Big questions in paleobiology and the role of numbers

Big questions in paleobiology and the role of numbers

What is paleobiology?

Paleobiology

• Paleontology– Stratigraphy– Taphonomy

• Biology – Ecology– Macroecology– Evolution– Macroevolution– Developmental biology– Community ecology– Phylogenetics– Biogeography

• Earth Science– Sedimentology– (Paleo)climatology– (Paleo)oceanography

• Physics-– Biomechanics– Geophysics

• Chemistry– Geochemistry, isotopes

• Math and Stats– Modeling and statistics– Morphometrics– Time series analyses– Branching theory

And the list goes on…..

Journals that publish paleobiology

Kenneth De Baets compilationhttps://sites.google.com/site/kennethdebaetswebpage/home/journals-in-paleontology-and-evolutionary-biology

Wordle made From the latest issue of Paleobiology (June 2013)

Sepkoski 1984 A kinetic-model of Phaneozoic taxonomic diversity Paleobiology

Div

ersi

ty

1. Diversity through time

MODEL

• Is there a carrying capacity for the number of species?

rtt oN N e

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t rto o

N KN

N K N e

1. Diversity through time

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

Crampton et al. 2006.The ark was full! Constant to declining Cenozoic shallow marine biodiversity on an isolated midlatitude continent. Paleobiology 32:509-532.

1. Diversity through time

Raup & Sepkoski 1982 Science

Mass Extinctions in the Fossil Record2a. Extinctions (Mass)

Harnik et al. TREE 2012

2b. Extinctions (Drivers)

Alroy 2008 PNAS

2b. Extinctions (Drivers)

Evidence for biotic drivers of extinction and origination, perhaps.

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.

2c. Extinctions (selectivity)

Saunders et al. Paleobiology 2008

Sniper action

Field of Bullets

P T

2c. Extinctions (selectivity)

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.

3. Phenotypic evolution

Hunt, G. (2007). "The relative importance of directional change, random walks, and stasis in the evolution of fossil lineages." PNAS104(47): 18404-18408.

3a. Phenotypic evolution (rate and direction)

Q1. 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

1. Size2. “geographic extent”3. Habitat4. Life habit5. Chemistry (of preserved

parts)6. Taxonomic practice

Preservation biases – organismal issues

Valentine, J. W., et al. (2006). "Assessing the fidelity of the fossil recordby using marine bivalves." PNAS 103(17): 6599-6604.

McKinney, M. L. (1997). "Extinction vulnerability and selectivity: Combining ecological and paleontological views." Annual Review of Ecology and Systematics 28: 495-516.

Remember this?2c. Extinctions (selectivity)

Many traits important for extinction risk

and preservation potential are CONFOUNDED!

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.

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

Standardizing samples: a now common approach

SIMULATIONS

Hannisdal, Henderiks & Liow. (2011). Global Change Biology.

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 toinform 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 areintegral 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.

Do we need the fossil record?/Is it useful?

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) 20101. Sampling from the FR(CF Koch)2. Estimation of taxonomic ranges from

the FR (Marshall) 3. Analysis of Morphological Data (M

Foote)4. Phylogenetic analysis and its

application in Evolutionary Paleobiology (DC Fisher)

5. Random Models in Paleobiology (PW Signor)

6. Population biology models in macroevolution (JJ Sepkoski)

7. The pace of taxonomic evolution (NL Gilinsky)

8. Taxonomic Survivorship curves (RZ German)

9. Bootstrapping and the FR (NL Gilinsky)

1. XXX2. Using confidence intervals to quantify

the uncertainty in the end points of stratigraphic ranges (Marshall)

3. 3 chapters (morphometrics, models of phenotypic evolution) including Hunt

4. Probabilistic phylogenetic inference in the FR (Wager and Marcot)

5. Xxx6. CMR (Liow and Nichols)7. Alroy, Liow and Nichols8. Alroy, Liow and Nichols9. Resampling methods in paleontology 10. 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): 246-267.

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.htmlR 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

• Sampling issues• Models • Simulations• The importance of the fossil record• The even greater importance of measuring

uncertainty (using confidence intervals, error bars, etc).