1. Squirrel Genetics (University of Sheffield) Melissa Gunn, Dave Coltman, Jon Slate, Andrew Leviston

2. Determination of paternity Development of paternal lineage/relatedness matrix enables: –Determination of multiple paternity –Analysis of inbreeding (present or absent) –Estimates of Ne/N –Analysis of population substructure –Re-estimates of maternal effects, heritability using animal model And probably lots more...

3. Step 1: Isolate microsatellites 6/13 working so far (Corey’s clones)

4. Find more microsatellites Get more sequences (aim for 20 polymorphic loci for paternity analysis) - make more clones Can use closely related species primers –Currently trying Eurasian red squirrel primers:

5. Step 2: Use microsatellites! Using microsats, obtain 20-locus genotype for each individual Assign paternity based on microsats (CERVUS), or relatedness (sib-groups) Reconstruct pedigree from known mothers, assigned fathers Determine multiple paternity –Is it correlated with differential survival of offspring? –Is it correlated with food availability?

6. Inbreeding? Determine if inbreeding occurs Estimate inbreeding coefficient (F) Is there correlation between F and reproductive success/growth rate/weight at weaning etc? Does inbreeding reduce phenotypic plasticity?

7. Population Structure Is there genetic flow between all grids (i.e. metapopulation)? Is there population structuring? –E.g. Does road stop gene flow? Estimate effective population size Ne

8. Heritability & Plasticity Using reconstructed pedigree, estimate heritability of traits (animal model) Maternal effects can also be re-estimated using full pedigree Phenotypic plasticity - between-year reaction norm measurements –Determination of plasticity versus genetic alterations in response to selection

9. Correlations Is survival to breeding age and/or lifetime reproductive success correlated with microsatellite heterozygosity? Are any loci associated with quantitative traits? --> eventually could lead to mapping, with sufficient loci. Develop many markers with this aim in view

10. Grant objectives: Test that the means and plasticities of reproductive traits show sig. V A Test for negative correlations between trait means and plasticities which may constrain selection Test for positive covariance between maternal and direct genetic effects on reproductive traits Test that selection gradients vary temporally, but overall favour earlier parturition, stable litter size and maternal investment Test that increased food availability increases selection intensity on parturition date and offspring growth rate, while increasing potential response to selection by reducing individual environmental variance, decoupling the influence of maternal effects