Below are the answers I received. Thanks to all who replied, sorry for the delay in reposting. - Sarah Gilman ----- Peter Unmack : I have a lab written up based on Mega and phylogeny. It is all very self contained / explained. This was based on mega version 4, I haven't checked the details on what changes would need to be made to make it compatible with version 5 (you can still download both versions). http://www.megasoftware.net/ From memory it takes around 1.5-2 hours or so to work through. Cheers Peter I've taught some "phylogeography" short courses in the past, and I've posted my labs as PDFs here: http://filogeografia.dna.ac/labs.html I hope 1 or 2 might be useful for you. Be aware some are a bit old, but the newest were updated in 2009. Some assume a specific data set, but most are general enough to be applied to any DNA sequence data matrix. Feel free to use or modify these labs to your own needs. I recently started to use GIS in conjunction with phylogeography/biogegraphy hypothesis testing, and I found this paper really useful (link above), because it tests several interesting hypothesis and also comes with tutorials to replicate their study. http://www.sciencedirect.com/science/article/pii/S1055790311000480 I have posted the materials for a phylogeny exercise I have done with high school students and high school teachers at http://www.eebweb.arizona.edu/Grads/mherron/Darwin/Darwin.html. This may be aimed a bit low, but I'm sure it could be adapted for advanced undergraduates. I would be very grateful for a summary of your responses. I don't have any prepared resources, but am aware of several on-line resources that might help. First, you could use genbank (at NCBI) and let them choose organisms and genes, then conduct a phylogenetic reconstruction. For element occurrence data, you might try NatureServe. I don't know how much that helps, but they're ideas for starters. If you choose to pursue either one and have questions, I'd be happy to help sort them out. Getting beginners up and running with GIS is tricky, b/c current Arc software is so complex. In my Conservation Biology course I use DIVA-GIS, which is free and downloadable - and there's a tutorial in this book: Gibbs, Hunter, and Sterling. 2008. Problem-solving in conservation biology and wildlife management, 2nd ed. Blackwell. Might be some other good stuff in there - I think the table of contents is available on-line. The tutorial took some re-working on my part but works OK - takes 3 weeks of 3 hour labs to do (1 as tutorial for novices, 2 to do the exercise). What textbook do you plan to use? Lomolino is very comprehensive and fairly affordable (still $100, but you get a lot for that) but has a jillion typos. We played "find the typo" in my class... I'd be interested in what other exercises people submit - my Biogeography class is lecture-only. My students were expected to find out if the plants from family Apiaceae that are edible or used as spices form a monophyletic group. We used the GenBank search command '"apioid superclade" rpl16 not genome' to obtain the sequences. They were analysed in RAxML. The students found researching food fascinating and the subsequent discussion about interpretation of the phylogeny yielded one of the most fruitful discussions in my course. I'm not sure if this is what you're looking for, but I had an interesting project in an Evolution class that went something like this: We were given about 15 cactus species and told to construct a phylogeny based on their morphology. We were to determine which characteristics we wanted to use. If you wanted to be sneaky, you could add in a non-cactus species that looked like a cactus (my entire class was fooled!). You could probably use other organisms, but cactus is really easy to work with. Hope this helps! ----- Sarah Gilman, Ph.D. Joint Science Department Keck Science Center The Claremont Colleges 925 N. Mills Avenue Claremont, CA 91711 http://faculty.jsd.claremont.edu/sgilman sgilman@jsd.claremont.edu 909-607-0715 SGilman@jsd.claremont.edu