http://amborella.net/2010PlantSystematics/DATA/3-24-APG%202003%20Bot%20J%20Linn%20Soc%20APGII.pdf

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II

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.

The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis

INTRODUCTION. Internal Organization of the Plant Body. Summary of Types of Cells and Tissues. General References. DEVELOPMENT OF THE SEED PLANT. The Embryo. From embryo to the Adult Plant. Apical Meristems and Their Derivatives. Differentiation, Specialization, and Morphogenesis. References. THE CELL. Cytoplasm. Nucleus. Plastids. Mitochondria. Microbodies. Vacuoles. Paramural Bodies. Ribosomes. Dictyosomes. Endoplasmic Reticulum. Lipid Globules. Microtubules. Ergastic Substances. References. CELL WALL. Macromolecular Components and Their Organization in the Wall. Cell Wall Layers. Intercellular Spaces. Pits, Primary Pit--Fields, and Plasmodesmata. Origin of Cell Wall During Cell Division. Growth of Cell Wall. References. PARENCHYMA AND COLLENCHYMA. Parenchyma. Collenchyma. References. SCLERENCHYMA. Sclereids. Fibers. Development of Sclereids and Fibers. References. EPIDERMIS. Composition. Developmental Aspects. Cell Wall. Stomata. Trichomes. References. XYLEM: GENERAL STRUCTURE AND CELL TYPES. Gross Structure of Secondary Xylem. Cell Types in the Secondary Xylem. Primary Xylem. Differentiation of Tracheary Elements. References. XYLEM: VARIATION IN WOOD STRUCTURE. Conifer Wood. Dicotyledon Wood. Some Factors in Development of Secondary Xylem. Identification of Wood. References. VASCULAR CAMBIUM. Organization of Cambium. Developmental Changes in the Initial Layer. Patterns and Causal Relations in Cambial Activity. References. PHLOEM. Cell Types. Primary Phloem. Secondary Phloem. References. PERIDERM. Structure of Periderm and Related Tissues. Development of Periderm. Outer Aspect of Bark in Relation to Structure. Lenticels. References. SECRETORY STRUCTURES. External Secretory Structures. Internal Secretory Structures. References. THE ROOT: PRIMARY STATE OF GROWTH. Types of Roots. Primary Structure. Development. References. THE ROOT: SECONDARY STATE OF GROWTH AND ADVENTITIOUS ROOTS. Common Types of Secondary Growth. Variations in Secondary Growths. Physiologic Aspects of Secondary Growth in Roots. Adventitious Roots. References. THE STEM: PRIMARY STATE OF GROWTH. External Morphology. Primary Structure. Development. References. THE STEM: SECONDARY GROWTH AND STRUCTURAL TYPES. Secondary Growth. Types of Stems. References. THE LEAF: BASIC STRUCTURE AND DEVELOPMENT. Morphology. Histology of Angiosperm Leaf. Development. Abscission. References. THE LEAF: VARIATIONS IN STRUCTURE. Leaf Structure and Environment. Dicotyledon Leaves. Monocotyledon Leaves. Gymnosperm Leaves. References. THE FLOWER: STRUCTURE AND DEVELOPMENT. Concept. Structure. Development. References. THE FLOWER: REPRODUCTIVE CYCLE. Microsporogenesis. Pollen. Male Gametophyte. Megasporogenesis. Female Gametophyte. Fertilization. References. THE FRUIT. Concept and Classification. The Fruit Wall. Fruit Types. Fruit Growths. Fruit Abscission. References. THE SEED. Concept and Morphology. Seed Development. Seed Coat. Nutrient Storage Tissues. References. EMBRYO AND SEEDLING. Mature Embryo. Development of Embryo. Classification of Embryos. Seedling. References. Glossary. Index.

Anatomy of Seed Plants

Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences

Calcium oxalate (CaOx) crystals are distributed among all taxonomic levels of photosynthetic organisms from small algae to angiosperms and giant gymnosperms. Accumulation of crystals by these organisms can be substantial. Major functions of CaOx crystal formation in plants include high-capacity calcium (Ca) regulation and protection against herbivory. Ultrastructural and developmental analyses have demonstrated that this biomineralization process is not a simple random physical-chemical precipitation of endogenously synthesized oxalic acid and environmentally derived Ca. Instead, crystals are formed in specific shapes and sizes. Genetic regulation of CaOx formation is indicated by constancy of crystal morphology within species, cell specialization, and the remarkable coordination of crystal growth and cell expansion. Using a variety of approaches, researchers have begun to unravel the exquisite control mechanisms exerted by cells specialized for CaOx formation that include the machinery for uptake and accumulation of Ca, oxalic acid biosynthetic pathways, and regulation of crystal growth.

CALCIUM OXALATE IN PLANTS: Formation and Function

Pollen aperture evolution--a crucial factor for eudicot success?

Microsporogenesis in Monocotyledons

Following recent phylogenetic studies of the families and genera of Dioscoreales, the identification of monophyletic infrageneric taxa in the pantropical genus Dioscorea is a priority. A phylogenetic analysis based on sequence data from the plastid genes rbcL and matK is presented, using 67 species of Dioscorea and covering all the main Old World and selected New World lineages. The analysis used 14 outgroup taxa, including Trichopus Gaertn., Tacca J.R. & G. Forster, Stenomeris Planch., Burmannia L. and Thismia Griff. The main findings are: a) that a clade of rhizomatous taxa is sister to the rest of Dioscorea; b) the main Old World groups (such as the right-twining D. sect. Enantiophyllum) are monophyletic and c) there are two distinct lineages among the endemic Malagasy taxa. The consequences of the results for infrageneric classification of Dioscorea is considered, in particular the possibility of greatly simplifying the classifications of Knuth and Burkill. The results are also used to present novel hypotheses of character evolution in selected underground.

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A Plastid gene phylogeny of the yam genus, Dioscorea : Roots, fruits and madagascar

Cladistic analysis of molecular data (plastid rbcL sequences) supports the interpretation of simultaneous microsporogenesis as an apomorphy for Asparagales (Lilianae), with a reversal in the most d...

Microsporogenesis and pollen sulcus type in Asparagales (Lilianae)

Microsporogenesis is highly labile in early‐branching angiosperms, i.e., those with mostly sulcate pollen, compared with the tricolpate and tricolpate‐derived eudicots. New records of microsporogenesis in basal angiosperms (19 taxa were examined), together with a review of the literature, demonstrate that the existing typology has been too strictly applied; several basal angiosperms have apparently intermediate forms and therefore do not fit easily into simultaneous or successive categories. Intermediate forms include the “modified simultaneous” type, where ephemeral cell plates are formed after the first meiotic division but then disperse, and simultaneous cleavage follows the second meiotic division. This relative diversity reflects a range of variation in number and position of pollen apertures in basal angiosperms, although both monosulcate and inaperturate pollen may occur in conjunction with either simultaneous or successive microsporogenesis. However, many taxa with inaperturate pollen have success...

Carol A. Furness

Papers

Pollen aperture evolution--a crucial factor for eudicot success?

Microsporogenesis in Monocotyledons

A Plastid gene phylogeny of the yam genus, Dioscorea : Roots, fruits and madagascar

Microsporogenesis and pollen sulcus type in Asparagales (Lilianae)

Evolution of Microsporogenesis in Angiosperms