FossilPlot, an Excel-Based Computer Application for Teaching Stratigraphic Paleontology Using the Se

Jun 20, 03:49 AM

Current Headlines: By Tapanila, Leif

ABSTRACT FossilPlot is a new Excel-based spreadsheet application of the Sepkoski Compendium designed for educational use in paleontology and historical geology courses. This free software allows students to compile any combination of marine animal genera to generate graphs depicting diversity curves and stratigraphic ranges for the Phanerozoic. Sample exercises are provided to show how this software can be integrated into lecture, lab and field studies in university-level paleontology courses. The large volume and full accessibility of the dataset gives instructors a versatile tool to enhance active learning of the dynamic history of life.

INTRODUCTION

In the current information age large geoscience datasets are becoming increasingly available, which has been a boon for creative activities in research and education (e.g., Digital Library for Earth System Education, The Paleobiology Database, The Paleontology Portal). These programs successfully illustrate the importance of making voluminous data both available and accessible for their varied audiences. For the purposes of education an effective archive should satisfy dual audiences - the instructor and the student - by providing qualities such as dataset versatility, the ease or implementation into the course curriculum, and the ease of use of the program by students, allowing them to focus their efforts on learning objectives.

Teaching the dynamic history of life is the core theme in university-level paleontology courses, where concepts in evolutionary theory are coupled with hands-on learning of fossil material both in the lab and in the field. Integrating a large faunal dataset within the course curriculum can facilitate these educational goals by encouraging students to explore the primary data used by professional paleontologiste to recognize patterns in organic evolution.

Among the faunal datasets available, the recently published monograph by Sepkoski (2002, hereafter referred to as the Sepkoski Compendium) is a stand-out, providing the stratigraphie ranges of more than 36,000 marine animal genera. This database forms the core of a new educational graphing application, which allows users to quickly and easily generate graphs that depict diversity curves and stratigraphie ranges for marine animals throughout the Phanerozoic. I nave designed this freeware program while teaching courses at the University of Utah (UU) and Idaho State University (ISU) in 2005- 2006, and it is now publicly available for educational use.

In this paper I outline the main functions of FossilPlot and give examples of how it can be incorporated into university-level paleontology courses to give students instructive and user-friendly access to Sepkoski's landmark database.

CONTENTS OF FOSSILPLOT

FossilPlot was designed in MicrosoftExcel 2000 for PC, and it also is fully compatible with MSExcel for MAC. This free software comes with a detailed User's Manual and a PowerPoint slideshow primer, but only the basic capabilities of the program will be described here. Science educators may download the current version of the software (FossilPlot version 1.1) and its supporting files at the dedicated website, http://geology.isu. edu/FossilPlot.

The database - During the 1980s and 1990s paleontologist J. John Sepkoski, Jr., and his associates compiled comprehensive databases on the stratigraphie ranges of marine animals (Sepkoski 1982, 1992, 2002). This work allowed for the first time quantitative and statistical analyses of patterns in the evolutionary record (see introduction in Sepkoski, 2002, for references). Following his death in 1999, the Sepkoski Compendium of marine genera was published as a 560-page monograph (Sepkoski, 2002J, making this body of work publicly available. Sepkoski's Compendium contains 36,340 marine animal genera, and for each genus it provides its known first and last stratigraphie occurrences, i.e., First Appearance Datum (FAD) and Last Appearance Datum (LAD). In FossilPlot, these stratigraphie FADs and LADs are converted to absolute ages in millions of years before present (Ma) in order to permit graphing functions. Absolute dates are based on the latest stratigraphie sources (e.g., primarily from Gradstein and Ogg, 2004; secondarily from Okulitch, 1999), and these values are cross-referenced throughout the program to accommodate future inevitable changes to stratigraphie benchmarks. Discrepancies exist in the geologic time scale used in the Sepkoski Compendium and the modern time scale (e.g., Tertiary vs. Paleogene- Neogene), however the latest version of FossilPlot (ver. 1.1) produces graphs using the latest time scale terminology. As the Geologic Time Scale evolves, new versions of FossilPlot will incorporate those updates.

Making graphs - To generate graph results, the user simply highlights the genera to be graphed from the database worksheet and copy/pastes them into one or more calculation worksheets. A series of protected calculation fields automatically generate the data necessary to plot the graphs (Figure 1). FossilPlot allows the user to plot any combination of genera, which affords great versatility in how the program can be utilized within the context of a course. The copy/paste methodology is both simple and fast. Students using the program for the first time were able to generate meaningful graphs within the initial minutes of use.

Types of graphs - The transfer of data to the calculation worksheets produces a series of graphs, each plotted in a separate worksheet that is ideal for printing. Four basic types of information are calculated and graphed by the program: generic diversity, generic originations, generic extinctions, and stratigraphie ranges. These data are presented in a variety of combinations and time-interval resolutions, including Epoch and Age scale. A special graph gives the database's highest possible time resolution of 2 Ma intervals across three of the major Phanerozoic mass extinction events, including the Late Ordovician, the Permian- Triassic and the CretaceousPaleogene.

Figure 1. Screen shots front FossilPlot showing database, calculation worksheet and two graph types derived from fossil bryozoan data. Users select genera from the Sepkoski Compendium database (A) and copy/paste these selections into a Calculation Worksheet (B) to produce a variety of graphs, including a stratigraphie range chart (C) and a graph (D) showing the diversity (thick line), origination (left bars) and extinction (right bars) values at the Epoch time scale. All bryozoan genera were selected for this example.

INTEGRATING THE DATABASE IN YOUR COURSE

The first introduction and primer on how to use FossilPlot can be demonstrated to students in less than one hour of laboratory time. In all trial classes, the majority of students were able to generate useful graphs quickly and consistently by the end of the primer. Once students are comfortable in independently using FossilPlot, the program can be incorporated into short take-home assignments and more extensive lab and field-integrated exercises. The following section describes four applications for the classroom, lab and field excursions where FossilPlot can augment pre-existing course activities.

Exploring aspects of evolution - The basic application of FossilPlot in the classroom is in providing diversity curves for particular taxa being taught during the lectures and the lab. For example, leading up to a lab on corals, the instructor may designate three students to generate and produce copies for the class of the Phanerozoic diversity curves for the Tabulate, the Rugosa and the Scleractinia. General diversity patterns can be explored for any marine animal grouping. When coupled with origination and extinction data, the diversity curves demonstrate the importance of input and output information in determining standing diversity. For introductory classes, the Bank Account Analogy is a useful way of describing how originations (deposits) and extinctions (withdraws) affect the standing diversity of faunas (account balance). For more advanced classes, students can be asked to examine rates of extinction or origination using the database. FossilPlot makes all of the stratigraphie ranges from the Sepkoski Compendium directly available to the student and instructor - a feature not readily available in other similar systematic databases.

Figure 2. Screen shot demonstrating the results from the Sample Exercise on Biostratigraphy. In this example, a dozen fossils collected in the field are identified to genus (inset) and plotted as a stratigraphie range chart in FossilPlot. A concurrent range zone occurring in the Caradoc (late Middle Ordovician) is easily visualized and quantified using this chart. Genera in this example are from collections of Black River Group fossils reported by Walker, 1972.

Dataset for the fossil notebook - Many paleontology and historical geology labs incorporate some type of 'fossil notebook' exercise, where students draw and describe a series of fossil taxa, focusing on different systematic groups each week. By the end of the semester, students will have drawn several dozen taxa, providing a familiarity with fossil material and an appreciation for the diversity of life. FossilPlot can add to the fossil notebook exercise by providing students the stratigraphie range and systematic taxonomy for each marine fossil they draw. Although data on stratigraphie ranges and systematic taxonomy are not unique to FossilPlot, this database provides a searchable (using the Edit/ Find function) and comprehensive tabulation of all marine animal genera and therefore it is an efficient resource for delivering these data to students. Teaching principles of biostratigraphy - An important utility of FossilPlot is its potential for demonstrating basic principles in biostratigraphy. The stratigraphie range graph (Figure 1C) can be used to display and organize a variety of genera, regardless of phylogenetic relationships. Individual genera can be copy/pasted into the calculation worksheet to represent an assemblage of taxa found in a single stratum. When these genera are sorted by FADs and LADs, the range graph nicely illustrates biozones (e.g., concurrent, interval and Oppel zones). This application of FossilPlot can enhance the typical fossil collection and identification exercises of a paleontology field trip. Once the collected fossils have been identified to the genus level in the lab, students can copy/paste the names of these genera into FossilPlot and generate a range graph for each of the outcrops visited. In me sample graph (Figure 2), twelve common fossil genera from the Black River Group limestones of New ork produce an 8.6 million year correlative range zone within the early to middle Caradoc (late Middle Ordovician). Students can calculate that for 460 million year old rocks, this correlative range zone differentiates strata to a resolution of less than 2% of this Ordovician time (8.6 m.y. interval + 460 m.y. age of Ordovician * 100% = 1.9%). This is a pragmatic and very effective way to demonstrate to students the relevance of paleontology in solving stratigraphie problems. Applying FossilPlot in the field is not restricted by geography or access to certain ages of fossils. Similar biostrahgraphic exercises were conducted by students at UU and ISU in Paleozoic and Mesozoic strata of Utah and Nevada, including the Cambrian Wheeler Shale, the Devonian Guilmette Formation, the Mississippian Chainman Formation, the Jurassic Carmel Formation, and the Cretaceous Mancos Shale.

Figure 3. Screen shot showing the remits from the Sample Exercise on Mass Extinction. Five animal groups are plotted across the K-T (i.e., Cretaceous-Paleogene) boundary using two million year intervals and Epoch-scale intervals to demonstrate the different effect of the mass extinction on various taxa. '+' = originations; '- ' = extinctions.

Examining mass extinction episodes - A detailed examination of mass extinction events is readily facilitated by using the FossilPlot approach. Students in my classes were asked to write a report about the Late Ordovician, the Permian-Triassic or the CretaceousPaleogene mass extinction. Using FossilPlot, they were asked to generate high-resolution diversity curves for a variety of animal groups during their specific mass extinction time interval. The number and types of animals to be analyzed was left to the discretion of the student, although they were cautioned to choose their Eoups wisely (e.g., pentamerids are not useful for the Pg boundary!). The student-generated graphs were submitted as part of the assignment (Figure 3I. second, the students were asked to research literature (including credible websites) to generate a list of hypothesized causes for their mass extinction event. Third, students were asked to interpret their diversity graphs by describing and quantifying changes in diversity across their mass extinction ooundary. Students were encouraged to recognize ecological differences among their taxa and at the same time to address the relevance of counting methods (e.g., percent versus numerical change) in determining diversity change across their boundary. The final component or the assignment was to use their interpretations of diversity to evaluate and argue for a fikely cause of their mass extinction. Assessment focused on how well students could select and synthesize the data to develop a sound argument for a cause of their extinction.

ADVANTAGES AND LIMITATIONS

FossilPlot's greatest strength lies in its versatility and ease of integration in all aspects of a paleontology course, from lectures to the lab and even the field. The sheer volume of the Sepkoski Compendium and the unencumbered access to its data gives both teacher and student a wide range of choices in their analysis of the fossil record. In practice, students were quick to learn the program, and most technical difficulties could be corrected immediately. As a result, students spend more time discovering intriguing aspects of the fossil record with FossilPlot rather than struggling to learn how to negotiate a new computer program.

Naturally there are some limitations to FossilPlot that need to De recognized. As with any static database that contains information from an active field of research, there always exists the possibility of errors and obsolete information. Since the publication of the Sepkoski Compendium, numerous refinements have been made to our understanding of the fossil record, including the phylogeny, taxonomy and the stratigraphy of various taxa reported in the database. Teachers and students using FossilPlot should refer to Sepkoski (2002) for methods in data acquisition and realize that some details in the Compendium are now obsolete (see Ausich and Peters, 2005).

Another limitation of the Compendium is that only marine animals are represented, i.e., no plants or terrestrial organisms are included. Alternative sources for these groups can be acquired through the Paleobiology Database (http://paleodb.org/).

The maximum group size to be analyzed in FossilPlot is limited by current computer speeds. For most computers, the upper limit of genera that can be analyzed is ~4000 (i.e., ~2 million calculations), but this size is adequate for analyzing any order, and most classes of taxa. As in any teaching scenario, the limitations posed by FossilPlot and the Sepkoski Compendium often can be redirected as opportunities to teach students how to evaluate the quality of raw scientific data and how to critically assess the validity and uncertainty of their resulting interpretations.

CONCLUDING REMARKS

FossilPlot is a new freeware computer application that uses the Sepkoski Compendium to generate graphs that depict diversity curves and stratigraphie ranges for marine animal genera. I have found tnis database easy to implement into various aspects of my paleontology courses, which has allowed my students to be more active in investigating the details of worldwide fossil occurrences and more quantitative in studying patterns of evolution. Because of the Sepkoski Compendium's large size, FossilPlot offers a remarkable versatility that permits it to be integrated into paleontology and historical geology courses taught in any geographic region andcustomized to appropriate levels of student abilities.

ACKNOWLEDGMENTS

I thank Tony Ekdale (University of Utah) for his encouragement and constructive suggestions as I designed this software, and for allowing me to test-run FossilPlot in his Paleobiology course. Trial runs of the software at UU and ISU benefited greatly from student input and I appreciate their contributions in refining the program. I also thank A. Pollington, J. Benner and E. Roberts for their suggestions on earlier versions of the program. Development of the manuscript was aided by constructive comments by S. Boss and S. Leslie.

REFERENCES

Ausich, W.I., and Peters, S.E., 2005, A revised macroevolutionary history from Ordovician-Early Silurian crinoids, PaleobioJogy, v. 31, p. 538-551.

Gradstein, P.M., and Ogg, J.G., 20IM, Geologic Time Scale 2004 - why, how, and where next?, Letnaia, v. 37, p. 175-181.

Okulitch, A.V., 1999, Geological Time Chart, GSC Open File 3040, supplement to Geolog, v. 29.

Sepkoski, JJ., Jr., 1981. A factor analytic description of the Phanerozoic marine fossil record. Paleobiology, 7:36-53.

Sepkoski, J.J., Jr., 1982, A compendium of fossil marine families, Milwaukee Public Museum Contribution to Biology and Geology, No. 51.

Sepkoski, J.J., Jr., 1992, A compendium of fossil marine families, 2nd Ed. Milwaukee Public Museum Contribution to Biology and Geology, No. 83.

Sepkoski, J.J., Jr., 2002, A compendium of fossil marine animal genera, Bulletins or American Paleontology, v. 363, p. 1-560.

Walker, K.R., 1972, Community ecology of the Middle Ordovician Black River Group of New York State, Geological Society of America Bulletin, v. 83, p. 2499-2524.

Leif Tapanila Department of Geosciences, Idaho State University, Pocatello, ID 83209-8072, tapaleif@isu.edu

Copyright National Association of Geoscience Teachers Mar 2007

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