Syllabus for

Stat 21 (W): Quantitative Paleobiology
Fall 2011
Prof. Steve C. Wang





OUTLINE OF TOPICS


I. Introduction

Topic: What is evolution?
What is evolution? What is natural selection? Is evolution a fact or a theory? What about intelligent design? Should we "teach the controversy"?
reading: Ken Miller lecture on youtube

Topic: Deep time
Topic: Meet the phyla
In which we meet the geological time scale and the cast of characters (brachiopods, molluscs, and arthropods, oh my!)

Methods: Likelihood
In which we examine a general framework for developing statistical methodology.
reading: Wang 2010

Topic: Does the fossil record give us an accurate picture of the history of life?
Methods: Measuring taphonomic fidelity
Guest: Rowan Lockwood, College of William and Mary
How accurately does the fossil record preserve characteristics of ecosystems? Can we trust the picture provided by fossils?
reading: Lockwood and Chastant 2006



II. Extinction

Topic: Estimating extinction times
Methods: Range extensions
How can you tell when a species goes extinct? Could dinosaurs still be hiding somewhere in the darkest jungle?
reading: Marshall 1990, Solow 1996, Marshall 1997, Solow 2003, Roberts and Solow 2003

Topic: Mass extinction: Sudden or gradual?
Methods: Signor-Lipps effect
Guest: Charles Marshall, UC Berkeley
What causes mass extinctions? Sudden events (e.g., asteroid impact) should leave a different signature from gradual ones (e.g., climate change). Can we distinguish these causes in the fossil record?
reading: Marshall 1995, Marshall and Ward 1996, Wang et al 2011

Topic: Extinction selectivity in the fossil record
Methods: Logistic regression
Guest: Jon Payne, Stanford U.
Do mass extinctions kill indiscriminately, or are there characteristics that distinguish survivors and victims? If the latter, are these the same characteristics that operate in "background" extinctions?
reading: Jablonski and Raup 1995, Smith and Jeffery 1998, Lockwood 2003, Payne and Finnegan 2007

Topic: Extinction today
Methods: Decision trees
Guest: Alison Boyer, U. of Tennessee
What factors are correlated with species that are endangered today?
reading: Davidson et al 2009



III. Evolution

Topic: Punctuated equilibria
Methods: Random walk models
Guest: Gene Hunt, Smithsonian Institution
Is evolution a slow and gradual process, or is evolutionary change concentrated in short bursts separating long periods of stability?
reading: Eldredge and Gould 1972, Hunt 2006, Hunt 2007

Topic: Does competition drive evolution?
Methods: Principal components analysis
Guest: Steve Brusatte, American Museum of Natural History/Columbia U.
Are major faunal changes driven by one group out-competing another group? What is the role of chance and historical contingency in evolution?
reading: Gould and Calloway 1980, Briggs 1998, Brusatte et al 2008

Topic: Is evolution progressive?
Methods: Change-vs-ancestor plots
Guest: Dan McShea, Duke U.
Does evolution mean species are getting better over time? What is progress, anyway?
reading: Gould 1988, McShea 1994, Alroy 1998

Topic: The history of diversity
Methods: Resampling, the bootstrap, randomization
Guest: John Alroy, Macquarie U.
How many species are there on earth now? How many have there been throughout the history of life? How many of them are we missing in the fossil record?
reading: Newman 2001, Alroy et al 2001, Alroy et al 2008


Questions? See the FAQ or email me.




BIBLIOGRAPHY
(incomplete; still under construction)


Alroy, J. 1998. Cope's rule and the dynamics of body mass evolution in North American fossil mammals. Science 280: 731-734.

Alroy, J., et al. 2001. Effects of sampling standardization on estimates of Phanerozoic marine diversification. PNAS 98: 6261-6266.

Alroy J, et al. 2008. Phanerozoic trends in the global diversity of marine invertebrates. Science 321: 97-100.

Briggs, J. C. 1998. Biotic replacements-extinction or clade interaction? BioScience 48: 389-395.

Brusatte, S. L., Benton, M. J., Ruta, M., and Lloyd, G. T. 2008. Superiority, competition, and opportunism in the evolutionary radiation of dinosaurs. Science 321: 1485-1488

Gould, S.J. 1988. Trends as changes in variance: a new slant on progress and directionality in evolution. Journal of Paleontology 62: 319-329.

Hunt, G. 2006. Fitting and comparing models of phyletic evolution: random walks and beyond, Paleobiology 32: 578-601.

Jablonski, D., and D. M. Raup. 1995. Selectivity of end-Cretaceous marine bivalve extinctions. Science 268: 389-391.

Lockwood, R. 2003. Abundance not linked to survival across the end-Cretaceous mass extinction: patterns in North American bivalves. PNAS 100: 2478-2482.

McShea, D.W. 1994. Mechanisms of large-scale trends. Evolution 48: 1747-1763.

Newman, M. 2001. A new picture of life's history on Earth. PNAS 98: 5955-5956.

Payne JL and Finnegan S. 2007. The effect of geographic range on extinction risk during background and mass extinction. PNAS 104: 10506-10511.

Smith, AB, and Jeffery, CH. 1998. Selectivity of extinction among sea urchins at the end of the Cretaceous period. Nature 392: 69-71.


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