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Phylogenetic Systematics

A laboratory exercise for undergraduate evolutionary biology courses


Hints for Instructors

Introduction:

Make sure students have read introductory material on how trees are constructed and understand the difference between ancestral and derived traits. Show class a phylogeny, with examples of progression. Ask them to identify which characters could be used to re-construct the same phylogeny. Are there alternate phylogenies? Discuss how convergent evolution might affect the construction of trees (homologous vs analogous structures).

Exercises:


Fastener phylogeny: Two optional families of related species: 1) Nails/screws - get a wide variety of flat-head nails, screws, wall hangers, etc. Nail history: http://www.glasgowsteelnail.com/nailmaking.htm 2) Paperclip family: metal / plastic paper clips, W type clips, binder clips, etc. Here is a web link to an archive of various sorts of historical paper clips http://www.officemuseum.com/paper_clips.htm

Alternative or addition to fastener phylogeny: 1) Echinoderm phylogeny: if facilities permit: order a variety of echionoderms and keep in aquaria (sand dollars, sea stars, brittle stars, sea cucumbers, etc). Get students to examine animals and  create phylogenies based on observed characters. Alternative to using live animals would be to use dry samples of sea stars, sea urchins, etc. If you have a bird collection or greenhouse available, it would also be a good source of specimens to examine.
echinos

GenBank Exercise


Make sure students have sufficient background in molecular biology : structure of DNA, substitutions, different types of changes in amino acide - transitions versus transversions (and the implications that different types of changes have for evolution).

Go over different types of methods to estimate phylogenetic relationships, and explain the benefits and problems with each.

NB: Maximum likelihood is conceptually difficult for most undergraduates, especially those with little statistical background - introduce method with coin flipping example - contrast probablity of getting 50/50 heads/tails if a coin is tossed 100x (which most students will be familiar with) and maximum likelihood method of using actual data from 100 tosses to determine model specifications.

Propose several hypothetical situations (fossil specimens, mtDNA information, small number of character states, etc) and ask students which would be the best method for resolving relationships among samples.

NCBI has a portion of their web site devoted to tutorials : http://www.ncbi.nlm.nih.gov/Education/index.html
which are very helpful. If students are having difficulty navigating GenBank, refer them to this site for help. The "nucleotide tutorial" has a nice guided search of Mycobacterium tuberculosis for sequences coding for penicillin resistance.

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