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/