Michael J. Donoghue

Phylogenetic relationships of Dipsacales based on rbcL sequences

Nucleotide sequences of the chloroplast gene rbcL were obtained from Lonicera, Sambucus, Adoxa, and Cornus. Phylogenetic analyses of these sequences, along with previously sequenced Dipsacales and placeholders for other Asteridae and Rosidae, lead to the following conclusions: (1) the genera of Caprifoliaceae (in any traditional sense) do not form a monophyletic group; (2) Symphoricarpos and Lonicera (representing Caprifoliaceae sens. str.) are related and are united with Valerianaceae and Dipsacaceae; and (3) Adoxa and Sambucus are directly linked and are possibly related to Viburnum

A LIKELIHOOD FRAMEWORK FOR INFERRING THE EVOLUTION OF GEOGRAPHIC RANGE ON PHYLOGENETIC TREES

Abstract At a time when historical biogeography appears to be again expanding its scope after a period of focusing primarily on discerning area relationships using cladograms, new inference methods are needed to bring more kinds of data to bear on questions about the geographic history of lineages. Here we describe a likelihood framework for inferring the evolution of geographic range on phylogenies that models lineage dispersal and local extinction in a set of discrete areas as stochastic events in continuous time. Unlike existing methods for estimating ancestral areas, such as dispersal‐vicariance analysis, this approach incorporates information on the timing of both lineage divergences and the availability of connections between areas (dispersal routes). Monte Carlo methods are used to estimate branch‐specific transition probabilities for geographic ranges, enabling the likelihood of the data (observed species distributions) to be evaluated for a given phylogeny and parameterized paleogeographic model. We demonstrate how the method can be used to address two biogeographic questions: What were the ancestral geographic ranges on a phylogenetic tree? How were those ancestral ranges affected by speciation and inherited by the daughter lineages at cladogenesis events? For illustration we use hypothetical examples and an analysis of a Northern Hemisphere plant clade (Cercis), comparing and contrasting inferences to those obtained from dispersal‐vicariance analysis. Although the particular model we implement is somewhat simplistic, the framework itself is flexible and could readily be modified to incorporate additional sources of information and also be extended to address other aspects of historical biogeography.

PATTERNS OF VARIATION IN LEVELS OF HOMOPLASY

Patterns of variation in levels of homoplasy were explored through statistical analyses of standardized consistency indexes. Data were obtained from 60 recent cladistic analyses of a wide variety of organisms based on several different kinds of characters. Consistency index is highly correlated with the number of taxa included in an analysis, with homoplasy increasing as the number of taxa increases. This observation is compatible with a simple model of character evolution in which 1) the probability of character‐state change increases with the total number of branches in a tree and 2) the number of possible states of a character is limited. Consistency index does not show a significant relationship to the number of characters utilized in an analysis or to the taxonomic rank of the terminal taxa. When the relationship between consistency index and number of taxa is taken into account, there is no significant difference between plant and animal data sets in the amount of homoplasy. Likewise, the level of homoplasy in morphological and molecular data sets does not appear to differ significantly, although there are still too few molecular studies to be confident of this result. Future comparisons of consistency indexes, including studies along the lines established here, must take into account the influence of the number of taxa on homoplasy.

Seed plant phylogeny and the origin of angiosperms: An experimental cladistic approach

We present a numerical cladistic (parsimony) analysis of seed plants plus progymnosperms, using characters from all parts of the plant body, outgroup comparison, and a method of character coding that avoids biases for or against alternative morphological theories. The robustness of the results was tested by construction of alternative trees and analysis of subsets of the data. These experiments show that although some clades are strongly supported, they can often be related to each other in very different but nearly equally parsimonious ways, apparently because of extensive homoplasy. Our results support Rothwell’s idea that coniferopsids are derived fromCallistophyton- like platyspermic seed ferns with saccate pollen, but the hypothesis that they evolved fromArchaeopteris- like progymnosperms and the seed arose twice is nearly as parsimonious. Meyen’s division of seed plants into radiospermic and primarily and secondarily platyspermic lines is highly unparsimonious, but his suggestion that ginkgos are related to peltasperms deserves attention. Angiosperms belong among the platyspermic groups, as the sister group of Bennettitales,Pentoxylon, and Gnetales, and this “anthophyte” clade is best related toCaytonia and glossopterids, although relationships with other combinations of Mesozoic seed fern taxa are nearly as parsimonious. These results imply that the angiosperm carpel can be interpreted as a modified pinnate sporophyll bearing anatropous cupules (=bitegmic ovules), while gnetalian strobili are best interpreted as aggregations of highly reduced bennettitalian flowers, as anticipated by Arber and Parkin and Crane. Our most parsimonious trees imply that the angiosperm line (though not necessarily all its modern features) extended back to the Triassic, but a later derivation of angiosperms from some species ofCaytonia or Bennettitales, which would be nearly as parsimonious, should also be considered. These results raise the possibility that many features considered key adaptations in the origin and rise of angiosperms (insectpollinated flowers, rapid reproduction, drought tolerance) were actually inherited from their gymnospermous precursors. The explosive diversification of angiosperms may instead have been a consequence of carpel closure, resulting in increased speciation rates due to potential for stigmatic isolating mechanisms and/or new means of dispersal. DNA sequencing of extant plants and better information on anatomy, chemistry, sporophyll morphology, and embryology of Bennettitales and Caytoniales and the morphological diversity of Mesozoic anthophytes could provide critical tests of relationships.RésuméNous présentons une analyse cladistique numérique (de parcimonie, ou économie d’hypothèses) des Spermatophytes plus Progymnospermes, utilisant des caractères de tous les organes du corps végétal, la comparaison extra-groupe, et une méthode de codification de caractères qui évite des prédispositions en faveur de ou contre les théories morphologiques alternatives. La solidité des résultats a été testé par la construction d’arbres phylétiques alternatifs et l’analyse de sous-ensembles des données. Selon ces expériences, certains phylums sont bien appuyés, mais ils peuvent être reliés de façons très différentes mais presque également économiques, apparemment à cause d’homoplasie répandue. Nos résultats confirment le concept de Rothwell, selon lequel les Coniféropsides sont dérivées de Ptéridospermes platyspermiques à pollen saccate proches deCallistophyton, mais l’hypothèse d’une dérivation de Progymnospermes proches d’Archaeopteris et d’une origine diphylétique de la graine est presque aussi économique. La division de Meyen des Spermatophytes en lignées radiospermiques et primairement et secondairement platyspermiques est très peu économique, mais son concept d’une affinité entre les Ginkgoales et les Peltaspermes mérite de l’attention. Les Angiospermes se situent parmi les groupes platyspermiques, comme groupe-frère des Bennettitales,Pentoxylon, et Gnetales, et le phylum ainsi constitué (“Anthophytes”) est le mieux lié àCaytonia et aux Glossoptérides, bien que des rapports avec d’autres combinaisons de taxons de Ptéridospermes mésozoïques soient presque aussi économiques. Ces résultats indiquent que le carpelle des Angiospermes peut être interprété comme une sporophylle pennée modifiée portant des cupules anatropes (=ovules bitégumentés), puisque les strobiles des Gnetales sont le mieux interprétés comme des agglomérations de fleurs bennettitaliennes fort réduites, comme l’a proposé Arber et Parkin et Crane. Nos arbres phylétiques les plus économiques supposent que la lignée des Angiospermes (mais pas forcément tous ses traits modernes) s’étend jusqu’au Trias, mais une origine plus récente à partir de quelque espèce deCaytonia ou de Bennettitales, hypothèses presque aussi économiques, doit aussi être considérée. Ces résultats suggèrent que plusieurs traits considérés comme des adaptationsclés dans l’origine ou l’expansion des Angiospermes (fleurs entomophiles, rapidité de reproduction, tolérance de sécheresse) étaient en fait hérités de leurs ancêtres gymnospermiques. La diversification explosive des Angiospermes pourrait plutôt être une conséquence de la clôture du carpelle, conduisant à un taux de spéciation élevé dû au potential pour des mécanismes d’isolement stigmatiques et/ou de nouveaux moyens de dispersion. L’étude de séquences d’ADN des végétaux actuels et de meilleurs renseignements sur l’anatomie, la phytochimie, la morphologie des sporophylles, et l’embryologie des Bennettitales et Caytoniales pourraient fournir des testes critiques de rapports phylétiques.

Rates of Molecular Evolution Are Linked to Life History in Flowering Plants

Variable rates of molecular evolution have been documented across the tree of life, but the cause of this observed variation within and among clades remains uncertain. In plants, it has been suggested that life history traits are correlated with the rate of molecular evolution, but previous studies have yielded conflicting results. Exceptionally large phylogenies of five major angiosperm clades demonstrate that rates of molecular evolution are consistently low in trees and shrubs, with relatively long generation times, as compared with related herbaceous plants, which generally have shorter generation times. Herbs show much higher rates of molecular change but also much higher variance in rates. Correlates of life history attributes have long been of interest to biologists, and our results demonstrate how changes in the rate of molecular evolution that are linked to life history traits can affect measurements of the tempo of evolution as well as our ability to identify and conserve biodiversity.

Angiosperm phylogeny: 17 genes, 640 taxa

PREMISE OF THE STUDY Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. METHODS We conducted two primary analyses based on 640 species representing 330 families. The first included 25260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19846 aligned bp from 13 genes (representing only the nucleus and plastid). KEY RESULTS Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms (Mesangiospermae), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae]. Eudicotyledoneae contains a basal grade subtending Gunneridae. Within Gunneridae, Gunnerales are sister to the remainder (Pentapetalae), which comprises (1) Superrosidae, consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae, comprising Berberidopsidales, Santalales, Caryophyllales, Asteridae, and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae, most deep-level relationships are resolved with strong support. CONCLUSIONS Our analyses confirm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.

A Critique of the Biological Species Concept and Recommendations for a Phylogenetic Alternative

Discussions that have accompanied biological species definitions often imply corre- spondence between breeding groups and morphological and ecological units. It is often assumed that the cause of such correspondences is gene flow or the lack of it. This has generated confusion because breeding, morphology, and ecology can be, and often are, uncoupled, and the effects of gene flow may be limited. Another source of confusion has been the failure to distinguish clearly between species themselves (taxa) and concepts of the species category. The biological concept fails to provide unambiguous criteria for grouping organisms (or for assigning species rank), and as a consequence, biological species may not be monophyletic. A phylogenetic species concept, which emphasizes monophyly, is more appropriate for purposes of phylogeny reconstruction, cladistic classification, and the study of evolutionary processes.

Evolutionary instability of ectomycorrhizal symbioses in basidiomycetes

Mycorrhizae, the symbiotic associations of plant roots and fungal hyphae, are classic examples of mutualisms. In these ecologically important associations, the fungi derive photosynthetic sugars from their plant hosts, which in turn benefit from fungus-mediated uptake of mineral nutrients. Early views on the evolution of symbioses suggested that all long-term, intimate associations tend to evolve toward mutualism. Following this principle, it has been suggested that mycorrhizal symbioses are the stable derivatives of ancestral antagonistic interactions involving plant parasitic fungi. Alternatively, mutualisms have been interpreted as inherently unstable reciprocal parasitisms, which can be disrupted by conflicts of interest among the partners. To determine the number of origins of mycorrhizae, and to assess their evolutionary stability, it is necessary to understand the phylogenetic relationships of the taxa involved. Here we present a broad phylogenetic analysis of mycorrhizal and free-living homobasidiomycetes (mushroom-forming fungi). Our results indicate that mycorrhizal symbionts with diverse plant hosts have evolved repeatedly from saprotrophic precursors, but also that there have been multiple reversals to a free-living condition. These findings suggest that mycorrhizae are unstable, evolutionarily dynamic associations.

A phylogenetic perspective on the distribution of plant diversity

Phylogenetic studies are revealing that major ecological niches are more conserved through evolutionary history than expected, implying that adaptations to major climate changes have not readily been accomplished in all lineages. Phylogenetic niche conservatism has important consequences for the assembly of both local communities and the regional species pools from which these are drawn. If corridors for movement are available, newly emerging environments will tend to be filled by species that filter in from areas in which the relevant adaptations have already evolved, as opposed to being filled by in situ evolution of these adaptations. Examples include intercontinental disjunctions of tropical plants, the spread of plant lineages around the Northern Hemisphere after the evolution of cold tolerance, and the radiation of northern alpine plants into the Andes. These observations highlight the role of phylogenetic knowledge and historical biogeography in explanations of global biodiversity patterns. They also have implications for the future of biodiversity.

Phylogenies and the analysis of evolutionary sequences, with examples from seed plants

Studies of character evolution have frequently relied on ahistorical correlations rather than on phylogenies. However, correlations do not estimate the number of times that a trait evolved, and they are insensitive to the direction or the temporal sequence of character transformation. In contrast, cladograms can provide this information. A cladistic test of the hypothesis that the evolution of dioecy is favored in animal‐dispersed plants indicates that dioecy may have originated somewhat more often in such lineages. Nevertheless, differences in rates of speciation or extinction must largely account for the observed species‐level correlation between dispersal and breeding system.