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.

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

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.

Volume 1. "This book outlines the steps in a phylogenetic analysis that follow the generation of most parsimonious trees. In addition, character reliability approaches and methods of analysis for morphometric characters are summarized. The algorithm used throughout the book is TNT, a freely available software package able to summarize and compare multiple trees produced by ambiguous datasets, or analyses of different datasets. Unstable taxa (wildcards or rogues), which may obscure the relationships of the other taxa, are discussed extensively, as well as their identification and handling with several options implemented in TNT"--

This book covers the latest techniques that enable us to study the genome in detail, the book explores what the genome tells us about life at the level of the molecule, the cell, and the organism

Our genome is the blueprint for our existence: it encodes all the information we need to develop from a single cell into a hugely complicated functional organism. Yet it is more than a static information store: our genome is a dynamic, tightly-regulated collection of genes, which switch on and off in many combinations to give the variety of cells from which our bodies are formed. But how do we identify the genes that make up our genome? How do we determine their function? And how do different genes form the regulatory networks that direct the processes of life? Introduction to Genomics is the most up-to-date and complete textbook for students approaching the subject for the first time. Lesk's engaging writing style brings a narrative to a disparate field of study and offers a fascinating insight into what can be revealed from the study of genomes. The book covers: the similarities and differences between organisms; how different organisms evolved; how the genome is constructed and how it operates; and what our understanding of genomics means in terms of our future health and wellbeing. The Online Resource Center accompanying Introduction to Genomics features: For students: *Extensive and imaginative weblems (web-based problems) for each chapter designed to give you practice with the tools required for further study and research in the field *Hints and answers to end-of-chapter problems and exercises support your self-directed learning *Guided tour of websites and major archival databanks in genomics offer a wealth of resources to springboard your own research *Journal club: links to related research articles on topics covered in the book are paired with engaging questions to improve your interpretation of the primary literature *Rotating figures allow you to visualize complex structures For instructors: *Downloadable figures from the book.

This book constitutes the proceedings of the workshops of the 23rd International Conference on Parallel and Distributed Computing, Euro-Par 2016, held in Grenoble, France in August 2016. The 65 full papers presented were carefully reviewed and selected from 95 submissions. The volume includes the papers from the following workshops: Euro-EDUPAR (Second European Workshop on Parallel and Distributed Computing Education for Undergraduate Students) – HeteroPar 2016 (the 14th International Workshop on Algorithms, Models and Tools for Parallel Computing on Heterogeneous Platforms) – IWMSE (5th International Workshop on Multicore Software Engineering) – LSDVE (Fourth Workshop on Large-Scale Distributed Virtual Environments) - PADABS (Fourth Workshop on Parallel and Distributed Agent-Based Simulations) – PBio (Fourth International Workshop on Parallelism in Bioinformatics) – PELGA (Second Workshop on Performance Engineering for Large-Scale Graph Analytics) – REPPAR (Third International Workshop on Reproducibility in Parallel Computing) – Resilience (9th Workshop in Resilience in High Performance Computing in Clusters, Clouds, and Grids) – ROME (Fourth Workshop on Runtime and Operating Systems for the Many-Core Era) – UCHPC (9th Workshop on UnConventional High-Performance Computing).

This volume constitutes the refereed proceedings of the 14th International Conference on Hybrid Artificial Intelligent Systems, HAIS 2019, held in León, Spain, in September 2019. The 64 full papers published in this volume were carefully reviewed and selected from 134 submissions. They are organized in the following topical sections: data mining, knowledge discovery and big data; bio-inspired models and evolutionary computation; learning algorithms; visual analysis and advanced data processing techniques; data mining applications; and hybrid intelligent applications.

This book constitutes the refereed proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2009, held in Tucson, Arisona, USA in May 2009. The 37 revised full papers presented were carefully reviewed and selected from 166 submissions. As the top conference in computational molecular biology, RECOMB addresses all current issues in algorithmic, theoretical, and experimental bioinformatics such as molecular sequence analysis, recognition of genes and regulatory elements, molecular evolution, protein structure, structural genomics, gene expression, gene networks, drug design, combinatorial libraries, computational proteomics, as well as structural and functional genomics.