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What do you expect evolution to look like in a microbial population? Check out our new study offering a view of that over 1000 generations in yeast in the lab. co-led by
@alex_nguyen_ba,@jireva, in@MichaelMDesai 's labhttps://www.nature.com/articles/s41586-019-1749-3 …Show this threadThanks. Twitter will use this to make your timeline better. UndoUndo -
Ivana Cvijovic Retweeted
Excited to announce a new preprint w/
@MortezaRoodgar on the ecological and evolutionary responses of the human gut microbiome during antibiotic treatment. https://www.biorxiv.org/content/10.1101/2019.12.21.886093v1?rss=1 …. A lot of surprises in here for me -- will post a longer summary after the holidays.Thanks. Twitter will use this to make your timeline better. UndoUndo -
Ivana Cvijovic Retweeted
Our approach generates high-resolution maps of
#AAV capsid sequence space, illuminating how capsids work and how to make them better. Here’s a visualization showing tolerance to substitutions (red:beneficial, white:neutral, blue:deleterious, this view isn't even in the paper!)pic.twitter.com/nWUekmzoKPShow this threadThanks. Twitter will use this to make your timeline better. UndoUndo -
Ivana Cvijovic Retweeted
This week on the Nature cover: Waves of mutation. Barcode system images evolutionary dynamics of laboratory yeast. Browse the issue here: https://go.nature.com/336w2ip pic.twitter.com/pe16RxYmiG
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Ivana Cvijovic Retweeted
A renewable barcoding system reveals the evolutionary dynamics of laboratory budding yeast, showing that fitness changes over time in a travelling wave of adaptation that can fluctuate owing to leapfrogging events, according to a Nature paper. https://go.nature.com/32NssJG pic.twitter.com/KH1aRQ68yS
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Ivana Cvijovic Retweeted
Here's a thread telling the story of our new technique for genetic recording of lineage history during long term evolution experiments. The work was co-led with
@alex_nguyen_ba and@ivana_cvijovic in@MichaelMDesai's lab. Read the paper here:http://nature.com/articles/s41586-019-1749-3 …Show this threadThanks. Twitter will use this to make your timeline better. UndoUndo -
Ivana Cvijovic Retweeted
Wonderful stuff! For those wondering about leapfrog, here's where Phil Gerrish & I introduced the idea: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.372.6402&rep=rep1&type=pdf … See Fig 7 for simple illustration, in which successively dominant genotypes may -- or not, in case of leapfrog -- represent sequential substitutions.
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But it also exists in a limit that we don't currently have a good quantitative description for. Instead of proceeding smoothly, the wave exhibits large fluctuations as mutations cause clones to continuously leapfrog over each other!
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We see that the population carries dozens of competing beneficial mutations, and that it forms a sort of 'traveling wave' if you look at its distribution of fitness. This agrees with theoretical predictions.
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I then developed an approach to use this lineage frequency data to reconstruct the clonal structure of the population and to detect individual beneficial mutations.
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By sequencing this genetic locus over time, we can measure the fractions of the population in different barcoded lineages.
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@alex_nguyen_ba and@jireva developed a remarkable new approach to continuously re-introduce enormous numbers of DNA barcodes into an evolving yeast population, one right next to the other in the genome.Show this threadThanks. Twitter will use this to make your timeline better. UndoUndo -
But it has been difficult to observe the majority of those mutations: theory had predicted that most would be lost before reaching fractions of the population detectable by available methods.
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We've known for the past couple of decades that many microbial populations adapt in an incredibly dynamic way, with large numbers of beneficial mutations continuously arising and competing.
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Ivana Cvijovic Retweeted
We have an open post-doc position in the lab! Core current interests are recombination/reassortment/HGT in microbial evolution, but we can get excited about other questions as well. Please share! https://neherlab.org/201910_BZ_postdoc.html …pic.twitter.com/tHqeE0Xt72
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Ivana Cvijovic Retweeted
Our Tn-Seq paper with
@_miloj, Alena Martsul and@MichaelMDesai is out in@sciencemagazine. https://science.sciencemag.org/content/366/6464/490 … Accompanied by a nice perspective by Craig Miller with a cool fitness landscape: https://science.sciencemag.org/content/366/6464/418 … Here is my original summary: https://twitter.com/skryazhi/status/1141821852047704064?s=20 …pic.twitter.com/Lu00tyqYUR
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Ivana Cvijovic Retweeted
Our work is out on
#bioRxiv! Check out how we altered substrate selectivity of an ABC transporter. Collaboration of@RachelleGaudet and@EvolvingMurray.https://www.biorxiv.org/content/10.1101/797100v1 …Thanks. Twitter will use this to make your timeline better. UndoUndo -
Ivana Cvijovic Retweeted
How do T cells access many spatial scales in vivo? Excited to share our results in my first
#zebrafish preprint, with Stephen Quake: https://www.biorxiv.org/content/10.1101/785964v1 … Comments from all communities welcome and with many thanks to#mblzebrafish 2017.Thanks. Twitter will use this to make your timeline better. UndoUndo -
Ivana Cvijovic Retweeted
How does the local neighborhood of mutations change across the combinatorially sprawling expanse of the fitness landscape? To find out, we did lots of yeast xformations and thunderdome all-v-all competitions (w/
@MichaelMDesai,@skryazhi, Alena Martsul): https://www.biorxiv.org/content/10.1101/675314v1 …pic.twitter.com/paMIY0CEJ1
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Ivana Cvijovic Retweeted
Distinguishing multiple-merger from Kingman coalescence using two-site frequency spectra http://biorxiv.org/cgi/content/short/461517v1 …
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