Dear EvolDir Members I had a few requests to post answers to my recent question about estimating founder population size. The original post and answers are at the bottom of this email. Many thanks to all that replied, most suggestions helpfully directed me to papers and software that have tackled similar problems. I hope this helps! Jacqui ORIGINAL POSTING Dear EvolDir members I am attempting to estimate founder population size for a recently introduced population (c. seven years/max 10 generations) of Anolis using microsatellite data. Standard estimates of effective population size are likely to be inappropriate in this case since mutation rate cannot be accurately estimated due to the recent nature of the introduction. I have come across a paper (Rasner et al 2004, Molecular Ecology) that attempts to answer the question using the number of alleles (n) within the most variable locus in the introduced population as an absolute minimum estimate of the founder population size. (Eight generations were assumed to have passed between founding and sampling). The paper then uses simulation to resample a specified number of 'founder individuals' from the native population 1000 times and calculates the proportion of times that at least this number (n) of alleles are captured in the samples. The smallest number of founders consistent with the data was taken to be the number that gave a probability > 0.05 of capturing n observed alleles (Rasner et al 2004). My questions are first, does anyone know of a method for estimating founder population size using microsatellite data in such a recently founded population? second, is there a program in the public domain that can handle a simulation such as that described above? It is presumably relatively easy to write such a program, unfortunately it is not my expertise! Many thanks for your anticipated help on this problem, Jacqui Eales Doctoral candidate, Bangor University, Wales, UK ANSWERS: "Andrew J. Bohonak" See the following papers (pdfs on my web site), in which I have simulated founding events similar to that you describe: Vandergast, A. G., A. J. Bohonak, D. B. Weissman and R. N. Fisher. 2007. Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus). Molecular Ecology 16: 977-992. Bohonak, A. J., N. Davies, F. X. Villablanca, and G. K. Roderick. 2001. Invasion genetics of New World medflies: testing alternative colonization scenarios. Biological Invasions 3: 103-111. Bohonak, A. J., and G. K. Roderick. 2001. Dispersal of invertebrates among temporary ponds: are genetic estimates accurate? Israel Journal of Zoology 47: 367-386. (Special Issue: Ecology of temporary pools) Hairston, N. G., Jr., L. J. Perry, A. J. Bohonak, M. Q. Fellows, C. M. Kearns and D. R. Engstrom. 1999. Population biology of a failed invasion: paleolimnology of Daphnia exilis in upstate New York. Limnology and Oceanography 44: 477-486. Dear Jacqui Eales, have a look at Wang (2005) Estimation of effective population size from data on genetic markers. Phil Trans R Soc B 360:1395-1409. and at his software page: http://www.zoo.cam.ac.uk/ioz/software.htm Maybe this helps, cheers, Rodolfo Jaffé Hi Jacqui, It may be worth looking at some of Mark Beaumont's programs: http://www.rubic.rdg.ac.uk/~mab/software.html There is a nice use of such approaches in Goossens et al. 2006 Plos Biol, 4(2) 0285-0291, looking at very recent bottlenecks in Orang-utans. Good luck, Mark de Bruyn Hi Jacqui, Check out E. C. Anderson and M. Slatkin, Estimation of the number of individuals founding colonized populations. 2007. Evolution 61: 927-983, and the corresponding software. Also see http://www.plosone.org/article/fetchArticle.action?articleURI=info:doi/10.1371/journal.pone.0000868 - an article of mine where I estimate founder population size for a North American invasive bee species (using forward simulations). Cheers, Amro Amro Zayed, PhD NSERC Postdoctoral Fellow Department of Entomology University of Illinois at Urbana-Champaign Hi Jacqui, Have you tried Rmetasim (Strand 2002)? We used this program to estimate the number of founders in non-native populations of bulllfrogs in Europe (Ficetola et al. 2008). We used mDNA data but it also works with microsatellites. I send you the two papers.I hope this helps. Aurélie Bonin, Grenoble Hi Jacqui, I wanted to do something similar for a species that had been introduced for biological control. I used msVAR, which is freeware. I used it to estimate current population sizes based on various reasonable priors, and then argued, that given that the introduction was so recent, the variation wasn't likely due to mutation, and so the estimate of population size was a reasonable estimate of the size of the founding population. If you search for msVAR is the attached Molecular Ecology paper, you should find what I did pretty quickly. Best, Ruth Ruth A. Hufbauer Associate Professor BSPM, GDPE, PRIMES Colorado State University Hi Jacqui you can use MULTSIM as described in Noor, M. A. F., M. Pascual, and K. R. Smith. 2000. Genetic variation in the spread of Drosophila subobscura from a nonequilibrium population. Evolution, 54: 696-703. Or the methodology described in Pascual, M.; Chapuis, MP.; Mestres, F.; Balanyà, J.; Huey, RB.; Gilchrist, GW.; Serra, L.; Estoup, A. 2007. Introduction history of Drosophila subobscura in the New World: a microsatellite based survey using ABC methods. Molecular Ecology, 16: 3069-3083. Arnaud Estoup has carried out done the estimations cheers Marta Marta Pascual Berniola Departament de Genetica Facultat de Biologia, Edifici annex Universitat de Barcelona Hi, In a similar case of estimating founder population after recently founded populations in an ant, I have calculated a crude estimator from the relatedness among individuals within populations compared to those in other populations. If all descend from one pair, their average r (queller & goodnight's program; also implemented in Fstat) across loci should be 0.5 in diploids. More founders will lower r. However this assumes that no alleles are lost by drift or inbreeding within the population during time, since this will inflate r. R is thus conversely associated with the number of founders and this measure will give a conservative maximum of Nf. I published it in "Conservation Genetics", came out late -07 or early -08. Best wishes, Kalevi Trontti, PhD University of Helsinki Finland Finally, Rich Glor (University of Rochester) has an R script for running simulations that resample from allele frequency distributions as described in Rasner et al 2004. Rich can be contacted by email: rglor@mail.rochester.edu bsp030@bangor.ac.uk