The fourteen case studies have been designed to demonstrate both the use of different data analysis methods in paleontology and the specific use of the functions in the program. The cases are taken from such diverse fields as morphology, taxonomy, paleoecology, paleoclimatology, sedimentology, extinction studies, and biostratigraphy. The examples are taken from both vertebrate and invertebrate paleontology, and they cover the whole of the Phanerozoic. These case studies are well suited for an introductory course in paleontological data analysis and have been tested in classroom situations. The cases are organized into four main subject areas: morphology and taxonomy, biogeography and paleoecology, time-series analysis, and biostratigraphy.

Case studies 1-5 involve the description and analysis of morphological variation of different sorts, while case study 6 targets some phylogenetic problems in a group of Cambrian trilobites and the mammals.
PE Note: The Case Study files are available from the PE site, and also directly from the author. The links below point to the author's site, which will, as time and the author proceed, contain updates and newer versions.

Case Study 1 investigates the external morphology of the Permian brachiopod Dielasma, developing ontogenic models for the genus and comparing the growth rates and outlines of different samples from in and around a Permian reef complex. In a more focused exercise, Case Study 2 uses spatial statistics to assess the mode of distribution of tubercles on the cranidium of the trilobite Paradoxides from the middle Cambrian.

Case Study 3 tackles the multivariate morphometrics of the Ordovician illaenid trilobite Stenopareia using Principal Components Analysis (PCA), Principal Coordinate Analysis (PCO), cluster and discriminant analyses to determine the validity of two species from Scandinavia.

Case Study 4 demonstrates the use of Elliptic Fourier shape analysis and principal components for detecting changes in trilobite cephalon shape through ontogeny.

In Case Study 5, aspects of the allometric growth of the Triassic rhynchosaur Scaphonyx are investigated using regression analysis.

Case Study 6 investigates the phylogenetic structure of the middle Cambrian Paradoxididae through cladistic analysis, using parsimony analysis and bootstrapping. Similar techniques can be applied to a matrix of 20 taxa of mammal; cladograms generated by the program can be compared with a cluster analysis of the data matrix.

Case studies 7-11 cover aspects of paleobiogeography and paleoecology. Case Study 7 analyzes a global dataset of late Ordovician brachiopod distributions. A series of provincial faunas were developed against a background of regression and cooler surface waters during the first strike of the late Ordovician (Hirnantian) glaciation. Through the calculation of similarity and distance coefficients together with cluster analysis, these data can be organized into a set of latitudinally controlled provinces. Seriation helps to develop any faunal, possibly climatically generated, gradients within the data structure.

In Case Study 8 faunal changes through a well-documented section in the upper Llanvirn rocks of central Wales are investigated graphically and by the calculation of diversity, dominance, and related parameters for each of ten horizons in the sections. The changes in faunas fingerprint environmental shifts through the section, shadowed by marked changes in lithofacies. This dataset is ripe for considerable experimentation.

Case Study 9 involves a re-evaluation of Ziegler's classic Lower Paleozoic depth-related communities from the Anglo-Welsh area. Using a range of multivariate techniques (similarity and distance coefficients, cluster analysis, detrended correspondence analysis, and seriation) the reality and mutual relationships of these benthic associations can be tested using a modified dataset.

Case Study 10 discusses some well-known Jurassic shelly faunas from England and France. The integrity and onshore – offshore distribution of six Corallian bivalve-dominated communities is investigated with diversity measures, cluster analysis and detrended correspondence analysis.

Case Study 11 completes the analysis of biotic assemblages with an investigation of the direction and orientation of a bedding-plane sample of brachiopod shells from the upper Ordovician rocks of Scotland.

Two cases involve the study of time series data. Case Study 12 investigates the periodicity of mass extinctions during the Permian to Recent time interval using spectral analysis. A number of diversity curves can be modeled for the Paleozoic and post-Paleozoic datasets available in Fossil Record 2, and turnover rates can be viewed for Phanerozoic biotas.

Case Study 13 addresses the periodicity of oxygen isotope data from ice cores representing the last million years of Earth history.

The final case study (Case Study 14) demonstrates the use of quantitative biostratigraphical correlation with the method of Unitary Associations. Eleven sections from the Eocene of Slovenia are correlated using alveolinid foraminiferans studied by Drobne.