Automated Taxon Identification in Systematics


Book Description

The automated identification of biological objects or groups has been a dream among taxonomists and systematists for centuries. However, progress in designing and implementing practical systems for fully automated taxon identification has been frustratingly slow. Regardless, the dream has never died. Recent developments in computer architectures an







Lizards of the World


Book Description

The first, definitive reference on the natural history and ecology of every one of the known 6500+ species of lizards, spanning the entire globe. Our planet is literally crawling with lizards. More than 6500 species are known to science, and new species are being discovered annually. In this monumental work, eminent researcher Gordon Rodda has created the first compilation of the natural histories of all the world's lizards and amphisbaenians, as well as the Tuatara. Although other books have attempted to survey the scope of adaptations present in the world's lizards, only Rodda has been able to quantify and summarize all species or higher taxa. Analyzing the relationships among traits such as morphologic characteristics, reproductive strategies, and food sources, Rodda uncovers novel insights into reptile ecology. Identifying 14 recurring character syndromes across all the world's lizards, he proposes a new lens for categorization. He also touches on • common names • geographic range • length • mass • age • maturation • differences between the sexes • nominal variables, including diel activity cycle and foraging mode • home range • predator avoidance tactics • thermal biology • social spacing • climate envelope • habitat and microhabitat • reproduction • parental care • diet • population density • conservation status • ecological business models Rodda's alphabetical taxon accounts provide an instantly retrievable sketch of every species, genus, and family. Outlining more than 1500 statistically significant associations extracted from a data matrix composed of more than 300 conditions tabulated—to the extent known—for all 6528 species of lizards, Lizards of the World will be the go-to source for the next generation of reptile ecologists, as well as herpetology students and serious herpetoculturists.




The Prokaryotes


Book Description

The revised Third Edition of The Prokaryotes, acclaimed as a classic reference in the field, offers new and updated articles by experts from around the world on taxa of relevance to medicine, ecology and industry. Entries combine phylogenetic and systematic data with insights into genetics, physiology and application. Existing entries have been revised to incorporate rapid progress and technological innovation. The new edition improves on the lucid presentation, logical layout and abundance of illustrations that readers rely on, adding color illustration throughout. Expanded to seven volumes in its print form, the new edition adds a new, searchable online version.




Scriptinformatics


Book Description

Scripts (writing systems) usually belong to specific languages and have temporal, spatial and cultural characteristics. The evolution of scripts has been the subject of research for a long time. This is probably because the long-term development of human thinking is reflected in the surviving script relics, many of which are still undeciphered today. The book presents the study of the script evolution with the mathematical tools of systematics, phylogenetics and bioinformatics. In the research described, the script is the evolutionary taxonomic unit (taxon), which is analogous to the concept of biological species. Among the methods of phylogenetics, phenetics classifies the investigated taxa on the basis of their morphological similarity, and does not primarily examine genealogical relationships. Due to the scarcity of morphological diversity of scripts’ features, random coincidences of evolution-independent features are much more common in scripts than in biological species, thus phenetic modelling based solely on morphological features can lead to erroneous results. For this reason, phenetic modeling has been extended with evolutionary considerations, thereby allowing the modelling uncertainties observed in the script evolution to be addressed due to the large number of random coincidences (homoplasies) characterizing each script. The book describes an extended phenetic method developed to investigate the script evolution. This data-driven approach helps to reduce the impact of the uncertainties inherent in the phenetic model due to the large number of homoplasies that occur during the evolution of scripts. The elaborated phenetic and evolutionary analyses were applied to the Rovash scripts used on the Eurasian Steppe (Grassland), including the Turkic Rovash (Turkic Runic/runiform) and the Székely-Hungarian Rovash. The evaluation of the extended phenetic model of the scripts, the various phenograms, the script spectra and the group spectra helped to reconstruct the main ancestors and evolutionary stages of the investigated scripts.




Python for Bioinformatics


Book Description

Programming knowledge is often necessary for finding a solution to a biological problem. Based on the author’s experience working for an agricultural biotechnology company, Python for Bioinformatics helps scientists solve their biological problems by helping them understand the basics of programming. Requiring no prior knowledge of programming-related concepts, the book focuses on the easy-to-use, yet powerful, Python computer language. The book begins with a very basic introduction that teaches the principles of programming. It then introduces the Biopython package, which can be useful in solving life science problems. The next section covers sophisticated tools for bioinformatics, including relational database management systems and XML. The last part illustrates applications with source code, such as sequence manipulation, filtering vector contamination, calculating DNA melting temperature, parsing a genbank file, inferring splicing sites, and more. The appendices provide a wealth of supplementary information, including instructions for installing Python and Biopython and a Python language and style guide. By incorporating examples in biology as well as code fragments throughout, the author places a special emphasis on practice, encouraging readers to experiment with the code. He shows how to use Python and the Biopython package for building web applications, genomic annotation, data manipulation, and countless other applications.




Paleozoology and Paleoenvironments


Book Description

Paleozoology and Paleoenvironments outlines the reconstruction of ancient climates, floras, and habitats on the basis of animal fossil remains recovered from archaeological and paleontological sites. In addition to outlining the ecological fundamentals and analytical assumptions attending such analyzes, J. Tyler Faith and R. Lee Lyman describe and critically evaluate many of the varied analytical techniques that have been applied to paleozoological remains for the purpose of paleoenvironmental reconstruction. These techniques range from analyses based on the presence or abundance of species in a fossil assemblage to those based on taxon-free ecological characterizations. All techniques are illustrated using faunal data from archaeological or paleontological contexts. Aimed at students and professionals, this volume will serve as fundamental resource for courses in zooarchaeology, paleontology, and paleoecology.




Methods in Stream Ecology


Book Description

Methods in Stream Ecology: Volume 2: Ecosystem Structure, Third Edition, provides a complete series of field and laboratory protocols in stream ecology that are ideal for teaching or conducting research. This new two-part edition is updated to reflect recent advances in the technology associated with ecological assessment of streams, including remote sensing. Volume two covers community interactions, ecosystem processes and ecosystem quality. With a student-friendly price, this new edition is key for all students and researchers in stream and freshwater ecology, freshwater biology, marine ecology and river ecology. This book is also supportive as a supplementary text for courses in watershed ecology/science, hydrology, fluvial geomorphology and landscape ecology. Methods in Stream Ecology, 3rd Edition, Volume 1: Ecosystem Structure, is also available now! - Provides a variety of exercises in each chapter - Includes detailed instructions, illustrations, formulae and data sheets for in-field research for students - Presents taxonomic keys to common stream invertebrates and algae - Includes website with tables and a links written by leading experts in stream ecology




The Timetree of Life


Book Description

The evolutionary history of life includes two primary components: phylogeny and timescale. Phylogeny refers to the branching order (relationships) of species or other taxa within a group and is crucial for understanding the inheritance of traits and for erecting classifications. However, a timescale is equally important because it provides a way to compare phylogeny directly with the evolution of other organisms and with planetary history such as geology, climate, extraterrestrialimpacts, and other features.The Timetree of Life is the first reference book to synthesize the wealth of information relating to the temporal component of phylogenetic trees. In the past, biologists have relied exclusively upon the fossil record to infer an evolutionary timescale. However, recent revolutionary advances in molecular biology have made it possible to not only estimate the relationships of many groups of organisms, but also to estimate their times of divergence with molecular clocks. The routineestimation and utilization of these so-called 'time-trees' could add exciting new dimensions to biology including enhanced opportunities to integrate large molecular data sets with fossil and biogeographic evidence (and thereby foster greater communication between molecular and traditional systematists). Theycould help estimate not only ancestral character states but also evolutionary rates in numerous categories of organismal phenotype; establish more reliable associations between causal historical processes and biological outcomes; develop a universally standardized scheme for biological classifications; and generally promote novel avenues of thought in many arenas of comparative evolutionary biology.This authoritative reference work brings together, for the first time, experts on all major groups of organisms to assemble a timetree of life. The result is a comprehensive resource on evolutionary history which will be an indispensable reference for scientists, educators, and students in the life sciences, earth sciences, and molecular biology. For each major group of organism, a representative is illustrated and a timetree of families and higher taxonomic groups is shown. Basic aspects ofthe evolutionary history of the group, the fossil record, and competing hypotheses of relationships are discussed. Details of the divergence times are presented for each node in the timetree, and primary literature references are included. The book is complemented by an online database(www.timetree.net) which allows researchers to both deposit and retrieve data.




Federal Register


Book Description