Journal ArticleDOI
Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness
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TLDR
A series of common pitfalls in quantifying and comparing taxon richness are surveyed, including category‐subcategory ratios (species-to-genus and species-toindividual ratios) and rarefaction methods, which allow for meaningful standardization and comparison of datasets.Abstract:
Species richness is a fundamental measurement of community and regional diversity, and it underlies many ecological models and conservation strategies. In spite of its importance, ecologists have not always appreciated the effects of abundance and sampling effort on richness measures and comparisons. We survey a series of common pitfalls in quantifying and comparing taxon richness. These pitfalls can be largely avoided by using accumulation and rarefaction curves, which may be based on either individuals or samples. These taxon sampling curves contain the basic information for valid richness comparisons, including category‐subcategory ratios (species-to-genus and species-toindividual ratios). Rarefaction methods ‐ both sample-based and individual-based ‐ allow for meaningful standardization and comparison of datasets. Standardizing data sets by area or sampling effort may produce very different results compared to standardizing by number of individuals collected, and it is not always clear which measure of diversity is more appropriate. Asymptotic richness estimators provide lower-bound estimates for taxon-rich groups such as tropical arthropods, in which observed richness rarely reaches an asymptote, despite intensive sampling. Recent examples of diversity studies of tropical trees, stream invertebrates, and herbaceous plants emphasize the importance of carefully quantifying species richness using taxon sampling curves.read more
Citations
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Journal ArticleDOI
The Theory of Island Biogeography
TL;DR: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols used xiii 1.
Journal ArticleDOI
Picante: R tools for integrating phylogenies and ecology
Steven W. Kembel,Peter Cowan,Matthew R. Helmus,William K. Cornwell,Hélène Morlon,David D. Ackerly,Simon P. Blomberg,Campbell O. Webb +7 more
TL;DR: Picante is a software package that provides a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities and performs tests for phylogenetic signal in trait distributions, community structure and species interactions.
Journal ArticleDOI
Global effects of land use on local terrestrial biodiversity
Tim Newbold,Lawrence N. Hudson,Samantha L. L. Hill,Sara Contu,Igor Lysenko,Rebecca A. Senior,Luca Börger,Dominic J. Bennett,Argyrios Choimes,Ben Collen,Julie Day,Adriana De Palma,Sandra Díaz,Susy Echeverría-Londoño,Melanie J. Edgar,Anat Feldman,Morgan Garon,Michelle L K Harrison,Tamera I Alhusseini,Daniel J. Ingram,Yuval Itescu,Jens Kattge,Victoria Kemp,Lucinda Kirkpatrick,Michael Kleyer,David L P Correia,Callum D. Martin,Shai Meiri,Maria Novosolov,Yuan Pan,Helen Phillips,Drew W. Purves,Alexandra N Robinson,Jake Simpson,Sean L. Tuck,Evan Weiher,Hannah J. White,Robert M. Ewers,Georgina M. Mace,Jörn P. W. Scharlemann,Andy Purvis +40 more
TL;DR: A terrestrial assemblage database of unprecedented geographic and taxonomic coverage is analysed to quantify local biodiversity responses to land use and related changes and shows that in the worst-affected habitats, pressures reduce within-sample species richness by an average of 76.5%, total abundance by 39.5% and rarefaction-based richness by 40.3%.
Journal ArticleDOI
Waste not, want not: why rarefying microbiome data is inadmissible.
Paul J. McMurdie,Susan Holmes +1 more
TL;DR: It is advocated that investigators avoid rarefying altogether and supported statistical theory is provided that simultaneously accounts for library size differences and biological variability using an appropriate mixture model.
Journal ArticleDOI
Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies
Anne Chao,Nicholas J. Gotelli,T. C. Hsieh,Elizabeth L. Sander,K. H. Ma,Robert K. Colwell,Robert K. Colwell,Aaron M. Ellison +7 more
TL;DR: In this article, the authors extended previous rarefaction and extrapolation models for species richness (Hill number q D, where q ¼ 0) to measures of taxon diversity incorporating relative abundance (i.e., for any Hill number qD, q. 0) and presented a unified approach for both individual-based (abundance) data and sample-based data.
References
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Journal ArticleDOI
The Theory of Island Biogeography
TL;DR: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols used xiii 1.
Book
The Theory of Island Biogeography
TL;DR: The Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201
Book
Ecological Diversity and its Measurement
TL;DR: In this paper, the authors define definitions of diversity and apply them to the problem of measuring species diversity, choosing an index and interpreting diversity measures, and applying them to structural and structural diversity.
Journal ArticleDOI
Diversity in tropical rain forests and coral reefs.
TL;DR: The commonly observed high diversity of trees in tropical rain forests and corals on tropical reefs is a nonequilibrium state which, if not disturbed further, will progress toward a low-diversity equilibrium community as mentioned in this paper.
Book
Resource competition and community structure
TL;DR: This book builds a mechanistic, resource-based explanation of the structure and functioning of ecological communities and explores such problems as the evolution of "super species," the differences between plant and animal community diversity patterns, and the cause of plant succession.