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Jake Barber

@jakenbarber.bsky.social

310 followers 170 following 15 posts

Evolutionary Biologist Postdoc with Alejandro Couce @ UPM, Spain Using Experimental Evolution to look at mutational biases in bacteria! Formerly of Mike McDonald @ http://mcdonald-lab.com Research Gate Profile: https://t.co/xhw63knBCj

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Jake Barber @jakenbarber.bsky.social · Jun 20

New pre-print is finally out! This is the first project from my postdoc with Alejandro Couce, looking at how mutation-bias influences adaptation across large population sizes, and how this may have real world consequences. Really happy with how this turned out :)

www.biorxiv.org/content/10.1...

www.biorxiv.org

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Reposted by Jake Barber

C. Brandon Ogbunu @cbo.bsky.social · 1d

www.pnas.org/doi/10.1073/...

In vivo directed evolution of an ultrafast Rubisco from a semianaerobic environment imparts oxygen resistance | PNAS

Carbon dioxide (CO2) assimilation by the enzyme Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) underpins biomass accumulation in photosy...

www.pnas.org

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Reposted by Jake Barber

Ákos T Kovács @evolvedbiofilm.bsky.social · 1d

Metabolic interplay drives population cycles in a cross-feeding microbial community

@natcomms.nature.com from @oventurelli2.bsky.social

www.nature.com/articles/s41...

Metabolic interplay drives population cycles in a cross-feeding microbial community - Nature Communications

Here the authors leverage a crossfeeding, engineered microbial community to demonstrate that strain abundance cycles are robust across environmental conditions. They pair this with a nonlinear dynamic model to elucidate population cycles.

www.nature.com

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Reposted by Jake Barber

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 2d

Pseudomonas aeruginosa lasR is a keystone gene in polymicrobial cultures https://www.biorxiv.org/content/10.1101/2025.10.06.680631v1

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🔬🌱 CBGP | Centro de Biotecnología y Genómica de Plantas @cbgpmadrid.bsky.social · 3d

#PaperCBGP 🆕📰‼️

Can we predict which bacteria will turn into #superbugs? 🦠

A study led by Dr. Alejandro Couce and published in PLoS Genetics (@plos.org) shows that a single DNA change can open “bridges” to modern resistances.

🔗 Read more here: https://shorturl.at/TRRwD

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🔬🌱 CBGP | Centro de Biotecnología y Genómica de Plantas @cbgpmadrid.bsky.social · 6d

#PaperCBGP 🆕📰‼️

🧬 Led by Alejandro Couce, researchers of the CBGP used experimental evolution to predict how the superbug enzyme KPC-2 could outsmart antibiotics

⚔️The study, published at @natecoevo.nature.com, lets us block it and protect our antibiotics

📎 shorturl.at/F7oOa

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Reposted by Jake Barber

Jeremy BOO! Yoder 🎃💀🕷️ @jbyoder.org · 8d

So this came online over the weekend: My dive into the "definition" of coevolution is online ahead of publication in @journal-evo.bsky.social!

Don’t ask "when is it coevolution?" — ask "how?"

doi.org/10.1093/evol...

Don’t ask “when is it coevolution?” — ask “how?”

Abstract. Coevolution has come to be widely understood as specific, simultaneous, reciprocal adaptation by pairs of interacting species. This strict-sense

doi.org

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Reposted by Jake Barber

Michael Brockhurst @brockhurstlab.bsky.social · 12d

Now peer-reviewed, improved and published in @microbiologysociety.org Microbiology - thanks to editor and reviewers!

www.microbiologyresearch.org/content/jour...

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Reposted by Jake Barber

Zamin Iqbal @zaminiqbal.bsky.social · 13d

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
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Ricard Solé @ricardsole.bsky.social · Jun 12

How can we build a general theory of mutualistic communities? After five years, we finally completed a new Neutral Theory of Cooperation that is fully solved analytically and displays remarkable properties @jordipinero.bsky.social @artemyte.bsky.social @manlius.bsky.social arxiv.org/abs/2506.09737

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Reposted by Jake Barber

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 15d

Mutation bias is a key predictor of adaptation rate https://www.biorxiv.org/content/10.1101/2025.09.22.677663v1

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Rike Stelkens @stelkens.bsky.social · 20d

We have a new paper out in Molecular Ecology, led by @devinbendixsen.bsky.social ! Reproductive isolation due to divergent ecological selection is accompanied by vast genomic instability in experimentally evolved yeast populations onlinelibrary.wiley.com/doi/10.1111/...

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Vaughn Cooper @vscooper.micropopbio.org · 21d

New in Evolution:
Historical effects during experimental evolution of multicellularity in Saccharomyces cerevisiae,
by Joleen Khey and Mike Travisano
academic.oup.com/evolut/artic...

Validate User

academic.oup.com

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Reposted by Jake Barber

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 22d

Ecological diversification in rapidly evolving populations https://www.biorxiv.org/content/10.1101/2025.09.15.676408v1

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Joanna Masel @joannamasel.bsky.social · 22d

Our new paper @asn-amnat.bsky.social develops a Grand Unified Theory including both exploitative and interference competition doi.org/10.1086/737628. The R* rule of ecology (that 2 species cannot coexist on a single resource), is widely broken, including via a new trade-off we describe. 1/9

A Mechanistically Integrated Model of Exploitative and Interference Competition over a Single Resource Produces Widespread Coexistence | The American Naturalist

Abstract Many ecological models treat exploitative competition in isolation from interference competition. Corresponding theory centers around the R* rule, according to which consumers that share a si...

doi.org

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Reposted by Jake Barber

Calum Gabbutt @calumgabbutt.bsky.social · 28d

Cancer is an evolutionary disease, but does knowing a cancer’s evolutionary past help predict its future? Out today in @nature, we learnt the evolution of 2000 lymphoid cancers and found it was highly correlated with clinical outcomes! (1/7)
rdcu.be/eFrrc

Fluctuating DNA methylation tracks cancer evolution at clinical scale

Nature - Cancer evolutionary dynamics are quantitatively inferred using a method, EVOFLUx, applied to fluctuating DNA methylation.

rdcu.be

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Reposted by Jake Barber

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 26d

Parallel but distinct adaptive routes in the budding and fission yeasts after 10,000 generations of experimental evolution https://www.biorxiv.org/content/10.1101/2025.09.11.675703v1

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Reposted by Jake Barber

Nature @nature.com · Sep 5

Nature research paper: Commensal yeast promotes Salmonella Typhimurium virulence

go.nature.com/4mTnRzG

Commensal yeast promotes Salmonella Typhimurium virulence - Nature

Commensal Candida albicans enhances the virulence and dissemination of Salmonella enterica subsp. enterica serovar Typhimurium.

go.nature.com

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Reposted by Jake Barber

Bryan Gitschlag @bryangitschlag.bsky.social · Sep 8

NEW PAPER! Some kinds of genetic mutations are more likely to arise than others. Such "biases" in mutation vary between species.

Analyzing data from 14 species, we show that this variation explains species differences in the genetics of adaptation!

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www.biorxiv.org/content/10.1...

Graph showing a positive correlation between "bias in adaptive outcome" on the vertical axis and "mutation bias" on the horizontal axis, with 14 data points representing 14 respective species, with a line of best fit equal to a slope of 0.82 on the log-scale axes. Each data point contains horizontal and vertical error bars to illustrate the uncertainty in both the mutational and adaptive data. The 95% confidence interval of the slope is shown in parentheses (0.44 to 1.24), based on 10,000 simulated data sets, where the simulated data sets are based on statistical resampling of the empirical data (i.e. "bootstrap" data sets). Regression lines based on these bootstrap data sets are shown as light gray lines.

The type of bias reported here refers to the ratio of transitions versus transversions, where transitions are a DNA mutation that preserves the basic structure of the DNA base (i.e. a purine-to-purine or pyrimidine-to-pyrimidine mutation), and transversions are mutations that alter the structure of the DNA base at a particular site (i.e. replacing a purine with a pyrimidine or vice versa). In other words, this graph shows that transitions contribute more toward adaptive evolution in species where transitions arise at a higher rate.

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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Sep 8

Mutational Biases and Selection in Mitochondrial Genomes: Insights from a Comparative Analysis of Natural and Experimental Populations of Caenorhabditis elegans https://www.biorxiv.org/content/10.1101/2025.09.03.674070v1

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Alexandra Dallaire @alexdallaire.bsky.social · Sep 3

I’m super happy to present the first discoveries of the RIKEN-Cambridge Joint Crop Symbiosis Research Team, based in Japan 🇯🇵

doi.org/10.1101/2025...

A thread 👇

Reductive evolution of the DNA replication machinery in endosymbiotic fungi

The molecular machinery for replicating and repairing DNA accurately is critically important for life and highly conserved across the Tree of Life. Here we show that two major lineages of fungi, Glome...

doi.org

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Reposted by Jake Barber

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Sep 6

Molecular adaptation reflects taxon-specific mutational biases https://www.biorxiv.org/content/10.1101/2025.09.03.674101v1

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Judith Behnsen @judith-behnsen.bsky.social · Sep 3

Excited to share our new publication, out today in Nature! www.nature.com/articles/s41.... @kanchanj.bsky.social led this fascinating fungal-bacterial interaction project. We are grateful for our wonderful collaborators Brian Peters and David Underhill.

Commensal yeast promotes Salmonella Typhimurium virulence - Nature

Commensal Candida albicans enhances the virulence and dissemination of Salmonella enterica subsp. enterica serovar Typhimurium.

www.nature.com

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Reposted by Jake Barber

Sam von der Dunk @derdunk.bsky.social · Sep 1

Excited with two new preprints on evolution of molecular structure, in RNA (doi.org/10.1101/2025..., @n-martin.bsky.social) and proteins (doi.org/10.1101/2025...). Both RNA and protein structures are often conserved across evolution, but the underlying reasons are very different.

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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Sep 1

Natural protein structures have evolved exceptional robustness to mutations https://www.biorxiv.org/content/10.1101/2025.08.27.672565v1

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Vivek Mutalik @vivekmutalik.bsky.social · Aug 31

Coevolutionary phage training expands phage host range: Driven by tail fiber mutations in Pseudomonas aeruginosa lytic phage?

#phage #phagesky #mevosky

www.sciencedirect.com/science/arti...

Coevolutionary phage training expands phage host range: Driven by tail fiber mutations in Pseudomonas aeruginosa lytic phage?

The rise of antibiotic-resistant bacteria, particularly multidrug-resistant Pseudomonas aeruginosa (P. aeruginosa), represents a critical challenge to…

www.sciencedirect.com

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