The Great Clade RaceTree-thinking activities for marine

scientistsSusan L. Richardson, Ph.D.

Wilkes Honors College, Florida Atlantic UniversityTeaching Oceanography Workshop: 18-20 June 2013

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

Plants

Mosses

Fungi

“Protists”

Bacteria

Animals

Cornflakes are here

Cotton socks

Fish supper

Athlete’s foot

You are

here

Muséum nationale d’Histoire Naturelle (Paris)

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)

Why Tree-thinking?Tree of Life

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

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 1028 SAR11 bacterial cells in ocean.

Brown et al. (2012). Global biogeography of SAR11 marine bacteria: Molecular Systems Biology, 8: 595.

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.

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

Why Tree-thinking?Conservation Applications

•Sequence 1

•>Unknown1

•GAAAATATATATTGTACAATAACCACAAGGCCACAGTATTATGTCCGTATTAAAAATAACTTATTTTATTGCATACTGTTATGTAACTTGTGCATGTATGTACTCCCACATAACCCATAGTAGTTAGTATTCCCCTGTGAATATGTATATGTACACATACTATGTATAATTGTGCATTCAATTATCTTCACTACGGAAGTTAAAGCCCGTATTAAATTTTATTAATTTTACATATTACATAATATTTATTAATAGTACAATAGTACATGTTCTTATGCATCCTCAGGTCATTCTAGACGGAATGACTCTTATGGCCGCTCCATTAGATCACGAGCTTAATCAGCATGCCGCGTGAAACCAGCAACCCGCTCGGCAGGGATCCCTCTTCTCGCACCGGGCCCATCAATCGTGGGGGTAGCTATTTAATGATCTTTATAAGACATCTGGTTCTTACTTCAGGACCATATTAACTTAAAATCGCCCACTC

http://www.cebl.auckland.ac.nz:9000/page/whales/title

htt

p:/

/ww

w.c

ebl.auck

land.a

c.nz:

90

00

/page/w

ftw

/meth

ods

ID’d as gray whale

http://www.cebl.auckland.ac.nz:9000/page/whales/title

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.

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.

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.

The Great Clade RaceRules

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.

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

Race.

The Great Clade RaceCorrect 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.

The Great Clade RaceOne Correct Tree

The Great Clade RaceAnother Correct Tree

Runners 1-4Alternative “tree” topologies

Runners 1-4Alternative “tree” topologies

Runners 5-8Alternative “tree” topologies

Examples of Student Trees