Download or read book Estimating Species Trees written by L. Lacey Knowles and published by John Wiley & Sons. This book was released on 2011-09-20 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent computational and modeling advances have produced methods for estimating species trees directly, avoiding the problems and limitations of the traditional phylogenetic paradigm where an estimated gene tree is equated with the history of species divergence. The overarching goal of the volume is to increase the visibility and use of these new methods by the entire phylogenetic community by specifically addressing several challenges: (i) firm understanding of the theoretical underpinnings of the methodology, (ii) empirical examples demonstrating the utility of the methodology as well as its limitations, and (iii) attention to technical aspects involved in the actual software implementation of the methodology. As such, this volume will not only be poised to become the quintessential guide to training the next generation of researchers, but it will also be instrumental in ushering in a new phylogenetic paradigm for the 21st century.
Download or read book Estimating Species Trees written by L. Lacey Knowles and published by John Wiley and Sons. This book was released on 2011-05-09 with total page 230 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent computational and modeling advances have produced methods for estimating species trees directly, avoiding the problems and limitations of the traditional phylogenetic paradigm where an estimated gene tree is equated with the history of species divergence. The overarching goal of the volume is to increase the visibility and use of these new methods by the entire phylogenetic community by specifically addressing several challenges: (i) firm understanding of the theoretical underpinnings of the methodology, (ii) empirical examples demonstrating the utility of the methodology as well as its limitations, and (iii) attention to technical aspects involved in the actual software implementation of the methodology. As such, this volume will not only be poised to become the quintessential guide to training the next generation of researchers, but it will also be instrumental in ushering in a new phylogenetic paradigm for the 21st century.
Download or read book Species Tree Inference written by Laura Kubatko and published by Princeton University Press. This book was released on 2023-03-14 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Inferring evolutionary relationships among a collection of organisms -- that is, their relationship to each other on the tree of life -- remains a central focus of much of evolutionary biology as these relationships provide the background for key hypotheses. For example, support for different hypotheses about early animal evolution are contingent upon the phylogenetic relationships among the earliest animal lineages. Within the last 20 years, the field of phylogenetics has grown rapidly, both in the quantity of data available for inference and in the number of methods available for phylogenetic estimation. The authors' first book, "Estimating Species Trees: Practical and Theoretical Aspects", published in 2010, gave an overview of the state of phylogenetic practice for analyzing data at the time, but much has changed since then. The goal of this book is to serve as an updated reference on current methods within the field. The book is organized in three sections, the first of which provides an overview of the analytical and methodological developments of species tree inference. Section two focuses on empirical inference. Section three explores various applications of species trees in evolutionary biology. The combination of theoretical and empirical approaches is meant to provide readers with a level of knowledge of both the advances and limitations of species-tree inference that can help researchers in applying the methods, while also inspiring future advances among those researchers with an interest in methodological development"--
Download or read book Tree Diversity Analysis written by R. Kindt and published by World Agroforestry Centre. This book was released on 2005 with total page 18 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Measuring Abundance written by Graham Upton and published by Pelagic Publishing Ltd. This book was released on 2020-10-12 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: Measuring the abundance of individuals and the diversity of species are core components of most ecological research projects and conservation monitoring. This book brings together in one place, for the first time, the methods used to estimate the abundance of individuals in nature. The statistical basis of each method is detailed along with practical considerations for survey design and data collection. Methods are illustrated using data ranging from Alaskan shrubs to Yellowstone grizzly bears, not forgetting Costa Rican ants and Prince Edward Island lobsters. Where necessary, example code for use with the open source software R is supplied. When appropriate, reference is made to other widely used programs. After opening with a brief synopsis of relevant statistical methods, the first section deals with the abundance of stationary items such as trees, shrubs, coral, etc. Following a discussion of the use of quadrats and transects in the contexts of forestry sampling and the assessment of plant cover, there are chapters addressing line-intercept sampling, the use of nearest-neighbour distances, and variable sized plots. The second section deals with individuals that move, such as birds, mammals, reptiles, fish, etc. Approaches discussed include double-observer sampling, removal sampling, capture-recapture methods and distance sampling. The final section deals with the measurement of species richness; species diversity; species-abundance distributions; and other aspects of diversity such as evenness, similarity, turnover and rarity. This is an essential reference for anyone involved in advanced undergraduate or postgraduate ecological research and teaching, or those planning and carrying out data analysis as part of conservation survey and monitoring programmes.
Download or read book Biomass Equations for Major Tree Species of the Northeast written by Louise M. Tritton and published by . This book was released on 1982 with total page 52 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Coalescent Theory written by John Wakely and published by Roberts. This book was released on 2016-04-22 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook provides the foundation for molecular population genetics and genomics. It shows the conceptual framework for studies of DNA sequence variation within species, and is the source of essential tools for making inferences about mutation, recombination, population structure and natural selection from DNA sequence data.
Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-07-09 with total page 1828 pages. Available in PDF, EPUB and Kindle. Book excerpt: A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.
Download or read book Bioinformatics and Phylogenetics written by Tandy Warnow and published by Springer. This book was released on 2019-04-08 with total page 410 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a compelling collection of state-of-the-art work in algorithmic computational biology, honoring the legacy of Professor Bernard M.E. Moret in this field. Reflecting the wide-ranging influences of Prof. Moret’s research, the coverage encompasses such areas as phylogenetic tree and network estimation, genome rearrangements, cancer phylogeny, species trees, divide-and-conquer strategies, and integer linear programming. Each self-contained chapter provides an introduction to a cutting-edge problem of particular computational and mathematical interest. Topics and features: addresses the challenges in developing accurate and efficient software for the NP-hard maximum likelihood phylogeny estimation problem; describes the inference of species trees, covering strategies to scale phylogeny estimation methods to large datasets, and the construction of taxonomic supertrees; discusses the inference of ultrametric distances from additive distance matrices, and the inference of ancestral genomes under genome rearrangement events; reviews different techniques for inferring evolutionary histories in cancer, from the use of chromosomal rearrangements to tumor phylogenetics approaches; examines problems in phylogenetic networks, including questions relating to discrete mathematics, and issues of statistical estimation; highlights how evolution can provide a framework within which to understand comparative and functional genomics; provides an introduction to Integer Linear Programming and its use in computational biology, including its use for solving the Traveling Salesman Problem. Offering an invaluable source of insights for computer scientists, applied mathematicians, and statisticians, this illuminating volume will also prove useful for graduate courses on computational biology and bioinformatics.
Download or read book Computational Phylogenetics written by Tandy Warnow and published by Cambridge University Press. This book was released on 2017-11-02 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the foundations of phylogeny estimation and technical material enabling researchers to develop improved computational methods.
Download or read book Forest Measurements written by Joan DeYoung and published by . This book was released on 2016 with total page 159 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This is a forest measurements textbook written for field technicians. Silvicultural applications and illustrations are provided to demonstrate the relevance of the measurements. Special “technique tips” for each skill are intended to help increase data collection accuracy and confidence. These include how to avoid common pitfalls, effective short cuts, and essentials for recording field data correctly. The emphasis is on elementary skills; it is not intended to be a timber cruising guide"--BC Campus website.
Download or read book Molecular Evolution written by Ziheng Yang and published by Oxford University Press. This book was released on 2014 with total page 509 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents and explains modern statistical methods and computational algorithms for the comparative analysis of genetic sequence data in the fields of molecular evolution, molecular phylogenetics, statistical phylogeography, and comparative genomics. The book offers numerous examples of real data analysis and numerical calculations to illustrate the theory, in addition to the working problems at the end of each chapter. The coverage of maximum likelihood and Bayesian methods are in particular up-to-date, comprehensive, and authoritative.
Download or read book The Timetree of Life written by S. Blair Hedges and published by OUP Oxford. This book was released on 2009-04-23 with total page 1237 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Comprehensive Database of Diameter based Biomass Regressions for North American Tree Species written by Jennifer Caroline Jenkins and published by . This book was released on 2004 with total page 52 pages. Available in PDF, EPUB and Kindle. Book excerpt: A database consisting of 2,640 equations compiled from the literature for predicting the biomass of trees and tree components from diameter measurements of species found in North America. Bibliographic information, geographic locations, diameter limits, diameter and biomass units, equation forms, statistical errors, and coefficients are provided for each equation, along with examples of how to use the database. The CD-ROM included with the paper version of this publication contains the complete database (Table 3) in spreadsheet format (Microsoft Excel 2002® with Windows XP®). The database files can also be viewed in both spreadsheet and pdf formats by directing your browser to the Global Change page at http://www.fs.fed.us/ne/global/pubs/books/index.html
Download or read book Measuring Biological Diversity written by Anne E. Magurran and published by John Wiley & Sons. This book was released on 2013-04-18 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: This accessible and timely book provides a comprehensive overview of how to measure biodiversity. The book highlights new developments, including innovative approaches to measuring taxonomic distinctness and estimating species richness, and evaluates these alongside traditional methods such as species abundance distributions, and diversity and evenness statistics. Helps the reader quantify and interpret patterns of ecological diversity, focusing on the measurement and estimation of species richness and abundance. Explores the concept of ecological diversity, bringing new perspectives to a field beset by contradictory views and advice. Discussion spans issues such as the meaning of community in the context of ecological diversity, scales of diversity and distribution of diversity among taxa Highlights advances in measurement paying particular attention to new techniques such as species richness estimation, application of measures of diversity to conservation and environmental management and addressing sampling issues Includes worked examples of key methods in helping people to understand the techniques and use available computer packages more effectively
Download or read book Urban Biodiversity written by Alessandro Ossola and published by Routledge. This book was released on 2017-11-28 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt: Urban biodiversity is an increasingly popular topic among researchers. Worldwide, thousands of research projects are unravelling how urbanisation impacts the biodiversity of cities and towns, as well as its benefits for people and the environment through ecosystem services. Exciting scientific discoveries are made on a daily basis. However, researchers often lack time and opportunity to communicate these findings to the community and those in charge of managing, planning and designing for urban biodiversity. On the other hand, urban practitioners frequently ask researchers for more comprehensible information and actionable tools to guide their actions. This book is designed to fill this cultural and communicative gap by discussing a selection of topics related to urban biodiversity, as well as its benefits for people and the urban environment. It provides an interdisciplinary overview of scientifically grounded knowledge vital for current and future practitioners in charge of urban biodiversity management, its conservation and integration into urban planning. Topics covered include pests and invasive species, rewilding habitats, the contribution of a diverse urban agriculture to food production, implications for human well-being, and how to engage the public with urban conservation strategies. For the first time, world-leading researchers from five continents convene to offer a global interdisciplinary perspective on urban biodiversity narrated with a simple but rigorous language. This book synthesizes research at a level suitable for both students and professionals working in nature conservation and urban planning and management.
Download or read book Comparative Genomics written by Mathieu Blanchette and published by Springer. This book was released on 2018-10-04 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the proceedings of the 16th International Conference on Comparative Genomics, RECOMB-CG 2018, held in Magog-Orford, QC, Canada, in October 2018. The 18 full papers presented were carefully reviewed and selected from 29 submissions. The papers cover topics such as: genome rearrangements; genome sequencing; applied comparative genomics; reconciliation and coalescence; and phylogenetics.
