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Real-time Phylogenomics: Joe Parker

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General science talk about the potential of real-time phylogenomics, delivered at the Jodrell Lecture Theatre, Kew Gardens, November 2nd 2015

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Real-time Phylogenomics: Joe Parker

  1. 1. Real-time phylogenomics Towards continuous analysis of environmental DNA
  2. 2. The Comparative Method
  3. 3. Images – Wikimedia commons CC BY-SA (clockwise from top left: Jeroen Rouwkema, @aGastya, author’s own, @RE73)
  4. 4. spectrum.ieee.orgIllumina.comflickr/stephenjjohnson Wikimedia commons CC BY-SA @Plindembaum NCBI (1985) ~1,000,000 base pairs NCBI (2015) 199,823,644,287 base pairs Wikimedia commons CC BY-SA @GSorby
  5. 5. Phylogenetics  Phylogenomics Stewart et al. (1987): 5 species 1 gene 130 amino acids 2 phylogenies doi:10.1038/330401a0 Parker et al. (2013): 22 species 2,326 genes 600,000 amino acids (~700,000,000 simulated) 14 test phylogenies 100 control phylogenies doi:10.1038/nature12511
  6. 6. Informatics & evolution VL 4 length Avg. neut VL 1 length ≤ 34 ≤ 27 > 27 > 34 Poor neut Broad neut
  7. 7. Steve Rossiter Georgia Tsagkogeorgia, James Cotton, Kalina Davies, Christopher Walker, Mahesh Pancholi
  8. 8. Phylogenetic incongruence
  9. 9. Phylogenetic incongruence
  10. 10. Real-time phylogenomics If collection and sequencing take hours or days, why do analysis and dissemination take months or years?
  11. 11. (demo)
  12. 12. Images – Wikimedia commons CC BY-SA (clockwise from top left: Jeroen Rouwkema, @Nelsonramirezdearellano, author’s own, @soerfm)
  13. 13. Implications of ubiquitous sequencing in real-time
  14. 14. Real-time phylogenomics Informatics: Field-based sequencing Real-time analyses Asynchronous computation Phylogenomics: Metrics on ‘tree space’ Relaxing orthology Neutral models of genomic evolution
  15. 15. Mechanisms of genomic evolution Gene family evolution Homeologues Horizontal transfer Aggregated genomic distributions of sitewise phenomena
  16. 16. Plant and Fungal Trees of Life (PAFTOL) • 2020 Output • Genus-level phylogenies inferred from genetic data for plants and fungi • You can help
  17. 17. Thanks – joe.parker@kew.org BI&SA: Abigail Barker, Rob Turner, John Iacona, James Crowe PAFTOL: Bill Baker, Delivery Group, Steering Group QMUL: Steve Rossiter, Kalina Davies, Georgia Tsagkogeorga WIMM/NDM: Guillaume Stewart-Jones, Emma Bowles SSI Fellowship • Software Sustainability Institute-funded hackathon series • Community building
  18. 18. Implications of ubiquitous sequencing in real-time

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