Better understanding of the functional biology of early angiosperms may clarify ecological factors surrounding their origin and early radiation. Phylogenetic studies identify Amborella, Nymphaeales (water lilies), Austrobaileyales, and Chloranthaceae as extant lineages that branched before the radiation of core angiosperms. Among living plants, these lineages may represent the best models for the ecology and physiology of early angiosperms. Here we combine phylogenetic reconstruction with new data on the morphology and ecophysiology of these plants to infer early angiosperm function. With few exceptions, Amborella, Austrobaileyales, and Chloranthaceae share ecophysiological traits associated with shady, disturbed, and wet habitats. These features include low and easily light-saturated photosynthetic rates, leaf anatomy related to the capture of understory light, small seed size, and clonal reproduction. Some Chloranthaceae, however, possess higher photosynthetic capacities and seedlings that recruit in canopy gaps and other sunny, disturbed habitats, which may have allowed Cretaceous Chloranthaceae to expand into more diverse environments. In contrast, water lilies possess ecophysiological features linked to aquatic, sunny habitats, such as absence of a vascular cambium, ventilating stems and roots, and floating leaves tuned for high photosynthetic rates in full sun. Nymphaeales may represent an early radiation into such aquatic environments. We hypothesize that the earliest angiosperms were woody plants that grew in dimly lit, disturbed forest understory habitats and/or shady streamside settings. This ecology may have restricted the diversity of pre-Aptian angiosperms and living basal lineages. The vegetative flexibility that evolved in the understory, however, may have been a key factor in their diversification in other habitats. Our inferences based on living plants are consistent with many aspects of the Early Cretaceous fossil record and can be tested with further study of the anatomy, chemistry, and sedimentological context of Early Cretaceous angiosperm fossils.

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.

Temporal diversity patterns have traditionally been analyzed by counting the number of families or genera present over a series of time periods. This approach has been criticized on the grounds that paraphyletic taxa might introduce artifacts. Sepkoski and Kendrick (1993) simulated phylogenetic trees and different classifications of those trees and concluded that paraphyletic taxa need not be rejected. We have reimplemented their model, extended it, and carried out statistical analyses under a variety of experimental conditions. Our results show that the focus on monophyly vs. paraphyly is misplaced. Instead, it appears that the number of groups in the classification and the distribution of the sizes of those groups have dramatic effects on the recovery of diversity information. Furthermore, the influence of these factors depends on whether the fossil record represents a low- or high-frequency sampling of lineages. When sampling is good, the best results are achieved by classifications with large numbers of small taxa. When sampling is poor, however, the best results are achieved by classifications that include some large and medium-sized groups as well as many smaller groups. This suggests that the best estimates of underlying diversity will be achieved by counting (in the same study) taxa assigned to different ranks, so as to best match the inferred quality of the paleontological sample. In practice this will mean abandoning the commitment to counting taxa at a single rank.

Approaches to patterns of diversification based on counting taxa at a given rank can be misleading, even when all taxa are monophyletic. Such “rank-based” approaches are unable to reflect a hierarchy of evolutionary events because taxa of the same rank cannot be nested within one another. Phylogenetic trees specify an order of origination of characters and clades and can therefore be used in some cases to test hypotheses on causal relationships between characters and changes in diversity. “Tree-thinking” also clarifies discussions of the age of groups, by distinguishing between splitting of the stem-lineage from its sister group and splitting of the crown-group into extant clades.

Cladistic evidence that Pentoxylon, Bennettitales, and Gnetales are the sister group of angiosperms implies that the angiosperm line (angiophytes) existed by the Late Triassic. The presence of primitive members of five basic angiosperm clades indicates that the crown-group (angiosperms) had begun to diversify by the mid-Early Cretaceous (Barremian-Aptian), but not necessarily much earlier. The greatest unresolved issue raised by cladistic analyses concerns the fact that the angiosperm tree can be rooted in two almost equally parsimonious positions. Trees rooted near Magnoliales (among “woody magnoliids”) suggest that the angiosperm radiation may have been triggered by the origin of intrinsic traits, e.g., a fast-growing, rhizomatous habit in the paleoherb and eudicot subgroup. However, trees rooted among paleoherbs, which are favored by rRNA data, imply that these traits are basic for angiosperms as a whole. This could mean that the crown-group originated not long before its radiation, or, if it did originate earlier, that its radiation was delayed due to extrinsic factors. Such factors could be a trend from environmental homogeneity and stability in the Jurassic to renewed tectonic activity and disturbance in the Early Cretaceous. Potentially relevant pre-Cretaceous fossils cannot be placed with confidence, but may be located along the stem-lineage (stem angiophytes); their generally paleoherb-like features favor the paleoherb rooting. The history of angiophytes may parallel that of Gnetales: some diversification of the stem-lineage in the Late Triassic, near disappearance in the Jurassic, and vigorous radiation of the crown-group in the Early Cretaceous.

Phylogeny and biogeography of Lentinula, which includes cultivated shiitake mushrooms, were investigated using parsimony analyses of an expanded nuclear ribosomal DNA dataset. Lentinula occurs in the New World as well as Asia and Australasia. The Asian–Australasian Lentinula populations appear to form a clade, but species limits within this group are controversial. We refer to the entire Asian–Australasian Lentinula clade as shiitake. Thirty-seven wild-collected isolates of shiitake were examined, representing Australia, Borneo, China, Japan, Korea, Nepal, New Zealand, Papua New Guinea (PNG), Tasmania and Thailand. Five isolates of the New World species, L. boryana, were included for rooting purposes. Levels of sequence divergence between North and Central American L. boryana isolates are higher than those between the most divergent shiitake isolates. In shiitake, five independent lineages of rDNA were identified, which we call groups I–V, but relationships among these lineages are not well resolved. Group I includes populations from northeast Asia to the South Pacific. Group II includes populations from PNG, Australia and Tasmania. Group III is limited to New Zealand. Group IV is from PNG. Finally, group V is from eastern China and Nepal. The distribution of rDNA lineages suggests a complex biogeographic history. Although many areas remain unsampled, our results suggest that certain areas have particularly high levels of diversity and should be targeted for further study and conservation.