Big questions in paleobiology and
the role of numbers
What is paleobiology?
Paleobiology
• Paleontology
– Stratigraphy
– Taphonomy
• Biology
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Ecology
Macroecology
Evolution
Macroevolution
Developmental biology
Community ecology
Phylogenetics
Biogeography
And the list goes on…..
• Earth Science
– Sedimentology
– (Paleo)climatology
– (Paleo)oceanography
• Physics– Biomechanics
– Geophysics
• Chemistry
– Geochemistry, isotopes
• Math and Stats
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Modeling and statistics
Morphometrics
Time series analyses
Branching theory
Journals that publish paleobiology
Kenneth De Baets compilation
https://sites.google.com/site/kennethdebaets
webpage/home/journals-in-paleontology-andevolutionary-biology
Wordle made From the latest issue of Paleobiology (June 2013)
Diversity
1. Diversity through time
Sepkoski 1984 A kinetic-model of Phaneozoic taxonomic diversity
Paleobiology
MODEL
1. Diversity through time
• Is there a carrying capacity for the number of species?
N t  N o e rt
Nt 
No K
N o  ( K  N o )e  rt
1. Diversity through time
Benton & Emerson. 2007. How did life become so diverse? The dynamics of diversification
according to the fossil record and molecular phylogenetics. Palaeontology 50:23-40.
1. Diversity through time
Sepkoski 1984 A kinetic-model of Phaneozoic taxonomic
diversity Paleobiology
Alroy et al. 2008. Phanerozoic trends in the global diversity of
marine invertebrates. Science 321:97-100
1. Diversity through time
Crampton et al. 2006.
The ark was full! Constant to declining Cenozoic shallow marine biodiversity on an isolated midlatitude continent.
Paleobiology 32:509-532.
2a. Extinctions (Mass)
Mass Extinctions in the Fossil Record
Raup & Sepkoski 1982 Science
2b. Extinctions (Drivers)
Harnik et al. TREE 2012
2b. Extinctions (Drivers)
Evidence for biotic drivers of
extinction and origination, perhaps.
Alroy 2008 PNAS
2c. Extinctions (selectivity)
2c. Extinctions (selectivity)
McKinney, M. L. (1997).
"Extinction vulnerability and selectivity:
Combining ecological and paleontological views."
Annual Review of Ecology and Systematics 28: 495-516.
Saunders et al. Paleobiology 2008
2c. Extinctions (selectivity)
Sniper action
PT
Field of Bullets
3. Phenotypic evolution
Eldredge, N. and S. J. Gould (1972). Punctuated
equilibria: an alternative to phyletic
gradualism. Models in Paleobiology T. J. M.
Schopf, W.H. Freeman & Company: 82–115.
3a. Phenotypic evolution (rate and direction)
Hunt, G. (2007). "The relative importance of directional change,
random walks, and stasis in the evolution of fossil lineages."
PNAS104(47): 18404-18408.
Q
1.
Diversity dynamics (temporal changes in diversity) – what are the
patterns?
2.
Diversity dynamics (temporal changes in extinction and
speciation/origination rates)
3.
Drivers of extinction (and speciation), selectivity of…
4.
What kinds of morphologies and function and why?
5.
Tempo and mode (space)
6.
Long term (morphological) trends
Science Today
• Alroy (2010). "The shifting balance of diversity among major marine
animal groups."
• Kiessling (2010). "Reefs as Cradles of Evolution and Sources of Biodiversity
in the Phanerozoic."
• Ezard (2011). "Interplay between changing climate and species' ecology
drives macroevolutionary dynamics."
• Hannisdal & Peters (2011). "Phanerozoic earth system evolution and
marine biodiversity."
• Quental & Marshall (2013). "How the Red Queen Drives Terrestrial
Mammals to Extinction."
Census and samples
“Technical” questions
• How “complete” is the fossil record?
• How well do changes we see in the fossil record reflect the
true course of diversity in the history of life? – How good is its
“fidelity”?
• How much time a “layer” represent?
• How many living species are represented as fossils?
• Did fossil X at time Y and space Z really “live” at time Y and
space Z?
• Do the “things” we measure really reflect what we mean to
study? (Measurement Theory see Houle et al. 2011)
The fossilization process
The fossilization process
Preservation biases – organismal issues
1.
2.
3.
4.
5.
Size
“geographic extent”
Habitat
Life habit
Chemistry (of preserved
parts)
6. Taxonomic practice
Valentine, J. W., et al. (2006). "Assessing the fidelity of the fossil record
by using marine bivalves." PNAS 103(17): 6599-6604.
Remember this?
2c. Extinctions (selectivity)
Many traits important for
extinction risk
and preservation potential
are CONFOUNDED!
McKinney, M. L. (1997).
"Extinction vulnerability and selectivity:
Combining ecological and paleontological views."
Annual Review of Ecology and Systematics 28: 495-516.
Sampling biases – geological issues
http://www.paleoportal.org/
http://macrostrat.org/
Sampling biases
• Incompleteness cf biases
Lloyd, G. T., et al. (2012). "Sampling bias and the fossil record of planktonic foraminifera
on land and in the deep sea." Paleobiology 38(4): 569-584.
Standardizing samples: a now common approach
Alroy et al. 2008. Phanerozoic trends in the global diversity of marine invertebrates. Science 321:97-100
SIMULATIONS
Hannisdal, Henderiks & Liow. (2011). Global Change Biology.
Do we need the fossil record?/Is it useful?
Condamine, F. L., et al. (2013). "Macroevolutionary perspectives to
environmental change." Ecology Letters 16(Supplement s1): 72-85.
“The most straightforward approach to examining the past to
inform the present is to analyse the fossil record”
Losos, J. B. (2011). "Seeing the forest for the trees: the limitations of
phylogenies in comparative biology." American Naturalist 177(6): 709-727.
“First, we must recognize that fossil data really are
integral to understanding what happened in the past.”
Quental, T. and C. R. Marshall (2010). "Diversity dynamics: molecular
phylogenies need the fossil record." Trends in Ecology & Evolution 25(8):
434–441.
“In fact, it appears that molecular phylogenies can only tell us
when there have been changes in diversification rates, but are blind to
the true diversity trajectories and rates of origination and extinction that
have led to the species alive today.
Very Quick Overview of
Quantitative Paleobiology
Error bars
“in many fields of science, the use of error bars is almost
automatic: one never plots a point or gives a measurement,
count or ratio with also expressing its uncertainty. In
paleobiology, error bars are common only in presentation of
means of series of measurements…. In general, however, if a
paleobiologist counts something or calculates a percentage or a
ratio from field data, the numbers are left to speak for
themselves. If an interested physicist happens to challenge the
absence of error bars, our reaction commonly is: “You don’t
understand, I merely counted what I found”” Raup 1991
(Analytical Paleobiology)
Comparing 1991 (6) 2010
1.
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7.
8.
9.
Sampling from the FR(CF Koch)
Estimation of taxonomic ranges from the
FR (Marshall)
Analysis of Morphological Data (M Foote)
Phylogenetic analysis and its application in
Evolutionary Paleobiology (DC Fisher)
Random Models in Paleobiology (PW
Signor)
Population biology models in
macroevolution (JJ Sepkoski)
The pace of taxonomic evolution (NL
Gilinsky)
Taxonomic Survivorship curves (RZ
German)
Bootstrapping and the FR (NL Gilinsky)
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10.
XXX
Using confidence intervals to quantify the
uncertainty in the end points of
stratigraphic ranges (Marshall)
3 chapters (morphometrics, models of
phenotypic evolution) including Hunt
Probabilistic phylogenetic inference in the
FR (Wager and Marcot)
Xxx
CMR (Liow and Nichols)
Alroy, Liow and Nichols
Alroy, Liow and Nichols
Resampling methods in paleontology
Foodwebs, macroecology, bayesian
approaches
• “….the mind’s capacity to see or even to
impose patterns where none exist… faces and
animals in the clouds of our lazy child
afternoons provide everyday evidence of this
capacity” – Signor and Gilinsky 1991
“That sampling effects can be so large should be
disconcerting to many palentogloists.” Koch 1991
• In biostratigraphic studies, many species will seem short
ranging due to sampling effects
• In biogeographic studies, the geographic area for which most
material is analyzed will seem to be an endemic center
• Major extinction events will seem to occur at the end of the
level for which most data have been assembled.
• As a minimum, studies…. should report data quantities in
some form such that other workers can make independent
judgments….
Reading List
• McKinney, M. L. (1997). "Extinction vulnerability and selectivity:
Combining ecological and paleontological views." Annual Review of
Ecology and Systematics 28: 495-516.
• Houle, D., et al. (2011). "Measurement and meaning in biology." Quarterly
Review of Biology 86(1): 3-34.
• Sepkoski, J. J. (1984). "A kinetic-model of Phaneozoic taxonomic diversity.
3. Post-paleozoic families and mass extinctions." Paleobiology 10(2): 246267.
Smart Entertainment: Steve Wang speaking at TED
• http://www.youtube.com/watch?v=lRHa82vMPhU
Suggested websites
Quantitative Paleontology (David Polly, Indiana University)
• http://www.indiana.edu/~g563/
Paleobiology Modeling and Analysis
(Michael Foote, University of Chicago)
• http://geosci.uchicago.edu/~foote/MODEL/2012/index.html
R primer for paleobiologists (Gene Hunt, Smithsonian Institute)
• http://paleobiology.si.edu/staff/individuals/hunt.cfm (scroll
down to “Resources”
http://pbdb.org/
http://www.r-project.org/
Today’s Summary
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Sampling issues
Models
Simulations
The importance of the fossil record
The even greater importance of measuring
uncertainty (using confidence intervals, error
bars, etc).