2016 05-31-wurm-social-chromosome
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The document discusses the genetic basis of social organization in fire ant populations. Researchers used RAD sequencing of haploid males to discover SNPs and genotype individuals at over 2,400 loci. Principal component analysis separated individuals into two clusters corresponding to their social form (single or multiple queen), with the first principal component explaining over 12% of the variance. A region on chromosome 13 containing the Gp-9 gene was completely associated with social form. This research identified a major gene influencing an important social trait using next-generation sequencing techniques.
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2016 05-31-wurm-social-chromosome
- 1. A major transition in social evolution & other tidbits y.wurm@qmul.ac.uk https://wurmlab.github.io
- 2. © Alex Wild & others
- 4. © National Geographic Atta leaf-cutter ants
- 5. © National Geographic Atta leaf-cutter ants
- 6. © National Geographic Atta leaf-cutter ants
- 8. Oecophylla Weaver ants © ameisenforum.de
- 10. © ameisenforum.de Oecophylla Weaver ants
- 12. Tofilski et al 2008 Forelius pusillus
- 13. Tofilski et al 2008 Forelius pusillus hides the nest entrance at night
- 14. Tofilski et al 2008 Forelius pusillus hides the nest entrance at night
- 15. Tofilski et al 2008 Forelius pusillus hides the nest entrance at night
- 16. Tofilski et al 2008 Forelius pusillus hides the nest entrance at night
- 17. Avant Workers staying outside die « preventive self-sacrifice » Tofilski et al 2008 Forelius pusillus hides the nest entrance at night
- 18. Dorylus driver ants: ants with no home © BBC
- 20. Animal biomass (Brazilian rainforest) from Fittkau & Klinge 1973 Other insects Amphibians Reptiles Birds Mammals Earthworms Spiders Soil fauna excluding earthworms, ants & termites Ants & termites
- 21. Well-studied: • behavior • morphology • evolutionary context
- 22. Well-studied: • behavior • morphology • evolutionary context • ecology Genetic basis?
- 25. REPORTS onMarch12,2013www.sciencemag.orgDownloadedfrom Solenopsis invicta fire ants are a big problem! verywellstudied! Ascunceetal2011
- 26. Solenopsis invicta fire ant: two social forms •1 large queen •Independent founding •Highly territorial •Many sizes of workers •2-100 smaller queens •Dependent founding •No inter-colony aggression •All workers similar size Single-queen form: Multiple-queen form:
- 27. Fire ants + Population genetics:Allozyme screen Ken Ross “starch gel”+ 1 2 3 L. Keller
- 28. Allozyme screen Social form associated to Gp-9 locus Frequency of the most common allele Locus! 0.3! 0.4! 0.5! 0.6! 0.7! 0.8! 0.9! 1.0! Single queen!Multiple queen! Est-6!Est-4! G 3pdh-1!C a-4!Pgm -4!Ddh-1!Pro-5! Pgm -3!Acoh-5!acoh-1!A cy-1!Pgm -1!Aat-2!Gp-9! Ken Ross and colleagues Laurent Keller and colleagues
- 29. Single queen form Multiple queen form Ken Ross and colleagues Laurent Keller and colleagues Social form completely associated to Gp-9 locus
- 30. bbbbBB BB Bb bb Ken Ross and colleagues Laurent Keller and colleagues Single queen form Multiple queen form Social form completely associated to Gp-9 locus (>15% )(< 5% )
- 31. bbBB BB Bb x Gp-9 bb females rare Ken Ross and colleagues Laurent Keller and colleagues Single queen form Multiple queen form Social form completely associated to Gp-9 locus (>15% )(< 5% )
- 32. BB BB Bb Ken Ross and colleagues Laurent Keller and colleagues Single queen form Multiple queen form Social form completely associated to Gp-9 locus (>15% )(< 5% )
- 33. BB BB Bb x Ken Ross and colleagues Laurent Keller and colleagues Single queen form Multiple queen form Social form completely associated to Gp-9 locus (>15% )(< 5% )
- 34. BB BB Bb x x Ken Ross and colleagues Laurent Keller and colleagues Social form completely associated to Gp-9 locus Single queen form Multiple queen form (>15% )(< 5% )
- 35. BB BB Bb x x x Ken Ross and colleagues Laurent Keller and colleagues Single queen form Multiple queen form (>15% )(< 5% ) Social form completely associated to Gp-9 locus
- 36. • Is this gene the single überregulator? Social form completely associated to Gp-9 locus
- 37. • Is this gene the single überregulator? maybe 1/14th of the genome? •Only 14 allozyme markers Locus! 0.3! 0.4! 0.5! 0.6! 0.7! 0.8! 0.9! 1.0! Single queen!Multiple queen! Est-6!Est-4! G 3pdh-1!C a-4!Pgm -4!Ddh-1!Pro-5! Pgm -3!Acoh-5!acoh-1!A cy-1!Pgm -1!Aat-2!Gp-9! Social form completely associated to Gp-9 locus
- 38. This changes everything. Any lab can sequence anything!
- 40. Single ♂: His brothers: 11× 4× (330bp-insert paired reads) (normal single-end reads)45× + Sequencing from haploid males (for easier assembly): (8,000 & 20,000bp-insert paired reads) B 20x The genome of a Gp-9 B fire ant Wurm et al 2011 PNAS 10,000 scaffolds (100 biggest scaffolds: 50% of genome) Total: 350,000,000 bp assembled.→ The other 150Mb: highly repetitive sequence
- 41. “RAD Genotyping.” Bb unfertilised eggs haploid ♂ Gp-9 B Gp-9 b Gp-9 B Gp-9 b Gp-9 b Gp-9 B 38 B♂ & 38 b♂
- 42. EcoR1 EcoR1 EcoR1 Gp-9 B RAD sequencing of haploid ♂ for SNP discovery & genotyping Wang & Wurm et al 2013 Nature
- 43. EcoR1 EcoR1 EcoR1 AACTG AACTG AACTG AACTG Gp-9 B RAD sequencing of haploid ♂ for SNP discovery & genotyping Gp-9 B
- 44. AACTG Gp-9 B Gp-9 B GGCCT Gp-9 B Gp-9 B AAGGT Gp-9 B Gp-9 B CCAGT Gp-9 b Gp-9 b TAAAT Gp-9 b Gp-9 b GGAAT Gp-9 b Gp-9 b 38 Gp-9 B males 38 Gp-9 b males RAD sequencing of haploid ♂ for SNP discovery & genotyping
- 45. Identify polymorphism individual x locus genotype table RADseq: sequencing the same 0.01% of the genome in many individuals A B C D E F L1 A C A A C C L2 G G T - T G L3 - A G A - G L4 C - - G G C L5 T T C T C - L6 G A A - - G 2419loci 38 B & 38 b 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20+ Amount of variance explained per principal component %VarianceExplained 051015202530 12.7% 6.1% 5.4% 4.8% 4.7% 3.9% 3.5% 3.2% 3.1% 2.9% 2.8% 2.6% 2.4% 2.3% 2.2% 2.0% 1.9% 1.7% 1.6% 30.2% 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20+ Amount of variance explained per principal component %VarianceExplained 051015202530 PCA: Principal Component Analysis
- 46. pc: 2 % variance: 6.073 pc:3%variance:5.441 -0.2 -0.1 0.0 0.1 0.2 -0.2 -0.1 0.0 0.1 0.2 pc: 2 % variance: 6.073 pc:3%variance:5.441 -0.2 -0.1 0.0 0.1 0.2 -0.2 -0.1 0.0 0.1 0.2 Principal Components: PC2 vs PC3 Gp-9 B Gp-9 b
- 47. pc: 1 % variance: 12.666 pc:2%variance:6.073 -0.2 -0.1 0.0 0.1 0.2 -0.10 -0.05 0.00 0.05 0.10 0.15 Principal Components: PC1 vs PC2 pc: 1 % variance: 12.666 pc:2%variance:6.073 -0.2 -0.1 0.0 0.1 0.2 -0.10 -0.05 0.00 0.05 0.10 0.15 Gp-9 B ♂ Gp-9 b ♂
- 49. • Is this gene the single überregulator? maybe 1/14th of the genome? •Only 14 allozyme markers Social form completely associated to Gp-9 locus BB BB Bb Single queen form Multiple queen form (>15% )(< 5% ) x xx ✖ ✔ Locus! 0.3! 0.4! 0.5! 0.6! 0.7! 0.8! 0.9! 1.0! Single queen!Multiple queen! Est-6!Est-4! G 3pdh-1!C a-4!Pgm -4!Ddh-1!Pro-5! Pgm -3!Acoh-5!acoh-1!A cy-1!Pgm -1!Aat-2!Gp-9!
- 50. Sex chromosomes X Y Gp-9 B Gp-9 b SB Sb ? 1.Why non-recombining? “Social chromosomes” = supergene 2.Are SB and Sb differentiated? 3.What are the differences?
- 51. Small portion (200,000bp) of social chromosome: SB♂ Sb♂ • Genome of a Gp-9 B ♂ • Genome of a Gp-9 b ♂ ➡SB vs Sb sequence comparison: small inversion 1. Why no recombination between SB & Sb? Sequenced (de novo):
- 52. Gp-9 B Gp-9 b SB Sb ≥5 major rearrangements 1. Why no recombination between SB & Sb?
- 53. 2. Are SB and Sb differentiated?
- 54. 2. Are SB and Sb differentiated? • Yes • Sb has (almost) no diversity (likeY) • Differences are homogeneously distributed (no evolutionary strata!) Roddy Pracana et al in prep
- 55. 3. What are the differences between SB and Sb?
- 56. X ♀ X X Y ♂ •Prediction: SBSB SB Sb Single queen colony Multiple queen colony Differences between SB and Sb? Sb is degenerating? •genes? Region contains 800 genes! no strong differences
- 57. SB Sb • More, larger repetitive DNA in Sb compared to SB • larger introns in Sb • larger intergenic regions in Sb • assembly worse (smaller scaffolds) in Sb • increased dN/dS [b] vs. [c]: p < 10-4 [a] vs. [c]: p < 10-7 Gp-9B male Gp-9b male Region: Genome assembly: Normally recombining regions from all 16 linkage groups Normally recombining regions from all 16 linkage groups Sb region without recombination in Gp-9 Bb queens SB region without recombination in Gp-9 Bb queens Scaffoldlength(bp) 0 1,000,000 2,000,000 3,000,000 4,000,000 5,000,000 6,000,000 [a] [a], [b] [a] [c] SB Sb Sb is degenerating?
- 58. X ♀ X X Y ♂ ≥5 rearrangements SBSB SB Sb Single queen colony Multiple queen colony Only small differences:Young age + Purifying selection because of ♂ haploidy •Prediction: Differences between SB and Sb? •genes? Region contains 800 genes! no strong differences Sb is degenerating?
- 59. Summary Fire ant Solenopsis invicta queen number determined by 1990s Gp-9 marker: •only BB workers ➔ single BB queen •with Bb workers ➔ multiple Bb queens Genome sequencing + RAD Genotyping >500 individuals •Gp-9 marks ~4% of genome ➔ social chromosomes: SB is like X; Sb is likeY >5 Structural differences between SB and Sb ➔ no recombination Ants are cool. Differentiation: Sb has (almost) no diversity (likeY) Differences are homogeneously distributed (no strata)
- 60. Formica selysi Purcell et al 2014 Convergent social chromosome architecture J Meunier Single queen form Multiple queen form Alpine silver ant Common ancestor with fire ant: 130 MYA
- 61. ≠ social chromosomes Purcell et al 2014 Solenopsis invicta social chromosome Formica selysi social chromosome
- 62. Social chromosome "supergenes" also for other major social transitions?
- 64. Research themes • Biomedical approaches • International population genomics surveys • Monitoring via sequencing • Major social transitions » social chromosomes » convergence » eusociality, queen number, parasitism... • Phenotypic plasticity • Strengths of selection • Candidate genes/pathway Pollinator health Genome evolution Social evolution
- 65. Pollinator health • Canonical Pesticide approval process. • Better: behaviour for everything • Our plan 1: RNAseq • Our plan II: Impact of pesticide exposure in the wild • Predict: evidence of positive selection on pesticide resistance alleles Joe Colgan with Richard Gill & Andres Acre @ Imperial
- 66. Modern Bioinformatics for Evolutionary Genomics • Reproducibility • Accuracy • Sustainability • Versioning • Open source • Agile & efficient data handling Our tools: https://wurmlab.github.io/tools •Sequenceserver: BLAST made easy •GeneValidator: Gene model quality visualization •oSwitch: One-line switch to any operating-system (e.g. biolinux) •BioNode: streaming scalable bioinformatics •Afra: crowd-sourcing gene model curation to students github in progress •Flo: transferring gene predictions between genome versions
- 67. y.wurm@qmul.ac.uk @yannick__ https://wurmlab.github.io @ Queen Mary U London Rodrigo Pracana Anurag Priyam @yeban Eckart Stolle Bruno Vieira @bmpvieira R Nichols & sbcsEvolve R Christie & T King / ITSR Apocrita Laurent Keller lab @ Lausanne J Wang, D Shoemaker,O Riba-Grognuz, M Nipitwattanaphon Ioannis Xenarios @ SIB DeWayne Shoemaker @ USDA Thanks!