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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.
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.
Much information is available for specific gravity and other properties of wood and bark, but it is widely scattered in the literature. This paper compiles information for estimation of biomass for 156 tree species found in North America for use in national forest inventory applications. We present specific gravities based on average green volume as well as 12 percent moisture content volume for calculation of oven-dry biomass. Additional information is included on bark thickness, bark voids, and bark percentages by species and green and dry weight of wood and bark. --
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.
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.
"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.
Studies of evolution at the molecular level have experienced phenomenal growth in the last few decades, due to rapid accumulation of genetic sequence data, improved computer hardware and software, and the development of sophisticated analytical methods. The flood of genomic data has generated an acute need for powerful statistical methods and efficient computational algorithms to enable their effective analysis and interpretation. Molecular Evolution: a statistical approach 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. Written by an expert in the field, the book emphasizes conceptual understanding rather than mathematical proofs. The text is enlivened with 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. This advanced textbook is aimed at graduate level students and professional researchers (both empiricists and theoreticians) in the fields of bioinformatics and computational biology, statistical genomics, evolutionary biology, molecular systematics, and population genetics. It will also be of relevance and use to a wider audience of applied statisticians, mathematicians, and computer scientists working in computational biology.
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
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.