Christopher R. Hardy

A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values

Abstract A phylogenetic analysis of the monocots was conducted on the basis of nucleotide sequence variation in two genes (atpA, encoded in the mitochondrial genome, and rbcL, encoded in the plastid genome). The taxon sample of 218 angiosperm terminals included 177 monocots and 41 dicots. Among the major results of the analysis are the resolution of a clade comprising four magnoliid lineages (Canellales, Piperales, Magnoliales, and Laurales) as sister of the monocots, with the deepest branch within the monocots between a clade consisting of Araceae, Tofieldiaceae, Acorus, and Alismatales, and a clade that includes all other monocots. Nartheciaceae are placed as the sister of Pandanales, and Corsiaceae as the sister of Liliales. The Triuridaceae, represented by three genera, including Lacandonia, are resolved as monophyletic and placed in a range of positions, generally within Pandanales. Dasypogonaceae and Arecaceae diverge sequentially from a clade that includes all other commelinid taxa, and within the latter group Poales s. lat. are sister of a clade in which Zingiberales and Commelinales are sisters. Within Poales s. lat., Trithuria (Hydatellaceae) and Mayaca appear to be closely related to some or all elements of Xyridaceae. A comparison was conducted of jackknife and bootstrap values, as computed using strict-consensus (SC) and frequency-within-replicates (FWR) approaches. Jackknife values tend to be higher than bootstrap values, and for each of these methods support values obtained with the FWR approach tend to exceed those obtained with the SC approach.

Intraspecific Variability and Timing in Ancestral Ecology Reconstruction: A Test Case from the Cape Flora

Thamnochortus (ca. 32 species) is an ecologically diverse genus of Restionaceae. Restionaceae comprise a major component of the southern African Cape flora, wherein eco-diversification might have been important in the generation of high levels of species richness. In an attempt to reconstruct the macroecological history of Thamnochortus, it was found that standard procedures for character state optimization make two inappropriate assumptions. The first is that ancestors are monomorphic (i.e., ecologically uniform) and the second is that eco-diversification follows, or is slower than, lineage diversification. We demonstrate a variety of coding schemes with which the assumption of monomorphy can be avoided. For unordered discrete ecological characters, presence coding and generalized frequency coding (GFC) are suboptimal because they occasionally yield illogical assignments of no state to ancestors. Polymorphism coding or use of the program DIVA are preferable in this respect but are applicable only with parsimony. For continuous eco-characters (e.g., a rainfall gradient, where individual species occur in ranges), GFC and MaxMin coding provide equally valid solutions to optimizing ranges with parsimony. However, MaxMin can be extended to likelihood approaches and is therefore preferable. With respect to rates and timing, all algorithms currently employed for ancestral ecology reconstruction bias toward slow rates of eco-diversification relative to lineage diversification. An alternative to this bias is provided by DIVA, which biases toward accelerated rates of eco-diversification and thus inferences of ecology-driven speciation. We see no way of choosing between these biases; however, phylogeneticists should be aware of them. Applying these methods to Thamnochortus, we find there to be important differences in details, yet general congruence, regarding the historical ecology of this clade. We infer the most recent common ancestor of Thamnochortus to have been a post-fire resprouting species distributed on rocky, well-drained, sandstone-derived soils at lower-middle elevations, in regions of moderate levels of yearly (primarily winter) rainfall. This species would have been distributed in habitats much like those of the southwestern Cape mountains today. Major ecological trends include shifts to lower rainfall regimes and shifts from sandstone to limestone-derived alkaline soils at lower altitudes.

Are mitochondrial genes useful for the analysis of monocot relationships

A phylogenetic analysis of monocots and related dicots was conducted, using a four-gene matrix consisting of two genes from the plastid genome (matK and rbcL) and two from the mitochondrial genome (atpA/atp1 and cob). The taxon sample includes 101 monocots and 36 dicots, and all four genes were sampled for all 137 taxa. Jackknife support was assessed for clades resolved by the four-gene analysis, and compared to support for the same clades by each of the four three-gene subset matrices, in order to quantify the degree to which each gene contributed to or detracted from support for each clade. Instances of positively and negatively correlated support for clades by genes of the same and different genomes were observed. In particular, the placement of Acorus within a clade that also includes Tofieldiaceae, Araceae, and Alismatales s.s., as opposed to its frequent placement as sister of all other monocots, is supported by atpA and matK. The results indicate that genes from the mitochondrial genome provide a unique test of relationships that have been inferred with plastid-encoded genes.

A PHYLOGENY FOR THE AFRICAN RESTIONACEAE AND NEW PERSPECTIVES ON MORPHOLOGY'S ROLE IN GENERATING COMPLETE SPECIES PHYLOGENIES FOR LARGE CLADES

Difficulties with obtaining complete species‐level phylogenies include (1) the accurate identification and sampling of species, (2) obtaining a complete species sampling, and (3) resolving relationships among closely related species. We addressed these in a study of 317 species and subspecies of the African Restionaceae. Accurate species identification and collection in the field was facilitated by a morphology‐based interactive key to all species. Despite intensive fieldwork, however, material for DNA extraction could not be obtained for 20 of the 292 species of the focal Restio subclade. Furthermore, the 6831 aligned nucleotides and 1685 parsimony‐informative sequence characters were insufficient to resolve relationships fully within the clade. A simulation indicated that an additional 5000–7000 bases may have been needed to achieve supported resolution in the neighborhood of 95%–100%. Instead of further sequencing, we investigated the phylogenetic utility of the large set of characters contained within the interactive key data set, exploiting recent advances in parsimony and Bayesian programs that allow multistate and supermultistate (including continuous for parsimony) morphological characters. On doing so, parsimony resolution increased 17% to nearly 100%, and overall support increased in both parsimony (bootstrap) and Bayesian (posterior probability) frameworks. Taxa for which DNA data were lacking could be placed in fully resolved positions. Experiments using the parsimony ratchet indicated that placement of these morphology‐only taxa may have been completely accurate 30% of the time, to within three nodes of accuracy 60% of time, and accurate to genus 96% of the time. Accurate placement of morphology‐only taxa through Bayesian analysis may require extensive effort devoted toward exploring tree and parameter space. We conclude that the increasingly available large morphological data sets associated with interactive keys or informatics initiatives represent convenient yet potentially powerful tools in overcoming many of the commonly encountered obstacles in molecular‐based species‐level phylogenetics.

Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity

Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction) and non-equilibrium dynamics on the evolutionary history of angiosperms, a clade well known for the abundance of some trait combinations and the rarity of others. Our analysis reveals that three character states (corolla present, bilateral symmetry, reduced stamen number) act synergistically as a key innovation, doubling diversification rates for lineages in which this combination occurs. However, this combination is currently less common than predicted at equilibrium because the individual characters evolve infrequently. Simulations suggest that angiosperms will remain far from the equilibrium frequencies of character states well into the future. Such non-equilibrium dynamics may be common when major innovations evolve rarely, allowing lineages with ancestral forms to persist, and even outnumber those with diversification-enhancing states, for tens of millions of years.

Plowmanianthus, a New Genus of Commelinaceae with Five New Species from Tropical America

Abstract A new Neotropical genus of Commelinaceae, Plowmanianthus, is described with five new species. Karyological and morphological data, as well as results of phylogenetic studies, support its inclusion in the subtribe Dichorisandrinae (tribe Tradescantieae) with four other genera (Cochliostema, Dichorisandra, Geogenanthus, and Siderasis). The occurrence of moniliform hairs along the distal margins of the petals is evidence of an even closer relationship with Cochliostema and Geogenanthus, this character being restricted in the family to these three genera. Plowmanianthus may be uniquely characterized as comprising small, perennial rosette herbs with usually one-cymed, axillary inflorescences borne among the lower leaves, an androecium reduced to three fertile stamens, annular, papillate stigmas, and uniseriate to partially biseriate seeds. Plants of the genus are shallowly rooted, the roots not penetrating deeper than the leaf-litter or humus-rich layers of their primary rainforest habitats. Plowmanianthus is also distinctive among the Commelinaceae in the unusually high frequency of cleistogamy in the genus, with some species for which only cleistogamous flowers are known. As currently understood, two species (P. panamensis and P. dressleri) are restricted to the Isthmus of Panama, whereas the remaining four taxa (P. grandifolius subsp. grandifolius, P. grandifolius subsp. robustus, P. perforans, and P. peruvianus) are restricted to lowland Amazonia.

Floral Organogenesis in Some Species of Tradescantia and Callisia (Commelinaceae)

The flowers of Tradescantia virginiana, Tradescantia ohioensis, and Callisia navicularis are polysymmetric and comprised of three sepals, three petals, six stamens in two whorls of three, and three connate carpels. Tradescantia and Callisia, as represented in this study, could be distinguished by the relative sizes and shapes of their floral apices. The apex of C. navicularis, for the duration of organ initiation, was considerably smaller and more convex than in either species of Tradescantia. In all three species, the sepals arise, in succession, first. The petals arise next in rapid succession in both Tradescantia species and in very rapid succession or more or less simultaneously in C. navicularis. The carpels arise last in very rapid succession and their connation is evident soon after their initiation. The inner (antepetalous) stamens appear simultaneously with the petals in C. navicularis, and, as with the petals, it is not always clear that these stamens arise sequentially rather than simultaneously. In both Tradescantia species, the inner (antepetalous) stamens arise in rapid succession concurrent with or immediately following the petals. In all three species, emergence of the outer (antesepalous) whorl occurs in rapid succession and usually begins before that of the inner whorl is complete; the last of the outer stamens does not appear until after all inner stamens are present. Therefore, as observed in this study, the two whorls of stamens arise in an overall, although slight, centrifugal sequence. Elsewhere in the family, only centripetal, slightly centripetal, and simultaneous patterns of stamen initiation have been reported. Elsewhere in the monocotyledons, centrifugal androecia are limited to certain polyandrous palm and alismatid genera, all of which are fundamentally different from and are not homologous to the tradescantioid centrifugal androecium.

Consistent phenological shifts in the making of a biodiversity hotspot: the Cape flora

BackgroundThe best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change have been little documented. Here we use phylogenies to reconstruct changes in distribution and flowering ecology of the Cape flora - South Africas biodiversity hotspot - through a period of past (Neogene and Quaternary) changes in the seasonality of rainfall over a timescale of several million years.ResultsForty-three distributional and phenological shifts consistent with past climatic change occur across the flora, and a comparable number of clades underwent adaptive changes in their flowering phenology (9 clades; half of the clades investigated) as underwent distributional shifts (12 clades; two thirds of the clades investigated). Of extant Cape angiosperm species, 14-41% have been contributed by lineages that show distributional shifts consistent with past climate change, yet a similar proportion (14-55%) arose from lineages that shifted flowering phenology.ConclusionsAdaptive changes in ecology at the scale we uncover in the Cape and consistent with past climatic change have not been documented for other floras. Shifts in climate tolerance appear to have been more important in this flora than is currently appreciated, and lineages that underwent such shifts went on to contribute a high proportion of the floras extant species diversity. That shifts in phenology, on an evolutionary timescale and on such a scale, have not yet been detected for other floras is likely a result of the method used; shifts in flowering phenology cannot be detected in the fossil record.

Floral Organogenesis in Plowmanianthus (Commelinaceae)

Floral organogenesis in three species of Plowmanianthus (subtribe Dichorisandrinae; tribe Tradescantieae) is described. Development begins as in other commelinaceous monosymmetric or monosymmetric‐derived flowers for which comparable data are available, with the precocious development of the upper (outer) sepal. Later, six stamen primordia emerge from the floral apex, but the lower three are soon aborted such that there are only three stamens at anthesis. Development of the lower petal is precocious. That is, although all three petals are at first similar in size and appearance following their simultaneous or nearly simultaneous initiation, the lower petal expands much more rapidly than either of the inner petals and initiates its fringe of moniliform hairs first. Early and middle phases of floral ontogeny in Plowmanianthus most closely resemble those of the closely related Cochliostema, especially in regards to suppression of the lower stamens and the laterally appressed, introrsely oriented, strongly curved anther thecae of the upper stamens. The staminal features unique to Cochliostema, such as union and curvature of the filaments, spiraling of the thecae, and development of filament‐borne structures enveloping the anthers, occur relatively late in development in this genus and are lacking in Plowmanianthus. Floral ontogenetic studies are still needed for other Dichorisandrinae, such as Geogenanthus, Siderasis, and additional species of the relatively large genus Dichorisandra, before an adequate understanding can be attained of how ontogenetic processes have evolved and shaped the remarkable floral diversity in this subtribe.

Simple Biodiversity Mashups for Non-Tech-Savvy Biologists: A Demonstration Using The Liana Flora of Pennsylvania, USA1

Abstract A step-by-step procedure is described and demonstrated using the liana flora of Pennsylvania, USA, for the creation of simple biodiversity informatics applications in the form of Web-mashups. The target audience is non-tech-savvy biologists. For each liana species, the Web-based Liana Atlas of Pennsylvania creates Species Pages by aggregating information or direct links to information on taxonomy, distribution, morphology, genetics, as well as photographs and general encyclopedic or bibliographic information, “live” from third-party websites including the Global Biodiversity Information Facility, the USDA PLANTS database, Wikipedia®, and GenBank®. The result is an original, information-rich, fully illustrated application providing more up-to-date information on Pennsylvanian lianas in one place than had previously been available elsewhere. More importantly, the procedure described and files available at the demonstration website are portable and customizable to many other biogeographic regions or taxa, and its application requires only basic knowledge of Web navigation and text editors. We hope that this procedure will encourage others, including biologists with limited IT knowledge or at smaller institutions with limited resources, to contribute their own informatics applications valuable to local or regional interest-groups such as educators, students, and amateurs.