Miracles can be achieved by mixture modelling of messy data.. Chromopainter/FineSTRUCTURE/Globetrotter.

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Presentation transcript:

Miracles can be achieved by mixture modelling of messy data.. Chromopainter/FineSTRUCTURE/Globetrotter

Mixture modelling of an English palette

How does the information from metagenomics compare with what we would know if we had full genome sequences?

Qizhi Cao, Jianzhong Zhang, China CDC, Xavier Didelot, Imperial College Not quite a metagenomics experiment

18 Helicobacter pylori sequenced from the same biopsy. All of them were different. 2 clades = 2 infections.

Reconstruction of recombination and mutation using ClonalFrame. Years in past Average import size 940bp

Interspersions in recombination events

Functional characterization of recombination events Proportion of genes recombined

Ancestral sequences show interactions between strains in the past And suggest longer mixed infection.

Classical metagenomic questions How many different infections? What proportion of the population does each infection account for? Microevolutionary questions What diversification has each infection undergone? What is the functional effect of diversification? Heroic questions How many infections were there in the past?

Ecological questions Which strains thrive in the same environment? Which strains thrive in the presence of each other? Which strains competitively exclude one another? What determines patterns of „succession“? What determines infection rates by different strains? Ecological genetic questions How do strains adapt to new environments?

Fran Colles, University of Oxford Campylobacter in chickens

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A rapid turnover of Campylobacter STs amongst individual birds Sequence types: Colles et al, Unpublished

Clonal complexes isolated from a broiler breeder flock over time Colles et al, Unpublished

Strains are sampled from a population...

Vibrio parahaemolyticus with Yujun Cui and Ruifu Yang

All the strains in CG1 The strains in CG1+S093 The strains in CG1+S093+CG2 +1 unrelated strain SNP density in 1Kbp windows

Oceanic gene pools

Amongst 53 unrelated strains, strong non-random associations between loci are almost entirely due to close genetic linkage

Not all populations are that simple...

Host-restricted and multihost lineages of C. jejuni

Multihost lineages of C. coli and C. jejuni

Association study Method: Word analysis ST-45 complex

9034 host associated words in ST-45 complex Map to 99 genes in total but 76% of words map to 10 contiguous genes (region 3)