distinct macroscopic body plans by the end of the Precambrian. Of potential “external” triggers there is no lack of candidates, including snowball earth episodes and a general increase in the oxygenation state of the world's oceans; the former could affect animal evolution by a mass extinction followed by ecological recovery, whereas the latter could affect the evolution of benthic animals through the transfer of reduced carbon from the pelagos to the benthos via fecal pellets. We argue that the most likely cause of the Cambrian explosion was the evolution of macrophagy, which resulted in the evolution of larger body sizes and eventually skeletons in response to increased benthic predation pressures. Benthic predation pressures also resulted in the evolution of mesozooplankton, which irrevocably linked the pelagos with the benthos, effectively establishing the Phanerozoic ocean. Hence, we suggest that the Cambrian explosion was the inevitable outcome of the evolution of macrophagy near the end of the Marinoan glacial interval.

Although Darwin was not the first to conceive directional selection as a mechanism of phenotypic change, it is his ideas that were received, and that have shaped population biology to this day. A significant change in his theoretical orientation occurred in the mid-1850s. About then he abandoned environmental selection in favor of competitive selection, and adopted relative adaptation with all its consequences as an alternative. These ideas changed his thinking fundamentally and shaped his argument throughout the writing of his great book. It is still these ideas that predominate today.

Here I examine Darwin's ideas in relation to his principle of divergence, sexual selection, and the nature and origin of species. Finally I suggest that had he not misunderstood the function of sexual communication he might well have understood the nature of species and provided a more penetrating resolution to Herschell's “mystery of mysteries,” with which he opened his book.

Improvements in our understanding of green plant phylogeny are casting new light on the connection between character evolution and diversification. The repeated discovery of paraphyly has helped disentangle what once appeared to be phylogenetically coincident character changes, but this has also highlighted the existence of sequences of character change, no one element of which can cleanly be identified as the “key innovation” responsible for shifting diversification rate. In effect, the cause becomes distributed across a nested series of nodes in the tree. Many of the most conspicuous plant “innovations” (such as macrophyllous leaves) are underlain by earlier, more subtle shifts in development (such as overtopping growth), which appear to have enabled the exploration of a greater range of morphological designs. Often it appears that these underlying changes have been brought about at the level of cell interactions within meristems, highlighting the need for developmental models and experiments focused at this level. The standard practice of attempting to identify correlations between recurrent character change (such as the tree growth habit) and clade diversity is complicated by the observation that the “same” trait may be constructed quite differently in different lineages (e.g., different forms of cambial activity), with some solutions imposing more architectural limitations than others. These thoughts highlight the need for a more nuanced view, which has implications for comparative methods. They also bear on issues central to Stephen Jay Gould's vision of macroevolution, including exaptation and evolutionary recurrence in relation to constraint and the repeatability of evolution.

Gould's Wonderful Life (1989) was a landmark in the investigation of the Cambrian radiation. Gould argued that a number of experimental body plans (“problematica”) had evolved only to become extinct, and that the Cambrian was a time of special fecundity in animal design. He focused attention on the meaning and significance of morphological disparity versus diversity, and provoked attempts to quantify disparity as an evolutionary metric. He used the Burgess Shale as a springboard to emphasize the important role of contingency in evolution, an idea that he reiterated for the next 13 years. These ideas set the agenda for much subsequent research. Since 1989 cladistic analyses have accommodated most of the problematic Cambrian taxa as stem groups of living taxa. Morphological disparity has been shown to be similar in Cambrian times as now. Konservat-Lagerstätten other than the Burgess Shale have yielded important new discoveries, particularly of arthropods and chordates, which have extended the range of recognized major clades still further back in time. The objective definition of a phylum remains controversial and may be impossible: it can be defined in terms of crown or total group, but the former reveals little about the Cambrian radiation. Divergence times of the major groups remain to be resolved, although molecular and fossil dates are coming closer. Although “superphyla” may have diverged deep in the Proterozoic, “explosive” evolution of these clades near the base of the Cambrian remains a possibility. The fossil record remains a critical source of data on the early evolution of multicellular organisms.

Stephen Jay Gould made impressive contributions to macroevolutionary theory; one of the topics in this area that particularly interested him was how to define and recognize species selection. Here we explore how and why Gould's ideas on concepts related to species selection evolved over 30 years, from the punctuated equilibria paper of 1972 to his “Structure of Evolutionary Theory” magnum opus published in 2002. Throughout his career his ideas on species selection shifted between three phases. Initially, Gould favored a definition of species selection that was more descriptive. Later, he came to distinguish between species sorting, which he called species selection in the broad sense, and true species selection, which is tied to the concept of species-level aptations. Finally, he came to view species selection in a broader, more inclusive way, effectively merging the two earlier viewpoints. His ideas on species selection changed over the years because he was trying to square his views on complex concepts like adaptation, natural selection, emergence, and the independence of macroevolutionary theory. Gould's thoughts on species selection not only help to define the history of debate on the concept but also help set a course for the future.

Neutral theory in ecology is based on the symmetry assumption that ecologically similar species in a community can be treated as demographically equivalent on a per capita basis—equivalent in birth and death rates, in rates of dispersal, and even in the probability of speciating. Although only a first approximation, the symmetry assumption allows the development of a quantitative neutral theory of relative species abundance and dynamic null hypotheses for the assembly of communities in ecological time and for phylogeny and phylogeography in evolutionary time. Although Steve Gould was not a neutralist, he made use of ideas of symmetry and of null models in his science, both of which are fundamental to neutral theory in ecology. Here I give a brief overview of the current status of neural theory in ecology and phylogeny and, where relevant, connect these newer ideas to Gould's work. In particular, I focus on modes of speciation under neutrality, particularly peripheral isolate speciation, and their implications for relative species abundance and species life spans. Gould was one of the pioneers in the study of neutral models of phylogeny, but the modern theory suggests that at least some of the conclusions from these early neutral models were premature. Modern neutral theory is a remarkably rich source of new ideas to test in ecology and paleobiology, the potential of which has only begun to be realized.

The fossil record displays remarkable stasis in many species over long time periods, yet studies of extant populations often reveal rapid phenotypic evolution and genetic differentiation among populations. Recent advances in our understanding of the fossil record and in population genetics and evolutionary ecology point to the complex geographic structure of species being fundamental to resolution of how taxa can commonly exhibit both short-term evolutionary dynamics and long-term stasis.

A simple principle predicts a tendency, or vector, toward increasing organismal complexity in the history of life: As the parts of an organism accumulate variations in evolution, they should tend to become more different from each other. In other words, the variance among the parts, or what I call the “internal variance” of the organism, will tend to increase spontaneously. Internal variance is complexity, I argue, albeit complexity in a purely structural sense, divorced from any notion of function. If the principle is correct, this tendency should exist in all lineages, and the resulting trend (if there is one) will be driven, or more precisely, driven by constraint (as opposed to selection). The existence of a trend is uncertain, because the internal-variance principle predicts only that the range of options offered up to selection will be increasingly complex, on average. And it is unclear whether selection will enhance this vector, act neutrally, or oppose it, perhaps negating it. The vector might also be negated if variations producing certain kinds of developmental truncations are especially common in evolution.

Constraint-driven trends—or what I call large-scale trends of the fourth kind—have been in bad odor in evolutionary studies since the Modern Synthesis. Indeed, one such trend, orthogenesis, is famous for having been discredited. In Stephen Jay Gould's last book, The Structure of Evolutionary Thought, he tried to rehabilitate this category (although not orthogenesis), showing how constraint-driven trends could be produced by processes well within the mainstream of contemporary evolutionary theory. The internal-variance principle contributes to Gould's project by adding another candidate trend to this category.

The thoughts and writings of Stephen Jay Gould have had an enormous impact on the shaping of macroevolutionary theory. The notion of punctuated equilibria (Eldredge and Gould 1972) remained prominent throughout his work. It also unleashed a storm of debate in paleontology and evolutionary theory. A second theme that recurs throughout Gould's opus is heterochrony (evolution by changes in the rates and timing of ontogenetic events, sensu Gould 1977a). His analyses of these two subjects have inspired many of us to explore further and add to them. My contribution discusses their expansion to encompass large numbers of lineages through long time, and the relationship of punctuated equilibria and heterochrony to physical environmental change, and to each other.

We outline a plausible evolutionary sequence that led from prokaryotes to the origin of the first nucleated cell. The nucleus is postulated to evolve after the archaebacterium and eubacterium merged to form the symbiotic ancestor of amitochondriate protists. Descendants of these amitochondriate cells (archaeprotists) today thrive in organic-rich anoxic habitats where they are amenable to study. Eukaryosis, the origin of nucleated cells, occurred by the middle Proterozoic Eon prior to the deposition in sediments of well-preserved microfossils such as Vandalosphaeridium and the spiny spheres in the Doushantou cherts of China.

Mass extinctions are important to macroevolution not only because they involve a sharp increase in extinction intensity over “background” levels, but also because they bring a change in extinction selectivity, and these quantitative and qualitative shifts set the stage for evolutionary recoveries. The set of extinction intensities for all stratigraphic stages appears to fall into a single right-skewed distribution, but this apparent continuity may derive from failure to factor out the well-known secular trend in background extinction: high early Paleozoic rates fill in the gap between later background extinction and the major mass extinctions. In any case, the failure of many organism-, species-, and clade-level traits to predict survivorship during mass extinctions is a more important challenge to the extrapolationist premise that all macroevolutionary processes are simply smooth extensions of microevolution. Although a variety of factors have been found to correlate with taxon survivorship for particular extinction events, the most pervasive effect involves geographic range at the clade level, an emergent property independent of the range sizes of constituent species. Such differential extinction would impose “nonconstructive selectivity,” in which survivorship is unrelated to many organismic traits but is not strictly random. It also implies that correlations among taxon attributes may obscure causation, and even the focal level of selection, in the survival of a trait or clade, for example when widespread taxa within a major group tend to have particular body sizes, trophic habits, or metabolic rates. Survivorship patterns will also be sensitive to the inexact correlations of taxonomic, morphological, and functional diversity, to phylogenetically nonrandom extinction, and to the topology of evolutionary trees. Evolutionary recoveries may be as important as the extinction events themselves in shaping the long-term trajectories of individual clades and permitting once-marginal groups to diversify, but we know little about sorting processes during recovery intervals. However, both empirical extrapolationism (where outcomes can be predicted from observation of pre- or post-extinction patterns) and theoretical extrapolationism (where mechanisms reside exclusively at the level of organisms within populations) evidently fail during mass extinctions and their evolutionary aftermath. This does not mean that conventional natural selection was inoperative during mass extinctions, but that many features that promoted survivorship during background times were superseded as predictive factors by higher-level attributes. Many intriguing issues remain, including the generality of survivorship rules across extinction events; the potential for gradational changes in selectivity patterns with extinction intensity or the volatility of target clades; the heritability of clade-level traits; the macroevolutionary consequences of the inexact correlations between taxonomic, morphological, and functional diversity; the factors governing the dynamics and outcome of recoveries; and the spatial fabric of extinctions and recoveries. The detection of general survivorship rules—including the disappearance of many patterns evident during background times—demonstrates that studies of mass extinctions and recovery can contribute substantially to evolutionary theory.