Knowing the structure and branching order of the evolutionary tree is essential to many studies of the evolutionary process and the history of life. Most attempts to reconstruct evolutionary trees are based on rectangular matrices, in which coded states are assigned for each character and each taxon under study. Everyone who has tried to infer the pattern of evolution from such character-taxon matrices is confronted with a great deal of “noise” and uncertainty. Often, there are multiple “most parsimonious trees” (those requiring the fewest evolutionary steps), which often differ significantly in topology; and many nodes in such trees are poorly supported; that is, there are contradictions and inconsistencies in the data. Some of this noise arises for reasons well known to phylogeneticists. Character states may arise multiple times, evolve in parallel, or reverse (homoplasy); taxa vary insufficiently among themselves; and diversification may be so rapid that data are insufficient to detect the order of branching. Polytomies are regarded as a nuisance rather than as real information. Characters may be coded inappropriately, so that there are too many redundancies, inapplicable character states, and multistate characters, as well as dependence among characters. Moreover, it is highly debatable whether evolution is parsimonious, and there are conflicts about how to establish the polarity of characters (primitive vs. derived). (For reviews and discussion see Sober 1988; Huelsenbeck and Crandall 1997.)

We show that the decline in the extinction rate during the Phanerozoic can be accurately described by a logarithmic fit to the cumulative total extinction. This implies that extinction intensity is falling off approximately as the reciprocal of time. We demonstrate that this observation alone is sufficient to explain the existence of the proposed power-law forms in the distribution of the sizes of extinction events and in the power spectrum of Phanerozoic extinction, results that previously have been explained by appealing to self-organized critical theories of evolutionary dynamics.

Paleotectonic reconstructions for the late Proterozoic have differed over the timing of the Cordilleran rifting between Laurentia and the East Gondwana cratons. Parsimony Analysis of Endemism (PAE) and phenetic clustering of the “Ediacara biota” were carried out, for comparison with competing paleotectonic hypotheses. All analyses show a common pattern of similarities among biotas. The biotas of Charnwood Forest and Newfoundland consistently group together, while the south Australian biota is closest to those of Baltica, northern Laurentia, and Siberia. The biota of southwest North America, though still poorly known, strikingly resembles that of Namibia—not that of northwestern Canada. This pattern is not obviously due to facies-related or preservational bias and is very different from Cambrian biogeographic patterns. The overall pattern is most consistent with the hypothesis that the western margin of Laurentia was in close contact with East Gondwana, with rifting taking place either during or just before the Vendian. This arrangement has been previously proposed as a paleotectonic hypothesis; however, most recent paleomagnetic and structural studies support the alternate hypothesis that this rifting took place more than 100 million years before the Vendian. Resolving this contradiction will require much more data on both organismal distribution and cratonal position.

The Cambrian Radiation marks the appearance of representatives of virtually all major skeletonized phyla in the fossil record and clearly represents a fundamental episode in the history of life. Furthermore, the tempo and mode of this evolutionary event have been the subject of intense debate. One area that has been debated is how so many phylum-level body plans can have evolved in such a geologically brief period. Some have argued that there was enhanced morphological flexibility and fewer evolutionary constraints at this time, leading to greater morphological disparity of Early Cambrian faunas. Others have claimed that this is not true because the evolution of most of the animal phyla significantly predates the radiation or because they failed to detect a signature of decreasing morphological disparity through time. At present, the higher-level patterns of diversification during this time period and the relevant implications for Early Cambrian uniqueness are areas of active research interest and debate. Recognizing this debate, we used both a phylogenetic and a morphometric framework to study whether there is a signature of increasing morphological constraint and decreasing flexibility through time within one of the clades that is a significant constituent of the Early Cambrian biota, specifically, the olenelloid trilobites. In this species-rich clade, we found no evidence that morphological changes were becoming either increasingly constrained or less flexible in one of the dominant Early Cambrian metazoan clades as it passed through the Cambrian Radiation.

Accretionary outlines of many brachiopods are closely matched by one or more episodes of logarithmic spiral growth where each episode has a constant growth gradient. An episodic model supports the observations of abrupt change, but not that of gradual change in accretionary growth. A reliable guide to the number of growth episodes is given by the pattern of residuals after fitting a single spiral to an outline. An episodic model exposes subtle variations in growth that are not easily described by visual examination. A three-episode model clarifies a shape difference between two species of the endemic New Zealand genus Neothyris. Direct observation, along with linear measurements and their ratios, was unable to pinpoint that the well-documented dorsoventral compression in one species arises from a growth episode in the ventral valve. Logarithmic spirals about a single coiling axis are not suited for large, disjunct changes in outline for which the moving-frame methods or aperture-deposition models are applicable.

Fish eagles (genus Haliaeetus) potentially have contributed the bones of their prey to many late Cenozoic concentrations of vertebrate microfossils. To evaluate possible biases in the taxa and skeletal elements preserved in assemblages accumulated by fish eagles, which could affect paleoecological and evolutionary interpretations derived from Cenozoic microfaunal localities, a sample of 1883 bones accumulated by modern African fish eagles (H. vocifer) was collected from a roost near Lake Turkana, Kenya. Characteristics of the bone assemblage include (1) taxonomic composition dominated by fish; (2) diverse but small-sized and ecologically restricted animals including inshore fish, aquatic birds, very small nocturnal mammals (which may have been contributed by other raptors), and small reptiles (possible predators on the roost); (3) poor survivorship for specific categories of skeletal elements; (4) considerable bone breakage for all but the smallest animals; and (5) a distinctive pattern of postcranial fragmentation for bird and mammal elements. The fish eagle element profile has some similarities to those of other diurnal raptors, but its cumulative signature can be distinguished from those of other bone accumulators and includes characteristics that would also be manifest in fossil assemblages. Examination of fossil microfaunas from the Plio-Pleistocene localities of Kanapoi (Kenya), Inolelo (Tanzania), and Olduvai Gorge (Tanzania) shows that the patterns of element preservation for Kanapoi and Inolelo do not match those of the Lake Turkana fish eagle roost. Nonetheless, some aspects of the Olduvai Gorge FLKN assemblage show taxonomic and skeletal similarites. In light of the selective choices of prey by fish eagles, the fauna recovered from Olduvai Gorge FLKN might not accurately reflect faunal diversity or patterns of abundance at this locality during the Pleistocene. Because fish eagles of the genus Haliaeetus are found on three continents, have a fossil record extending to the Miocene, and deposit bones in a habitat conducive to preservation, the taxa preserved at many other late Cenozoic microfaunal sites also might be biased. Therefore, taphonomic profiles of late Cenozoic microfaunal assemblages should be compared against the taphonomic profiles typical of fish eagle roosts before faunal characterizations of sites are applied in analyses of paleoecological evolution.

In this paper we analyze the ontogenies of four species of pachypleurosaur (Reptilia: Sauropterygia) occurring in Triassic-age deposits in the Monte San Giorgio region, Switzerland. Preservation of multiple complete specimens representing a growth series from each taxon allows the comparison of ontogenetic trajectories through a space composed of nine variables important in the evolution of the clade. Trajectories are characterized using the multivariate generalization of the allometry equation and then compared through calculations of the angles between allometry vectors. Individual coefficients of vectors are compared after calculation of bootstrapped confidence intervals. Pachypleurosaur ontogeny is found to be allometric and generally conserved, although significant differences between taxa exist. Shape-disassociated allometric changes characterize the transition between Serpianosaurus and Neusticosaurus, while allometric changes within Neusticosaurus are less significant. N. edwardsii is inferred to have arisen through hypermorphosis. Interpretation of whole-body heterochrony in multivariate analysis is discussed.

In this paper we reconstruct the phylogeny of a clade of pachypleurosaurs (Reptilia: Sauropterygia) occurring in Triassic-age deposits in the Monte San Giorgio region, Switzerland. We also present the phylogeny of this clade as a case study for two paradigms of phylogeny reconstruction: cladistics and phenetic/stratigraphic methods. While this dichotomy is not held rigidly by all workers, its advancement by cladists leads us to retain it initially for rhetorical purposes. We review the philosophical bases of species, species concepts, and speciation, as well as cladograms and phylogenies, before introducing the experimental system.

Data are presented from cladistic analyses, phenetic analyses, and stratigraphic information. Phylogeny of the clade is interpreted from both paradigms, and the interpretations are found to be inconsistent. Resolution of the phylogeny rests on the emphasis of one type of data over another. An interpretation of cladogenesis within the genus Neusticosaurus entails rejection of suggestive phenetic and stratigraphic data, whereas an anagenetic interpretation entails reversal of autapomorphies in ancestral taxa. Anagenesis is deemed to be the more probable interpretation, based on the strength of the stratigraphic and phenetic data relative to the character data. Implications of the test case results for phylogeny reconstruction in general are discussed, ending with a call for pluralism in approach.

Addition of the recently discovered fossil Nalacetus to a phylogenetic analysis of basicranial, cranial, dental, postcranial, and soft morphological characters reveals that it is the most basal cetacean, and that mesonychians form the monophyletic sister group to Cetacea. The molars of Nalacetus elucidate transformations in dental morphology that occurred early in the cetacean radiation and clarify certain derived differences in molar cusp position between cetaceans and the extinct clade, Mesonychia, hypothesized to be their sister taxon. Nalacetus and other archaic cetaceans share derived vertically elongate shearing facets on the lower molars. Applying the Extant Phylogenetic Bracket, we advance the hypothesis that these facets are an osteological correlate of aquatic predation. Our functional interpretation of this character and its distribution within Cetacea indicates that a behavioral change in tooth use characterized the origin of the clade. Comparison of the transformation of this dental character with that of the cetacean pelvis indicates that a change in tooth use (feeding behavior) occurred before loss of the ability to engage in terrestrial locomotion.

The most parsimonious phylogenetic hypothesis presented here has a significant fit with the stratigraphic record as determined by the Manhattan Stratigraphic Measure, which is corroborated by retention indices of stratigraphic data. Ghost lineages necessitated by the phylogenetic hypothesis extend the stratigraphic range of Cetacea into the middle Paleocene (Torrejonian), ten million years earlier than the oldest cetacean fossil currently known. Primitive features of Nalacetus, the large number of synapomorphies diagnosing Cetacea, and the implied ghost lineage suggest that the early cetacean radiation was much more extensive than has been previously recognized.