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. Real-time phylogenomics Towards continuous analysis of environmental DNA
- 3. Images – Wikimedia commons CC BY-SA (clockwise from top left: Jeroen Rouwkema, @aGastya, author’s own, @RE73)
- 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. 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. Informatics & evolution VL 4 length Avg. neut VL 1 length ≤ 34 ≤ 27 > 27 > 34 Poor neut Broad neut
- 7. Steve Rossiter Georgia Tsagkogeorgia, James Cotton, Kalina Davies, Christopher Walker, Mahesh Pancholi
- 10. Real-time phylogenomics If collection and sequencing take hours or days, why do analysis and dissemination take months or years?
- 11. (demo)
- 12. Images – Wikimedia commons CC BY-SA (clockwise from top left: Jeroen Rouwkema, @Nelsonramirezdearellano, author’s own, @soerfm)
- 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. Mechanisms of genomic evolution Gene family evolution Homeologues Horizontal transfer Aggregated genomic distributions of sitewise phenomena
- 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. 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
Notes de l'éditeur
- Sequence data will become ubiquitous, as compouters are now -much of it available real-time and collected by non-experts Exploiting this requires informatics Talk about virus stuff relate progress to HIV seq compendium ebola monitoring programme
- Why we are interested in evolution etc Evolutionary biology mechanisms as well as facts
- My central thesis is that comparative analyses of evolutionary processes using genetic data must be statistical… … only informatics approaches let us do this properly… … in the very near future all of us will be comparative statistical evolutionary genomicists, or Phylogenomics bods BGI leader Jun Wang and others (mick watson) have even suggested even that AI is needed
- Genbank doubling ~18monthly (2007) ENA doubling ~10monthly My central thesis is that comparative analyses of evolutionary processes using genetic data must be statistical… … only informatics approaches let us do this properly… … in the very near future all of us will be comparative statistical evolutionary genomicists, or Phylogenomics bods Total holdings: As of 15 August 2015, GenBank release 209.0 has 187,066,846 loci, 199,823,644,287 bases, from 187,066,846 reported sequences.[3] Like going from the 7 books pictured to nearly a million…
- My evidence for showing phylogenetics phylogenomics? Some past work Showing how informatics enables statistical application of the comparative method to biological questions --- Basis of our method Two convergence hypotheses Large numbers of loci, including sensory Simulated sites Random control tree correction 22 mammals, 2326 loci, ~600,000 sites Convergence signals across genome? Loci linked to sensory perception?
- My evidence for showing phylogenetics phylogenomics? Some past work Showing how informatics enables statistical application of the comparative method to biological questions
- The phylogenies
- OK that’s the ‘genomics’ bit covered. Now the ‘real time’ bit Analysing, as fast as sequencing, in the field / real-time Science fiction? The MinION Iterative analysis key to doing better science, not just more Place natural variation into context Reduce ascertainment bias, increase taxon discovery Make use of cloud resources and get phylogenetics into the field
- DEMO 0) delete extra reads in m/raw Start metrichor + workflow (1-D MAP 005) “app store” Start RRA and tidy windows “prototype” Copy reads from pooled -> raw “simulate” Cross fingers
- Microscope? Is ‘camera’ more apt? From a specialised unwieldy device to commercialised one with thousands of users, app store, magazines, forums etc Where will we be in 2020? 20205? My central thesis is that comparative analyses of evolutionary processes using genetic data must be statistical… … only informatics approaches let us do this properly… … in the very near future all of us will be comparative statistical evolutionary genomicists, or Phylogenomics bods BGI leader Jun Wang and others (mick watson) have even suggested even that AI is needed
- future work – implications of the RTP / MinION and fellows Real-time phylogenomics and the minion for monitoring, turbotaxonomy / ID Applications, use cases Whacky theoretical stuff
- OK that’s the ‘genomics’ bit covered. Now the ‘real time’ bit Analysing, as fast as sequencing, in the field / real-time Science fiction? The MinION Iterative analysis key to doing better science, not just more Place natural variation into context Reduce ascertainment bias, increase taxon discovery Make use of cloud resources and get phylogenetics into the field
- Of course I think the tools are cool but I’m a scientist not a tech for a reason By which we mean evolution on genomes and their landscape/architecture: gene family evolution, homology/paralogy/orthology horizontal transfer non independence of sitewise processes (fourier etc)
- What it is Genus level phylogenies dynamically (automatically, continuously) inferred from genomic data Challenges ∫A LOT of data needed Implications of ubiquitous sequencing Data deluge My WP How you can help, tissue etc now minIONs with you in a few years?
- Thank people involved so far
- future work – implications of the RTP / MinION and fellows Real-time phylogenomics and the minion for monitoring, turbotaxonomy / ID Applications, use cases Whacky theoretical stuff