1. Teaching about time a biologists perspective Biochemistry Physiology Ecology Evolution Origins of biodiversity and estimates of divergence times TIME Integrative Courses Vertebrate or Invertebrate Zoolgy Comparative Anatomy Biogeography 10 -6 s 10 9 years *not drawn to scale

2. Biologist’s 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

4. Teaching deep time through macroevolution and phylogenetics

5. Stories of evolution through phylogenies of many topologies

6. Biomedcentral.com

7. Genetic diversity/no morphological diversity Plethodontid salamanders Desmognathus wrighti (pygmy salamander) P. hubrichti RM 1 RM 2 SI 1 SI 2 CW 1 CW 2 BM 1 BM 2 DG VA 1 GF 1 GF 2 WT VA1 DG VA 2 WT VA 2 RBB 1 RBB 2 BR 1 CM 1 CM 2 BR 2 PG 1 SM. 1 SM. 2 PG 2 ML 1 ML 2 CD 1 CD 2 N1 N2 S1 S2 S3 N1 N2 S3 S2 S1 mt DNA sequenceCombination mtDNA and allozyme 3.1 mya (Pliocene)

8. BMC Genetics 2004, 5:23 Genetic variation among Indian groups of peoples

9. Phylogeography of Drosophila in Hawaii (Bromham and Penny, 2003)

10. Molecular clocks 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 Zuckerkandl and Pauling 1962

12. Inquiry-based integrated instructional unit: Phylogenetic analysis of the bony fishes: Morphological and mtDNA sequence 3-4 week module Comparative Anatomy Evolution Genetics Molecular Biology Ichthyology, etc Introductory Biology

13. What are the phylogenetic relationships among orders of Actinopterygii? 150 mya 200 mya 250 mya 300 mya

14. 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]

15. 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 that’s it.

16. Goals of this workshop (for me) 1.Learn more formal pedagogy behind teaching deep time 2.Learn how to integrate cognitive science in pedagogy of phylogenetics Analogy Diagram reasoning (“tree thinking” Catley and Novick,2009) 3.Form collaborations with geoscientists to generate a working group interested in integrating teaching methods of deep time from geoscience and evolutionary biology perspectives.

18. Molecular clocks When 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?

19. Deuterostome phylogeny: Morphology

20. Morphological Analysis

21. Genomic/mt DNA extraction PCR target gene sequence DNA sequence Alignment Phylogenetic analysis

22. Variation in mutation rates among genomic regions Hartl & Clark, Principles of Population Genetics

24. 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)

25. Molecular clocks When is a molecule not appropriate? Saturation (homoplasy)