Refining Phylogenetic Analyses

Refining Phylogenetic Analyses

Author: Pablo A. Goloboff

Publisher: CRC Press

Published: 2022-07-22

Total Pages: 312

ISBN-13: 1000603989

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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 Features Discusses the treatment of ambiguity in phylogenetic analyses in depth, for summarizing results or comparing trees Reviews literature on arguments and methods for weighting morphological characters and their practical application Describes theory and application of methods for evaluating strength of group support, based on either resampling or comparisons with suboptimal trees Discusses the use of morphometric characters in phylogenetic analysis Presents extensive information on commands and options of the TNT computer program, including the use and creation of scripts


Book Synopsis Refining Phylogenetic Analyses by : Pablo A. Goloboff

Download or read book Refining Phylogenetic Analyses written by Pablo A. Goloboff and published by CRC Press. This book was released on 2022-07-22 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 Features Discusses the treatment of ambiguity in phylogenetic analyses in depth, for summarizing results or comparing trees Reviews literature on arguments and methods for weighting morphological characters and their practical application Describes theory and application of methods for evaluating strength of group support, based on either resampling or comparisons with suboptimal trees Discusses the use of morphometric characters in phylogenetic analysis Presents extensive information on commands and options of the TNT computer program, including the use and creation of scripts

Analysis of Phylogenetics and Evolution with R

Analysis of Phylogenetics and Evolution with R

Author: Emmanuel Paradis

Publisher: Springer Science & Business Media

Published: 2011-11-06

Total Pages: 401

ISBN-13: 1461417430

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The increasing availability of molecular and genetic databases coupled with the growing power of computers gives biologists opportunities to address new issues, such as the patterns of molecular evolution, and re-assess old ones, such as the role of adaptation in species diversification. In the second edition, the book continues to integrate a wide variety of data analysis methods into a single and flexible interface: the R language. This open source language is available for a wide range of computer systems and has been adopted as a computational environment by many authors of statistical software. Adopting R as a main tool for phylogenetic analyses will ease the workflow in biologists' data analyses, ensure greater scientific repeatability, and enhance the exchange of ideas and methodological developments. The second edition is completed updated, covering the full gamut of R packages for this area that have been introduced to the market since its previous publication five years ago. There is also a new chapter on the simulation of evolutionary data. Graduate students and researchers in evolutionary biology can use this book as a reference for data analyses, whereas researchers in bioinformatics interested in evolutionary analyses will learn how to implement these methods in R. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered: manipulation of phylogenetic data, phylogeny estimation, tree drawing, phylogenetic comparative methods, and estimation of ancestral characters. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.


Book Synopsis Analysis of Phylogenetics and Evolution with R by : Emmanuel Paradis

Download or read book Analysis of Phylogenetics and Evolution with R written by Emmanuel Paradis and published by Springer Science & Business Media. This book was released on 2011-11-06 with total page 401 pages. Available in PDF, EPUB and Kindle. Book excerpt: The increasing availability of molecular and genetic databases coupled with the growing power of computers gives biologists opportunities to address new issues, such as the patterns of molecular evolution, and re-assess old ones, such as the role of adaptation in species diversification. In the second edition, the book continues to integrate a wide variety of data analysis methods into a single and flexible interface: the R language. This open source language is available for a wide range of computer systems and has been adopted as a computational environment by many authors of statistical software. Adopting R as a main tool for phylogenetic analyses will ease the workflow in biologists' data analyses, ensure greater scientific repeatability, and enhance the exchange of ideas and methodological developments. The second edition is completed updated, covering the full gamut of R packages for this area that have been introduced to the market since its previous publication five years ago. There is also a new chapter on the simulation of evolutionary data. Graduate students and researchers in evolutionary biology can use this book as a reference for data analyses, whereas researchers in bioinformatics interested in evolutionary analyses will learn how to implement these methods in R. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered: manipulation of phylogenetic data, phylogeny estimation, tree drawing, phylogenetic comparative methods, and estimation of ancestral characters. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.

From Observations to Optimal Phylogenetic Trees

From Observations to Optimal Phylogenetic Trees

Author: Pablo A. Goloboff

Publisher: CRC Press

Published: 2022-07-22

Total Pages: 289

ISBN-13: 1000550060

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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.


Book Synopsis From Observations to Optimal Phylogenetic Trees by : Pablo A. Goloboff

Download or read book From Observations to Optimal Phylogenetic Trees written by Pablo A. Goloboff and published by CRC Press. This book was released on 2022-07-22 with total page 289 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Alignment- and Alignment-refining Algorithms

Alignment- and Alignment-refining Algorithms

Author: Yichen Zheng

Publisher:

Published: 2015

Total Pages:

ISBN-13:

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This dissertation consists of a study of the effects of multiple-alignment method on phylogenetic analyses. First, I investigated the effects of multiple-sequence alignment quality on branch-length estimation, which can influence downstream bioinformatic analyses such as estimating rates of evolution and divergence times. To quantify the accuracy of branch-length estimates, I devised a scale-free measure of branch length proportionality between two phylogenetic trees that contain the same taxa and topology. This measure was named "normalized tree distance" (NTD). NTD is an ideal measure for detecting coevolutionary processes, in addition to measuring the accuracy of branch-length estimates. Using NTD as an error measure, I investigated the effects of multiple-sequence alignment quality on branch-length estimation. I simulated coding sequences and estimated the effects of multiple evolution parameters and choice of alignment- and alignment-filtering algorithms on the accuracy of branch-length estimation. I demonstrated that branch-length accuracy is indeed dependent on the method of alignment. Alignments with high-accuracy algorithms combined with methods for filtering out unreliable sites produce significantly better branch-length estimates. The optimal method combination depends on the evolutionary scenario. Thus, different alignment algorithms and different combinations of algorithms yield better branch-length estimates under different evolutionary conditions. A judicious choice of alignment- and alignment filtering algorithms is recommended for phylogenetic studies. Second, I studied the correlation between two types of purifying selection: against nonsynonymous mutations and against deletions using mammalian genomic protein-coding sequences. Intuitively, a codon that is intolerant of amino-acid altering substitutions is expected to be also intolerant of deletion. However, there has not been any comprehensive study on this purported correlation. In addition to the nine-species alignments of 8,595 genes, I simulated coding sequences along the same phylogenetic trees. The real data showed a much stronger correlation than the simulated sequences. I demonstrated that the correlation between amino-acid replacement and deletion rates exists and cannot be explained solely by alignment errors. Further investigations on nonsynonymous and synonymous mutations showed that this is most likely due to selection rather than mutation rates. Understanding selection on different types of mutations would help strengthen the link between population genetics and sequence evolution.


Book Synopsis Alignment- and Alignment-refining Algorithms by : Yichen Zheng

Download or read book Alignment- and Alignment-refining Algorithms written by Yichen Zheng and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation consists of a study of the effects of multiple-alignment method on phylogenetic analyses. First, I investigated the effects of multiple-sequence alignment quality on branch-length estimation, which can influence downstream bioinformatic analyses such as estimating rates of evolution and divergence times. To quantify the accuracy of branch-length estimates, I devised a scale-free measure of branch length proportionality between two phylogenetic trees that contain the same taxa and topology. This measure was named "normalized tree distance" (NTD). NTD is an ideal measure for detecting coevolutionary processes, in addition to measuring the accuracy of branch-length estimates. Using NTD as an error measure, I investigated the effects of multiple-sequence alignment quality on branch-length estimation. I simulated coding sequences and estimated the effects of multiple evolution parameters and choice of alignment- and alignment-filtering algorithms on the accuracy of branch-length estimation. I demonstrated that branch-length accuracy is indeed dependent on the method of alignment. Alignments with high-accuracy algorithms combined with methods for filtering out unreliable sites produce significantly better branch-length estimates. The optimal method combination depends on the evolutionary scenario. Thus, different alignment algorithms and different combinations of algorithms yield better branch-length estimates under different evolutionary conditions. A judicious choice of alignment- and alignment filtering algorithms is recommended for phylogenetic studies. Second, I studied the correlation between two types of purifying selection: against nonsynonymous mutations and against deletions using mammalian genomic protein-coding sequences. Intuitively, a codon that is intolerant of amino-acid altering substitutions is expected to be also intolerant of deletion. However, there has not been any comprehensive study on this purported correlation. In addition to the nine-species alignments of 8,595 genes, I simulated coding sequences along the same phylogenetic trees. The real data showed a much stronger correlation than the simulated sequences. I demonstrated that the correlation between amino-acid replacement and deletion rates exists and cannot be explained solely by alignment errors. Further investigations on nonsynonymous and synonymous mutations showed that this is most likely due to selection rather than mutation rates. Understanding selection on different types of mutations would help strengthen the link between population genetics and sequence evolution.

The Phylogenetic Handbook

The Phylogenetic Handbook

Author: Marco Salemi

Publisher: Cambridge University Press

Published: 2009-03-26

Total Pages: 750

ISBN-13: 0521877105

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A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.


Book Synopsis The Phylogenetic Handbook by : Marco Salemi

Download or read book The Phylogenetic Handbook written by Marco Salemi and published by Cambridge University Press. This book was released on 2009-03-26 with total page 750 pages. Available in PDF, EPUB and Kindle. Book excerpt: A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.

The Future of Phylogenetic Systematics

The Future of Phylogenetic Systematics

Author: David Williams

Publisher: Cambridge University Press

Published: 2016-07-21

Total Pages: 509

ISBN-13: 1316688186

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Willi Hennig (1913–76), founder of phylogenetic systematics, revolutionised our understanding of the relationships among species and their natural classification. An expert on Diptera and fossil insects, Hennig's ideas were applicable to all organisms. He wrote about the science of taxonomy or systematics, refining and promoting discussion of the precise meaning of the term 'relationship', the nature of systematic evidence, and how those matters impinge on a precise understanding of monophyly, paraphyly, and polyphyly. Hennig's contributions are relevant today and are a platform for the future. This book focuses on the intellectual aspects of Hennig's work and gives dimension to the future of the subject in relation to Hennig's foundational contributions to the field of phylogenetic systematics. Suitable for graduate students and academic researchers, this book will also appeal to philosophers and historians interested in the legacy of Willi Hennig.


Book Synopsis The Future of Phylogenetic Systematics by : David Williams

Download or read book The Future of Phylogenetic Systematics written by David Williams and published by Cambridge University Press. This book was released on 2016-07-21 with total page 509 pages. Available in PDF, EPUB and Kindle. Book excerpt: Willi Hennig (1913–76), founder of phylogenetic systematics, revolutionised our understanding of the relationships among species and their natural classification. An expert on Diptera and fossil insects, Hennig's ideas were applicable to all organisms. He wrote about the science of taxonomy or systematics, refining and promoting discussion of the precise meaning of the term 'relationship', the nature of systematic evidence, and how those matters impinge on a precise understanding of monophyly, paraphyly, and polyphyly. Hennig's contributions are relevant today and are a platform for the future. This book focuses on the intellectual aspects of Hennig's work and gives dimension to the future of the subject in relation to Hennig's foundational contributions to the field of phylogenetic systematics. Suitable for graduate students and academic researchers, this book will also appeal to philosophers and historians interested in the legacy of Willi Hennig.

Phylogenetics

Phylogenetics

Author: E. O. Wiley

Publisher: John Wiley & Sons

Published: 2011-10-11

Total Pages: 444

ISBN-13: 1118017870

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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.


Book Synopsis Phylogenetics by : E. O. Wiley

Download or read book Phylogenetics written by E. O. Wiley and published by John Wiley & Sons. This book was released on 2011-10-11 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Refining Phylogenetic Hypotheses Using Chloroplast Genomics and Incomplete Data Sets in Lasthenia (Madieae, Asteraceae)

Refining Phylogenetic Hypotheses Using Chloroplast Genomics and Incomplete Data Sets in Lasthenia (Madieae, Asteraceae)

Author: Joseph Frederic Walker

Publisher:

Published: 2014

Total Pages: 62

ISBN-13:

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The genus Lasthenia (Madieae, Asteraceae), consists of predominantly annual plant species that are largely endemic to the California Floristic Province of western North America and occupy a large range of habitat types. With high levels of morphological and ecological diversity, Lasthenia is a robust tool, capable of providing a natural non-model organism for answering a diverse array of ecological and evolutionary questions. Future studies would benefit greatly from a strong phylogenetic hypothesis and more molecular resources, such as the whole plastome sequence for a representative species in the genus. Over a decade ago there was a study that laid a strong foundation for a molecular phylogenetic hypothesis, however, many critical nodes still remained ambiguous. Since that study was conducted, there have emerged new statistical and biological methods to maximize the information obtained from the sequence data. With the advent of next-generation sequencing, it is now simpler than ever to obtain molecular resources for a genus, and it is possible to apply some of those molecular resources to resolving the phylogenetic relationships in Lasthenia. My research has two specific outcomes: 1) I have provided the first whole plastome in the tribe Madieae of the Asteraceae and used the plastome to analyze rates of evolution across the regions of other sequenced plastomes in the Asteraceae, and 2) Through the use of modern phylogenetic methods and incomplete data sets consisting of freely available and newly obtained sequence data, I have for the first time resolved all seven sections of the Lasthenia genus with moderate to high bootstrap support.


Book Synopsis Refining Phylogenetic Hypotheses Using Chloroplast Genomics and Incomplete Data Sets in Lasthenia (Madieae, Asteraceae) by : Joseph Frederic Walker

Download or read book Refining Phylogenetic Hypotheses Using Chloroplast Genomics and Incomplete Data Sets in Lasthenia (Madieae, Asteraceae) written by Joseph Frederic Walker and published by . This book was released on 2014 with total page 62 pages. Available in PDF, EPUB and Kindle. Book excerpt: The genus Lasthenia (Madieae, Asteraceae), consists of predominantly annual plant species that are largely endemic to the California Floristic Province of western North America and occupy a large range of habitat types. With high levels of morphological and ecological diversity, Lasthenia is a robust tool, capable of providing a natural non-model organism for answering a diverse array of ecological and evolutionary questions. Future studies would benefit greatly from a strong phylogenetic hypothesis and more molecular resources, such as the whole plastome sequence for a representative species in the genus. Over a decade ago there was a study that laid a strong foundation for a molecular phylogenetic hypothesis, however, many critical nodes still remained ambiguous. Since that study was conducted, there have emerged new statistical and biological methods to maximize the information obtained from the sequence data. With the advent of next-generation sequencing, it is now simpler than ever to obtain molecular resources for a genus, and it is possible to apply some of those molecular resources to resolving the phylogenetic relationships in Lasthenia. My research has two specific outcomes: 1) I have provided the first whole plastome in the tribe Madieae of the Asteraceae and used the plastome to analyze rates of evolution across the regions of other sequenced plastomes in the Asteraceae, and 2) Through the use of modern phylogenetic methods and incomplete data sets consisting of freely available and newly obtained sequence data, I have for the first time resolved all seven sections of the Lasthenia genus with moderate to high bootstrap support.

Foundations of Phylogenetic Systematics

Foundations of Phylogenetic Systematics

Author: Johann Wolfgang Wägele

Publisher:

Published: 2005

Total Pages: 376

ISBN-13:

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Phylogeny inference and the classification of organisms are indispensable for all fields of biology. On the basis of a well corroborated tree of life it is possible to understand the evolution of structure and function, of genomes, of gene families, of cascades of developmental genes, and the origin of genes of medical importance. Ecologists need a stable classification of organisms to identify organisms, to find their correct names and thus further information on relevant species. This book offers an introduction to the theory of Phylogenetic Systematics and is a companion for all biologists who want to analyze morphological or molecular data with classical methods or with modern computer programs. The first part of the book explains the epistemological basis that is independent of the type of method used to construct phylogenetic trees. Unlike other empirical sciences, the estimation of data quality in phylogenetics is still little developed and very often neglected. Here a theoretical basis is presented that enables the systematist to assess critically and objectively the quality of different data sets and to make statements on the plausibility of results. This requires a conception of the notions of information content, probability of homology, probability of cognition, probability of events, the principle of parsimony, the differentiation of phenomenological and modelling methods. Willi Hennig's original method is compared with modern numerical systematics and an updated Hennigian procedure of data analysis is discussed. The difference between phenetic and phylogenetic cladistics is explained. Popular tools for data evaluation implemented in computer programs are explained including their axiomatic assumptions, sources of error and possible applications. For the more common tools the mathematical background is explained in a simple, easy-to-understand way.Johann-Wolfgang Wagele was until recently head of the Department for Animal Systematics (Lehrstuhl fur Spezielle Zoologie) at the University of Bochum and is now director of the Museum Alexander Koenig in Bonn (Germany). His main research interests are the taxonomy, phylogeny and biodiversity of Isopoda, which implies observations of life history, biogeography and ecology in combination with phylogeny inference. Further subjects include arthropod phylogeny and tools for explorative data analyses. The author is president of the Gesellschaft fur Biologische Systematik, a Central European society of systematists, and he is actively promoting biodiversity research.


Book Synopsis Foundations of Phylogenetic Systematics by : Johann Wolfgang Wägele

Download or read book Foundations of Phylogenetic Systematics written by Johann Wolfgang Wägele and published by . This book was released on 2005 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylogeny inference and the classification of organisms are indispensable for all fields of biology. On the basis of a well corroborated tree of life it is possible to understand the evolution of structure and function, of genomes, of gene families, of cascades of developmental genes, and the origin of genes of medical importance. Ecologists need a stable classification of organisms to identify organisms, to find their correct names and thus further information on relevant species. This book offers an introduction to the theory of Phylogenetic Systematics and is a companion for all biologists who want to analyze morphological or molecular data with classical methods or with modern computer programs. The first part of the book explains the epistemological basis that is independent of the type of method used to construct phylogenetic trees. Unlike other empirical sciences, the estimation of data quality in phylogenetics is still little developed and very often neglected. Here a theoretical basis is presented that enables the systematist to assess critically and objectively the quality of different data sets and to make statements on the plausibility of results. This requires a conception of the notions of information content, probability of homology, probability of cognition, probability of events, the principle of parsimony, the differentiation of phenomenological and modelling methods. Willi Hennig's original method is compared with modern numerical systematics and an updated Hennigian procedure of data analysis is discussed. The difference between phenetic and phylogenetic cladistics is explained. Popular tools for data evaluation implemented in computer programs are explained including their axiomatic assumptions, sources of error and possible applications. For the more common tools the mathematical background is explained in a simple, easy-to-understand way.Johann-Wolfgang Wagele was until recently head of the Department for Animal Systematics (Lehrstuhl fur Spezielle Zoologie) at the University of Bochum and is now director of the Museum Alexander Koenig in Bonn (Germany). His main research interests are the taxonomy, phylogeny and biodiversity of Isopoda, which implies observations of life history, biogeography and ecology in combination with phylogeny inference. Further subjects include arthropod phylogeny and tools for explorative data analyses. The author is president of the Gesellschaft fur Biologische Systematik, a Central European society of systematists, and he is actively promoting biodiversity research.

Species Problems and Beyond

Species Problems and Beyond

Author: John S. Wilkins

Publisher: CRC Press

Published: 2022-06-14

Total Pages: 383

ISBN-13: 1000549798

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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, USA Species, 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.


Book Synopsis Species Problems and Beyond by : John S. Wilkins

Download or read book Species Problems and Beyond written by John S. Wilkins and published by CRC Press. This book was released on 2022-06-14 with total page 383 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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, USA Species, 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.