Very many thanks to all those who replied to my query about null alleles and population structure. I had around 50 answers, which is testament to the extent of the problem. Shortly before my submission Chapuis & Estoup published a simulation of the effects of various ways of estimating the frequency of "the" null allele and adjusting Fst estimates. They have also developed software to do this, which will surely become an essential resource to many: Chapuis & Estoup 2007. Microsatellite null alleles and estimation of population differentiation. Mol. Biol. Evol. 24: 621-631. http://www.montpellier.inra.fr/URLB/ Cock van Oosterhout's MICROCHECKER (the current version is a major update from the last time I looked) applies one of these and is available here: http://www.microchecker.hull.ac.uk/ van Oosterhout, C., D. Weetman, and W. F. Hutchinson. 2006. Estimation and adjustment of microsatellite null alleles in nonequilibrium populations. Mol Ecol Notes 6:255-256. So, if you are prepared to live with the assumptions of these (the main ones being that your problem is due to a single null, and no Wahlund effects) there is great scope for Fst-style analyses. A nice surprise to me is that an imminent release of STRUCTURE allows treating loci as dominant markers so allowing analyses of potential sub-structure despite nulls. This is not available yet, but is to be released soon on the STRUCTURE website and Daniel Falush and colleagues have a paper (again, just out) in MEN on this. http://www.blackwell-synergy.com/doi/abs/10.1111/j.1471-8286.2007.01758.x http://pritch.bsd.uchicago.edu/structure.html It may be worth mentioning here that there are also methods for relatedness and parentage: Wagner AP, Creel S, Kalinowski ST (2006) Estimating relatedness and relationships using microsatellite loci with null alleles. Heredity 97:336-345. I will not send all the responses I received out on EvolDir, as these are lengthy and the new developments bypass many of them, but I have compiled most of the answers here: http://bio.st-and.ac.uk/supplemental/ritchie/NullResponses.html I would like to finish with two nice quotes: My instincts are to think a lot about the data, keep your eye on the biology and total evidence, and be prepared to argue your case with editors. Sometimes they are unreasonable, but that can happen on any issue. - Paul Sunnucks If we combine our problems, maybe there is food for an article "S.O.S. - Save Our Samples: survival guide to get the best out of the worst". This might get a lot of citations. - Dieter Anseeuw Best wishes & thanks again, Mike Mike Ritchie Phone 0 (44 outside UK) 1334 463495 Environmental & Evolutionary Biology Fax 0 (44 outside UK) 1334 463366 Dyers Brae House University of St Andrews E-mail mgr@st-andrews.ac.uk St Andrews, Fife Scotland KY16 9TH Website: http://bio.st-andrews.ac.uk/staff/mgr.htm Research website via: http://tiree.st-and.ac.uk/cegg/research.html mgr@st-andrews.ac.uk