Teaching about time a biologists perspective

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Teaching about timea biologists perspective
Biochemistry
Physiology
Ecology
Evolution Origins of biodiversity and estimates
of divergence times
TIME
10-6s
109 years
not drawn to scale
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Biologists general modus operandus

• We had no training on how to teach about deep
  time other than memorizing the chart
• We focus on teaching biological processes, not so
  much the time scales during which they proceed
• We make modest attempts to talk about deep time
  (give out handouts)
• We give our geology/paleontology colleagues
  absolute authority to provide dates of events
  (with no discussion of error, methods, etc.)
• We do not assess whether students grasp time
  concepts within evolution
• We avoid confrontations with students who
  challenge us with biblical timelines of events

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Teaching deep time through macroevolution and
phylogenetics
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Stories of evolution through phylogenies of many
topologies
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Biomedcentral.com
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Genetic diversity/no morphological diversity
Plethodontid salamanders
P. hubrichti RM 1 RM 2
N1
BM 1 BM 2 DG VA 1 GF 1 GF 2 WT VA1 DG VA 2 WT VA
2
N2
Desmognathus wrighti (pygmy salamander)
N1
3.1 mya (Pliocene)
SI 1 SI 2 CW 1 CW 2
S1
N2
RBB 1 RBB 2
S3
BR 1 CM 1 CM 2 BR 2 PG 1 SM. 1 SM. 2
S2
S2
S1
PG 2 ML 1 ML 2 CD 1 CD 2
S3
mt DNA sequence
Combination mtDNA and allozyme
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Genetic variation among Indian groups of peoples
BMC Genetics 2004, 523
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Phylogeography of Drosophila in Hawaii (Bromham
and Penny, 2003)
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Molecular clocks
Zuckerkandl and Pauling 1962

• Implicitly used when choosing a region to assay
  for variation given the expected evolutionary
  distance of interest
• Explicitly used when attempting to date
  divergence times
• Need to calibrate divergence times estimated with
  DNA variation with historical geological
  dates/events
• Lots of debate and criticism about the use of
  molecular clocks

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Inquiry-based integrated instructional
unitPhylogenetic analysis of the bony fishes
Morphological and mtDNA sequence

• 3-4 week module
• Comparative Anatomy
• Evolution
• Genetics
• Molecular Biology
• Ichthyology, etc
• Introductory Biology

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What are the phylogenetic relationships among
orders of Actinopterygii?
150 mya
200 mya
250 mya
300 mya
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Learning activities

1. Students assign traits to a set of sea shells and
   generate a tree based on the similarity of
   characters--this is done by hand. cladograms are
   visual representations of calculated
   relationships
2. Students create character matrix and extract DNA/
   sequence the 28s rRNA gene. scaled up
   repetition, base pair differences are empirically
   determined
3. Students align sequences, calculate the number of
   differences among taxa and use a computer program
   to generate a phylogenetic tree more complex
   iteration of initial exercise introduces
   bioinformatics
4. Students download cytb sequence and generate
   another tree for the same taxa repeat tree
   making skills

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Assessment

• Exam questions
• What is a molecular clock, and how is it
  relevant to phylogenetic analysis?
• Compare the cytb tree to the tree you
  constructed from the 28S rRNA gene you made
  earlier in the week. Which gave a more robust
  hypothesis (and why), and what are the reasons
  why the two genes resolved different hypotheses?
• .but thats it.

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Goals of this workshop (for me)

• Learn more formal pedagogy behind teaching deep
  time
• Learn how to integrate cognitive science in
  pedagogy of phylogenetics
• Analogy
• Diagram reasoning (tree thinking Catley and
  Novick,2009)
• Form collaborations with geoscientists to
  generate a working group interested in
  integrating teaching methods of deep time from
  geoscience and evolutionary biology perspectives.

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Molecular clocksWhen is a molecule not
appropriate? Questions to ask yourself
Do molecular clocks tick evenly through time? Is
there a geological or climatic date/event for
calibration? Are geological calibrations
accurate? Molecules can evolve at different rates
than organisms (or other molecules)! Is the clock
ticking at different rates among lineages?
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Deuterostome phylogeny Morphology
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Morphological Analysis
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Genomic/mt DNA extraction
PCR target gene sequence
DNA sequence
Alignment
Phylogenetic analysis
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Variation in mutation rates among genomic regions
Hartl Clark, Principles of Population Genetics
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Biological factors that affect molecular clocks
Neutral Theory
Limitations

1. Gene to gene variation in rates of mutation
2. Lineage to lineage variation in rates of mutation
3. Variation if portions of genome under selection
   (vs. neutral)

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Molecular clocksWhen is a molecule not
appropriate?
Saturation (homoplasy)