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Melissa Gunn, Dave Coltman, Jon Slate, Katie Hartnup, Andrew Leviston

Red Squirrel Genetics. Melissa Gunn, Dave Coltman, Jon Slate, Katie Hartnup, Andrew Leviston. Microsatellites. 100. Panel 1. Panel 2. Size (bp). 400. Microsatellites. 19 polymorphic m’sats working ~10 alleles per locus 200 extra clones available ~460 individuals genotyped (tissue)

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Melissa Gunn, Dave Coltman, Jon Slate, Katie Hartnup, Andrew Leviston

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  1. Red Squirrel Genetics Melissa Gunn, Dave Coltman, Jon Slate, Katie Hartnup, Andrew Leviston

  2. Microsatellites 100 Panel 1 Panel 2 Size (bp) 400

  3. Microsatellites • 19 polymorphic m’sats working • ~10 alleles per locus • 200 extra clones available • ~460 individuals genotyped (tissue) • 2003/2004 Sulphur, Kloo, Agnes all extracted • 80% of loci scored • Robot re-calibrated, hair extraction kit ready to go • ~40 days to extract 2500 hairs • All hair samples catalogued • PCR may need re-optimising for hair samples

  4. Parentage Assignment • Cervus V.2 • Currently assigning 58% sires • known mother genotyped (95% confidence) • Assigning 54% sires • no mother genotyped • More sires assigned if all males included • Chase males don’t seem to get all paternities

  5. Offspring ID Known parent ID KP class 0-KP loci mismatching Candidate parent ID O-CP loci mismatching LOD Delta Confidence KL36 KL40 Typed 0 SUL18 1 1.02E+01 8.00E+00 * KL68 KL30 Typed 0 KL81 0 9.93E+00 6.27E+00 * KL18 KL10 Typed 0 KL5 0 1.29E+01 7.38E+00 * KL144 Untyped 0 KL53 1 6.49E+00 4.41E+00 * KL145 Untyped 0 KL53 0 7.12E+00 5.66E+00 * KL48 KL11 Typed 0 KL89 0 1.17E+01 3.72E+00 * KL172 Untyped 0 KL9 1 7.08E+00 3.63E+00 * KL71 Untyped 0 KL9 1 6.52E+00 3.98E+00 * SUL28 SUL19 Typed 0 SUL41 0 1.45E+01 1.09E+01 * SUL93 SUL19 Typed 2 SUL7 1 1.13E+01 9.72E+00 * SUL102 Untyped 0 SUL11 3 5.20E+00 2.45E+00 * SUL99 Untyped 0 SUL4 1 6.58E+00 2.35E+00 * SUL154 SUL14 Typed 1 SUL16 2 9.10E+00 7.15E+00 * SUL166 SUL12 Typed 1 SUL41 1 1.32E+01 9.52E+00 * SUL114 SUL17 Typed 2 SUL2 2 1.16E+01 8.61E+00 * SUL167 SUL17 Typed 1 SUL2 1 1.13E+01 6.89E+00 * Assigned Parent Output

  6. Papers • Primer note – “Microsatellites for Tamiasciurus hudsonicus and their cross-utility in other rodents”

  7. Papers & Ideas • Heritability of plasticity of birthdate • Estimate including maternal effect 0.89±0.6/4.9 (av) • Plasticity measured as birthdate/log cone previous year • Based on 156 mothers with multiple births • Later analyses will include probable fathers • Probable covariates incl. juv. growth rate, weight at birth, number of maternal breeding events • Population structure & migration – observed migrations vs. genetic effects • Productivity vs. genetic diversity • Agnes vs. Kloo? Between-individuals?)

  8. Other Results & Ideas • NeEstimator - Effective pop. size = ~4.6/56/109 (c.f 456 individuals used for test) • How large an Ne is required to maintain evolvability ? • Compare with Ne from previous years? • Depends on good hair genotyping • Is selection still favouring plastic females? • More tissue • mainly new juv’s • Some adults still need sampling • Comparison with island populations (Ne, birthdate, etc)?

  9. Acknowledgements Thanks for access to the database, all squirrel sample collectors, and providers of other DNA samples and primers: Roland Ashford, Chris Faulkes, Chris Barnard, Marie Hale, Amy Plowman, Deborah Dawson, Terry Burke, Pippa Thomson, Corey Davis

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