American Journal of Botany

Although the chloroplast genome contains many noncoding regions, relatively few have been exploited for interspecific phylogenetic and intraspecific phylogeographic studies. In our recent evaluation of the phylogenetic utility of 21 noncoding chloroplast regions, we found the most widely used noncoding regions are among the least variable, but the more variable regions have rarely been employed. That study led us to conclude that there may be unexplored regions of the chloroplast genome that have even higher relative levels of variability. To explore the potential variability of previously unexplored regions, we compared three pairs of single‐copy chloroplast genome sequences in three disparate angiosperm lineages: Atropa vs. Nicotiana (asterids); Lotus vs. Medicago (rosids); and Saccharum vs. Oryza (monocots). These three separate sequence alignments highlighted 13 mutational hotspots that may be more variable than the best regions of our former study. These 13 regions were then selected for a more detailed analysis. Here we show that nine of these newly explored regions (rpl32‐trnL^(UAG), trnQ^(UUG)‐5′rps16, 3′trnV^(UAC)‐ndhC, ndhF‐rpl32, psbD‐trnT^(GGU), psbJ‐petA, 3′rps16–5′trnK^(UUU), atpI‐atpH, and petL‐psbE) offer levels of variation better than the best regions identified in our earlier study and are therefore likely to be the best choices for molecular studies at low taxonomic levels.

Chloroplast DNA sequences are a primary source of data for plant molecular systematic studies. A few key papers have provided the molecular systematics community with universal primer pairs for noncoding regions that have dominated the field, namely trnL‐trnF and trnK/matK. These two regions have provided adequate information to resolve species relationships in some taxa, but often provide little resolution at low taxonomic levels. To obtain better phylogenetic resolution, sequence data from these regions are often coupled with other sequence data. Choosing an appropriate cpDNA region for phylogenetic investigation is difficult because of the scarcity of information about the tempo of evolutionary rates among different noncoding cpDNA regions. The focus of this investigation was to determine whether there is any predictable rate heterogeneity among 21 noncoding cpDNA regions identified as phylogenetically useful at low levels. To test for rate heterogeneity among the different cpDNA regions, we used three species from each of 10 groups representing eight major phylogenetic lineages of phanerogams. The results of this study clearly show that a survey using as few as three representative taxa can be predictive of the amount of phylogenetic information offered by a cpDNA region and that rate heterogeneity exists among noncoding cpDNA regions.

A classification of the architectural features of dicot leaves—i.e., the placement and form of those elements constituting the outward expression of leaf structure, including shape, marginal configuration, venation, and gland position—has been developed as the result of an extensive survey of both living and fossil leaves. This system partially incorporates modifications of two earlier classifications: that of Turrill for leaf shape and that of Von Ettingshausen for venation pattern. After categorization of such features as shape of the whole leaf and of the apex and base, leaves are separated into a number of classes depending on the course of their principal venation. Identification of order of venation, which is fundamental to the application of the classification, is determined by size of a vein at its point of origin and to a lesser extent by its behavior in relation to that of other orders. The classification concludes by describing features of the areoles, i.e., the smallest areas of leaf tissue surrounded by veins which form a contiguous field over most of the leaf. Because most taxa of dicots possess consistent patterns of leaf architecture, this rigorous method of describing the features of leaves is of immediate usefulness in both modern and fossil taxonomic studies. In addition, as a result of this method, it is anticipated that leaves will play an increasingly important part in phylogenetic and ecological studies.

Phylogenetic analysis of 330 plastidmatKgene sequences, representing 235 genera from 37 of 39 tribes, and four outgroup taxa from eurosids I supports many well‐resolved subclades within the Leguminosae. These results are generally consistent with those derived from other plastid sequence data (rbcLandtrnL), but show greater resolution and clade support overall. In particular, the monophyly of subfamily Papilionoideae and at least seven major subclades are well‐supported by bootstrap and Bayesian credibility values. These subclades are informally recognized as theCladrastisclade, genistoid sensu lato, dalbergioid sensu lato, mirbelioid, millettioid, and robinioid clades, and the inverted‐repeat‐lacking clade (IRLC). The genistoid clade is expanded to include genera such asPoecilanthe,Cyclolobium,Bowdichia, andDiplotropisand thus contains the vast majority of papilionoids known to produce quinolizidine alkaloids. The dalbergioid clade is expanded to include the tribe Amorpheae. The mirbelioids include the tribes Bossiaeeae and Mirbelieae, with Hypocalypteae as its sister group. The millettioids comprise two major subclades that roughly correspond to the tribes Millettieae and Phaseoleae and represent the only major papilionoid clade marked by a macromorphological apomorphy, pseudoracemose inflorescences. The robinioids are expanded to includeSesbaniaand members of the tribe Loteae. The IRLC, the most species‐rich subclade, is sister to the robinioids. Analysis of thematKdata consistently resolves but modestly supports a clade comprising papilionoid taxa that accumulate canavanine in the seeds. This suggests a single origin for the biosynthesis of this most commonly produced of the nonprotein amino acids in legumes.

• 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.

The wide size range of conifer tracheids and angiosperm vessels has important consequences for function. In both conduit types, bigger is better for conducting efficiency. The gain in efficiency with size is maximized by the control of conduit shape, which balances end‐wall and lumen resistances. Although vessels are an order of magnitude longer than tracheids of the same diameter, they are not necessarily more efficient because they lack the low end‐wall resistance of tracheids with torus‐margo pits. Instead, vessels gain conducting efficiency over tracheids by achieving wider maximum diameters. End‐walls contributed 56–64% to total xylem resistance in both conduit types, indicating that length limits conducting efficiency. Tracheid dimensions may be more limited by unicellularity and the need to supply strength to homoxylous wood than by the need to protect against cavitation. In contrast, the greater size of the multicellular vessel is facilitated by fibers that strengthen heteroxylous wood. Vessel dimensions may be most limited by the need to restrict intervessel pitting and cavitation by air‐seeding. Stressful habitats that promote narrow vessels should favor coexistence of conifers and angiosperms. The evolution of vessels in angiosperm wood may have required early angiosperms to survive a phase of mechanic and hydraulic instability.

The field of plant molecular systematics is expanding rapidly, and with it new and refined methods are coming into use. This paper reviews recent advances in experimental methods and data analysis, as applied to the chloroplast genome. Restriction site mapping of the chloroplast genome has been used widely, but is limited in the range of taxonomic levels to which it can be applied. The upper limits (i.e., greatest divergence) of its application are being explored by mapping of the chloroplast inverted repeat region, where rates of nucleotide substitution are low. The lower limits of divergence amenable to restriction site study are being examined using restriction enzymes with 4‐base recognition sites to analyze polymerase chain reaction (PCR)‐amplified portions of the chloroplast genome that evolve rapidly. The comparison of DNA sequences is the area of molecular systematics in which the greatest advances are being made. PCR and methods for direct sequencing of PCR products have resulted in a mushrooming of sequence data. In theory, any degree of divergence is amenable to comparative sequencing studies. In practice, plant systematists have focused on two slowly evolving sequences (rbcL and rRNA genes). More rapidly evolving DNA sequences, including rapidly changing chloroplast genes, chloroplast introns, and intergenic spacers, and the noncoding portions of the nuclear ribosomal RNA repeat, also are being investigated for comparative purposes. The relative advantages and disadvantages of comparative restriction site mapping and DNA sequencing are reviewed. For both methods, the analysis of resulting data requires sufficient taxon and character sampling to achieve the best possible estimate of phylogenetic relationships. Parsimony analysis is particularly sensitive to the issue of taxon sampling due to the problem of long branches attracting on a tree. However, data sets with many taxa present serious computational difficulties that may result in the inability to achieve maximum parsimony or to find all shortest trees.

Symbiotic associations between plants and arbuscular mycorrhizal fungi are ubiquitous and ecologically important in many grasslands. Differences in species responses to mycorrhizal colonization can have a significant influence on plant community structure. The growth responses of 36 species of warm‐ and cool‐season tallgrass prairie grasses and 59 tallgrass prairie forbs to arbuscular mycorrhizal (AM) fungal colonization were assessed in greenhouse studies to examine the extent of interspecific variation in host‐plant benefit from the symbiosis and patterns of mycorrhizal dependence among host plant life history (e.g., annual, perennial) and taxonomic (e.g., grass, forb, legume, nonlegume) groups and phenological guilds. There was a strong and significant relationship between phenology of prairie grasses and mycorrhizal responsiveness, however this relationship was less apparent in forbs. Perennial warm‐season C₄ grasses and forbs generally benefited significantly from the mycorrhizal symbiosis, whereas biomass production of the cool‐season C₃ grasses was not affected. The root systems of the cool‐season grasses were also less highly colonized by the AM fungi, as compared to the warm‐season grasses or forbs. Unlike the native perennials, annuals were generally not responsive to mycorrhizal colonization and were lower in percentage root colonization than the perennial species. Plant growth responsiveness and AM root colonization were positively correlated for the nonleguminous species, with this relationship being strongest for the cool‐season grasses. In contrast, root colonization of prairie legumes showed a significant, but negative, relationship to mycorrhizal growth responsiveness.

In this paper, we focus on dinoflagellate ecology, toxin production, fossil record, and a molecular phylogenetic analysis of hosts and plastids. Of ecological interest are the swimming and feeding behavior, bioluminescence, and symbioses of dinoflagellates with corals. The many varieties of dinoflagellate toxins, their biological effects, and current knowledge of their origin are discussed. Knowledge of dinoflagellate evolution is aided by a rich fossil record that can be used to document their emergence and diversification. However, recent biogeochemical studies indicate that dinoflagellates may be much older than previously believed. A remarkable feature of dinoflagellates is their unique genome structure and gene regulation. The nuclear genomes of these algae are of enormous size, lack nucleosomes, and have permanently condensed chromosomes. This chapter reviews the current knowledge of gene regulation and transcription in dinoflagellates with regard to the unique aspects of the nuclear genome. Previous work shows the plastid genome of typical dinoflagellates to have been reduced to single‐gene minicircles that encode only a small number of proteins. Recent studies have demonstrated that the majority of the plastid genome has been transferred to the nucleus, which makes the dinoflagellates the only eukaryotes to encode the majority of typical plastid genes in the nucleus. The evolution of the dinoflagellate plastid and the implications of these results for understanding organellar genome evolution are discussed.

The relationship between near‐infrared reflectance at 800 nm (NIRR) from leaves and characteristics of leaf structure known to affect photosynthesis was investigated in 48 species of alpine angiosperms. This wavelength was selected to discriminate the effects of leaf structure vs. chemical or water content on leaf reflectance. A quantitative model was first constructed correlating NIRR with leaf structural characteristics for six species, and then validated using all 48 species. Among the structural characteristics tested in the reflectance model were leaf trichome density, the presence or absence of both leaf bicoloration and a thick leaf cuticle (>1 μm), leaf thickness, the ratio of palisade mesophyll to spongy mesophyll thickness (PM/SM), the proportion of the mesophyll occupied by intercellular air spaces (%IAS), and the ratio of mesophyll cell surface area exposed to IAS (A_mes) per unit leaf surface area (A), or A_mes/A. Multiple regression analysis showed that measured NIRR was highly correlated with A_mes/A, leaf bicoloration, and the presence of a thick leaf cuticle (r² = 0.93). In contrast, correlations between NIRR and leaf trichome density, leaf thickness, the PM/SM ratio, or %IAS were relatively weak (r² < 0.25). A model incorporating A_mes/A, leaf bicoloration, and cuticle thickness predicted NIRR accurately for 48 species (r² = 0.43; P < 0.01) and may be useful for linking remotely sensed data to plant structure and function.