Geology 393/591L
Quantitative Paleontology
Spring 2015
Instructor: Dr. Thomas W. Kammer
Office:
243 Brooks Hall
Phone:
293-9663
E-mail:
tkammer@wvu.edu
Web Page: http://www.geo.wvu.edu/~kammer/welcome.htm
Class Web Page: http://www.geo.wvu.edu/~kammer/geol591.htm
Office Hours: it's best to make an appointment, although I am around much of the time.
Classroom: 305 Brooks Hall
Computer Lab: 425 Brooks Hall – reserved every Thursday
Research Lab: 265 Brooks Hall
FORMAT
The course will be conducted in a seminar-tutorial-project format. We will
explore various topics together and the professor may range from an expert, to something
of a tour guide, to even a co-explorer with the students. Learning is a life-long
experience for all of us, so learning how to teach yourself is an important skill. Students
are expected to take an active role in discussion of assigned readings and use of software.
This course will emphasize analyzing data sets from the paleontologic literature.
PURPOSE
This course is a survey of typical quantitative approaches in paleontology,
although it is far from exhaustive on the topic. Students will have the opportunity to
improve their quantitative skills in analyzing paleontologic data for pattern recognition
and hypothesis testing. Many of the skills learned are transferrable to analysis of other
types of geologic data sets. The ultimate goal of the course is to improve your ‘tool kit’
for conducting research specifically in paleontology, and geology in general.
GRADES
Class Participation
25%
Exercises and Presentations
50%
Term Project, due May 4, noon
25%
(Project title due March 31; Outline and Reference List due April 14)
Term Project: Each student will do their own term project chosen in consultation with the instructor. The
goal of the project is to conduct an in-depth quantitative analysis of patterns associated with a fossil group
or topic (e.g. diversity comparisons, evolutionary rates, or paleoecologic analyses) applying the techniques
covered in this course. Students will either generate their own data set, or work with available data sets. A
more extensive and in-depth report will be expected from graduate students. The paper format will be that
of a scientific paper with an abstract, introduction, methods, data, results, discussion, conclusions, list of
cited references, and figures. See handout describing procedures. Make sure you are absolutely clear about
how not to plagiarize when writing a scientific paper or report.
2
SOFTWARE
Many of the class exercises will require use of either Microsoft Excel or PAST.
Excel is a very useful spreadsheet program that you should be familiar with and is
available on department computers. PAST stands for PAlaeontological STatistics and is
freeware available at: folk.uio.no/ohammer/past/ You should download a copy of the
software and reference manual to the computer(s) you work at.
Fossil Plot: http://www.fossilplot.org/
PAUP – Phylogenetic Analysis Using Parsimony
TOPICS

Evaluating sample completeness – Rarefaction methods

Quantitative analysis of Phanerozoic fossil diversity patterns for studying
macroevolutionary trends.

Quantitative analysis of stratigraphic ranges for studying evolutionary rates in
specific fossil groups.

Univariate statistics in paleontology: e.g., t-Test, p values, Chi-square, Binomial
Distribution, Runs Tests

Multivariate techniques in paleontology: e.g., Cluster Analysis, MultiDimensional Scaling and Ordination, Correspondence Analysis, Principal
Components and Factor Analysis

Cladistics for phylogenetic analysis: theory and practice
FIELD TRIPS
Carnegie Museum of Natural History - a one-day trip, on a Thursday, probably April 2.
We will start an exercise on cladistic methods by coding characters on the dinosaurs on
exhibit. We will then bring that data back to WVU for computer analysis using
parsimony-based methods.
Fossil collecting: Cincinnatian of Maysville, Kentucky, or Richmond, Indiana –
overnight trip, Saturday and Sunday, April 18-19, to collect Upper Ordovician marine
invertebrate fossils. Students will research the paleontology and stratigraphy of the
Cincinnatian of Indiana/Ohio/Kentucky and make class presentations prior to the trip.
Each student will be responsible for a different topic.
3
SCHEDULE:
Week
1
Date
Jan. 12
2
Jan. 19
3
4
Jan. 26
Feb. 2
5
6
7
Feb. 9
Feb. 16
Feb. 23
8
9
10
11
12
13
14
15
March 2
March 9
March 16
March 30
April 6
April 13
April 20
April 27
Tuesday – Room 305, Teaching Lab
Thursday – Room 425, Computer Lab
Course Intro. Counting Ames fossils for Rarefaction analysis using PAST and
rarefaction analysis.
Excel – Exercise 1
Rarefaction analysis continued: Ames
Rarefaction analysis using PAST and
exercise, plus Mississippian crinoids
Excel – Exercise 2
Global diversity patterns, part 1
Fossil Plot software and exercises
Global diversity patterns, part 2:
Fossil Plot software and exercises with
choosing your own group from Sepkoski your own group from Sepkoski (2002)
(2002)
Calculating evolutionary rates - theory
Calculating evolutionary rates - theory
Calculating evolutionary rates – crinoids Calculating evolutionary rates – crinoids
Calculating evolutionary rates –
Calculating evolutionary rates – working
choosing your own group from Sepkoski with your own group from Sepkoski
(2002)
(2002)
Univariate statistics
Univariate statistics
Univariate statistics
Univariate statistics
Multivariate techniques
Multivariate techniques
Multivariate techniques
Multivariate techniques
Multivariate techniques
Multivariate techniques
Cladistics
Cladistics
Cladistics
Cladistics
Work on final projects
Work on final projects
Monday, May 4, Final work due at noon.
Primary References:
Foote, M., and A.I. Miller. 2007. Principles of Paleontology, Third Edition. W.H. Freeman and
Co., 354 p. Rarefaction Method, p. 19; Ch. 7, Evolutionary Rates and Trends; Ch. 8,
Global Diversification and Extinction.
Hammer, O. and D.A.T. Harper. 2006. Paleontological Data Analysis. Blackwell Publishing, 351
p.
Davis, J.C. 1986, 2002. Statistics and Data Analysis in Geology. John Wiley and Sons, New
York, second or third editions are equally good.
McKillup, S. and M. Darby Dyar. 2010. Geostatistics Explained. Cambridge University Press,
396 p.
Published Data Sets:
Ausich, W.I., and T.W. Kammer. 2013. Mississippian crinoid biodiversity, biogeography, and
macroevolution. Palaeontology, 56:727-740.
Kammer, T.W., and W.I. Ausich. 2006. The “Age of Crinoids”: a Mississippian biodiversity
spike coincident with widespread carbonate ramps. Palaios, 21:238-248.
Kammer, T.W. and A.M. Lake. 2001. Salinity ranges of Late Mississippian invertebrates of the
central Appalachian basin. Southeastern Geology, 40:99-116.
4
Lebold, J.G. and T.W. Kammer. 2006. Gradient analysis of faunal distributions associated with
rapid transgression and low accommodation space in a Late Pennsylvanian marine
embayment: Biofacies of the Ames Member (Glenshaw Formation, Conemaugh Group)
in the northern Appalachian Basin, USA. Palaeogeography, Palaeoclimatology,
Palaeoecology, 231:291-314.
Sallan, L.C., T. W. Kammer, W.I. Ausich, L. A. Cook. Persistent predator-prey dynamics
revealed by mass extinction. PNAS, Proceedings of the National Academy of Sciences,
108(20):8335-8338.
Sepkoski, J.J. 2002. A compendium of fossil marine animal genera. Bulletins of American
Paleontology, Number 363, 560 p.
Additional References
Cladistics
Carlson, S.J. 1999. Phylogenetic systematics and palaeontology, p. 41-91. In: D.A.T. Harper
(ed.), Numerical Palaeobiology, John Wiley and Sons.
Carlson, S.J. 1999. Evolution and systematics, p. 95-117. In: J. Scotchmoor and D.A. Springer
(eds.), Evolution, Investigating the Evidence. Paleontological Society, Special
Publication, Volume 9.
Foote, M., and A.I. Miller. 2007. Systematics, Chapter 4, p. 85-120. In: Principles of
Paleontology, Third Edition. W.H. Freeman and Co.
PAUP data sets: http://palaeo.gly.bris.ac.uk/services.html University of Bristol, Palaeontology
Group. See Cladestore for downloadable data sets.
Dinosaurs – for cladistics
Benton, M. J. 2005. Vertebrate Palaeontology, Third Edition. Blackwell Publishing. Ch. 8, The
Age of Dinosaurs, p. 187-255.
Fastovsky, D. E. and D. B. Weishampel 2005. The Evolution and Extinction of the Dinosaurs,
Second Edition. Cambridge University Press, 485 p.
Martin, A. J. 2006. Introduction to the Study of Dinosaurs, Second Edition. Blackwell
Publishing, 560 p.
Sereno, P.C. 1999. The evolution of dinosaurs. Science, 284:2137-2147. PDF
Readings on the Ordovician of the Cincinnati Arch for Field Trip
Meyer, D.L. and R.A. Davis. 2009. A Sea without Fish, Life in the Ordovician Sea of the
Cincinnati Region. Indiana University Press, 346 p.
Cincinnatian Fossils and Strata: http://strata.uga.edu/cincy/index.html