Pluralism and diversity: trends in the use and application of ordination methods 1990‐2007

Question: What are the trends and patterns in the application of ordination techniques in vegetation science since 1990? Location: Worldwide literature analysis. Methods: Evaluation of five major journals of vegetation science; search of all ISI‐listed ecological journals. Data were analysed with ANCOVAs, Spearman rank correlations, GLMs, biodiversity indices and simple graphs. Results: The ISI search retrieved fewer papers that used ordinations than the manual evaluation of five selected journals. Both retrieval methods revealed a clear trend in increasing frequency of ordination applications from 1990 to the present. Canonical Correspondence Analysis was far more frequently detected by the ISI search than any other method. Applications such as Correspondence Analysis/Reciprocal Averaging and Detrended Correspondence Analysis have increasingly been used in studies published in “applied” journals, while Canonical Correspondence Analysis, Redundancy Analysis and Non‐Metric Multidimensional Scaling were more frequently used in journals focusing on more “basic” research. Overall, Detrended Correspondence Analysis was the most commonly applied method within the five major journals, although the number of publications slightly decreased over time. Use of Non‐Metric Multidimensional Scaling has increased over the last 10 years. Conclusion: The availability of suitable software packages has facilitated the application of certain techniques such as Non‐Metric Multidimensional Scaling. However, choices of ordination techniques are currently less driven by the constraints imposed by the software; there is also limited evidence that the choice of methods follows social considerations such as the need to use fashionable methods. Methodological diversity has been maintained or has even increased over time and reflects the researcher's need for diverse analytical tools suitable to address a wide range of questions.     

Book Review Essays

Archaeology and Burials: Bodies of Evidence: Reconstructing History through Skeletal Analysis. Anne L. Grauer, ed.
Archaeology and Burials: Regional Approaches to Mortuary Analysis. Lane Anderson Beck, ed. New York: Plenum Press, 1995. 280 pp.     

Reviews

Book reviewed in this article:
Phylogenetic Analysis of DNA Sequences -M. M. Miyamoto and J. Cracraft(eds.)
Phylogenetic Analysis of DNA Sequence -Michael M. Miyamoto and Joel Cracraftv (eds.)
Phylogeny and the Classfication of Ffossil and Recent Organisms: Proceedings of A Symposium Organized by the Deutsche Forschungsgemeinschaft.-N. Schmidt Kittler and R. Willmann (eds.)     

The spatial and temporal distribution of the grain aphid Sitobion avenae in winter wheat

The spatial and temporal distribution of the grain aphid Sitobion avenae F. (Homoptera: Aphididae) was studied within a field of winter wheat during the summer of 1996. Sampling was done using four nested grids comprising 133 locations. Analysis by Taylor's power law gave results typical for insect populations. Analysis by SADIE (Spatial Analysis by Distance Indices) showed spatial pattern due to edge effects and sampling scale, and positive but mild spatial association, although spatial patterns were ephemeral. Reasons for these findings and the implications for integrated crop management are discussed.     

Book reviews

Books reviewed in this article:
GORDON, A. D. Classification, 2nd edition.
LEHMANN, E. L. Elements of Large-Sample Theory.
VON STORCH, H. and ZWIERS, W. Statistical Analysis in Climate Research.
CHOW, S. -C. and LIU, J.-P. Design and Analysis of Bioavailability and Bioequivalence Studies, 2nd edition.
FEDEREI, W. T. Statistical Design and Analysis for Intercropping Experiments Vol. 11: Three or More Crops.
LUTZ, M. and KENAKIN, T. Quantitative Molecular Pharmacology and Informatics in Drug Discovery.
OTT, J. Analysis of Human Genetic Linkage, Third Edition.
RASCH, D., VERDOOREN, L. R., and GOWERS, J. I. Fundamentals in the Design and Analysis of Experiments and Surveys-Grundlagen der Planung und Auswertung von Versuchen und Erhebungen.
RIFFENBURGH, R. H. Statistics in Medicine.
FISHER, R. A. The Genetical Theory of Natural Selection: A Complete Variorum Edition
GOOD, P. I. Resampling Methods: A Practical Guide to Data Analysis.
RONDEL, R. K., VARLEY, S. A. and WEBB, C. V., eds. Clinical Data Management, 2nd edition.
LEFKOVITS, I. and WALDMANN, H. Limiting Dilution Analysis of Cells in the Immune System, 2nd edition.     

NanoString nCounter分析系统进行多基因表达计数的评价

目的:Nano String n Counter是近年发展起来的进行基因表达谱检测的新平台,它利用分子条形码直接对基因表达进行多重计数。本实验通过对m RNA表达量的检测,分析n Counter系统进行基因表达计数的可靠性。方法:应用Nano String公司提供的CAE Kit试剂盒,通过杂交(m RNA样品与报告探针和捕获探针杂交)、纯化(清洗未结合探针)和计数(读取m RNA的条数)三个步骤,检测由人参考RNA和人脑RNA构成的4个样品中48个目的基因的m RNA表达量;对获得的未进行标准化的原始数据,应用Excel 2007软件进行线性分析,从再现性、稳定性、准确性方面对n Counter分析系统进行评估。结果:再现性分析所有R2均大于0.998,线性拟合良好;试剂盒中阳性控制所有R2均大于0.99,高于质控要求的0.95;样品H70B30和H30B70的预期表达量与实测值线性R2大于0.999,预期值与实测值一致性良好。结论:n Counter分析系统稳定性好,准确性高,检测m RNA表达可靠。     

Book Reviews

Books reviewed in this article:
COLES, S. An Introduction to Statistical Modeling of Extreme Values.
DOWNES, B. J., BARMUTA, L. A., FAIRWEATHER, P.G., FAITH, D. P., KEOUGH, M. J., LAKE, P. S., MAPSTONE, B. D. and QUINN, G. P. Monitoring Ecological Impacts: Concepts and Practice in Flowing Waters.
BRUNNER, E., DOMHOF, S. and LANGER, F. Nonparametric Analysis of Longitudinal Data in Factorial Experiments.
LANGE, K. Mathematical and Statistical Methods for Genetic Analysis, 3rd edition.
MILLIKEN, G. A. and JOHNSON, D. E. Analysis of Messy Data, Volume III: Analysis of Covariance.
SMITH, P. J. Analysis of Failure and Survival Data.
JONES, P. W. and SMITH, P. Stochastic Processes: An Introduction.
PERCUS, J. K. Mathematics of Genome Analysis.
ROSENBAUM, P. Observational Studies, 2nd edition.
THODE, H. C., Jr. Testing for Normality.
GLAZ, J., NAUS, J. and WALLENSTEIN, S. Scan Statistics.
TOWNEND, J. Practical Statistics for Environmental and Biological Scientists.
REDDY, M. V. Statistics for Mental Health Care Research.     

Graphics for Statistics and Data Analysis with R by KEEN,K. J.

Graphics for Statistics and Data Analysis with R (K. J. Keen) Michael Friendly Hidden Markov Models for Time Series: An Introduction Using R (W. Zucchini and I. L. MacDonald) Peter Guttorp Bayesian Adaptive Methods for Clinical Trials (S. M. Berry, B. P. Carlin, J. J. Lee, J. J. and P. Muller) Say Beng Tan SAS and R Data Management, Statistical Analysis, and Graphics (K. Kleinman and N. Horton) Juan P. Steibel Numerical Analysis for Statisticians, 2nd edition (K. Lange) Maria Rizzo Statistical Methods for Disease Clustering (T. Tango) Lance A. Waller Brief Reports by the Editor Survival Analysis Using SAS: A Practical Guide (P. D. Allison) Design and Analysis of Quality of Life Studies in Clinical Trials (D. L. Fairclough) Nonparametric Statistical Inference (J. D. Gibbons and S. Chakraborti) Stochastic Processes: An Introduction (P. W Jones and P. Smith)
     

Book review

Book review in this article:
Epithelial Transport: A Guide to Methods and Experimental Analysis . Edited by N. K. Wills, L. Reuss and Simon A. Lewis.     

Reviews

Modern Methods of Plant Analysis , New Series, Vol. 13, Plant Toxin Analysis . Ed. by H. F. L inskens & J. F. J ackson
Plant Disease Control – Principles and Practice. By O tis C. M alov
Orchid Biology : Reviews and Perspectives , IV and V. Ed. by J oseph A rditti
The Ecology of Mangrove and Related Systems: Proceedings of the International Symposium held at Mombasa, Kenya, September 1990 . Ed. by V ictor J accarini &E ls M artens
Climate Change: Science, Impacts and Policy , Ed. by J. J äger &H.L. F erguson
Quaternary of Scotland. Ed. by J. E. G ordon &D. G. S utherland     

Turning over the pieces of the post-genomic jigsaw puzzle

NMHCC Second International Conference: Post-Genomic Analysis of Therapeutic Targets preceded by a Preconference Symposium: Genomic Disease Modeling and Targeting, San Diego, CA, USA, 3–4 August 1998.     

Circadian Rhythmicity of Grooming Behavior During Pregnancy in a Marmoset (Callithrix jacchus) Family Group in Captivity

One family group of common marmoset ( Callithrix jacchus ) was observed in captivity under natural environmental conditions to describe the circadian pattern of grooming behavior during the pregnancy of the reproductive female. The animals were observed by focal sampling, from the beginning to the end of animal's active phase, during two non-consecutive days per week, from August to November 1996. The duration of self-grooming and social grooming behavior of each animal were totalled each hour. The time series obtained were analyzed by Cluster Analysis and by Sin gle Cosinor Analysis. The daily patterns of grooming behavior during pregnancy were divided by Cluster Analysis into two stages, one corresponding to the second half of the third month of pregnancy, and the other from the last half of the third month to the last week before parturition. The confidence intervals of acrophases overlapped in all stages. The acrophases values of the first stage occurred between 10:09 h and 11:00 h, and on the second stage between 8:51 h and 11:13 h. The daily pattern of grooming behavior of adult male and female showed a trend to increase in the first hours of the active phase. This trend to advance grooming behavior during the second stage of pregnancy may be due to an effect of the coming parturition itself or to seasonal influences.     

Interactive InterPro-based comparisons of proteins in whole genomes

MOTIVATION: The SWISS-PROT group at the EBI has developed the Proteome Analysis Database utilizing existing resources and providing comprehensive and integrated comparative analysis of the predicted protein coding sequences of the complete genomes of bacteria, archaea and eukaryotes. The Proteome Analysis Database is accompanied by a program that has been designed to carry out interactive InterPro proteome comparisons for any one proteome against any other one or more of the proteomes in the database.     

The Minority Voice in Educational Reform: An Analysis by Minority and Women College of Education Deans

The Minority Voice in Educational Reform: An Analysis by Minority and Women College of Education Deans. Louis A. Castenell and Jill M. Tarule, eds. Greenwich, CT: Ablex Publishing Corporation, 1997. 170 pp.     

Book Reviews

Book reviews in this article:
Immunohistochemistry edited by A. C. Cuello.
Methods of Enzymatic Analysis, 3rd Edition, Vol. 1: Fundamentals edited by H. U. Bergmeyer, J. Bergmeyer, and M. Grassl.     

Applied Spatial Data Analysis with R. by BIVAND, R. S., PEBESMA, E. J., and GOMEZ-RUBIO, V.

Applied Spatial Data Analysis with R (R. S. Bivand, E. J. Pebesma, and V. Gomez‐Rubio) Jay M. Ver Hoef Bayesian Disease Mapping: Hierarchical Modeling in Spatial Epidemiology (A. B. Lawson) J. Law Disease Surveillance: A Public Health Informatics Approach (J. S. Lombardo and D. L. Buckeridge, editors) Iris Pigeot Survival Analysis for Epidemiologic and Medical Research (S. Selvin) M. G. Valsecchi Survival and Event History Analysis: A Process Point of View (O. O. Aalen, O. Borgan, and H. K. Gjessing) Patricia Grambsch Nonlinear Dimensionality Reduction (J. A. Lee and M. Verleysen) Haonan Wang Model Selection and Model Averaging (G. Claeskens and N. L. Hjort) Thomas M. Loughin Meta‐Analysis of Binary Data Using Profile Likelihood (D. Böhning, R. Kuhnert, and S. Rattanasiri) Eloise Kaizar Wavelet Methods in Statistics with R (G. P. Nason) Jeffrey S. Morris Adaptive Design Theory and Implementation Using SAS and R (M. Chang) Feifang Hu Ecological Models and Data in R (B. M. Bolker) Rachel M. Fewster Applied Multiway Data Analysis (P. M. Kroonenberg) Renato Coppi Brief Reports by the Editor Sampling of Populations: Methods and Applications, 4th edition (P. S. Levy and S. Lemeshow) Applied Survival Analysis: Regression Modeling of Time‐to‐Event Data, 2nd edition (D. W. Hosmer, S. Lemeshow, and S. May) SAS for Data Analysis: Intermediate Statistical Methods (M. G. Marasinghe and W. J. Kennedy) Advances in Mathematical and Statistical Modeling (B. C. Arnold, N. Balakrishnan, J. M. Sarabia, and R. Mínguez, editors) An Introduction to Generalized Linear Models, 3rd edition (A. J. Dobson and A. G. Barnett) Design and Analysis of Bioavailability and Bioequivalence Studies, 3rd edition (S.‐C. Chow and J.‐P. Liu)     

Circadian Rhythmicity of Grooming Behavior During Pregnancy in a Marmoset (Callithrix jacchus) Family Group in Captivity

One family group of common marmoset (Callithrix jacchus) was observed in captivity under natural environmental conditions to describe the circadian pattern of grooming behavior during the pregnancy of the reproductive female. The animals were observed by focal sampling, from the beginning to the end of animal's active phase, during two non-consecutive days per week, from August to November 1996. The duration of self-grooming and social grooming behavior of each animal were totalled each hour. The time series obtained were analyzed by Cluster Analysis and by Sin gle Cosinor Analysis. The daily patterns of grooming behavior during pregnancy were divided by Cluster Analysis into two stages, one corresponding to the second half of the third month of pregnancy, and the other from the last half of the third month to the last week before parturition. The confidence intervals of acrophases overlapped in all stages. The acrophases values of the first stage occurred between 10:09 h and 11:00 h, and on the second stage between 8:51 h and 11:13 h. The daily pattern of grooming behavior of adult male and female showed a trend to increase in the first hours of the active phase. This trend to advance grooming behavior during the second stage of pregnancy may be due to an effect of the coming parturition itself or to seasonal influences.     

Book Reviews

Book reviewed in this article:
Methods of Enzymatic Analysis, 3rd Edition, Vol. 2: Samples, Reagents, Assessment of Results; Vol. 3: Enzymes 1: Oxidoreductases, Transferases edited by H. U. Bergmeyer, J. Bergmeyer, and M. Grassl.
Growth and Maturation Factors, Vol. 1 edited by G. Guroff.     

Epiphytic macrolichen communities along regional gradients in northern Norway

Abstract. Question: What are the relative influences of human impact, macroclimate, geographic location and habitat related environmental differences on species composition of boreal epiphytic macrolichen communities? Location: Troms county in northern Norway. Methods: Detrended Correspondence Analysis revealed the main gradient structure in lists of epiphytic macrolichen species from deciduous forests. By Canonical Correspondence Analysis with variance partitioning, the relative amount of variance in macrolichen species composition attributable to human impact, macroclimate, spatial context and environmental differences was quantified. Results: There was no significant effect of human impact on species composition of epiphytic macrolichens of deciduous forests. Macroclimate was the most important factor determining epiphytic macrolichen communities, which were also strongly influenced by ecological differences such as forest stand properties. Conclusions: Epiphytic macrolichen communities are determined by a macroclimatic gradient from the coastline to the interior of central north Norway. In marked contrast, the species composition of epiphytic macrolichen communities seems to be unaffected by human impact in the study area, where air pollution was marginal.