This project was prepared as part of a BioQUEST faculty development workshop entitled BioQUEST Summer Workshop 2007 at Beloit College in June 2007. The BioQUEST Curriculum Consortium is committed to the reform of undergraduate biology instruction through an emphasis on engaging students in realistic scientific practices. This approach is sometimes characterized as an inquiry driven approach and is captured in BioQUEST's three P's (problem-posing, problem-solving, and peer-persuasion). As part of this workshop groups of faculty were encouraged to initiate innovative curricular projects. We are sharing these works in progress in the hope that they will stimulate further exploration, collaboration and development. Please see the following links for additional information:

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Trees from the Seas
Authors          Audiences          Overview           Materials          Resources           Future Directions



Marsha Timmerman
La Salle University

Linda Weinland
Edison College

William Bromer
University of St. Francis

K. Rebecca Thomas
Montgomery College


Possible Audiences:

Introductory College Biology, Evolution, Bioinformatics, High School AP Biology  


Brief Overview:

This project provides a case study introducing students to patterns of relationships and evolution among economically important dinoflagellates, the causative agents of red tides. Using nucleotide sequences, students build a tree of relationships among dinoflagellate taxa. They use their tree (along with phylogenetic hypotheses derived from the literature) to explore the evolution of morphological and/or ecological characters in dinoflagellates. As broader applications, students learn to compare and evaluate hypotheses of evolutionary relationships. Additionally, because the case study focuses on dinoflagellates that have evolved toxicity, it can be used to further explore the biological and economic impacts of red tides.  


Project Materials:

The DinoflagelaltesAll2 is a file that we used in MESQUITE to analyze trees, nucleotides and morphological data. The file DNAsequences4ClustalWTEXT1.txt is a text file that contains the nucleotide sequences of the SSUrRNA of 15 dinoflagellate species from 13 genera.  


Resources and References:


Anderson, DM. 2007. The Harmful Algae Page, Woods Hole Oceanographic Institute.

Anderson, DM. 2007. Human illness associated with harmful algae. Woods Hole Oceanographic Institute.

Brevetoxin B

Burkholder, JM; Glasgow, HB; Deamer-Melia, NJ; Springer, J; Parrow, MW; Zhang, C; and Cancellieri PJ. 2001. Species of the toxic Pfiesteria complex, and the importance of functional type in data interpretation. Environmental Health Perspectives 109:667-679.

Clamp, M.; Cuff, J.; Searle, SM; and Barton, GJ. 2004. The Jalview Java Alignment Editor. Bioinformatics 20:426-7


European Bioinformatics Institute

EBI Tools: ClustalW

Faust, MA and Gulledge RA. 2002. Identifying Harmful Marine Dinoflagellates, Smithsonian Institution

Fish and Wildlife Research Institute. Regional red tide summaries and status reports


Hackett, JD; Anderson, DM; Erdner, DL; and Bhattacharya, D. 2004. Dinoflagellates: A remarkable evolutionary experiment. Am J Bot 91:1523-34.

Jalview A Multialignment Editor

Maddison, WP and Madison, DR. 2006. Mesquite: A Modular System for Evolutionary Analysis, version 1.12

Murray, S; Jorgensen, MF; Ho SYW; Patterson DJ; and Jermiin LS. 2005. Improving the analysis of dinoflagellate phylogeny based on rDNA. Protist 156:269-286.

Saldarriaga, JF; McEwen, ML; Fast, NM; Taylor, FJR; and Keeling, PJ. 2003b. Multiple protein phylogenies show that Oxyrrhis marina and Perkinsus marinus are early branches of the dinoflagellate lineage. Int J Syst Evol Microbiol 53:355-65.

Saxitoxin: Essential data

Solutions to Avoid Red Tide (START)

SDSC Biology Workbench

Vogelbein, WK; Lovko, VJ; Shields, JD; Reese, KS; Mason, PL; Haas, LW; and Walker, CC. 2002. Pfiesteria shumwayae kills fish by micropredation not exotoxin secretion. Nature 418:967-70.

Yoon, SH; Hackett, JD; and Bhattacharya D. 2002. A single origin of the peridinin- and fucoxanthin- containing plastids in dinoflagellates through tertiary endosymbiosis. PNAS 99(18): 11724-11729



Future Directions:

  • Map and analyze LSU rRNA data.
  • Connect case more strongle with ecological and economic issues.
  • Find and analyze some dinoflagellate specific molecular data such as plastid sequneces, toxin production.
  • Apply this model to other economically important species.