The fossil record of angiosperms has more potential than ever for contributing to the resolution of major questions in the evolution of the flowering plants due to the better understanding of the significance of leaf and pollen records and because of the increasingly complete and informative fossil record of flowers. Nonetheless, the record has fallen short of its potential (and of its potentially synergistic value) because, although it is better understood than ever, there are still problems in identifying fossils' affinities that have not been fully resolved and that have major implications with respect to determining timing in angiosperm evolution with either molecular clock–based models or minimum-age node mapping. This issue is of particular significance with respect to early angiosperm radiation, where more careful studies of existing specimens seem to have unrealized value for increasing our comprehension of floral evolution and homology, potentially in the context of strides in understanding MADS-box genes. Subjective methods with typological overtones are still often used in identifying fossils, even though phylogenetic context is available. Identification using phylogenetic context, among other things, does not obscure relative character changes within monophyletic groups, does not lend itself to facultative interpretation of affinities to suit outcomes of various models, and, thus, does not impede our understanding of angiosperm evolutionary history. Nonetheless, a reasonably good fossil record of angiosperms is emerging from the combined efforts of many laboratories and, when carefully evaluated, reveals an interesting and possibly informative pattern of flowering plant evolution. One of its most striking aspects is the rapid radiation of angiosperm taxa that are now unusually diverse around two particular times in geological history: the Turonian and Early Tertiary. Possible reasons for these intervals of rapid radiation among angiosperms will be discussed.

In the past decade, there has been a rise in interest in the plant fossil record. Fossils potentially provide information for assessing homology and evolutionary change (e.g., the popular missing link phenomenon), character evidence that affects phylogenetic conclusions and, thus, our understanding of modern relationships, evidence of past distributions that can aid in understanding biogeographic histories, and estimates of minimum ages of the clades to which they belong. Recently, many molecular biologists have used fossils in their analyses as a way of providing a calibration point for evolutionary models used to approximate ages for the nodes of phylogenetic trees. However, there has been little, if any, discussion of the criteria by which calibration fossils can be selected for these studies. When considering the use of a fossil as a calibration point, it is critical to take into account the quality of preservation, the method and details of identification (reliability of the taxonomic placement), and the accuracy of the published age. Here, we provide basic criteria for the use of fossils to calibrate molecular evolutionary models. These approaches not only provide better primary estimates for ages of clades, but also provide more reliable sources for those molecular biologists wishing to clean up their molecular clocks.

In recent years, most systematics studies have focused on phylogenetic analyses of molecular data sets. The latest trend has been to add molecular dating to these phylogenies utilizing methods such as nonparametric rate smoothing (NPRS) and penalized likelihood (PL) and calibrating these analyses using (often only one or very few) fossils. The success of such approaches is dependent on several assumptions, including a local clocklike behavior of evolution, the accuracy of the phylogeny, the correct phylogenetic placement of fossils, and the consistency of particular fossils in extrapolating rates throughout a given phylogenetic tree. An example of such an analysis of the Nymphaeales is provided to illustrate inappropriate use of fossils in this context and faulty results based on inadequate and/or inappropriate analyses. Neither fossil identifications nor a particular method of molecular dating should be called into question based on the disparity of a single analysis. Indeed, fossil observations and molecular dating are often at odds due to failure of the data to meet minimum assumptions of a clocklike behavior and poor or inadequate sampling of extant taxa, molecular sequence data, and/or fossils. Rejection or acceptance of either the fossils or the molecular dates resulting from their use should be considered in light of direct analysis of the fossils and compared to other analyses using other fossils and/or other extant data sets. Rejection of fossils based on unexpected results is merely verificationism.

Our efforts to reconstruct accurate, complete records of events in vegetation history and in plant evolutionary history depend on accuracy in dating sediments, interpretation of structures preserved, reconstruction of whole organisms or communities from the preserved material, and interpretation of the interaction between past abundance and fossil presence. This contribution examines the interaction between past abundance of a target plant and the probability of retrieval of that species in the fossil record. By examining records of recolonization in volcanic areas, records of invasive species spread, succession in disturbed habitats, and historical migration patterns, we can provide estimates of the likelihood of appearance in the potential fossil record of newly evolved and reasonably successful species. The lag in discovery, recognition, and publication of a fossil as an important representative of a critical clade is also evaluated and is highlighted as a more important constraint on the use of fossils in testing evolutionary and ecological hypotheses than the recolonization rate. The lag between discovery and publication is particularly relevant in areas of the modern world where fossil plant–bearing deposits are either rare or inaccessible. Greater awareness of the density and reliability of the plant record should allow evolutionary biologists and paleoecologists to bracket not only time intervals but also geographic regions where the fossil record can be interpreted largely at face value. At the same time, more effort should be focused on intense collecting efforts and training in areas where fossil deposits are potentially present, but poorly collected and evaluated.

A major challenge in the post-genomics era will be to integrate molecular sequence data from extant organisms with morphological data from fossil and extant taxa into a single, coherent picture of phylogenetic relationships; only then will these phylogenetic hypotheses be effectively applied to the study of morphological character evolution. At least two analytical approaches to solving this problem have been utilized: (1) simultaneous analysis of molecular sequence and morphological data with fossil taxa included as terminals in the analysis, and (2) the molecular scaffold approach, in which morphological data are analyzed over a molecular backbone (with constraints that force extant taxa into positions suggested by sequence data). The perceived obstacles to including fossil taxa directly in simultaneous analyses of morphological and molecular sequence data with extant taxa include: (1) that fossil taxa are missing the molecular sequence portion of the character data; (2) that morphological characters might be misleading due to convergence; and (3) character weighting, specifically how and whether to weight characters in the morphological partition relative to characters in the molecular sequence data partition. The molecular scaffold has been put forward as a potential solution to at least some of these problems. Using examples of simultaneous analyses from the literature, as well as new analyses of previously published morphological and molecular sequence data matrices for extant and fossil Chiroptera (bats), we argue that the simultaneous analysis approach is superior to the molecular scaffold approach, specifically addressing the problems to which the molecular scaffold has been suggested as a solution. Finally, the application of phylogenetic hypotheses including fossil taxa (whatever their derivation) to the study of morphological character evolution is discussed, with special emphasis on scenarios in which fossil taxa are likely to be most enlightening: (1) in determining the sequence of character evolution; (2) in determining the timing of character evolution; and (3) in making inferences about the presence or absence of characteristics in fossil taxa that may not be directly observable in the fossil record.

Floral architecture and floral organ shape are interrelated to some extent as can be seen in the diversity of extant angiosperm groups. The shape of fragmentary fossil material, such as single organs, may therefore give hints for the reconstruction of the architecture of a flower. This study is partly a review and partly provides original material and new points of view on organ-architecture interrelationships. Several topics are illustrated with examples: (1) autonomous and imprinted shape, exemplified by cuneate organs, especially stamens; (2) conditions for valvate anther dehiscence; (3) lability in number and shape of reduced organs that have decreased in size and lost their original function; (4) long hairs as filling material of irregular spaces; (5) architectural conditions for the presence of orthotropous ovules; (6) structural differences between exposed and covered organ parts in bud; and (7) sepal aestivation and petal elaboration.

Appreciation for the role of ontogeny in plant evolution has been heightened by advances in studying development using molecular techniques, with a growing number of specific structural features now understood in terms of the genetic, regulatory, and biochemical mechanisms by which they are produced. Paleontological approaches to plant development provide a vehicle for extending that understanding to the ontogeny and evolution of whole organisms through time. Recent studies have shown that developmentally diagnostic features can be identified in the fossil record, where they represent fingerprints for gene-mediated regulatory pathways. The first paleontological evidence for the regulation of cambial activity via the polar axial flow of auxin consists of circular patterns of tracheary elements above buds and branch junctions in the wood of the 375-million-year-old fossil progymnosperm Archaeopteris Dawson. That evidence strongly supports homology of secondary vascular tissues in progymnosperms and seed plants, and monophylesis of the lignophytes (progymnosperms and seed plants). Similar anatomical patterns at the same position have now been identified in the wood of tree-sized fossil equisetophytes and arborescent lycophytes that belong to independent lineages, demonstrating that a similar mechanism involving the regulation of secondary vascular tissue production by the polar axial flow of auxin characterizes those clades as well. These data imply that the wood in lignophytes, lycophytes, and equisetophytes originated in conjunction with the parallel evolution of regulation of secondary tissue production by auxin in each clade. The independent origins of secondary vascular tissue in three major clades of Paleozoic plants sensu Kenrick and Crane (1997) reveal evolutionary patterns that are not represented in the living flora and illuminate promising avenues for combining future paleontological studies with molecular and genetic studies to substantially impact our understanding of the role of developmental regulation in vascular plant evolution.

Biogeography is one of the most synthetic of biological undertakings; it requires placing a substantiated phylogenetic model in a geological, climatological, and ecological context, all of which shift through time. In the past two decades, the application of cladistic and molecular techniques has diversified our grasp on phylogeny. This has allowed the formulation of hypotheses of past distribution patterns based on samples from available living material and algorithms for their interpretation. Fossils contribute to these cladistic approaches by adding morphological checkpoints to character associations in time and by providing a basis for estimates of rates of divergence. However, fossils also check these hypotheses by direct occurrence (does a fossil of the taxon occur where predicted?) and by ecological suitability (is it reasonable that the taxon could occur in the predicted environment?). The first test is straightforward if difficult, requiring the finding of a specific fossil in a specific place and time. The second is based on the assumption of physiological uniformitarianism—that fossil and modern taxa united by a common morphology possess similar physiologies. If correct, then hypotheses of past distribution must accord with the predicted physiological tolerances of the taxon in question. Application of physiological uniformitarianism to phylogeographic hypotheses, together with new paleontological data, suggest (a) the validity of many established phylogeographic hypotheses; (b) the need to reevaluate others; and (c) the recognition that the North Atlantic land bridge likely functioned as a link between the Old and New Worlds into the Later Tertiary, contrary to this author's earlier papers.

The paleoecology of plants as a modern discipline, distinct from traditional floristics or biostratigraphy, has undergone an enormous expansion in the past 20 years. In addition to baseline studies characterizing extinct plants and plant assemblages in terms of their growth habits, environmental preferences, and patterns of association, paleoecology has converged on neoecology and represents a means to extend our basic understanding of the world and to contribute to the theoretical framework of ecology, writ large. Reconstruction of whole plants, including studies of physiology and developmental biology, and analyses of biomechanics have become mainstays of autecological studies. Assemblage studies now are informed by sophisticated taphonomic models that have helped guide sampling strategies and helped with the interpretation of statistical data. Linkages of assemblage patterns in space and time with sedimentology, geochemical proxies for atmospheric composition and climate, paleosol analyses, and increasingly refined geochronological and sequence stratigraphic data have permitted paleoecologists to examine rates and extents of vegetational response to environmental change and to time intervals of quiescent climatic conditions. Studies of plant-animal interaction, explicit consideration of phylogenetic information in assessing assemblage time-space dynamics, and examination of ecological structure in terms of developing metabolic scaling theory are all having direct impact on paleoecological as well as neoecological studies. The growth of paleoecology shows no sign of diminishment—closer linkages with neoecology are needed.