Counting the Uncountable: Statistical Approaches to Estimating Microbial Diversity

All biologists who sample natural communities are plagued with the problem of how well a sample reflects a community's “true” diversity. New genetic techniques have revealed extensive microbial diversity that was previously undetected with culture-dependent methods and morphological

[1]  T. Dobzhansky A Critique of the Species Concept in Biology , 1935, Philosophy of Science.

[2]  F. W. Preston The Commonness, And Rarity, of Species , 1948 .

[3]  Paul R. Ehrlich,et al.  Has the Biological Species Concept Outlived Its Usefulness , 1961 .

[4]  F. L. WATERHOUSE,et al.  Insect Ecology , 1967, Nature.

[5]  G. Seber The estimation of animal abundance and related parameters , 1974 .

[6]  M. Bulmer On Fitting the Poisson Lognormal Distribution to Species-Abundance Data , 1974 .

[7]  G. Belle,et al.  Explicit Calculation of the Rarefaction Diversity Measurement and the Determination of Sufficient Sample Size , 1975 .

[8]  S. Zahl,et al.  JACKKNIFING AN INDEX OF DIVERSITY , 1977 .

[9]  G. Sugihara Minimal Community Structure: An Explanation of Species Abundance Patterns , 1980, The American Naturalist.

[10]  Terry L. Erwin,et al.  TROPICAL FORESTS: THEIR RICHNESS IN COLEOPTERA AND OTHER ARTHROPOD SPECIES , 1982 .

[11]  J. Heltshe,et al.  Estimating species richness using the jackknife procedure. , 1983, Biometrics.

[12]  P. Raven The Challenge of Tropical Biology , 1983 .

[13]  G. Belle,et al.  Nonparametric estimation of species richness , 1984 .

[14]  A. Chao Nonparametric estimation of the number of classes in a population , 1984 .

[15]  J. Lawton,et al.  INSECTS ON PLANTS. COMMUNITY PATTERNS AND MECHANISMS. , 1987 .

[16]  Cannibalism, Food Availability, and Reproduction in Mosquitofish: A Critique , 1986, The American Naturalist.

[17]  R. G. Hughes Theories and Models of Species Abundance , 1986, The American Naturalist.

[18]  N. Pace,et al.  The Analysis of Natural Microbial Populations by Ribosomal RNA Sequences , 1986 .

[19]  J. Raaijmakers,et al.  Statistical analysis of the Michaelis-Menten equation. , 1987, Biometrics.

[20]  A. Chao Estimating the population size for capture-recapture data with unequal catchability. , 1987, Biometrics.

[21]  H. A. Orr,et al.  Do We Need a New Species Concept , 1988 .

[22]  A. Magurran Ecological Diversity and Its Measurement , 1988, Springer Netherlands.

[23]  H. Spencer,et al.  Why we need a new genetic species concept , 1989 .

[24]  M. Palmer,et al.  The Estimation of Species Richness by Extrapolation , 1990 .

[25]  A. Chao,et al.  Estimating the Number of Classes via Sample Coverage , 1992 .

[26]  N. Pace,et al.  Differential amplification of rRNA genes by polymerase chain reaction , 1992, Applied and environmental microbiology.

[27]  Á. Baltanás,et al.  On the use of some methods for the estimation of species richness , 1992 .

[28]  Jorge SoberónM.,et al.  The Use of Species Accumulation Functions for the Prediction of Species Richness , 1993 .

[29]  A. Chao,et al.  Stopping rules and estimation for recapture debugging with unequal failure rates , 1993 .

[30]  Robert K. Colwell,et al.  Estimating terrestrial biodiversity through extrapolation. , 1994, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[31]  G. Bills,et al.  Abundance and diversity of microfungi in leaf litter of a lowland rain forest in Costa Rica , 1994 .

[32]  M. Samways Insect Conservation Biology , 1994 .

[33]  S. Giovannoni,et al.  Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities , 1995 .

[34]  K. Schleifer,et al.  Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.

[35]  L. Raeymaekers,et al.  A commentary on the practical applications of competitive PCR. , 1995, Genome research.

[36]  J. Borneman,et al.  Molecular microbial diversity of an agricultural soil in Wisconsin , 1996, Applied and environmental microbiology.

[37]  Kevin J. Gaston,et al.  Biodiversity : a biology of numbers and difference , 1996 .

[38]  K. Gaston Species richness : measure and measurement , 1996 .

[39]  S. Hubbell,et al.  SPECIES-AREA AND SPECIES-INDIVIDUAL RELATIONSHIPS FOR TROPICAL TREES : A COMPARISON OF THREE 50-HA PLOTS , 1996 .

[40]  S. Giovannoni,et al.  Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR , 1996, Applied and environmental microbiology.

[41]  M. Watve,et al.  Problems in measuring bacterial diversity and a possible solution , 1996, Applied and environmental microbiology.

[42]  S. Giovannoni,et al.  Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina , 1997 .

[43]  R. Lande,et al.  Species diversity in vertical, horizontal, and temporal dimensions of a fruit‐feeding butterfly community in an Ecuadorian rainforest , 1997 .

[44]  Hans H. Cheng,et al.  Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA , 1997, Applied and environmental microbiology.

[45]  J. Borneman,et al.  Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation , 1997, Applied and environmental microbiology.

[46]  J. T. Staley,et al.  Biodiversity: are microbial species threatened? , 1997, Current opinion in biotechnology.

[47]  Jim Schieck,et al.  Biased detection of bird vocalizations affects comparisons of bird abundance among forested habitats , 1997 .

[48]  Robert K. Colwell,et al.  Statistical methods for estimating species richness of woody regeneration in primary and secondary rain forests of northeastern Costa Rica , 1998 .

[49]  S. Morand,et al.  Comparative performance of species richness estimation methods , 1998, Parasitology.

[50]  J. Tiedje,et al.  Characterization of the Dominant and Rare Members of a Young Hawaiian Soil Bacterial Community with Small-Subunit Ribosomal DNA Amplified from DNA Fractionated on the Basis of Its Guanine and Cytosine Composition , 1998, Applied and Environmental Microbiology.

[51]  James F. Quinn,et al.  ESTIMATING THE EFFECTIVENESS OF FURTHER SAMPLING INSPECIES INVENTORIES , 1998 .

[52]  D. Karl,et al.  Diversity of deep-sea hydrothermal vent Archaea from Loihi Seamount, Hawaii , 1998 .

[53]  J. Prosser,et al.  Molecular Analysis of Bacterial Community Structure and Diversity in Unimproved and Improved Upland Grass Pastures , 1999, Applied and Environmental Microbiology.

[54]  D. Relman,et al.  Bacterial diversity within the human subgingival crevice. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[55]  John Dunbar,et al.  Levels of Bacterial Community Diversity in Four Arid Soils Compared by Cultivation and 16S rRNA Gene Cloning , 1999, Applied and Environmental Microbiology.

[56]  J. Doré,et al.  Direct Analysis of Genes Encoding 16S rRNA from Complex Communities Reveals Many Novel Molecular Species within the Human Gut , 1999, Applied and Environmental Microbiology.

[57]  J. Hellmann,et al.  BIAS, PRECISION, AND ACCURACY OF FOUR MEASURES OF SPECIES RICHNESS , 1999 .

[58]  H. Heuer,et al.  Polynucleotide Probes That Target a Hypervariable Region of 16S rRNA Genes To Identify Bacterial Isolates Corresponding to Bands of Community Fingerprints , 1999, Applied and Environmental Microbiology.

[59]  G. Muyzer DGGE/TGGE a method for identifying genes from natural ecosystems. , 1999, Current opinion in microbiology.

[60]  Kinzig,et al.  Self-similarity in the distribution and abundance of species , 1999, Science.

[61]  Gerard Muyzer,et al.  Quantifying Microbial Diversity: Morphotypes, 16S rRNA Genes, and Carotenoids of Oxygenic Phototrophs in Microbial Mats , 1999, Applied and Environmental Microbiology.

[62]  D. Zelmer,et al.  Robust estimation of parasite component community richness. , 1999, The Journal of parasitology.

[63]  R. Lande,et al.  When species accumulation curves intersect: implications for ranking diversity using small samples. , 2000 .

[64]  G. Daily,et al.  Countryside Biogeography of Moths in a Fragmented Landscape: Biodiversity in Native and Agricultural Habitats , 2001 .