Dear Colleagues, I received many very useful replies to my query for computer programs to demonstrate experimental evolution, and in general various evolutionary topics, for students. Thanks so very much to all those who kindly sent replies and information. I list below an overview of the suggestions received and further below replies in full so that they may be of use for others. Best regards, Else Fjerdingstad OVERVIEW: - PopG by J. Felsenstein (earlier called Simul8) (ftp://evolution.gs.washington.edu/pub/popgen/popg.html) Free and downloadable. Allows manipulating fitness of different genotypes, population size, mutation rates for two different alleles, number of populations, migration rate between subpopulations, and then carry out simulations to give a graphic output on allele frequency changes and allele fixations. - Populus by D. Alstad (http://www.cbs.umn.edu/software/populus.html/), free and downloadable, and allows illustrating a large number of different evolutionary topics (selection, genetic drift, co-evolution, heritability, genetic drift etc.) - Ecobeaker (http://www.simbio.com/) a cellular automaton, not free. - EvoBeaker (http://www.simbio.com/EvoBeaker.html), Not free -one can download a free demo if teaching at colleges or in highschools. Has very detailed manuals. - Darwinian snails, PopCycle and AlleleA1 by J. Herron (the first later included in modified version in EvoBeaker) Darwinian snails can de found at (http://wps.prenhall.com/esm_freeman_evol_3) or (http://fac- ulty.washington.edu/~herronjc/SoftwareFolder/software.html) ; PopCycle at http://wps.prenhall.com/esm_freeman_evol_3/0,8018,849183- ,00.html , and AlleleA1 at http://wps.prenhall.com/esm_freeman_evol_3/0,8018,849255- ,00.html PopCycle allows setting mutation rates, survival rates and migration rates for a test population. AlleleA1 is a single locus, two allele simulation illustrating how the balance among drift, selection, and mutation influence the rates of change and the maintenance of variation. - XLGene, by C. M Austin & R. Carr. Ask for permission to use it (chris.austin@cdu.edu.au) & (rodney.carr@deakin.edu.au). The program is allows simulating genetic drift and tweaking various Hardy-Weinberg population parameters, while giving a graphical output showing frequency of alleles. - WinPop 2.5 , P. Nuin, ( http://www.genedrift.org/winpop.php) - an upgraded version called ----- PopGene.S^2 will be released (contact P. Nuin : nuin@terra.com.br - Evolve, distributed by BioQuest: (http://bioquest.org/BQLibrary/library/evolve.html ) , one must buy a site-licence or an individual license to access the programs. - Evotutor ( http://www.evotutor.org/TutorA.html). Very graphical and treats a series of topics in different simulations (mutation, genetic drift, adaptation, gene flow, speciation, phylogenetics, sexual selection). - Evolution tutorials from Ridley's Evolution textbook which has website resources - one of which are virtual experiments ( http://www.blackwellpublishing.com/ridley/experiments/) Also, the site below has a lot of lessons for various types of evolution related questions: ( http://www.indiana.edu/%7Eensiweb/home.html) - Matlab functions to illustrate a series of evolutionary and population genetic topics (fitness surfaces, frequency dependent selection, stochastic fertility selection, fitness under epistasis, genetic drift and many more) by L. Revel, can be found at http://iguana.wustl.edu/~liam/evol_theory/matlab/ by following the link to the old page (more details on running these in the full reply from Revel listed below, towards the very end. REPLIES IN FULL: __________ From: "Lauren Chan" To: Sent: Friday, September 08, 2006 1:19 PM Subject: Re: Other: experimental evolution computer programs Hi Else, The program AlleleA1 by Jon Herron might suit your needs. http://faculty.washington.edu/~herronjc/SoftwareFolder/AlleleA1.html It is a single locus, two allele simulation with a lot of really nice features. I find it very easily to use and it does a great job of illustrating how the balance among drift, selection, mutation, etc influences matters to rates of change and the maintenance of variation. Best, -Lauren __________________ From: "Joe Felsenstein" To: "Else Fjerdingstad" Sent: Friday, September 08, 2006 11:56 AM Subject: Re: Other: experimental evolution computer programs There are a number of these. Try "Simulate gene frequencies" in Google. The one from my lab (which isn't found that way) is: ftp://evolution.gs.washington.edu/pub/popgen/popg.html (note this is an "ftp:" URL, not an "http:" one). J.F. ---- Joe Felsenstein joe@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 357730, Seattle, WA 98195-7730 USA __________________From: "USORHANNUS" To: Sent: Friday, September 08, 2006 12:49 PM Subject: Programs Ø Dear Else, I think what you are looking for is POPULUS - I use it in my evolution course. You will find it at http://www.cbs.umn.edu/software/populus.html/ With best regards, Ulf Sorhannus Deparment of Biology Edinboro University of Pennsylvania Edinboro, PA 16444 USA __________________ From: Carmen Bessa Gomes To: Else.Fjerdingstad@snv.jussieu.fr Sent: Friday, September 08, 2006 12:50 PM Subject: Re: Other: experimental evolution computer programs Dear Else, For my ecology courses, I often use Ecobeaker, a cellular automaton quite attractive to students (http://www.simbio.com/). Ecobeaker dicobeaksposes of several "labs" addressing distinct problems. I use it more for examining ecological questions than evolutionary, but I think you may find labs addressing evolutionary issues. In addition, it exists also a software specific for evolutionary biology named EvoBeaker. I hope this may be of some use to you and that all is well. Best regards Carmen __________________ From: "Miguel de Navascués" To: Sent: Friday, September 08, 2006 10:41 AM Subject: Re: Other: experimental evolution computer programs Ø Dear Else, There use to be a DOS program called Simul8 or something similar but I do not know its availability at the moment. Good luck, Miguel Miguel de Navascués, BScHon, PhD http://m.navascues.googlepages.com/ __________________ From: "Miguel Ángel Toro Ibáñez" To: Sent: Friday, September 08, 2006 8:51 AM Subject: RE: Other: experimental evolution computer programs Ø I think that the computer program called POPULUS of D. Alstad (University of Minnesota) is quite useful. It allows not only to play with selection, genetic drift, etc but also ecological models Miguel Angel Toro Ibañez Departamento de Mejora Genética Animal Instituto Nacional de Investigación y Tecnología Agraria y Agroalimentaria (INIA) Carretera La Coruña km. 7 28040 Madrid ESPAÑA Telf: 34 913476807 Fax: 34 913572293 e-mail: toro@inia.es __________________ From: "Alexander s. Dixson" To: Sent: Friday, September 08, 2006 8:57 AM Subject: Re: Other: experimental evolution computer programs Ø Hello, I'm a PhD student studying evolution, sexual selection and development in an insect system at Victoria Uni, Wellington, New Zealand. I get various jobs as a teacher assistant in which evolution simulation programmes are used. So far the programs used here are mostly from John Herron, they are all free to download and may well meet the requirements you listed in your evoldir posting. The link to his site is: http://faculty.washington.edu/~herronjc/SoftwareFolder/software.html I have also been working with an instructor here trying to get the program EvoBeaker taken on for future courses. It is mentioned on Dr. Herron's site and is very much more detailed program, a bit more visually appealing, and much nicer to work with. A link to this is: http://www.simbio.com/fr_index.html?/EvoBeaker.html However, Evolbeaker is not free and requires, I think, that number of students using be registered to meet copyright requirement for reprinting the very detailed manuals for each of the labs on the program. The company will send instructors a copy of evobeaker for nothing plus samples of the lab manual paperwork. It's really good though, I've enjoyed playing around with it! Hope this helps. Kind regards, Alexander Dixson dixsonalex@student.vuw.ac.nz From: "Jean-Nicolas Jasmin" To: Sent: Friday, September 08, 2006 8:19 AM Subject: Re: Other: experimental evolution computer programs Ø Chère Dr. Fjerdingstaf, j'ai utilisé le logiciel PopG du Dr. Felsenstein de l'Université de Washington lors d'un cours de génétique à l'Université d'Ottawa. Ce logiciel et ses conditions d'utilisation sont disponibles à l'adresse suivante: ftp://evolution.gs.washington.edu/pub/popgen/popg.html Je crois que le logiciel permet de manipuler toutes les variables que vous mentionnez dans votre courriel, à l'exception de ceux qui concernent la structure spatiale des populations. Au plaisir, Jean-Nicolas University of California at San Diego __________________ From: Mark Schultz To: Else.Fjerdingstad@snv.jussieu.fr Sent: Friday, September 08, 2006 8:06 AM Subject: YES! XLGene. RE: Other: experimental evolution computer programs Yes, I know a great program. It is called XLGene, and was written by my supervisor and genetecist Prof Chris M Austin and his biometrician colleague Rodney Carr. You can contact Chris to ask permission on chris.austin@cdu.edu.au, or Rodney on rodney.carr@deakin.edu.au I'm sure they would both be happy for you to use it. The program is perfect for simulating genetic drift and tweaking various Hardy-Weinberg population parameters, while giving a graphical output showing frequency of alleles. Regards, Mark Mark Schultz Charles Darwin University C/- Arafura Timor Research Facility PO Box 41775 Casuarina NT 0811 Ph: +61 (0)8 8920 9292 Fax: +61 (0)8 8920 9222 __________________ From: "Paulo Nuin" To: Sent: Friday, September 08, 2006 1:28 PM Subject: Re: Other: experimental evolution computer programs Ø Dear Else Take a look on the package WinPop 2.5 at http://www.genedrift.org/winpop.php it might not be exactly what you want but it has some good features. Also we will be releasing an upgraded version of it called PopGene.S^2 soon. IF you have any suggestion for a possible module that can be added to the program we might try to include it. Regards Paulo Nuin From: "David W. Hall" To: Sent: Friday, September 08, 2006 12:50 PM Subject: Re: Other: experimental evolution computer programs Ø Else, You might try www.evotutor.org. Cheers, Dave From: "JOHANNE BRUNET" To: Sent: Friday, September 08, 2006 2:45 PM Subject: Re: Other: experimental evolution computer programs Ø Try Populus. It has both a section on ecology and one on population genetics. There is also a book you can buy describing the programs. Easy to use. From: Ken Weiss To: Else.Fjerdingstad@snv.jussieu.fr Sent: Friday, September 08, 2006 3:18 PM Subject: Re: Other: experimental evolution computer programs You might give a look at Populus, free and downloadable. From: "David H. A. Fitch" To: Sent: Friday, September 08, 2006 3:29 PM Subject: experimental evolution computer programs Hi Else, For my evolution course, I use the free PopG by Joe Felsenstein: ftp://evolution.gs.washington.edu/pub/popgen/popg.html or Evolve, distributed by BioQuest: http://bioquest.org/ Have fun! Dave Fitch -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~ ~ - - ~ David H. A. Fitch ~ \ / / / ~ Associate Professor ~ \/ / / ~ Department of Biology ~ \ / / ~ New York University ~ [] / / ~ Main Building, Room 1009 ~ \ / / ~ 100 Washington Square East ~ \/ / ~ New York, NY 10003 ~ \ / ~ U S A ~ \/ ~ Tel.: (212) 998-8254 ~ \ ~ Fax: (212) 995-4015 ~ \ ~ e-mail: david.fitch@nyu.edu ~ From: "Jennifer Gleason" To: Sent: Friday, September 08, 2006 4:10 PM Subject: Re: Other: experimental evolution computer programs Ø Hi, I know of a some programs that do some, but probably not all of what you are looking for. They are available on the website for the Freeman & Herron textbook, Evolutionary Analysis (http://wps.prenhall.com/esm_freeman_evol_3 ). Once you enter the website, on the lefthand column is a link called "Simulations." There you will find various simulations illustrating different points. They are pretty good though the documentation is out of date (it refers to the 2nd edition of the book, though if you are not using the book, the references are irrelevant). I use the programs when I teach Evolutionary Biology. Jon Herron wrote the programs and now he is contributing to the EvoBeaker programs http://www.simbio.com/fr_index.html?/EvoBeaker.html ) instead of developing these more. EvoBeaker is very good, but it isn't free. Cheers, Jenny ---------- Dr. Jennifer Gleason Assistant Professor University of Kansas Ecology and Evolutionary Biology 1200 Sunnyside Ave., Haworth Room 6006 Lawrence, KS 66045 785-864-5858 785-864-5321 (FAX) jgleason@ku.edu http://www.ku.edu/~eeb/faculty/gleason.html ____________________ From: "Renate Wesselingh" To: Sent: Friday, September 08, 2006 4:28 PM Subject: Re: Other: experimental evolution computer programs Ø Dear Else, try EvoTutor http://www.evotutor.org/TutorA.html. Best regards, Renate Wesselingh ------------------- Renate A. Wesselingh Unité d'Ecologie et de Biogéographie Biodiversity Research Centre Université catholique de Louvain Croix du Sud, 4-5 B-1348 Louvain-la-Neuve Belgium phone: +32 10 473447 fax: +32 10 473490 e-mail: wesselingh@ecol.ucl.ac.be From: "Daria Koscinski" To: Sent: Friday, September 08, 2006 5:27 PM Subject: Re: Other: experimental evolution computer programs Ø Hi, I don't have any sure answers for you but I've been looking around for evolution tutorials and found a couple of pages of interest. One is from Ridley's Evolution textbook which has website resources - one of which are virtual experiments. I can't try them since they are only available for PC but they might be what you are looking for: http://www.blackwellpublishing.com/ridley/experiments/ The site below has lots of lessons for various types of evolution related questions: http://www.indiana.edu/%7Eensiweb/home.html Hope it helps. Good luck! Daria Koscinski From: "Jeremy M. Brown" To: Cc: Sent: Friday, September 08, 2006 5:41 PM Subject: Re: Other: experimental evolution computer programs Ø Else, I'm not sure this is exactly what you're looking for, but try the website: www.evotutor.org It was written by a friend of mine and fellow graduate student here at the Univ. of Texas-Austin, Alan Lemmon. It allows you to manipulate most evolutionary parameters independently (but perhaps not jointly?). I know this website is used in several evol. biol. courses around the US. Best, Jeremy Ø _____________________ From: "Bronwyn Heather Bleakley" To: Sent: Friday, September 08, 2006 6:15 PM Subject: RE: Other: experimental evolution computer programs Ø Hi Else, I've used PopG 2.0, which runs on windows and Mac to do exactly what you want with students. It's written and distributed for free by Joe Felsenstein at University of Washington. I copied the relevant information from the website (http://depts.washington.edu/genetics/courses/genet453/2002/) below for you. --Heather From: "Kirsten Fisher" To: Sent: Friday, September 08, 2006 5:02 PM Subject: Re: Other: experimental evolution computer programs Ø Hi, you might check out Evobeaker: http://www.simbio.com/fr_index.html?/EvoBeaker.html I think they have a demo you can order. In particular, the Columbine exercise might be useful for you. best wishes, kirsten _____________________________ From: "Paul Hohenlohe" To: Sent: Friday, September 08, 2006 8:11 PM Subject: Re: Other: experimental evolution computer programs Else- I have used the Ecobeaker package of programs for teaching beginning undergraduate students in an evolution course, and I would highly recommend it. It has a number of ecological and evolutionary simulations that are fairly user-friendly and visual. The same company also produces "Evobeaker", an evolutionary package, that I have not used -- this may be useful to you also. These can all be found at the website www.simbio.com Good luck, Paul =<>=<>=<>=<>=<>=<>=<>=<>=<>=<>=<>=<>=<>=<>= Paul Hohenlohe, Postdoctoral Researcher Department of Zoology Oregon State University Corvallis, OR 97331 Center for Ecology and Evolutionary Biology University of Oregon Eugene, OR 97403 hohenlo@uoregon.edu ph: 541-760-9233 fax: 541-737-0501 From: "Yampolsky, Lev" To: Sent: Friday, September 08, 2006 7:54 PM Subject: RE: Other: experimental evolution computer programs Have you tried Populus (http://www.cbs.umn.edu/populus/)? It's not ideal, but it certainly fits most of what you describe. From: "kevin livingstone" To: Sent: Saturday, September 09, 2006 6:52 PM Ø Dear Else- while not everything you might want, we have used the programs alleleA1 and popcycle that are a part of Freeman and Herron's evolution textbook (but available for free) to demonstrate evolution to our undergraduate classes. cheers -Kevin popcycle: http://wps.prenhall.com/esm_freeman_evol_3/0,8018,849183-,00.html alleleA1 http://wps.prenhall.com/esm_freeman_evol_3/0,8018,849255-,00.html From: "Liam J. Revell" To: Sent: Sunday, September 10, 2006 5:59 PM Subject: re: TeachingEvol.ComputerPrograms Ø Dear Dr. Fjerdingstaf - I have no idea if this is what you're looking for, but I used to have available online a set of simple matlab functions to illustrate some concepts in population genetics. The functions include: - one that generates an animated cobweb plot and Wrightian fitness surface for p(t) by p(t+1) for arbitrary genotypic fitnesses (specified by user), - one that generates a cobweb plot for frequency dependent selection, - one that simulates stochastic fertility selection, - one that plots the erosion of LD while simulating the erosion of LD and comparing it to the prediction, - one that plots 3D fitness surfaces under various forms of epistasis (e.g., ad x ad, ad x dom). - one that simulates and animates the process of genetic drift, - one that simulates the coalescent process, - and several others. Although I took the page down while I update my website, you can still get to it by going to http://iguana.wustl.edu/~liam/evol_theory/matlab/ and following the link to the old page. Matlab (http://www.mathworks.com/products/matlab/) is both a high level programming language and environment. My matlab functions might also run in Octave (http://www.gnu.org/software/octave/) or SciLab (http://www.scilab.org/), which are both open-source, free packages (although many of the animated features might not work). I hope this is of some help. Liam Liam Revell Washington University, Department of Biology web: http://iguana.wustl.edu/~liam/ email: ljrevell@artsci.wustl.edu From: Alessia Guggisberg To: Else.Fjerdingstad@snv.jussieu.fr Sent: Monday, September 11, 2006 8:53 AM Subject: Re: Other: experimental evolution computer programs You may check the EvoTutor webpage ( http://www.evotutor.org/TutorA.html). Dr. Else J. FJERDINGSTAD Laboratoire d'Ecologie, CNRS UMR 7625 Université Pierre et Marie Curie 7 Quai St-Bernard, Bâtiment A, 7ème étage, case 237 F-75252 Paris Cedex 05 FRANCE Email: Else.Fjerdingstad@snv.jussieu.fr Tél. +33 1 44 27 34 20, Fax. +33 1 44 27 35 16 Have a heart that never hardens, a temper that never tires - Charles Dickens