The reconstruction of phylogenies using cladistic methods is a powerful and well-established tool for evolutionary biologists and paleobiologists. Indeed, the construction of rigorous phylogenetic hypotheses has become widely accepted as an essential first step in the analysis of historical patterns for both extant and extinct organisms. In the past few years, there has arisen a healthy and constructive debate as to the exact methods that will lead to the most accurate tree (for example whether statistical inference or stratigraphic information has any part to play in phylogenetic reconstruction). Although important, this debate has tended to focus on the problems of tree construction and divert attention away from the applications of tree-based research. The construction of a phylogeny is, after all, only a first step, and phylogenetic trees provide the starting point from which to address a wide range of interesting biological and geological topics.

One of the most extensively studied aspects of phylogenetic tree shape is balance, which is the extent to which nodes divide a tree into clades of equal size. Several authors have stressed the importance of tree balance for understanding patterns of evolution. It has been remarked that paleontological studies commonly produce very unbalanced trees (also called pectinate cladograms or “Hennigian combs”). This claim is tested here by comparing the balance of 50 paleontological trees and 50 neontological trees, all taken from the recent literature. Each tree was reanalyzed from the published data matrix to ensure its accuracy. The results confirm that paleontological trees tend to be more imbalanced than neontological trees.

That paleontological trees are more imbalanced has been represented as a shortcoming of fossil data sets, but here it is argued that this is the expected result. Even under a simple Markovian model in which all speciations and extinctions occur randomly and with equal probability in all parts of the tree, trees based on taxa from a single time period (e.g., the present day) are generally more balanced than trees based on all taxa that ever existed within the clade. Computer simulation is used to calculate the expected balance and standard deviation of trees for up to 40 terminal taxa over the entire history of a model clade. The balance is measured using Colless's index, Ic, and the expected balance conforms well with published paleontological trees. The study underlines the difficulty of applying neontological tree statistics in paleontology.

Heterochrony is considered to be an important and ubiquitous mechanism of evolutionary change. Three components are necessary to describe heterochrony: phylogenetic relationships, size and shape change, and timing of developmental events. Patterns and processes of heterochrony are all too often invoked before all three components have been investigated. Phylogenetic hypotheses affect the interpretation of heterochrony in three ways: rooting of a clade, topology of a clade, and character polarity. To study these effects we examined the distribution of shell microstructure, lophophore support structures, and body size in four different phylogenetic hypotheses of thecideide brachiopods (Triassic to Recent), a group of minute, cryptic, benthic marine invertebrates.

Thecideides are consistently monophyletic in experiments using terebratulide, strophomenate, and spire-bearing outgroups together and separately, varying ingroup membership, and experimentally withholding certain character complexes. Thecideide monophyly is also supported by bootstrap analysis. Hypotheses of heterochrony in thecideide origins and evolution are therefore not merely artifacts of classification and can be pursued further. Using either strophomenate or spire-bearing outgroups, Triassic Thecospira is the most primitive thecideide. Trees constructed using terebratulide outgroups are rooted instead at Eudesella, a taxon derived in every other phylogenetic reconstruction, and the Triassic thecideides occupy derived rather than primitive positions.

Our phylogenetic results support the traditional interpretation of the reduction or loss of the secondary fibrous shell layer as a paedomorphic pattern, whereas the evolution of lophophore support structures suggests a peramorphic pattern. Reduction in thecideide adult body size is gradual, phylogenetically, and results in an overall paedomorphic pattern. Heterochrony in these three character suites may play a role in the subsequent evolution of the clade, but apparently not in the origin of the clade, as is commonly thought. Heterotopy, rather than—or in addition to—heterochrony, may account for both the origin and evolution of the lophophore support structures and in the reduction and loss of the secondary shell layer. These phylogenetic hypotheses suggest that heterochrony can result from a complex mosaic of processes and provide specific, testable predictions about the processes responsible for producing the patterns, whether heterochronic or not. Categorizing an entire clade (such as thecideides), rather than individual characters, as globally paedomorphic may allow interesting peramorphic patterns in individual characters to be overlooked.

Phylogenies provide a rich source of information that should be exploited in designing quantitative hypothesis tests in paleobiological contexts. Viewing such data analysis problems through the prism of phylogenetically structured comparisons can help add realism and depth to paleobiological data-analysis strategies. Two examples of the importance of adopting a phylogenetic perspective are discussed. In the first example, a phylogenetic-comparative approach is used to test correlations between ecological, morphological, and biological characteristics of planktonic foraminifera. Results suggest that the presence of spines and photosynthetic symbionts in Neogene-Recent species are not adaptations to living in shallow-intermediate planktonic depth habitats. In the second, a phylogenetic-comparative approach is used to reveal the presence of morphological correlations with locomotor function in a mammalian carnivore data set. Paleontologists can play an active role in improving comparative data analyses by (1) helping to develop improved phylogenies, especially those that provide better estimates of branch lengths, and (2) helping to resolve a number of outstanding issues surround the question of ancestral character-state specification.

The association between mass extinction in the marine realm and eustatic sea-level change in the Mesozoic is well documented, but perplexing, because it seems implausible that sea-level change could actually cause a major extinction. However, large-scale cycles of sea-level change can and do alter the ratio of shallow to deep marine continental-shelf deposits preserved in the rock record both regionally and globally. This taphonomic megabias alone could be driving patterns of first and last occurrence and standing diversity because diversity and preservation potential both change predictably with water depth. We show that the Cenomanian/Turonian faunal event in western Europe has all the predicted signatures expected if taphonomic megabias was the cause. Grade taxa terminating in pseudoextinction and Lazarus taxa are predominantly found in the onshore facies that disappear for extended periods from the rock record. Before other mass extinctions are taken at face value, a much more careful analysis of biases in the rock record needs to be carried out, and faunal disappearances need to be analyzed within a phylogenetic framework.

Evolutionary interpretation of paleontological patterns requires a hypothesis of phylogeny, but our phylogenetic hypotheses may not perfectly mirror organismal phylogeny. Tree summary methods less conservative than strict consensus may increase resolution, but these methods may present a biased summary of the full set of most parsimonious trees. When we fail to acknowledge all equally optimal topologies, we risk disregarding trees that are closer to the correct phylogeny. We discuss a case where two subsets of trees were recovered in the set of most parsimonious trees, each with a profoundly different interpretation of character evolution near the root of Echinodermata. This was caused by the presence of a bimodally labile taxon in the matrix with two different topological subsets, each equally parsimonious but differing in the number of consistent trees. Majority-rule consensus favors the subset with the largest number of trees consistent with the placement of the rogue taxon. This bias favors clusters not because of the biological implications of the tree, but on the basis of great inequality in the sizes of the islands of parsimony. We thus recommend that majority-rule consensus trees not be used to summarize the results of a phylogenetic analysis.

A phylogeny of 54 Recent and fossil species of Soritacea (Foraminifera) was used to test the hypothesis that endosymbiosis has driven the evolution of the clade. Endosymbiosis with photosynthetic eukaryotes is the plesiomorphic condition for the entire clade Soritacea. Living species dwell in tropical-subtropical, shallow-water habitats and are characterized by the possession of rhodophyte, chlorophyte, or dinophyte photosymbionts. Two distinct changes in endosymbiont type are recognized when endosymbiont type is mapped in the cladogram of Soritacea: (1) a change from rhodophyte to chlorophyte endosymbionts occurred in the stem lineage of the least inclusive clade containing New clade B, Orbiculinida, and Soritida; and (2) a change from chlorophyte to dinophyte endosymbionts occurred in the stem lineage of the least inclusive clade containing New clade G, New clade H, New clade I, Sorites, Amphisorus, and Orbitolites. When habitat and ontogeny are optimized on the cladogram of Soritida, the acquisition of dinophyte endosymbionts appears as a key innovation that facilitated a switch in habitat from free-living to attached living on nonphytal and phytal substrata. A subsequent change in the attached habitat from nonphytal to predominantly phytal (seagrasses and macroalgae) substrata is accompanied by a peramorphic trend in the megalospheric tests. The diversification (adaptive radiation) of the crown Soritida subclade resulted from the interplay between the acquisition of a key innovation (dinophyte endosymbionts) and the subsequent change in the ecology of the group (radiation to phytal substrates).

Hypotheses about constraints, selection, and other evolutionary processes often predict different rates of change among different characters. For example, it is thought that gross soft anatomical characters change less frequently than do general shell characters. However, some shell characters on primitive gastropods, such as the sinus and selenizone, are thought to be linked to soft anatomy. If both premises are true, then selenizone/sinus characters should change less frequently than other characters. Workers also have documented active trends among gastropod shell characters. One explanation is a driven trend, where the rate of change in one direction (i.e., gain or loss, increase or decrease) is greater than the rate of change in the opposite direction.

Hypotheses about relative rates and biased change are tested here for lophospiroid gastropods. Likelihood analyses test whether hypotheses positing many different rates predict data significantly better than do hypotheses positing few rates. One tree-based approach assumes that a phylogeny is known and thus treats a tree as a model. A second tree-based approach treats phylogeny as an additional hypothesis. This multiparameter approach allows competing rate hypotheses to “assume” a phylogeny that maximizes their likelihoods.

Likelihood tests reject hypotheses of low rate heterogeneity among lophospiroid characters. The most likely hypothesis (which treats phylogeny as an unknown) posits seven rates, with biased changes among three characters (preferential reduction of both sinus depth and sinus width and preferential addition of ornament). The distribution of rates among different character classes is consistent with the prediction that characters associated with internal anatomy should show generally lower rates of change than those associated with gross shell morphology. Evaluating significance when contrasting hypotheses posit different phylogenies is problematic, but the difference in support (log-likelihood) is overwhelming. Even if a model phylogeny is used, we still reject all hypotheses using fewer than six rates and not invoking trends in sinus characters. Thus, it is difficult to avoid rejecting the hypothesis that shell characters are uniformly plastic.

Radiations are commonly believed to be linked to the evolutionary appearance of a novel morphology or ecology. Previous studies have demonstrated a close relationship between the evolutionary appearance of algal photosymbiosis in planktonic foraminifera and evolutionary diversification of Paleogene photosymbiotic clades. For example, the evolution of photosymbiosis was synchronous with the abrupt evolution of four major groups of Paleogene planktonic foraminifera including two clades within the genus Morozovella, as well as the genera Acarinina and Igorina. Our new isotopic and biogeographic data suggest that the acarininids evolved from a photosymbiotic ancestor (which we identify as Praemurica inconstans or early representatives of Praemurica uncinata), but also demonstrate that photosymbiosis did not trigger an immediate species-level radiation in this group. Instead, the acarininids remained a low-diversity taxon restricted to high latitudes for nearly 1.8 million years before radiating ecologically and taxonomically. The eventual radiation of the acarininids is tied to an expansion of their geographic range into the mid and low latitudes. Biogeographic analyses of modern plankton suggest that high-latitude environments may be less conducive to establishing radiations simply because there are fewer niches available to be filled than there are in the tropics. Accordingly, the acarininids may have initially failed to diversify because they started off in environments that presented few opportunities to sustain a large radiation. The high-latitude origin of the acarininids continued to retard their overall diversification until they were able to develop strategies that allowed them to expand into tropical environments and fully exploit their photosymbiotic ecology.

Populations of planktic foraminifera display “proportionate” coiling (approximately 50% sinistral and dextral individuals given the data at hand) or may have “biased“ coiling, in which populations are dominated by either sinistral or dextral individuals. The major radiations of planktic foraminifera in the Late Cretaceous, the Paleocene to early Eocene, the middle Eocene, and the Neogene were each initiated by clades with proportionate coiling but subsequently accumulated sinistral and dextral species over time. Upper Maastrichtian foraminifera were predominantly dextral, but only the small number of species with proportionate coiling actually survived the Cretaceous/Paleogene mass extinction. The first Paleocene species with biased coiling appeared about four million years after the extinction and gradually came to represent as much as 50–60% of the tropical species diversity by the latest Paleocene. Tropical taxa with biased coiling suffered a second extinction in the late early Eocene and renewed a trend toward an increased abundance of species with biased coiling in the middle Eocene.

Our results for the Paleogene reflect a recurring theme in foraminifer evolution. In each radiation, once the founding species of a clade developed a biased-coiling mode, the descendants tended to maintain biased coiling until the extinction of the clade. The iterative evolution of biased coiling appears to represent an example in which a fundamental feature of development becomes fixed in a clade and inhibits reversion to an ancestral state. Apparently, coiling patterns are heritable in contrast with previous interpretations that coiling is environmentally controlled. On evolutionary timescales, species with proportionate coiling are less susceptible to extinction than species dominated by sinistral or dextral forms. Differential survivorship ensures that each radiation is initiated from founders with proportionate coiling following mass extinction. Hence, coiling preferences represent a case where the establishment of an evolutionary trend is caused by drift away from a “limiting boundary,” much like the evolution of large body size from ubiquitous small ancestors.

A spatial approach was employed to test whether the conchological differentiation of the Recent land snail Albinaria terebra from southern central Crete (Greece) is decreased in areas that have been more recently colonized by the species. The eastern Mediterranean genus Albinaria has produced more than 120 species, probably in pre-Tortonian events of radiation. A. terebra occupies a compact range of 550 km2 consisting partly of late Cenozoic deposits of different ages, partly of pre-Cenozoic formations. The morphological study was based on 300 samples distributed over the entire range of the species. Shell size, shape, whorls, and teleoconch rib densities exhibited no evident correlation with environment but were subjected to considerable spatial variations. The differentiation, determined as the difference of the mentioned shell parameters between one population and another population 2–4 km distant, was found to increase continuously with the time (1–12 Myr) the land has been exposed to air. The populations with the highest degrees of spatial variation came from two areas that have never been submerged in the late Cenozoic, possibly the oldest populations of the species. It is plausible that the other areas were colonized by range expansion after late Neogene periods of tectonic uplift. The results are consistent with previous conclusions derived from molecular studies setting the radiation of Albinaria prior to the Tortonian and imply that we might be in possession of a new tool to detect information on the phylogeographic history of land snail species.

Teleost otoliths are located in the membranous labyrinth and are mainly composed of aragonite and a small amount of organic matrix. Their rhythmic growth may provide important data about age, growth, maturity, and life-history events.

This article presents insights into paleoecological and evolutionary details from a study of the otolith microstructure of Trisopterus kasselensis, Trisopterus sculptus, and Pterothrissus umbonatus (Oligo-Miocene, North Sea Basin). Otoliths of Recent Trisopterus minutus were analyzed using the same methods (light and electron microscopy, thin slides) as a basis for comparison with the fossil sample.

Growth structures similar in size and aspect to the seasonal and daily growth increments in living fish indicate both individual age and early life transitions in habitat and life strategy suggesting planktonic larvae and benthic juveniles. The aspect of rhythmic growth patterns is due to lunar periodicity, a common feature in fish otoliths. Moreover, fossil Trisopterus show an phylogenetic increase in otolith—and consequently—somatic growth, indicating a change of life strategy during evolution (Oligocene to Recent).

Thus the internal structure of fossil otoliths allows the determination of growth, age composition, and early life history of fossil fish, as well as their direct comparison with living relatives.

The Neogene paleoisland from the area of Gargano, Italy, has yielded numerous fossil vertebrates, some of them showing extraordinary morphological peculiarities due to island evolution. Among them, Microtia (Freudenthal 1976) is the dominant rodent genus in the Gargano palaeofauna and is represented by at least three evolutionary lineages. The incisors are used to describe the size evolution in these lineages, and we come to the conclusion that these lineages did not follow the same evolutionary trend: two of them evolve toward larger size, while the third one shows a slight decrease in size. In addition, we describe the evolution of the curvature of the lower incisor, compared with that of body-size. The evolution of Microtia is characterized by a specialization for burrowing, which may be accompanied by either an increase or a decrease in size. Finally, we propose that the evolutionary change among these three sympatric lineages allowed Microtia to minimize competition between species, by avoiding size overlaps.

Clypeasteroid echinoids are a familiar and easily defined clade with a cryptic origin. They first appear in the late Paleocene and are believed to have arisen from cassiduloid ancestry, but identifying sister-group relationships more precisely has proved difficult. Two factors are responsible for this problem, the extreme morphological conservatism of cassiduloids, which has given rise to high levels of character exhaustion, and the origin of crown-group clypeasteroids through paedomorphosis. Previous analyses, based on extant representatives alone or including all Mesozoic to Recent genera, have proved unsatisfactory.

Here a parsimony analysis is undertaken using a restricted set of all stem-group clypeasteroids and cassiduloid taxa that existed immediately prior to the appearance of crown-group clypeasteroids. Inclusion of Togocyamus, the fossil taxon lying closest to the origin of crown-group clypeasteroids, is phylogenetically uninformative because that taxon is highly paedomorphic and has only generalized juvenile characteristics. However, earlier stem-group plesions provide critical data that identify Apatopygidae as extant sister group to the Clypeasteroida. Stratigraphically restricted analyses cannot eradicate the problems that arise from character exhaustion, but can minimize these with respect to specific phylogenetic questions.

The degree of hierarchical structure of organisms—the number of levels of nesting of lower-level entities within higher-level individuals—has apparently increased a number of times in the history of life, notably in the origin of the eukaryotic cell from an association of prokaryotic cells, of multicellular organisms from clones of eukaryotic cells, and of integrated colonies from aggregates of multicellular individuals. Arranged in order of first occurrence, these three transitions suggest a trend, in particular a trend in the maximum, or an increase in the degree of hierarchical structure present in the hierarchically deepest organism on Earth. However, no rigorous documentation of such a trend—based on operational and consistent criteria for hierarchical levels—has been attempted. Also, the trajectory of increase has not been examined in any detail. One limitation is that no hierarchy scale has been developed with sufficient resolution to document more than these three major increases. Here, a higher-resolution scale is proposed in which hierarchical structure is decomposed into levels and sublevels, with levels reflecting number of layers of nestedness, and sublevels reflecting degree of individuation at the highest level. The scale is then used, together with the body-fossil record, to plot the trajectory of the maximum. Two alternative interpretations of the record are considered, and both reveal a long-term trend extending from the Archean through the early Phanerozoic. In one, the pattern of increase was incremental, with almost all sublevels arising precisely in order. The data also raise the possibility that waiting times for transitions between sublevels may have decreased with increasing hierarchical level (and with time). These last two findings—incremental increase in level and decreasing waiting times—are tentative, pending a study of possible biases in the fossil record.