Real-time phylogenomics

Towards continuous analysis of environmental DNA

The Comparative Method

Images – Wikimedia commons CC BY-SA (clockwise from top left: Jeroen Rouwkema, @aGastya, author’s own, @RE73)

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

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

Informatics & evolutionVL 4 length

Avg. neut

VL 1 length

≤ 34

≤ 27

> 27

> 34

Poor neut

Broad neut

Steve RossiterGeorgia Tsagkogeorgia,

James Cotton, Kalina Davies, Christopher

Walker, Mahesh Pancholi

Phylogenetic incongruence

Phylogenetic incongruence

Real-time phylogenomics

If collection and sequencing take hours or days, why do analysis and dissemination take months or years?

(demo)

Images – Wikimedia commons CC BY-SA (clockwise from top left: Jeroen Rouwkema, @Nelsonramirezdearellano, author’s own, @soerfm)

Implications of ubiquitous

sequencing in real-time

Real-time phylogenomicsInformatics:

Field-based sequencing

Real-time analysesAsynchronouscomputation

Phylogenomics:

Metrics on ‘tree space’

Relaxing orthologyNeutral models ofgenomic evolution

Mechanisms of genomic evolution

Gene family evolution

Homeologues

Horizontal transfer

Aggregated genomic distributions of

sitewise phenomena

Plant and Fungal Trees of Life (PAFTOL)

• 2020 Output• Genus-level

phylogenies inferred from genetic data for plants and fungi

• You can help

Thanks – joe.parker@kew.orgBI&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

Implications of ubiquitous

sequencing in real-time