Real-time Phylogenomics: Joe Parker
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Transcript of Real-time Phylogenomics: Joe Parker
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Real-time phylogenomics
Towards continuous analysis of environmental DNA
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The Comparative Method
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Images – Wikimedia commons CC BY-SA (clockwise from top left: Jeroen Rouwkema, @aGastya, author’s own, @RE73)
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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
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Phylogenetics Phylogenomics
Stewart et al. (1987):5 species1 gene130 amino acids2 phylogeniesdoi:10.1038/330401a0
Parker et al. (2013):22 species
2,326 genes600,000 amino acids
(~700,000,000 simulated)
14 test phylogenies100 control phylogenies
doi:10.1038/nature12511
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Informatics & evolutionVL 4 length
Avg. neut
VL 1 length
≤ 34
≤ 27
> 27
> 34
Poor neut
Broad neut
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Steve RossiterGeorgia Tsagkogeorgia,
James Cotton, Kalina Davies, Christopher
Walker, Mahesh Pancholi
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Phylogenetic incongruence
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Phylogenetic incongruence
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Real-time phylogenomics
If collection and sequencing take hours or days, why do analysis and dissemination take months or years?
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(demo)
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Images – Wikimedia commons CC BY-SA (clockwise from top left: Jeroen Rouwkema, @Nelsonramirezdearellano, author’s own, @soerfm)
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Implications of ubiquitous
sequencing in real-time
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Real-time phylogenomicsInformatics:
Field-based sequencing
Real-time analysesAsynchronouscomputation
Phylogenomics:
Metrics on ‘tree space’
Relaxing orthologyNeutral models ofgenomic evolution
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Mechanisms of genomic evolution
Gene family evolution
Homeologues
Horizontal transfer
Aggregated genomic distributions of
sitewise phenomena
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Plant and Fungal Trees of Life (PAFTOL)
• 2020 Output• Genus-level
phylogenies inferred from genetic data for plants and fungi
• You can help
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Thanks – [email protected]&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
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Implications of ubiquitous
sequencing in real-time