List of mother plants
- Two genotypes of R. ursinus x armeniacus: are these apomictic or sexual?
- One genotype of R. ursinus x pensilvanicus: is this apomictic or sexual?
- R. ursinus: expect to see sexual recombination (dioecious)
- R. armeniacus: expect ~90% asexual progeny
- R. pensilvanicus: expect to see mostly asexual progeny
- R. ulmifolius: an extra control; should reproduce sexually
- Another clone that is similar to R. armeniacus: also expect to see ~90% asexual progeny. This clone is included because it was unexpected that we found a second invasive clone on the West Coast, and so characterizing it in general would be a good idea.
These are chosen based on how much heterozygosity they show in our mother plants of interest.
- CBA15 - only really useful in the R. armeniacus types
- CBA28 - should be especially useful
- RUB126 - also should be very useful
The simplest thing to do is, for each group of mother plus progeny, calculate a pairwise distance matrix between individuals. Then we will look at the distributions of within-group distances. Shorter distances indicate apomixis, while larger distances indicate sexual reproduction. Mother plants that have a mix of the two reproductive modes should show a bimodal distribution.
A more complex analysis could involve looking at the probabilities of seeing certain genotypes under the hypotheses of sexual and asexual reproduction. Theoretically we should expect 100% identical genotypes under asexual reproduction, but we should leave some wiggle room for mutations or scoring errors.
- Ellstrand & Scierenbeck: Hybridization as a stimulation for the evolution of invasiveness in plants? 
- Kollmann et al.: Evidence of sexuality in European Rubus species based on AFLP and allozyme analysis. 
- Amsellem et al.: Evidence for a switch in reproductive biology of Rubus alceifolius towards apomixis, between its native range and area of introduction 
- Werlemark & Nybom: Pollen donor impact on the progenies of pseudogamous blackberries. 
PCR Run today
Stella, you can put whatever notes you like in here about what you are doing.