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Ambrosia Beetle Genotype-by-sequencing
- 1. Population structure ina haplo-diploid fungus farming beetle New insights from genotype-by-sequencing male Caroline Storer & Jiri Hulcr University of Florida female
- 2. Ambrosia beetles buildgalleries in the xylem of dying trees for farming their symbiotic fungus
- 3. The Xyleborini area hyper-diverse (~1,200 species) tribe of Ambrosia beetles
- 4. The Xyleborini havebizarre genetics
- 5. The Xyleborini havebizarre genetics Haplo-diploid: Females produce many diploid daughters and one haploid son haploid son diploid mother
- 6. The Xyleborini havebizarre genetics Haplo-diploid: Females produce many diploid daughters and one haploid son Inbreed: The haploid son mates with its sisters haploid son diploid mother
- 7. 1) What isthe effect of haplo-diploid inbreeding on genetic diversity and population structure?
- 8. 1) What isthe effect of haplo-diploid inbreeding on genetic diversity and population structure? 2) Are new high-throughput genotype-bysequencing methods suitable for these near-clonal organisms?
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- 11. Why genotype-by-sequencing? o Fast - No marker development - Sample prep takes days
- 12. Why genotype-by-sequencing? o Fast - No marker development - Sample prep takes days o High-throughput - 100s of individuals - 100s of genotypes
- 13. Why genotype-by-sequencing? o Fast - No marker development - Sample prep takes days o High-throughput - 100s of individuals - 100s of genotypes o Robust - High-quality sequence data - Biological signals are recoverable (Buerkle & Gompert 2013)
- 14. Why genotype-by-sequencing? o Fast - No marker development - Sample prep takes days o High-throughput - 100s of individuals - 100s of genotypes o Robust - High-quality sequence data - Biological signals are recoverable (Buerkle & Gompert 2013)
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- 16. Xylosandrus crassiusculus 1 mm o Abundant
- 17. Xylosandrus crassiusculus 1 mm o Abundant o Exotic (in the US)
- 18. Xylosandrus crassiusculus 1 mm o Abundant o Exotic (in the US) o Sometimes pest
- 19. Xylosandrus crassiusculus Maryland Northern NC 1 mm Southern NC South Carolina o Abundant o Exotic (in the US) North Florida Central Florida o Sometimes pest 2-3 beetles sequenced from 6 locations
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- 22. restriction-site associated sequencing (RADseq) ddRADseqenables the sequencing of the same genomic region in many taxonomically related individuals Petterson et al. 2012
- 24. 1 Sequences are sortedby an individual’s unique barcode...
- 25. 1 Sequences are sortedby an individual’s unique barcode... 2 then assembled into locus stacks based on sequence similarity Stack 1 Stack 2 Stack X
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- 29. 89,429 stacks in catalog 21,860stacks shared across individuals
- 30. 89,429 stacks in catalog 21,860stacks shared across individuals 2,984 SNP loci genotyped
- 31. Inbreeding detected atmost loci 1 0.8 0.6 FIS 0.4 FIS > 0 inbreeding 0.2 0 -‐0.2 -‐0.4 -‐0.6 FIS < 0 outbreeding -‐0.8 -‐1 locus
- 32. No population structureassociated with geographic location Central Florida North Florida South Carolina Southern North Carolina Northern North Carolina Maryland Principal coordinate 2 (14.54%) Principal coordinate 1 (35.34%)
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- 34. In summary... o Genotype-by-sequencingis possible
- 35. In summary... o Genotype-by-sequencingis possible o High inbreeding (>0.8) at most loci, but some outbreeding may occur
- 36. In summary... o Genotype-by-sequencingis possible o High inbreeding (>0.8) at most loci, but some outbreeding may occur o No genetic structure associated with geographic location
- 37. In summary... o Genotype-by-sequencingis possible o High inbreeding (>0.8) at most loci, but some outbreeding may occur o No genetic structure associated with geographic location o High genetic similarity between some individuals, but not clonal
- 38. o What isthe global population structure ambrosia beetles?
- 39. o What isthe global population structure ambrosia beetles? o How does population structure differ between outbreeding and inbreeding ambrosia beetles?
- 40. o What isthe global population structure ambrosia beetles? o How does population structure differ between outbreeding and inbreeding ambrosia beetles? Native and exotic?
- 41. o What isthe global population structure ambrosia beetles? o How does population structure differ between outbreeding and inbreeding ambrosia beetles? Native and exotic? o Is population structure correlated with fungal symbiont biodiversity?
- 42. o What isthe global population structure ambrosia beetles? o How does population structure differ between outbreeding and inbreeding ambrosia beetles? Native and exotic? o Is population structure correlated with fungal symbiont biodiversity? o Are species complexes a phenotypically plastic single species or distinct cryptic species?
- 43. The Forest Entomology Labat University of Florida Dr. Jiri Hulcr Andrew Johnson Martin Kostovcik Polly Harding (not shown) Craig Bateman UF Graduate Student Council
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- 45. 1e+06 8e+05 stacks per library 6e+05 sequences per library 00005 50,000 800,000 00006 60,000 1,000,000 600,000 4e+05 00004 40,000 400,000 2e+05 200,000 total sequences total_seqs quality filtered sequences filtered_seqs used sequences used_seqs stacks unique_seqs >40,000 sequence targets for marker discovery 00002 20,000 00003 30,000
- 46. o 58% ofstacks identical between individuals o 9,054 stacks contain putative SNPs o Calling genotypes: – Present in > 80% of individuals – 5 sequences (RAD-tags) required to confirm each genotype within an individual – Minimum minor allele frequency of 0.1 o 2,948 loci genotyped in 16 individuals