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

In the analysis of sequence-based data matrices, the use of different methods of treating gaps has been demonstrated to in? fluence the resulting phylogenetic hypothe? ses (e.g., Eernisse and Kluge, 1993; Vogler and DeSalle, 1994; Simons and Mayden, 1997). Despite this influence, a well-justi? fied, uniformly applied method of treating gaps is lacking in sequence-based phyloge? netic studies. Treatment of gaps varies widely from secondarily mapping gaps onto the tree inferred from base characters

/pdf/gaps-as-characters-in-sequence-based-phylogenetic-analyses-4hdlrw0k0r.pdf

Gaps as Characters in Sequence-Based Phylogenetic Analyses

Seed dormancy is an innate seed property that defines the environmental conditions in which the seed is able to germinate. It is determined by genetics with a substantial environmental influence which is mediated, at least in part, by the plant hormones abscisic acid and gibberellins. Not only is the dormancy status influenced by the seed maturation environment, it is also continuously changing with time following shedding in a manner determined by the ambient environment. As dormancy is present throughout the higher plants in all major climatic regions, adaptation has resulted in divergent responses to the environment. Through this adaptation, germination is timed to avoid unfavourable weather for subsequent plant establishment and reproductive growth. In this review, we present an integrated view of the evolution, molecular genetics, physiology, biochemistry, ecology and modelling of seed dormancy mechanisms and their control of germination. We argue that adaptation has taken place on a theme rather than via fundamentally different paths and identify similarities underlying the extensive diversity in the dormancy response to the environment that controls germination.

/pdf/seed-dormancy-and-the-control-of-germination-4tdhm2985s.pdf

Seed dormancy and the control of germination

Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous

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

The {ITS} region of nuclear ribosomal {DNA}: {A} valuable source of evidence on angiosperm phylogeny

THE SCIENCE OF PLANT SYSTEMATICS - What Do We Mean by Plant? - What Do We Mean by Systematics? - A Phylogenetic Approach - The Practice of Plant Systematics - Why is Systematics Important? - Aims and Organization of This Book - PRINCIPLES OF BIOLOGICAL SYSTEMATICS - What is a Phylogeny? - Determining Evolutionary History - Constructing a Classification - Summary - CLASSIFICATION AND SYSTEM IN FLOWERING PLANTS: THE HISTORICAL BACKGROUND - Classification, Nature, and Stability - Understanding Relationships - Classifications and Memory - Higher Taxa and Their Formation - Plant Groupings - Summary - TAXONOMIC EVIDENCE: STRUCTURAL AND BIOCHEMICAL CHARACTERS - Morphology - Pollination Biology - Inflorescences, Fruits, and Seeds - Anatomy - Embryology - Chromosomes - Palynology - Secondary Plant Compounds - Proteins - Summary - MOLECULAR SYSTEMATICS - Plant Genomes - Generating Molecular Data - Types of Molecular Data - Analysis of Molecular Data - Molecular Characters - Summary - THE EVOLUTION OF PLANT DIVERSITY - Plant Diversity Is the Result of Evolution - Variation in Plant Populations and Species - Speciation - Species Concepts - Summary - AN OVERVIEW OF PLANT EVOLUTION - Endosymbiotic Events - Miscellaneous 'Algae' - Green Plants - Land Plants - Vascular Plants - Seed Plants - Flowering Plants - PHYLOGENETIC RELATIONSHIPS OF LYCOPHYTES, FERNS AND THEIR ALLIES, AND GYMNOSPERMS - Lycophytes - Ferns and Their Allies - Gymnosperms - Cycads - Ginkgos - Conifers - Gnetophytes - PHYLOGENETIC RELATIONSHIPS OF ANGIOSPERMS - 'Basal Families' - Amborellales - Nymphaeales - Austrobaileyales - Magnoliid Complex - Magnoliales - Laurales - Canellales - Piperales - Monocots - Alismatales - Petaloid Monocots (Liliales, Asparagales, Dioscoreales) - Commelinoid Monocots (Arecales, Commelinales, Poales, Zingiberales) - Eudicots (Tricolpates) - 'Basal Tricolpates' - Ranunculales, Proteales, and several small groups - Core Eudicots - Caryophyllid Clade (Caryophyllales, Polygonales) - Santalales - Rosid Clade - Saxifragales - Vitales - Myrtales - Eurosids I (Zygophyllales, Oxalidales, Celastrales, Malpighiales, - Fabales, Rosales, Cucurbitales, Fagales) - Eurosids II (Brassicales, Malvales, Sapindales) - Asterid clade (Sympetalae) - Cornales - Ericales - Euasterids I (Solanales, Gentianales, Lamiales) - Euasterids II (Aquifoliales, Apiales, Dipsacales, Asterales) - - Appendix 1. Botanical Nomenclature - Appendix 2. Specimen Preparation and Identification - Glossary - Taxonomic Index - Subject Index

Plant Systematics: A Phylogenetic Approach

Erratum: The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny (Annals of the Missouri Botanical Garden (1995) 82 (247-277))

Phylogenetic relationships among 88 genera of Rosaceae were investigated using nucleotide sequence data from six nuclear (18S, gbssi1, gbssi2, ITS, pgip, and ppo) and four chloroplast (matK, ndhF, rbcL, and trnL-trnF) regions, separately and in various combinations, with parsimony and likelihood-based Bayesian approaches. The results were used to examine evolution of non-molecular characters and to develop a new phylogenetically based infrafamilial classification. As in previous molecular phylogenetic analyses of the family, we found strong support for monophyly of groups corresponding closely to many previously recognized tribes and subfamilies, but no previous classification was entirely supported, and relationships among the strongly supported clades were weakly resolved and/or conflicted between some data sets. We recognize three subfamilies in Rosaceae: Rosoideae, including Filipendula, Rubus, Rosa, and three tribes; Dryadoideae, comprising the four actinorhizal genera; and Spiraeoideae, comprising Lyonothamnus and seven tribes. All genera previously assigned to Amygdaloideae and Maloideae are included in Spiraeoideae. Three supertribes, one in Rosoideae and two in Spiraeoideae, are recognized.

http://www.bergianska.se/polopoly_fs/1.68351.1325501360!/menu/standard/file/Potter_et_al_2007.pdf

Christopher S. Campbell

Papers

The {ITS} region of nuclear ribosomal {DNA}: {A} valuable source of evidence on angiosperm phylogeny

Plant Systematics: A Phylogenetic Approach

Plant Systematics: A Phylogenetic Approach

Erratum: The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny (Annals of the Missouri Botanical Garden (1995) 82 (247-277))

Phylogeny and classification of Rosaceae