Biological diversity : frontiers in measurement and assessment / edited by Anne E. Magurran and Brian J. McGill.

Includes bibliographical references and index.

Machine generated contents note: 1. Challenges and opportunities in the measurement and assessment of biological diversity / Brian J. McGill -- 1.1. Introduction -- 1.2. State of the field -- 1.3. What is in this book -- Acknowledgements -- pt. I Basic Measurement Issues -- 2. An overview of sampling issues in species diversity and abundance surveys / Norman Mercado-Silva -- 2.1. Introduction -- 2.2. State of the field -- 2.2.1. Setting objectives -- 2.2.2. An important partner: the statistician -- 2.2.3. What species to sample -- 2.2.4. Where to sample -- 2.2.5. Bias, sampling error, and precision -- 2.2.6. How to sample -- 2.2.7. Quantifying the sample -- 2.2.8. When to sample -- 2.2.9. How many samples to collect -- 2.2.10. Comparing information from different surveys -- 2.2.11. Preparing for the field -- 2.3. Prospectus -- 2.4. Key points -- 3. Biodiversity monitoring: the relevance of detectability / Stuart E. Newson -- 3.1. Introduction -- 3.2. State of the field: which biodiversity measure?

3.3. Detectability: are species counts relevant for monitoring biodiversity? -- 3.3.1. Individual detectability -- 3.3.2. Estimating individual detectability -- 3.3.3. Species detectability -- 3.4. Case study: the UK Breeding Bird Survey -- 3.5. Discussion -- 3.6. Prospectus -- 3.7. Key points -- Acknowledgements -- pt. II Diversity -- 4. Estimating species richness / Robert K. Colwell -- 4.1. Introduction -- 4.2. State of the field -- 4.2.1. Sampling models for biodiversity data -- 4.2.2. The species accumulation curve -- 4.2.3. Climbing the species accumulation curve -- 4.2.4. Species richness versus species density -- 4.2.5. Individual-based rarefaction -- 4.2.6. Sample-based rarefaction -- 4.2.7. Assumptions of rarefaction -- 4.2.8. Estimating asymptotic species richness -- 4.2.9. Comparing estimators of asymptotic species richness -- 4.2.10. Software for estimating species richness from sample data -- 4.3. Prospectus -- 4.4. Key points -- Acknowledgements -- 5. Measurement of species diversity / Brian J. McGill -- 5.1. Introduction -- 5.2. State of the art.

880-01 7.4.3. Using species abundance distributions to evaluate change -- 7.4.4. Assessing change using biodiversity indexes -- 7.5. Measuring change in the rate of change -- 7.6. Using temporal change to shed light on community structure -- 7.7. Partitioning diversity in space and time -- 7.8. Prospectus -- 7.9. Key points -- pt. III Distribution -- 8. Commonness and rarity / Peter A. Henderson -- 8.1. Introduction -- 8.2. State of the field -- 8.3. Commonness and rarity: ecological context -- 8.4. Assessing commonness and rarity -- 8.5. Prospectus -- 8.6. Key points -- 9. Species abundance distributions / Brian J. McGill -- 9.1. Introduction -- 9.2. State of the field -- 9.2.1. Visual approaches to SADs -- 9.2.2. Parametric approaches to SADs -- 9.2.3. Non-parametric approaches to SADs -- 9.2.4. Multivariate approaches to SADs -- 9.3. Identifying a useful, parsimonious subset of SAD metrics -- 9.3.1. Efficiency and bias -- 9.3.2. Independence of measures -- 9.3.3. Overall assessment of useful, parsimonious metrics of SADs -- 9.4. Prospectus -- 9.5. Key points -- Acknowledgements.

10. Fitting and empirical evaluation of models for species abundance distributions / Maria Dornelas -- 10.1. Introduction -- 10.2. State of the field -- 10.2.1. Species abundance models -- 10.2.2. Obtaining predicted abundances -- 10.2.3. Choosing parameters -- 10.2.4. Goodness-of-fit testing -- 10.2.5. Model selection -- 10.3. Prospectus -- 10.3.1. Sampling theory for species abundance models -- 10.3.2. Parameter estimation -- 10.3.3. Goodness-of-fit testing -- 10.3.4. Model selection -- 10.3.5. Conclusions -- 10.4. Key points -- 11. Species occurrence and occupancy / Fangliang He -- 11.1. Introduction -- 11.2. State of the field -- 11.2.1. Occupancy-area relationships -- 11.2.2. Occupancy-abundance relationships -- 11.2.3. Species occupancy distributions -- 11.3. Prospectus -- 11.4. Key points -- Acknowledgements -- 12. Measuring the spatial structure of biodiversity / Brian J. McGill -- 12.1. Introduction -- 12.1.1. What spatial structure is of interest? -- 12.1.2. Number of variables recorded -- pattern or association? -- 12.1.3. Types of data.

12.2. State of the art -- 12.2.1. Estimating intensity (first-order effects) -- 12.2.2. Studying effects at a distance (second-order effects) -- 12.2.3. Associations between two variables -- 12.2.4. Software available -- 12.3. Prospectus -- 12.4. Key points -- Acknowledgements -- pt. IV Alternative measures of diversity -- 13. A primer of trait and functional diversity / Evan Weiher -- 13.1. Introduction -- 13.1.1. General definitions -- 13.1.2. General importance -- 13.1.3. A brief history of trait and functional diversity -- 13.2. State of the field -- 13.2.1. Overview -- 13.2.2. Indices of trait and functional diversity -- 13.2.3. Partitioning the components of trait diversity -- 13.2.4. Methodological issues -- 13.2.5. Conceptual issues -- 13.3. Prospectus -- 13.3.1. Recommendations -- 13.3.2. Future directions -- 13.4. Key points -- Acknowledgements -- 14. Measuring phylogenetic biodiversity / Arne Ø. Mooers -- 14.1. Introduction -- 14.1.1. Overview -- 14.1.2. Approaching the study of phylogenetic diversity.

14.2. State of the field -- 14.2.1. Null models -- 14.2.2. Simulation analyses -- 14.2.3. Simulation results -- 14.3. Prospectus -- 14.3.1. Phylogenetic diversity in conservation -- 14.3.2. Phylogenetic diversity in community ecology -- 14.3.3. Abundance vs presence-absence data -- 14.4. Key points -- 15. Genetic methods for biodiversity assessment / Hans-Werner Herrmann -- 15.1. Introduction -- 15.2. Genetic methods in biodiversity assessment -- 15.2.1. Mitochondrial, chloroplast, and nuclear DNA -- 15.2.2. Genome technologies -- 15.3. Biodiversity assessments -- 15.3.1. Phylogenies for biodiversity assessment using mtDNA and nuclear DNA -- 15.3.2. Non-invasively monitoring for biodiversity -- 15.3.3. DNA barcoding for biodiversity assessment -- 15.3.4. Genome technologies for biodiversity assessment -- 15.4. Prospectus -- 15.5. Key points -- pt. V Applications -- 16. Microbial diversity and ecology / Thomas P. Curtis -- 16.1. Introduction -- 16.2. The diversity concept -- 16.3. Phylogeny -- 16.4. rRNA as an evolutionary chronometer.

16.5. Methods for assessing diversity -- 16.5.1. PCR-based methods -- 16.5.2. Pyrosequencing -- 16.5.3. Metagenomics -- 16.6. Sampling, scale, and thresholds -- 16.7. Mathematical tools for estimating diversity -- 16.7.1. Collectors curves -- 16.7.2. Chao's non-parametric estimators -- 16.7.3. Parametric estimators that assume a distribution -- 16.7.4. Estimating diversity by inferring a distribution from the data -- 16.8. Estimation of required sample size -- 16.9. In-depth metagenome analyses -- 16.10. Prospectus -- 16.11. Key points -- 17. Biodiversity and disturbance / Karl Inne Ugland -- 17.1. Introduction -- 17.2. What is a disturbance? -- 17.2.1. Source of the disturbance -- 17.2.2. Timescale -- 17.2.3. Spatial scale -- 17.2.4. Intensity -- 17.2.5. Specificity -- 17.2.6. Summary -- 17.3. State of the field: measuring the effects of disturbance on biodiversity -- 17.3.1. Univariate metrics -- 17.3.2. Species abundance distribution based metrics -- 17.3.3. Multivariate analysis -- 17.4. Prospectus -- 17.5. Key points -- Acknowledgements.

18. Measuring biodiversity in managed landscapes / Melodie A. McGeoch -- 18.1. Introduction -- 18.2. State of the field -- 18.2.1. Variation in biodiversity measurement goals -- 18.2.2. Bioindicators and monitoring -- 18.2.3. Measuring biodiversity for management -- 18.2.4. Matrices for measurement -- 18.3. Prospectus -- 18.4. Key points -- Acknowledgements -- 19. Estimating extinction with the fossil record / S. Kathleen Lyons -- 19.1. Introduction -- 19.2. State of the field -- 19.2.1. Basic metrics -- 19.2.2. Survivorship curves -- 19.2.3. The importance of sampling -- 19.2.4. Relevant studies -- 19.2.5. Occurrence-based diversity estimates -- 19.2.6. Gap analyses -- 19.3. Prospectus -- 19.4. Key points.

20. Estimating species density / Chi Yuan -- 20.1. Introduction -- 20.1.1. The problem: what is the density of species? -- 20.1.2. Defining the density of species -- 20.1.3. Species density takes on new importance in an era of environmental concern -- 20.2. Data set -- 20.2.1. Data description -- 20.2.2. Data manipulation -- 20.2.3. NP: our surrogate for A -- 20.3. Density estimates -- 20.3.1. First density estimate -- 20.3.2. Density estimates for subsets with a uniform plot size -- 20.4. Curvature in SPARs -- 20.5. Reducing the bias -- 20.5.1. Extrapolation -- 20.5.2. Estimators based on the frequency of scarce species -- 20.6. Applying bias reduction -- 20.7. Checking our results on the scale of all of Virginia -- 20.8. Why species density? -- 20.8.1. Species density as an environmental indicator -- 20.8.2. Species density as a topic of study -- 20.9. Key points -- Acknowledgements -- pt. VI Conclusions -- 21. Conclusions / Anne E. Magurran.

Print version record.

Biological Diversity provides an up to date, authoritative review of the methods of measuring and assessing biological diversity, together with their application. The book's emphasis is on quantifying the variety, abundance, and occurrence of taxa, and on providing objective and clear guidance for both scientists and managers. This is a fast-moving field and one that is the focus of intense research interest. However the rapid development of new methods, the inconsistentand sometimes confusing application of old ones, and the lack of consensus in the literature about the best approach, means that there is a real need for a current synthesis. Biological Diversity covers fundamental measurement issues such as sampling, re-examines familiar diversity metrics (including species richness, diversity statistics, and estimates of spatial and temporal turnover), discusses species abundance distributions and how best to fit them, explores species occurrence and the spatial structure of biodiversity, and investigates alternative approaches used to assess trait, phylogenetic, and genetic diversity. The final section of the book turnsto a selection of contemporary challenges such as measuring microbial diversity, evaluating the impact of disturbance, assessing biodiversity in managed landscapes, measuring diversity in the imperfect fossil record, and using species density estimates in management and conservation.

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