Paleontological Data Analysis

by Hammer, Ø; yvind; Harper, David A. T.

• ISBN13: 9781405115445
• ISBN10: 1405115440
• Format: Paperback
• Copyright: 2005-11-04
• Publisher: Wiley-Blackwell

Summary

During the last 10 years numerical methods have begun to dominate paleontology. These methods now reach far beyond the fields of morphological and phylogenetic analyses to embrace biostratigraphy, paleobiogeography, and paleoecology. The availability of cheap computing power, together with a wide range of software products, have made increasingly complex algorithms accessible to the vast majority of paleontologists. Paleontological Data Analysis explains the key numerical techniques in paleontology, and the methodologies employed in the software packages now available. Following an introduction to numerical methodologies in paleontology, and to univariate and multivariate techniques (including inferential testing), are chapters on morphometrics, phylogenetic analysis, paleobiogeography and paleoecology, time series analysis, and quantitative biostratigraphy. Each chapter describes a range of techniques in detail, with worked examples, illustrations, and appropriate case histories. The purpose, type of data required, functionality, and implementation of each technique are described, together with notes of caution where appropriate. The book and the accompanying PAST software package available through www.blackwellpublishing.com/hammer are important investigative tools in a rapidly developing field characterized by many exciting new discoveries and innovative techniques. Paleontological Data Analysis is an invaluable tool for all students and researchers involved in quantitative paleontology.

Author Biography

Dr Øyvind Hammer is currently a Researcher in Paleontology at the Geological Museum in Oslo, and in Geobiology at the research center “Physics of Geological Processes”. In addition to a number of research publications, he is the author of the popular data-analysis software PAST.

David Harper is Professor of Paleontology and Deputy Director of Geology at the Natural History Museum of Denmark, University of Copenhagen. His research interests include the history of biodiversity; fossil brachiopods from the Palaeozoic rocks of NW Europe, North America, and China, and from the Cretaceous and Cenozoic rocks of the Caribbean; computer-based methods for the analysis and modeling of fossils and their distributions.

Table of Contents

Preface	ix
Acknowledgments	xi
Introduction	1	(7)
The nature of paleontological data	1	(3)
Advantages and pitfalls of paleontological data analysis	4	(3)
Software	7	(1)
Basic statistical methods	8	(53)
Introduction	8	(4)
Statistical distributions	12	(7)
Shapiro-Wilk test for normal distribution	19	(3)
F test for equality of variances	22	(1)
Student's t test and Welch test for equality of means	23	(4)
Mann-Whitney U test for equality of medians	27	(3)
Kolmogorov--Smirnov test for equality of distribution	30	(3)
Bootstrapping and permutation	33	(2)
One-way ANOVA	35	(4)
Kruskal--Wallis test	39	(3)
Linear correlation	42	(4)
Non-parametric tests for correlation	46	(2)
Linear regression	48	(5)
Reduced major axis regression	53	(4)
Chi-square test	57	(4)
Introduction to multivariate data analysis	61	(17)
Approaches to multivariate data analysis	61	(1)
Multivariate distributions	62	(1)
Parametric multivariate tests -- Hotelling's T2	63	(3)
Non-parametric multivariate tests -- permutation test	66	(1)
Hierarchical cluster analysis	67	(8)
K-means cluster analysis	75	(3)
Morphometrics	78	(79)
Introduction	78	(1)
The allometric equation	79	(4)
Principal components analysis (PCA)	83	(8)
Multivariate allometry	91	(5)
Discriminant analysis for two groups	96	(4)
Canonical variate analysis (CVA)	100	(3)
MANOVA	103	(2)
Fourier shape analysis in polar coordinates	105	(3)
Elliptic Fourier analysis	108	(4)
Eigenshape analysis	112	(3)
Landmarks and size measures	115	(2)
Procrustes fitting	117	(4)
PCA of landmark data	121	(1)
Thin-plate spline deformations	122	(6)
Principal and partial warps	128	(4)
Relative warps	132	(2)
Regression of warp scores	134	(2)
Disparity measures and morphospaces	136	(5)
Point distribution statistics	141	(4)
Directional statistics	145	(12)
Case study: The ontogeny of a Silurian trilobite	148	(9)
Phylogenetic analysis	157	(26)
Introduction	157	(3)
Characters	160	(1)
Parsimony analysis	161	(5)
Character state reconstruction	166	(2)
Evaluation of characters and trees	168	(1)
Consensus tree	168	(2)
Consistency index	170	(1)
Retention index	171	(1)
Bootstrapping	172	(2)
Bremer support	174	(1)
Stratigraphic congruency indices	175	(3)
Phylogenetic analysis with maximum likelihood	178	(5)
Case study: The systematics of heterosporous ferns	179	(4)
Paleobiogeography and paleoecology	183	(71)
Introduction	183	(3)
Biodiversity indices	186	(7)
Taxonomic distinctness	193	(3)
Comparison of diversity indices	196	(2)
Abundance models	198	(4)
Rarefaction	202	(4)
Diversity curves	206	(2)
Size-frequency and survivorship curves	208	(3)
Association similarity indices for presence/absence data	211	(5)
Association similarity indices for abundance data	216	(5)
ANOSIM and NPMANOVA	221	(2)
Correspondence analysis	223	(10)
Principal coordinates analysis (PCO)	233	(3)
Non-metric multidimensional scaling (NMDS)	236	(4)
Seriation	240	(14)
Case study: Ashgill brachiopod-dominated paleocommunities from East China	244	(10)
Time series analysis	254	(25)
Introduction	254	(1)
Spectral analysis	255	(5)
Autocorrelation	260	(3)
Cross-correlation	263	(3)
Wavelet analysis	266	(3)
Smoothing and filtering	269	(2)
Runs test	271	(8)
Case study: Sepkoski's generic diversity curve for the Phanerozoic	273	(6)
Quantitative biostratigraphy	279	(38)
Introduction	279	(2)
Parametric confidence intervals on stratigraphic ranges	281	(2)
Non-parametric confidence intervals on stratigraphic ranges	283	(3)
Graphic correlation	286	(5)
Constrained optimization	291	(7)
Ranking and scaling	298	(8)
Unitary associations	306	(8)
Biostratigraphy by ordination	314	(1)
What is the best method for quantitative biostratigraphy?	315	(2)
Appendix A: Plotting techniques	317	(11)
Appendix B: Mathematical concepts and notation	328	(5)
References	333	(12)
Index	345