1. The Great Clade Race Tree-thinking activities for marine scientists Susan L. Richardson, Ph.D. Wilkes Honors College, Florida Atlantic University Teaching Oceanography Workshop: 18-20 June 2013

2. Why Tree-thinking? Understanding how to interpret phylogenetic, or evolutionary trees, is an essential skill in modern biology. Trees are generated from computer analyses of morphological (phenotypic characters) and/or molecular sequence (DNA, RNA, etc.) data sets. http://www.utexas.edu/features/2008/tree/ Phylogenetic tree of 3,000 species: <1% of known species are depicted

3. Plants Mosses Fungi “Protists” Bacteria Animals Cornflakes are here Cotton socks Fish supper Athlete’ s foot You are here

4. Muséum nationale d’Histoire Naturelle (Paris)

5. Why Tree-thinking? Evolution underlies biological diversity Most current biology textbooks portray the evolutionary relationships of organisms in the form of phylogenetic trees. Life in modern oceans is more abundant and diverse than on land. Life evolved in the ocean and radiated to freshwater and terrestrial habitats. “Water” by Giuseppe Arcimboldo (1566)

6. Why Tree-thinking? Tree of Life

7. Why Tree-thinking? Unculturable Marine Microbes Environmental sequencing of seawater has illuminated the vast diversity of genes in the ocean. Some groups of marine microbes (and viruses) are only known from gene sequences. http://ucsdnews.ucsd.edu/thisweek/2006/oct/10_16_venter.asp Craig Venter on Sorcerer II

8. Why Tree-thinking? Unculturable Marine Microbes Some groups of marine microbes are only known from gene sequences The SAR11 clade is a group of alpha-proteobacteria identified primarily from ribosomal gene sequences identified in DNA extracted from seawater. The global biomass of SAR11 bacteria is greater than all the fish in the ocean; their abundance is estimated to be 2.4 X 10 28 SAR11 bacterial cells in ocean. Brown et al. (2012). Global biogeography of SAR11 marine bacteria: Molecular Systems Biology, 8: 595.

9. Why Tree-thinking? Conservation Applications Trees are used in marine conservation biology to identify illegally harvested marine life. Legal: Minke whales; fin whales? Illegal: Humpback whales; dolphins Baker & Palumbi (1994). Which whales are hunted? A molecular genetic approach to monitoring whaling: Science, v. 265, p. 1538-1539.

10. Why Tree-thinking? Conservation Applications Witness for the Whales is a service for the identification of cetaceans (whales, dolphins and porpoises) using DNA sequences. http://www.cebl.auckland.ac.nz:9000/page/wftw/intro

11. Why Tree-thinking? Conservation Applications Sequence 1 >Unknown1 GAAAATATATATTGTACAATAACCACAAGGCCACAGTATTATGTCCGT ATTAAAAATAACTTATTTTATTGCATACTGTTATGTAACTTGTGCATGTA TGTACTCCCACATAACCCATAGTAGTTAGTATTCCCCTGTGAATATGT ATATGTACACATACTATGTATAATTGTGCATTCAATTATCTTCACTACG GAAGTTAAAGCCCGTATTAAATTTTATTAATTTTACATATTACATAATAT TTATTAATAGTACAATAGTACATGTTCTTATGCATCCTCAGGTCATTCT AGACGGAATGACTCTTATGGCCGCTCCATTAGATCACGAGCTTAATCA GCATGCCGCGTGAAACCAGCAACCCGCTCGGCAGGGATCCCTCTTC TCGCACCGGGCCCATCAATCGTGGGGGTAGCTATTTAATGATCTTTAT AAGACATCTGGTTCTTACTTCAGGACCATATTAACTTAAAATCGCCCA CTC http://www.cebl.auckland.ac.nz:9000/page/whales/title

12. http://www.cebl.auckland.ac.nz:9000/page/wftw/methods ID’d as gray whale http://www.cebl.auc kland.ac.nz:9000/pa ge/whales/title

14. Why Tree-thinking? Trees show evolutionary trends Lim et al. (2010). Phylogeny of hammerhead sharks (Family Sphyrinidae) inferred from mitochondrial and nuclear genes. Mol. Phylog. & Evol. 55: 572-579.

16. The Great Clade Race These cards represent cards carried by eight runners in an imaginary race through the woods. The racecourse is made of diverging paths. As runners encounter a fork in the path, they choose to go to the right or the left, and continue in this manner to the finish line. Although each runner starts the race at the same place, each runner finishes the race at a separate finish line. Goldsmith (2003). The Great Clade Race. American Biology Teacher 65(9):679-682.

17. The Great Clade Race Along the stretches between the forks in the path are check-in stations; each check- in station has a unique stamp. As runners pass a station, they stop to collect a stamp on their card. Using the collections of stamps on each card, students must reconstruct the pattern of the racecourse that shows: the forks in the path, the location of the check-in stations & the finish line for each runner.

18. The Great Clade Race Rules 1. All runners must complete the race. They cannot drop out of the race. 2. When the path branches, it only branches into two new paths, never three or more. 3. Once two paths have branched off from one another, they can never reconnect. 4. Check-in stations along the legs between the forks in the path.

19. Work in groups to map out the “racecourse” for the Great Clade Race.

20. The Great Clade Race Correct Trees There are several correct trees that contain the same information. The pattern of branching is what is relevant; branches can be rotated around each node and still portray the same information. Branch length is not important for our example. Shape (square, curved, etc.) of trees is not important; orientation is not important.

21. The Great Clade Race One Correct Tree

22. The Great Clade Race Another Correct Tree

23. Runners 1-4 Alternative “tree” topologies

25. Runners 5-8 Alternative “tree” topologies

26. Examples of Student Trees