I would like to thank all of you who have made suggestions to my question about evolutionary lab activities or offered to donate fossils for my teaching. Below, after the repeat of my original email, is a compilation of all the suggestions I have received about lab exercises, in the order of arrival. I have also attached the two files I received, which I hope will be successfully sent to the email list. Hope these suggestions and documents will be helpful to some of you. ~Xianfa On 12/3/11 2:57 AM, "Xianfa Xie" wrote: Dear colleagues, I am designing an upper-level undergraduate Evolutionary Biology Laboratory course, as an addition to the lecture. I am seeking suggestions on what lab activities will be good for this 2-hour 1-credit course. Ideally, I would like to have different activities for the lab, including computer simulations (on genetic drift, etc.), exercise in taxonomy and molecular phylogeny, and wet-lab experiments. I would like to hear your opinions on what computer programs are particularly good for the first two types of activities, and I will greatly appreciate your suggestions on experimental lab activities which could be run in the time of one class, across a few weeks or the whole semester and can potentially produce publishable results. If you have taught any of the above lab activities, I would like to hear from you on what works, what does not, and your suggestions for improvement. I will compile the suggestions and comments received and make them available here. In addition, I am trying to put together a fossil collection for teaching purpose. If you have some fossils you think could be used for teaching and would like to donate, please send me a note and I will provide you the address where they can be sent to. Sorry I cannot afford to buy your fossils, but I plan to reimburse you for the shipping cost. Thanks a lot, Xianfa Xie Xianfa.Xie@gmail.com ------ Forwarded Message From: Tom Gilbert Date: Sat, 3 Dec 2011 09:07:31 +0100 To: Subject: Re: Other: Evolution lab suggestions Dear Xianfa I am not sure what range of experiments you are considering, but there is one very simple one that always goes down well that demonstrates very nicely the power/significance of drift, bottlenecks etc in genetic data. The classic 'resampling beads' experiment. If you don't know it its very simple. You need, per group, a bag, and a selection of beads. Ideally say 100 of 3+ different colours (100 red, 100 blue, 100 yellow) Basic idea is you start them by putting predetermined mix of 100 beads in a bag. Then to simulate bottlenecks, or drift, they just pick an appropriate number of beads randomly from the bag, which of course will vary a bit from the original ratio due to stochasticity. Then you get them to count and record the new frequency, multiply them up to 100 by adding new beads at the same ratio, and then repeat. After about 4-5 generations they can really see how the frequency is drifting away. Its a real eye opener for many students who don't initially get how drift can happen. Of course you can easily simulate bottlenecks, expansions, etc. Very cheap. Very obvious. Very easy to modify to more or less complex situations. There are computer programs that do this too, but frankly the hands on way is in my experience way more fruitful. As many are sceptical of computers...they think its preprogrammed to do it. But actually seeing drift first hand... Hope this helps Tom Gilbert ------ Forwarded Message From: Anuschka Faucci Date: Fri, 02 Dec 2011 22:30:26 -1000 To: Subject: Evolution Labs Hi, not sure you know about the attached paper (the evolution of the chocolate bar). I use a simplified version for our Intro to ecology and evolution Lab as a warm-up before the Caminalcule Lab designed by Rob Gendron. He has some great ideas on his page as well: http://nsm1.nsm.iup.edu/rgendron/Caminalcules.shtml Good luck, and I'd love to see all the responses. Anuschka ------ Forwarded Message From: Susan Cousineau Reply-To: Date: Sat, 3 Dec 2011 10:00:13 +0100 To: Subject: Evolution lab Hi Xianfa I'm a Masters student in the Erasmus Mundus Evolutionary Biology programme (MEME) in my second year of studies. We did some practicals in our first year that were very helpful, and I can make a few recommendations from my current 6-month projects. I don't know how familiar you are with the world of evolutionary biology so it's hard to know if these suggestions will be totally naive and unhelpful... so bear with me! For one suggestion... A practical that involves a series of steps from getting sequences, to aligning and editing (good idea might be something with indels and other known "problems"), either raw or cDNA sequences; then building a tree and making inferences about molecular evolution. I think this could be done over a series of labs quite tractably (1/ getting and aligning sequences; 2/ editing sequences and building the tree; 3/evolutionary models of molecular evolution). So software would include of course an online BLAST search (or similar database); I would recommend free SeaView for editing sequences over BioEdit, as the latter is (while easy to use at first glance and very intuitive, also very "buggy" and has limited utility at higher levels); since Geneious is often prohibitively expensive (except, naturally, pirated version), it may well be unavailable to students at other points in their careers so they may benefit from learning to work in less powerful/freeware programs... For tree-building I've used RaxML, TreeView, FigTree and others; and for testing evolutionary models, HyPhy and PAML are the real powerhouses. I would highly recommend students get some experience in using these as command-line programs rather than the click-through GUI of Datamonkey (HyPhy), for instance. This could all be done as a presentation-style/longer project, where students must search sequences pertaining to a particular question; then try to answer it through these methods and make some conclusions from their findings.  Must run but if other ideas would be helpful feel free to let me know. Best, Susan 2)  -- "I never trust anyone who's more excited about success than about doing the thing they want to be successful at." BSc. Ecology University of Calgary Hon 1st Erasmus Mundus Master Program in Evolution (MEME) 2012 University of Montpellier II, France University of Groningen, Netherlands ------ Forwarded Message From: "Mohammad S. Al - Zein" Reply-To: "Mohammad S. Al - Zein" Date: Sat, 3 Dec 2011 02:44:52 -0800 (PST) To: "Xianfa.Xie@gmail.com" Subject: Re: Other: Evolution lab suggestions I suggest you check Populus developed by Dan Alstad (http://www.cbs.umn.edu/populus). The software is available free of charge and an accompanying set of excercises may be purchased from Sinnaeur Associates. In general biology laboratory manuals, you may also be able to locate several "hands on" activities in which evolution is simulated. One that comes to mind now is simulating populations with marbles, but this may be more of a population genetics excercise. Please compile all the suggestions you get (or a summary thereof) and share them with us. Best regards, Mohammad ------ Forwarded Message From: "Yampolsky, Lev" Date: Sat, 3 Dec 2011 13:56:31 +0000 To: "Xianfa.Xie@gmail.com" Subject: RE: Other: Evolution lab suggestions I am not sure about publishable results, but here is a meaningful Drosophila lab demonstrating selection and drift: http://www.bioone.org/doi/abs/10.1525/abt.2010.72.1.4 I can send you a pdf if you like. Best regards, Lev Yampolsky ------ Forwarded Message From: Emily Weigel Date: Sat, 3 Dec 2011 10:03:12 -0500 To: Subject: Evolution Lab Suggestions If you want something hands-on, my students have enjoyed working with Avida-Ed. See here: http://avida-ed.msu.edu/ They have worked with this system to understand the effect of mutations, logisitic population growth, and fitness. The system also allows for them to design their own experiments, and is completely scalable and free. I'd highly recommend it. Have a great weekend! -- Emily -- Emily Weigel Graduate Student Boughman Lab Zoology Department Ecology, Evolutionary Biology and Behavior Program Michigan State University https://www.msu.edu/user/weigelem/index.html weigelem@msu.edu 404-788-2023 ----- -- ------ Forwarded Message From: Kathryn Perez Date: Sat, 3 Dec 2011 11:00:27 -0600 To: Subject: Re: Other: Evolution lab suggestions A complete evolution lab course online: http://faculty.virginia.edu/evolutionlabs/ Drosophila wet lab: http://faculty.virginia.edu/evolutionlabs/DrosophilaEvoBioscenev28-2p3-6.pdf Also Craig Nelson formerly at Indiana has a series of websites with evol labs posted. Kathryn E. Perez, Ph.D. Department of Biology University of Wisconsin at La Crosse 1725 State Street La Crosse, WI 54601 Office (Room 3009): 608-785-6998 Laboratory (Room 323): 608-785-8257 http://www.uwlax.edu/biology/faculty/perez/ ------ Forwarded Message From: Ronny C Woodruff Date: Sat, 3 Dec 2011 09:41:48 -0500 To: "brian@helix.biology.mcmaster.ca" Subject: Re: Other: Evolution lab suggestions Resent-To: Resent-Date: Sat, 3 Dec 2011 16:58:24 -0500 Go to the Drosophila Information Service [p http://www.ou.edu/journals/dis/], then to Teaching Articles, then to my name and you will find a lot of them. Ron Woodruff -- R. C. Woodruff Distinguished Research Professor CoEditor-in-Chief , GENETICA Fellow, AAAS Department of Biological Sciences Corner Merry and N. College Life Sciences Building Bowling Green State University Bowling Green, Ohio 43403 Telephone: 419-372-0376 Fax: 419-372-2024 email: rwoodru@bgsu.edu ------ Forwarded Message From: Pat Barry Date: Sat, 3 Dec 2011 10:12:11 -0900 To: "brian@helix.biology.mcmaster.ca" Subject: Re: Other: Evolution lab suggestions Resent-To: Resent-Date: Sat, 3 Dec 2011 16:59:01 -0500 Hi Dr. Xie, I have taught an ecology lab using the program PopG (http://evolution.gs.washington.edu/popgen/popg.html). I find that it does a good job simulating migration and fitness. For simulating drift we used the program p.14 by Mork, but is a bit dated. Hope this helps. Patrick ------ Forwarded Message From: Henry Schaffer Date: Sat, 3 Dec 2011 20:57:29 -0500 To: Subject: computer simulations for course Xianfa, I saw your request on evoldir. Here is one computer simulation I wrote: http://www.cals.ncsu.edu/gn/ex/mit-eve.html and a bit of discussion about it: http://www.cals.ncsu.edu/gn/ex/mit-eve-disc.html I also did a similar one on the inheritance/drift for the Y chromosome. I also have some simulations dealing with inbreeding - both selfing (single seed descent) and full sib inbreeding. Let me know if you'd like to see more of these. Best wishes, --henry schaffer ------ Forwarded Message From: Dusan Misevic Date: Sun, 4 Dec 2011 02:10:36 -0800 (PST) To: Subject: evolution labs Dear Xianfa, I would suggest two simulation platforms that you could use for lab exercises. The first one is Avida-ed, and it's more developed, stable and user friendly. http://avida-ed.msu.edu/ Look around the website, download the software, and look for support material for teachers and sample exercises under the Information tab. There have been many science publications with the research version of the software, you can easily google them or find many of them listed at http://devolab.msu.edu/ A somewhat similar software, but more directed towards research than education, is Aevol. You can download the software here: http://gforge.liris.cnrs.fr/projects/aevol/ and can find more information in some of the publications listed here: http://liris.cnrs.fr/~cknibbe/ specifically the early ones. Hope that helps. And you collect and sort through the answers from the people on EvolDir, it would be great if you could also share those answers with us! Best of luck! Dule tinyurl.com/duleweb ------ Forwarded Message From: Francesco Montinaro Date: Mon, 5 Dec 2011 09:18:00 +0000 To: Subject: Re: Other: Evolution lab suggestions Hi Xianfa, A good simulation software program to start is Simcoal2. It could semm hard but actually is quite easy. However there is a nice tool called m4s (modeler for simcola http://popgen.eu/soft/m4s2/) that automatize the simulation of several evolutionary scenario. Once you have simulated these scenario, you can simply run it with arlequin and  compare some summary statistics. Another quite easy software is BEAST ( http://beast.bio.ed.ac.uk/Main_Page) that performs several philogenetics analysis, and the website contains sveral well explained Tutorial. I hope that this could help you Best regards Francesco Montinaro ------ Forwarded Message From: "Beck, Christopher" Date: Mon, 5 Dec 2011 12:55:40 +0000 To: "Xianfa.Xie@gmail.com" Subject: evolution lab ideas Xianfa, We have several experimental labs using the bean beetle model system posted at www.beanbeetles.org/protocols. You can also look for evolution labs on the website of the Association for Biology Laboratory Education (www.ableweb.org/proceedings). Chris Dr. Christopher Beck Department of Biology Emory University 1510 Clifton Rd. Atlanta, GA 30322 christopher.beck@emory.edu ------ Forwarded Message From: "Forbes, Andrew A" Date: Mon, 5 Dec 2011 14:25:12 +0000 To: Xianfa Xie Subject: labs Hi Xianfa ... Iım sending the bare-bones descriptions of the two labs I conducted this Fall. Both worked very well and the students enjoyed them. Iıd be happy to give you more information on either once youıve had a chance to look at them. Sorry, I thought I had more. I did find the attached worksheet on apple maggots which works as a dry lab/ thought exerciseŠ and then Iıve used this before: http://ats.doit.wisc.edu/biology/ev/sp/sp.htm ... Andrew Andrew A. Forbes Assistant Professor Department of Biology The University of Iowa 434A Biology Building Iowa City, IA 52242 Tel: (319) 335-3006 andrew-forbes@uiowa.edu ------ Forwarded Message From: Mary Kuhner Date: Mon, 5 Dec 2011 15:09:08 -0800 (PST) To: Subject: ideas for evolution course I have designed some successful labs around the PopG program of Joe Felsenstein, which simulates populations with drift, mutation, migration and selection. It can be found on his website: http://evolution.gs.washington.edu/popg/popg.html This is good for asking questions like "How much gene flow does it take to prevent two populations from diverging?" and "What is the chance that a gene with a small advantage will fix?" (Both of these have non-intuitive answers and really benefit from the "try it yourself" approach.) For phylogenetics the MacClade program allows you to hand-optimize a parsimony tree in a graphical way, and is very good for showing the basic principles. It's available at: http://www.macclade.org/download.html Hope this helps, Mary Kuhner mkkuhner@uw.edu Department of Genome Sciences, University of Washington ------ Forwarded Message From: David Tallmon Reply-To: Date: Mon, 5 Dec 2011 16:49:41 -0900 To: Subject: lab suggestions Hi Xianfa- I, too, run an upper division evolutionary biology course. I have a few suggestions that might be of use. I would also love to see the suggestions you get from others on course content. Could you forward that to me? I'm curious to know what peers are doing. Anyway, here are a few things we do that I have found helpful. 1) I use the model PopG from Joe Felsenstein in several labs. It simulates drift, migration, and selection under simple situations that help students to understand these concepts. You can find and download the software at: http://evolution.gs.washington.edu/popgen/popg.html It is easy to design computer lab exercises that lead the student through use of this software. 2) I also use software that was designed to work with the textbook "Evolutionary Analysis" by Freeman and Herron. Specifically, I use the software on heritability Xianfa Xie