Dear list members, My query about different nuclear genomes but the same mitochondrial genome in Australian limpets got an overwhelming number of responses, so rather than reply to everyone in person, I've included a list of suggestions below. The following explanations were suggested: contamination, convergent evolution, mitochondrial capture, highly variable flanking regions (more variable than mtDNA), heteroplasmy, primer annealing sites located on transposable elements present in only a portion of the population (resulting in sequence lengths too large to amplify), and accidental amplification of a parasite. The explanation that I found most convincing was "mitochondrial capture", where hybridization has resulted in the introgression of mtDNA haplotypes from one species to another. This seems to be quite common in a wide variety of taxa, including mammals, birds and frogs, and it seems very likely that there would be hybridization between local and introduced species in the vicinity of Sydney harbour. There is in fact a recent paper in Molecular Ecology dealing with this that I completely overlooked (because of the bad habit of ignoring most papers that don't deal with marine biology): Good et al. 2008, Ancient hybridization and mitochondrial capture between two species of chipmunks. Mol Ecol 17:1313-1327. What convinced me was that we're finding this strict segregation in our limpets either the one set of primers work, or the other. One recent development is that we seem to have found our first non-hybrid specimen it is morphologically slightly different, the same microsat primers work for it than in the 10% of the samples, but at the mitochondrial level it seems to be so different that the COI gene has repeatedly failed to amplify using the Folmer primers. I've now amplified it using some alternative COI primers and am also sequencing some nuclear introns to see if the patterns we're getting from the microsats hold up. Thanks to everyone for their suggestions, and I hope those of you who told me that they've run into the same problem can now test whether they've got a case of mitochondrial capture in their species. The lesson here seems to be that hybrid zones and places where lots of aliens are likely to have established themselves are better avoided when selecting samples for designing microsat libraries. But it seems that what started off as a bit of a disaster has now turned into an interesting challenge. Best wishes, Peter Dr Peter R. Teske Postdoctoral Researcher Molecular Ecology Lab Dept. of Biological Sciences, E8C Macquarie University Sydney, NSW 2109 Australia Phone: +61 2 9850 9251 Fax: +61 2 9850 8245 E-mail: Peter.Teske@bio.mq.edu.au Website: http://www.bio.mq.edu.au/molecularecology/people.htm Publications: http://www.ru.ac.za/academic/departments/botany_research/peter/