Species and Systematics – serie

This volume discusses the aspects of a phylogenetic analysis that go beyond basic calculation of most parsimonious trees. Practical application of all principles discussed is illustrated by reference to TNT, a freely available software package that can perform all the steps needed in a phylogenetic analysis. The first problem considered is how to summarize and compare multiple trees (including identification and handling wildcard taxa). Evaluation of the strength of support for groups, another critical component of any phylogenetic analysis, is given careful consideration. The different interpretations of measures of support are discussed and connected with alternative implementations. The book reviews rationales for estimating character reliability on the basis of homoplasy, with particular attention to morphological characters. The main methods for character weighting and their practical implementation, several of them unique to TNT, are discussed ad libitum. Also unique to TNT is the ability to directly analyze morphometric data (including landmarks), on the same footing as discrete characters. Finally, the scripting language of TNT is introduced. With scripting, it is possible to "program" TNT to create personalized routines and automate complex calculations, taking analyses to the next level and allowing exploration of new methods and ideas.Key FeaturesDiscusses the treatment of ambiguity in phylogenetic analyses in depth, for summarizing results or comparing treesReviews literature on arguments and methods for weighting morphological characters and their practical applicationDescribes theory and application of methods for evaluating strength of group support, based on either resampling or comparisons with suboptimal treesDiscusses the use of morphometric characters in phylogenetic analysisPresents extensive information on commands and options of the TNT computer program, including the use and creation of scripts

Species Problems and Beyond offers a collection of up-to-date essays discussing from an interdisciplinary perspective the many ramifications of the ‘Species Problem.’ The authors represent experts in the philosophy of biology, in species-level evolutionary investigations, and in biodiversity studies and conservation. Some of the topics addressed concern the context sensitivity of the term ‘species’; species as individuals, processes, natural kinds, or as ‘operative concepts’; species delimitation in the age of Big (genomic) Data; and taxonomic inflation and its consequences for conservation strategies. The carefully edited volume will be an invaluable resource for philosophers of biology and evolutionary biologists alike. – Olivier Rieppel, Rowe Family Curator of Evolutionary Biology, Negaunee Integrative Research Center, Field Museum, USASpecies, or ‘the Species Problem’, is a topic in science, in the philosophy of science, and in general philosophy. In fact, it encompasses many aspects of the same problem, and these are dealt with in this volume. Species are often thought of as fundamental units of biological matter to be used in ecology, conservation, classification, and biodiversity. The chapters in this book present opposing views on the current philosophical and conceptual issues of the Species Problem in biology.Divided into four sections, Concepts and Theories, Practice and Methods, Ranks and Trees and Names, and Metaphysics and Epistemologies, the book is authored by biologists, philosophers, and historians, many leaders in their fields. Topics include ontology of species, definitions of both species category and units, species rank, speciation issues, nomenclature, ecology, and species conservation.Species Problems and Beyond aims to clarify the contemporary issues of the Species Problem. It is ideal for use in upper-level seminars and courses in Evolutionary Biology, Philosophy of Science, Philosophy of Biology, Systematics and Taxonomy, and Phylogenetics/Cladistics, and for any scholar in these fields.

This volume reviews the historical roots and theoretical foundations of biological systematics in an approachable text. The author outlines the structure and main tasks of systematics. Conceptual history is characterized as a succession of scientific revolutions. The philosophical foundations of systematic research are briefly reviewed as well as the structure and content of taxonomic theories. Most important research programs in systematics are outlined. The book includes analysis of the principal problematic issues as "scientific puzzles" in systematics. This volume is intended for professional taxonomists, biologists of various specialties, students, as well as all those interested in the history and theory of biology and natural sciences.Key Features Considers the conceptual history of systematics as the framework of evolutionary epistemology Builds a hierarchically organized quasi-axiomatic system of taxonomic theory Contends that more reductionist taxonomic concepts are less objective Supports taxonomic pluralism by non-classic philosophy of science as a normal condition of systematics Documents that "taxonomic puzzles" result from conflict between monistic and pluralistic attitudesRelated Titlesde Queiroz, K. et al., eds. Phylonyms: A Companion to the PhyloCode (ISBN 978-1-1383-3293-5)Sigwart, J. D. What Species Mean: A User's Guide to the Units of Biodiversity (ISBN 978-1-4987-9937-9)Rieppel, O. Phylogenetic Systematics: Haeckel to Hennig (ISBN 978-1-4987-5488-0)Wilkins, J. S. Species: The Evolution of the Idea, 2nd ed. (ISBN 978-1-1380-5574-2)

Over time the complex idea of "species" has evolved, yet its meaning is far from resolved. This comprehensive work is a fresh look at an idea central to the field of biology by tracing its history from antiquity to today. Species is a benchmark exploration and clarification of a concept fundamental to the past, present, and future of the natural sciences. In this edition, a section is added on the debate over species since the time of the New Synthesis, and brings the book up to date. A section on recent philosophical debates over species has also been added. This edition is better suited non-specialists in philosophy, so that it will be of greater use for scientists wishing to understand how the notion came to be that living organisms form species.Key Selling Features:Covers the philosophical and historical development of the concept of "species"Documents that variation was recognized by pre-Darwinian scholarsIncludes a section on the debates since the time of the New SynthesisBetter suited to non-philosophers

A persistent argument among evolutionary biologists and philosophers revolves around the nature of natural selection. Evolution by Natural Selection: Confidence, Evidence and the Gap explores this argument by using a theory of persistence as an intentional foil to examine ways in which similar theories can be misunderstood. It discusses Charles Darwin’s theory of natural selection, including what the theory says, what it aims to explain, and how it manages to explain natural selection.Darwin’s theory is so familiar today that it feels universally understood. However, the fact that there are so divergent views about the theory means that not everyone who thinks he or she understands it can be right. This book describes the history of evolutionary theory as a sequence of theoretical developments, not all of which can be considered improvements. In particular, it suggests that some attempts to use the theory of natural selection end up reshaping the concepts involved so that they can be applied more easily to the world. As a result, the theory is stripped of some of its explanatory power and becomes detached from the empiricism that good scientific examination requires.With these issues in mind, Evolution by Natural Selection shows there are aspects of the theory of natural selection that are not totally understood. These misunderstandings create problems in uses of the theory. At a time when selectionist explanations are being brought forward to explain an ever-widening range of phenomena, this book analyzes the explanatory structure of Darwin’s theory. It takes a much-needed thoughtful look into the working parts of the theory of natural selection to provide better understanding of the theory and its role in contemporary science and life.

This volume reviews the historical roots and theoretical foundations of biological systematics in an approachable text. The author outlines the structure and main tasks of systematics. Conceptual history is characterized as a succession of scientific revolutions. The philosophical foundations of systematic research are briefly reviewed as well as the structure and content of taxonomic theories. Most important research programs in systematics are outlined. The book includes analysis of the principal problematic issues as "scientific puzzles" in systematics. This volume is intended for professional taxonomists, biologists of various specialties, students, as well as all those interested in the history and theory of biology and natural sciences.Key Features Considers the conceptual history of systematics as the framework of evolutionary epistemology Builds a hierarchically organized quasi-axiomatic system of taxonomic theory Contends that more reductionist taxonomic concepts are less objective Supports taxonomic pluralism by non-classic philosophy of science as a normal condition of systematics Documents that "taxonomic puzzles" result from conflict between monistic and pluralistic attitudesRelated Titlesde Queiroz, K. et al., eds. Phylonyms: A Companion to the PhyloCode (ISBN 978-1-1383-3293-5)Sigwart, J. D. What Species Mean: A User's Guide to the Units of Biodiversity (ISBN 978-1-4987-9937-9)Rieppel, O. Phylogenetic Systematics: Haeckel to Hennig (ISBN 978-1-4987-5488-0)Wilkins, J. S. Species: The Evolution of the Idea, 2nd ed. (ISBN 978-1-1380-5574-2)

This book is an extended argument for abandoning the species rank. Instead, the author proposes that the rank of "species" be replaced by a pluralistic and multi-level view. In such a view, all clades including the smallest identifiable one would be named and studied within a phylogenetic context. What are currently called "species" represent different sorts of things depending on the sort of organisms and processes being considered. This is already the case, but is not formally recognized by those scientists using the species rank in their work. Adopting a rankless taxonomy at all levels would enhance academic studies of evolution and ecology and yield practical benefits in areas of public concern such as conservation. The Open Access version of this book, available at http://www.taylorfrancis.com/books/e/9781498714549, has been made available under a Creative Commons Attribution-Non Commercial license.KEY FEATURES • Proposes the replacement of restrictive species concepts with a pluralistic view • Suggests abandoning the formal taxonomic rank of "species" • Considers zoological, botanical, and microbiological aspects of the species level • Deals with practical issues such as conservation, inventories, and field guides

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 systematics. Written in English, the book presents a unique perspective on a vast body of German biological literature.The book also offers a perspective on German biology in the Third Reich. The author looks at how idealistic morphology and phylogenetic systematics represented two antagonistic traditions in German biology, the first organicist-holistic, the latter empiricist-positivistic. In addition, he explains the ways in which both traditions acquired socio-political and ideological connotations, culminating in their accommodation to different strands of Nazi ideology.The book’s nine chapters summarize a century of the conceptual development of systematics, describe both the history and philosophy of phylogenetic approaches to the understanding of the history of life, examine the role of important people such as Haeckel, Gegenbauer, Portman, von Bertalanffy, Stresemann, and Hennig, and critically evaluate the impact and influence of Nazism on evolutionary biology.Chapter titles include: The Evolutionary Turn in Comparative Anatomy; Of Parts and Wholes; The Turn against Haeckel; The Rise of Holism in German Biology; The Rise of German ("Aryan") Biology; Ganzheitsbiologie; The Ideological Instrumentalization of Biology; A New Beginning: From Speciation to Phylogenetics; and Grundzüge: The Conceptual Foundations of Phylogenetic Systematics.

To unravel the complex shared history of the Earth and its life forms, biogeographers analyze patterns of biodiversity, species distribution, and geological history. So far, the field of biogeography has been fragmented into divergent systematic and evolutionary approaches, with no overarching or unifying research theme or method. In this text, Lynne Parenti and Malte Ebach address this discord and outline comparative tools to unify biogeography. Rooted in phylogenetic systematics, this comparative biogeographic approach offers a comprehensive empirical framework for discovering and deciphering the patterns and processes of the distribution of life on Earth. The authors cover biogeography from its fundamental ideas to the most effective ways to implement them. Real-life examples illustrate concepts and problems, including the first comparative biogeographical analysis of the Indo-West Pacific, an introduction to biogeographical concepts rooted in the earth sciences, and the integration of phylogeny, evolution and earth history.

The complex idea of 'species' has evolved over time, yet its meaning is far from resolved. This comprehensive work takes a fresh look at an idea central to the field of biology by tracing its history from antiquity to today. John S. Wilkins explores the essentialist view, a staple of logic from Plato and Aristotle through the Middle Ages to fairly recent times, and considers the idea of species in natural history - a concept often connected to reproduction. Tracing 'generative conceptions' of species back through Darwin to Epicurus, Wilkins provides a new perspective on the relationship between philosophical and biological approaches to this concept. He also reviews the array of current definitions. "Species" is a benchmark exploration and clarification of a concept fundamental to the past, present, and future of the natural sciences.

The complex idea of 'species' has evolved over time, yet its meaning is far from resolved. This comprehensive work takes a fresh look at an idea central to the field of biology by tracing its history from antiquity to today. John S. Wilkins explores the essentialist view, a staple of logic from Plato and Aristotle through the Middle Ages to fairly recent times, and considers the idea of species in natural history - a concept often connected to reproduction. Tracing 'generative conceptions' of species back through Darwin to Epicurus, Wilkins provides a new perspective on the relationship between philosophical and biological approaches to this concept. He also reviews the array of current definitions. "Species" is a benchmark exploration and clarification of a concept fundamental to the past, present, and future of the natural sciences.

Molecular studies reveal highly ordered geographic patterns in plant and animal distributions. The tropics illustrate these patterns of community immobilism leading to allopatric differentiation, as well as other patterns of mobilism, range expansion, and overlap of taxa. Integrating Earth history and biogeography, "Molecular Panbiogeography of the Tropics" is an alternative view of distributional history in which groups are older than suggested by fossils and fossil-calibrated molecular clocks. The author discusses possible causes for the endemism of high-level taxa in tropical America and Madagascar, and overlapping clades in South America, Africa, and Asia. The book concludes with a critique of adaptation by selection, founded on biogeography and recent work in genetics.

The Evolution of Phylogenetic Systematics aims to make sense of the rise of phylogenetic systematics - its methods, its objects of study, and its theoretical foundations - with contributions from historians, philosophers, and biologists. This volume articulates an intellectual agenda for the study of systematics and taxonomy in a way that connects classification with larger historical themes in the biological sciences, including morphology, experimental and observational approaches, evolution, biogeography, debates over form and function, character transformation, development, and biodiversity. It aims to provide frameworks for answering the question: how did systematics become phylogenetic?

Taxonomists specializing in different groups once based phylogenetic analysis only on morphological data; molecular data was used more rarely. Although molecular systematics is routine today, the use of morphological data continues to be important, especially for phylogenetic placement of many taxa known only from fossils and rare or difficult to collect species. In addition, morphological analyses help identify potential biases in molecular analyses. And finally, scenarios with respect to morphology continue to motivate biologists: the beauty of a cheetah or a baobab does not lie in their DNA sequence, but instead on what they are and do! This book is an up-to-date revision of methods and principles of phylogenetic analysis of morphological data. It is also a general guide for using the computer program TNT in the analysis of such data. The book covers the main aspects of phylogenetic analysis and general methods to compare classifications derived from molecules and morphology. The basic aspects of molecular analysis are covered only as needed to highlight the differences with methods and assumptions for analysis of morphological datasets.

Taxonomists specializing in different groups once based phylogenetic analysis only on morphological data; molecular data was used more rarely. Although molecular systematics is routine today, the use of morphological data continues to be important, especially for phylogenetic placement of many taxa known only from fossils and rare or difficult to collect species. In addition, morphological analyses help identify potential biases in molecular analyses. And finally, scenarios with respect to morphology continue to motivate biologists: the beauty of a cheetah or a baobab does not lie in their DNA sequence, but instead on what they are and do! This book is an up-to-date revision of methods and principles of phylogenetic analysis of morphological data. It is also a general guide for using the computer program TNT in the analysis of such data. The book covers the main aspects of phylogenetic analysis and general methods to compare classifications derived from molecules and morphology. The basic aspects of molecular analysis are covered only as needed to highlight the differences with methods and assumptions for analysis of morphological datasets.

Species Problems and Beyond offers a collection of up-to-date essays discussing from an interdisciplinary perspective the many ramifications of the ‘Species Problem.’ The authors represent experts in the philosophy of biology, in species-level evolutionary investigations, and in biodiversity studies and conservation. Some of the topics addressed concern the context sensitivity of the term ‘species’; species as individuals, processes, natural kinds, or as ‘operative concepts’; species delimitation in the age of Big (genomic) Data; and taxonomic inflation and its consequences for conservation strategies. The carefully edited volume will be an invaluable resource for philosophers of biology and evolutionary biologists alike. – Olivier Rieppel, Rowe Family Curator of Evolutionary Biology, Negaunee Integrative Research Center, Field Museum, USASpecies, or ‘the Species Problem’, is a topic in science, in the philosophy of science, and in general philosophy. In fact, it encompasses many aspects of the same problem, and these are dealt with in this volume. Species are often thought of as fundamental units of biological matter to be used in ecology, conservation, classification, and biodiversity. The chapters in this book present opposing views on the current philosophical and conceptual issues of the Species Problem in biology.Divided into four sections, Concepts and Theories, Practice and Methods, Ranks and Trees and Names, and Metaphysics and Epistemologies, the book is authored by biologists, philosophers, and historians, many leaders in their fields. Topics include ontology of species, definitions of both species category and units, species rank, speciation issues, nomenclature, ecology, and species conservation.Species Problems and Beyond aims to clarify the contemporary issues of the Species Problem. It is ideal for use in upper-level seminars and courses in Evolutionary Biology, Philosophy of Science, Philosophy of Biology, Systematics and Taxonomy, and Phylogenetics/Cladistics, and for any scholar in these fields.

This volume discusses the aspects of a phylogenetic analysis that go beyond basic calculation of most parsimonious trees. Practical application of all principles discussed is illustrated by reference to TNT, a freely available software package that can perform all the steps needed in a phylogenetic analysis. The first problem considered is how to summarize and compare multiple trees (including identification and handling wildcard taxa). Evaluation of the strength of support for groups, another critical component of any phylogenetic analysis, is given careful consideration. The different interpretations of measures of support are discussed and connected with alternative implementations. The book reviews rationales for estimating character reliability on the basis of homoplasy, with particular attention to morphological characters. The main methods for character weighting and their practical implementation, several of them unique to TNT, are discussed ad libitum. Also unique to TNT is the ability to directly analyze morphometric data (including landmarks), on the same footing as discrete characters. Finally, the scripting language of TNT is introduced. With scripting, it is possible to "program" TNT to create personalized routines and automate complex calculations, taking analyses to the next level and allowing exploration of new methods and ideas.Key FeaturesDiscusses the treatment of ambiguity in phylogenetic analyses in depth, for summarizing results or comparing treesReviews literature on arguments and methods for weighting morphological characters and their practical applicationDescribes theory and application of methods for evaluating strength of group support, based on either resampling or comparisons with suboptimal treesDiscusses the use of morphometric characters in phylogenetic analysisPresents extensive information on commands and options of the TNT computer program, including the use and creation of scripts

Everyone uses species. All human cultures, whether using science or not, name species. Species are the basic units for science, from ecosystems to model organisms. Yet, there are communication gaps between the scientists who name species, called taxonomists or systematists, and those who use species names—everyone else. This book opens the "black box" of species names, to explain the tricks of the name-makers to the name-users. Species are real, and have macroevolutionary meaning, and it follows that systematists use a broadly macroevolution-oriented approach in describing diversity. But scientific names are used by all areas of science, including many fields such as ecology that focus on timescales more dominated by microevolutionary processes. This book explores why different groups of scientists understand and use the names given to species in very different ways, and the consequences for measuring and understanding biodiversity.Key selling features:Explains the modern, multi-disciplinary approach to studying species evolution and species discovery, and the role of species names in diverse fields throughout the life sciencesDocuments the importance and urgent need for high-quality taxonomic work to address today’s most pressing problemsSummarises controversies in combining different—sometimes quite different—datasets used to estimate global biodiversityFocusses throughout on a central theme—the disconnect between the makers and the users of names—and seeks to create the rhetorical foundation needed to bridge this disconnectAnticipates the future of taxonomy and its role in studies of global biodiversity

The Hierarchies in Biological Systematics: A Conceptual Perspective examines the diverse hierarchies shaping the field of biology. From the overarching cognitive frameworks to the specific classifications that define biological taxonomy, this book is a comprehensive analysis of hierarchical structures and their inherent complexities.Through a conceptual lens, the author explores the fundamental parameters of hierarchies, their fuzziness, and the principles guiding their substantiation, elaboration, and implementation. The book also delves into the ongoing debate between ranked and rankless taxonomic hierarchies, highlighting the author’s view of the unique rationality of ranked systems while critically assessing their limitations. Whether you are a researcher, student, or professional in biological systematics, this book offers valuable insights into the conceptual underpinnings of hierarchical classifications and their role in advancing scientific understanding.

Over time the complex idea of "species" has evolved, yet its meaning is far from resolved. This comprehensive work is a fresh look at an idea central to the field of biology by tracing its history from antiquity to today. Species is a benchmark exploration and clarification of a concept fundamental to the past, present, and future of the natural sciences. In this edition, a section is added on the debate over species since the time of the New Synthesis, and brings the book up to date. A section on recent philosophical debates over species has also been added. This edition is better suited non-specialists in philosophy, so that it will be of greater use for scientists wishing to understand how the notion came to be that living organisms form species.Key Selling Features:Covers the philosophical and historical development of the concept of "species"Documents that variation was recognized by pre-Darwinian scholarsIncludes a section on the debates since the time of the New SynthesisBetter suited to non-philosophers

A persistent argument among evolutionary biologists and philosophers revolves around the nature of natural selection. Evolution by Natural Selection: Confidence, Evidence and the Gap explores this argument by using a theory of persistence as an intentional foil to examine ways in which similar theories can be misunderstood. It discusses Charles Darwin’s theory of natural selection, including what the theory says, what it aims to explain, and how it manages to explain natural selection.Darwin’s theory is so familiar today that it feels universally understood. However, the fact that there are so divergent views about the theory means that not everyone who thinks he or she understands it can be right. This book describes the history of evolutionary theory as a sequence of theoretical developments, not all of which can be considered improvements. In particular, it suggests that some attempts to use the theory of natural selection end up reshaping the concepts involved so that they can be applied more easily to the world. As a result, the theory is stripped of some of its explanatory power and becomes detached from the empiricism that good scientific examination requires.With these issues in mind, Evolution by Natural Selection shows there are aspects of the theory of natural selection that are not totally understood. These misunderstandings create problems in uses of the theory. At a time when selectionist explanations are being brought forward to explain an ever-widening range of phenomena, this book analyzes the explanatory structure of Darwin’s theory. It takes a much-needed thoughtful look into the working parts of the theory of natural selection to provide better understanding of the theory and its role in contemporary science and life.

This book is an extended argument for abandoning the species rank. Instead, the author proposes that the rank of "species" be replaced by a pluralistic and multi-level view. In such a view, all clades including the smallest identifiable one would be named and studied within a phylogenetic context. What are currently called "species" represent different sorts of things depending on the sort of organisms and processes being considered. This is already the case, but is not formally recognized by those scientists using the species rank in their work. Adopting a rankless taxonomy at all levels would enhance academic studies of evolution and ecology and yield practical benefits in areas of public concern such as conservation. The Open Access version of this book, available at http://www.taylorfrancis.com/books/e/9781498714549, has been made available under a Creative Commons Attribution-Non Commercial license.KEY FEATURES • Proposes the replacement of restrictive species concepts with a pluralistic view • Suggests abandoning the formal taxonomic rank of "species" • Considers zoological, botanical, and microbiological aspects of the species level • Deals with practical issues such as conservation, inventories, and field guides

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 systematics. Written in English, the book presents a unique perspective on a vast body of German biological literature.The book also offers a perspective on German biology in the Third Reich. The author looks at how idealistic morphology and phylogenetic systematics represented two antagonistic traditions in German biology, the first organicist-holistic, the latter empiricist-positivistic. In addition, he explains the ways in which both traditions acquired socio-political and ideological connotations, culminating in their accommodation to different strands of Nazi ideology.The book’s nine chapters summarize a century of the conceptual development of systematics, describe both the history and philosophy of phylogenetic approaches to the understanding of the history of life, examine the role of important people such as Haeckel, Gegenbauer, Portman, von Bertalanffy, Stresemann, and Hennig, and critically evaluate the impact and influence of Nazism on evolutionary biology.Chapter titles include: The Evolutionary Turn in Comparative Anatomy; Of Parts and Wholes; The Turn against Haeckel; The Rise of Holism in German Biology; The Rise of German ("Aryan") Biology; Ganzheitsbiologie; The Ideological Instrumentalization of Biology; A New Beginning: From Speciation to Phylogenetics; and Grundzüge: The Conceptual Foundations of Phylogenetic Systematics.