Phylogenetics often uncovers contradicting hypotheses regarding the relationships within the same group of organisms, a phenomenon known since the beginning of the molecular systematics era. While, historically, single marker-based analyses produced discordance, nowadays entire cellular genomes or portions of the same genomic compartment conflict with others or the rest, respectively. In contrast to the beginning of the molecular systematics era, when adding markers and taxa offered a way out of systematic errors, genome inference-based incongruences cannot be addressed and explained easily. Disagreeing phylogenomic hypotheses might originate from various evolutionary processes, including but not limited to hybridization or incomplete lineage sorting, thereby leading to gene tree-versus species tree-associated discrepancies. Today, this can be expanded to genome discordance, where phylogenomic signals of organellar genomes (plastid, mitochondrial) and the nuclear genome disagree due to intrinsically different coalescent paths or phenomena like organelle capture.

The field of plant taxonomy has transformed rapidly over the past fifteen years, especially with regard to improvements in cladistic analysis and the use of new molecular data. The second edition of this popular resource reflects these far-reaching and dramatic developments with more than 3,000 new references and many new figures. Synthesizing current research and trends, Plant Taxonomy now provides the most up-to-date overview in relation to monographic, biodiversity, and evolutionary studies, and continues to be an essential resource for students and scholars. This text is divided into two parts: Part 1 explains the principles of taxonomy, including the importance of systematics, characters, concepts of categories, and different approaches to biological classification. Part 2 outlines the different types of data used in plant taxonomic studies with suggestions on their efficacy and modes of presentation and evaluation. This section also lists the equipment and financial resources required for gathering each type of data. References throughout the book illuminate the historical development of taxonomic terminology and philosophy while citations offer further study. Plant Taxonomy is also a personal story of what it means to be a practicing taxonomist and to view these activities within a meaningful conceptual framework. Tod F. Stuessy recalls the progression of his own work and shares his belief that the most creative taxonomy is done by those who have a strong conceptual grasp of their own research.

This volume presents a compelling collection of state-of-the-art work in algorithmic computational biology, honoring the legacy of Professor Bernard M.E. Moret in this field. Reflecting the wide-ranging influences of Prof. Moret’s research, the coverage encompasses such areas as phylogenetic tree and network estimation, genome rearrangements, cancer phylogeny, species trees, divide-and-conquer strategies, and integer linear programming. Each self-contained chapter provides an introduction to a cutting-edge problem of particular computational and mathematical interest. Topics and features: addresses the challenges in developing accurate and efficient software for the NP-hard maximum likelihood phylogeny estimation problem; describes the inference of species trees, covering strategies to scale phylogeny estimation methods to large datasets, and the construction of taxonomic supertrees; discusses the inference of ultrametric distances from additive distance matrices, and the inference of ancestral genomes under genome rearrangement events; reviews different techniques for inferring evolutionary histories in cancer, from the use of chromosomal rearrangements to tumor phylogenetics approaches; examines problems in phylogenetic networks, including questions relating to discrete mathematics, and issues of statistical estimation; highlights how evolution can provide a framework within which to understand comparative and functional genomics; provides an introduction to Integer Linear Programming and its use in computational biology, including its use for solving the Traveling Salesman Problem. Offering an invaluable source of insights for computer scientists, applied mathematicians, and statisticians, this illuminating volume will also prove useful for graduate courses on computational biology and bioinformatics.

The modified mouthparts group is perhaps the largest of the four major Hawaiian Drosophila clades, yet has received relatively little taxonomic attention during the past 40 years. This study reviews unplaced species and the ceratostoma, freycinetiae, semifuscata, and setiger subgroups, with descriptions of 22 new species. We hope this work encourages greater study of the biology of this important group.

When Rolf Dahlgren and I embarked on preparing this book series, Rolf took prime responsibility for monocotyledons, which had interested him for a long time. After finishing his comparative study and family classification of the monocots, he devoted much energy to the acquisition and editing of family treatments for the present series. After his untimely death, Peter Goldblatt, who had worked with him, continued to handle further incoming monocot manuscripts until, in the early 1990s, his other obligations no longer allowed him to continue. At that time, some 30 manuscripts in various states of perfection had accumulated, which seemed to form a solid basis for a speedy completion of the FGVP monocots; with the exception of the grasses and orchids which would appear in separate volumes. I felt a strong obligation to do everything to help in publishing the manuscripts that had been put into our hands. I finally decided to take charge of them personally, although during my life as a botainst I had never seriously been interested in monocots.

Although they are relative latecomers on the evolutionary scene, having emerged only 135?170 million years ago, angiosperms—or flowering plants—are the most diverse and species-rich group of seed-producing land plants, comprising more than 15,000 genera and over 350,000 species. Not only are they a model group for studying the patterns and processes of evolutionary diversification, they also play major roles in our economy, diet, and courtship rituals, producing our fruits, legumes, and grains, not to mention the flowers in our Valentine’s bouquets. They are also crucial ecologically, dominating most terrestrial and some aquatic landscapes. This fully revised edition of Phylogeny and Evolution of the Angiosperms provides an up-to-date, comprehensive overview of the evolution of and relationships among these vital plants. Incorporating molecular phylogenetics with morphological, chemical, developmental, and paleobotanical data, as well as presenting a more detailed account of early angiosperm fossils and important fossil information for each evolutionary branch of the angiosperms, the new edition integrates fossil evidence into a robust phylogenetic framework. Featuring a wealth of new color images, this highly synthetic work further reevaluates long-held evolutionary hypotheses related to flowering plants and will be an essential reference for botanists, plant systematists, and evolutionary biologists alike.

Plastid Genome Evolution, Volume 85 provides a summary of recent research on plastid genome variation and evolution across photosynthetic organisms. It covers topics ranging from the causes and consequences of genomic changes, to the phylogenetic utility of plastomes for resolving relationships across the photosynthetic tree of life. This newly released volume presents thorough, up-to-date information on coevolution between the plastid and nuclear genomes, with chapters on plastid autonomy vs. nuclear control over plastid function, establishment and genetic integration of plastids, plastid genomes in alveolate protists, plastid genomes of glaucophytes, the evolution of the plastid genome in chlorophyte and streptophyte green algae, and more. Provides comprehensive coverage of plastid genome variation by leading researchers in the field Presents a broad range of taxonomic groups, ranging from single and multicellular algae, to the major clades of land plants Includes thorough, up-to-date information on coevolution between the plastid and nuclear genomes

The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as the first, with many exciting developments yet to come. This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography—the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics. The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes: Parsimony and parsimony analysis Parametric phylogenetics including maximum likelihood and Bayesian approaches Phylogenetic classification Critiques of evolutionary taxonomy, phenetics, and transformed cladistics Specimen selection, field collecting, and curating Systematic publication and the rules of nomenclature Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology.

Phylogenetic Systematics: Haeckel to Hennig traces the development of phylogenetic systematics against the foil of idealistic morphology through 100 years of German biology. It starts with the iconic Ernst Haeckel-the German Darwin from Jena-and the evolutionary morphology he developed. It ends with Willi Hennig, the founder of modern phylogenetic