Jake Barber
@jakenbarber.bsky.social
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
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
Pinned
Jake Barber
@jakenbarber.bsky.social
· Jun 20
www.biorxiv.org
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/content/10.1...
Reposted by Jake Barber
Another new preprint from former PhD student Daniel Wong (now @ ENS) has been a long time in the making, and builds on our recent efforts to model eco-evolutionary feedbacks in rapidly evolving microbial populations that compete for different resources (1/n)
November 17, 2025 at 2:14 PM
Another new preprint from former PhD student Daniel Wong (now @ ENS) has been a long time in the making, and builds on our recent efforts to model eco-evolutionary feedbacks in rapidly evolving microbial populations that compete for different resources (1/n)
Reposted by Jake Barber
Happy to share our new review on oligonucleotide chemical evolution on early Earth. We discuss how iterative sequence selection and diversification could have shaped RNA pools, facilitating sequence exploration and the emergence of ribozymes.
www.jstage.jst.go.jp/article/biop...
www.jstage.jst.go.jp/article/biop...
Selection–diversification interplay in oligonucleotide chemical evolution
The emergence of catalytic RNAs (ribozymes) may have set the stage for an “RNA world” preceding protein evolution. The probability of ribozyme emergen …
www.jstage.jst.go.jp
November 7, 2025 at 2:27 PM
Happy to share our new review on oligonucleotide chemical evolution on early Earth. We discuss how iterative sequence selection and diversification could have shaped RNA pools, facilitating sequence exploration and the emergence of ribozymes.
www.jstage.jst.go.jp/article/biop...
www.jstage.jst.go.jp/article/biop...
Reposted by Jake Barber
New online! Microbial genomics for antimicrobial resistance ecology and action
Microbial genomics for antimicrobial resistance ecology and action
Nature Reviews Genetics, Published online: 03 November 2025; doi:10.1038/s41576-025-00909-zMicrobial genomics can improve our understanding of antimicrobial resistance dynamics across ecosystems. In this Comment, Kathryn Holt emphasizes the interconnectedness of human, animal and environmental health and calls for greater integration of microbial genomic data through robust analytical frameworks to unravel the complexity of antimicrobial resistance dynamics.
www.nature.com
November 3, 2025 at 1:07 PM
New online! Microbial genomics for antimicrobial resistance ecology and action
Reposted by Jake Barber
Out now at @plosbiology.org we evaluate the potential for antibiotic efflux and cell wall biogenesis as targets for reversing drug resistance and preventing its de novo evolution in Escherichia coli. Link below:
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
Impeding pathways of intrinsic resistance in Escherichia coli confers antibiotic sensitization and resistance proofing
Intrinsic resistance pathways in E. coli can be exploited to enhance antibiotic sensitivity and limit resistance evolution. This study shows that genetic inhibition of efflux pumps and cell envelope b...
journals.plos.org
October 25, 2025 at 1:47 AM
Out now at @plosbiology.org we evaluate the potential for antibiotic efflux and cell wall biogenesis as targets for reversing drug resistance and preventing its de novo evolution in Escherichia coli. Link below:
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
Reposted by Jake Barber
New in JB: Black and Wakeman review the challenges of treating polymicrobial infections in various body sites, a topic near and dear to my heart.
journals.asm.org/doi/10.1128/...
@asm.org #JBacteriology
journals.asm.org/doi/10.1128/...
@asm.org #JBacteriology
October 23, 2025 at 12:20 PM
New in JB: Black and Wakeman review the challenges of treating polymicrobial infections in various body sites, a topic near and dear to my heart.
journals.asm.org/doi/10.1128/...
@asm.org #JBacteriology
journals.asm.org/doi/10.1128/...
@asm.org #JBacteriology
Reposted by Jake Barber
Evolution of One Species Increases Resistance to Invasion in a Simple Synthetic Community
Microbial Ecology
link.springer.com/article/10.1...
Microbial Ecology
link.springer.com/article/10.1...
Evolution of One Species Increases Resistance to Invasion in a Simple Synthetic Community - Microbial Ecology
The species that make up a microbial community determine its potential function. A major goal of microbial ecology is to make assemblages of microbes — synthetic communities — with targeted applicatio...
link.springer.com
October 21, 2025 at 6:11 AM
Evolution of One Species Increases Resistance to Invasion in a Simple Synthetic Community
Microbial Ecology
link.springer.com/article/10.1...
Microbial Ecology
link.springer.com/article/10.1...
Reposted by Jake Barber
A fun little side project I've been working on with @stepadenisov.bsky.social , Mato Lagator, and Andreas Wagner: "Strong promoters are mutationally robust". Briefly...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Strong promoters are mutationally robust
Mutational robustness is the persistence of a phenotype upon mutation. It facilitates molecular evolution and has been characterized in a variety of biological systems, but studies of prokaryotic prom...
www.biorxiv.org
October 21, 2025 at 8:02 AM
A fun little side project I've been working on with @stepadenisov.bsky.social , Mato Lagator, and Andreas Wagner: "Strong promoters are mutationally robust". Briefly...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jake Barber
Massive undertaking with @teppo-h.bsky.social and others out. We studied 4 years (!!!) of synthetic 23 microbial species community evolution with/without antibiotic. Resistance mutations occurring over years led to stepwise restructuring and ultimately recovery of undisturbed community composition.
Evolution induced state shifts in a long-term microbial community experiment www.biorxiv.org/content/10.1...
Evolution induced state shifts in a long-term microbial community experiment
Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain poorly understood. Understanding how Darwinian evoluti...
www.biorxiv.org
October 11, 2025 at 5:00 AM
Massive undertaking with @teppo-h.bsky.social and others out. We studied 4 years (!!!) of synthetic 23 microbial species community evolution with/without antibiotic. Resistance mutations occurring over years led to stepwise restructuring and ultimately recovery of undisturbed community composition.
Reposted by Jake Barber
Reposted by Jake Barber
Metabolic interplay drives population cycles in a cross-feeding microbial community
@natcomms.nature.com from @oventurelli2.bsky.social
www.nature.com/articles/s41...
@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
October 7, 2025 at 7:09 PM
Metabolic interplay drives population cycles in a cross-feeding microbial community
@natcomms.nature.com from @oventurelli2.bsky.social
www.nature.com/articles/s41...
@natcomms.nature.com from @oventurelli2.bsky.social
www.nature.com/articles/s41...
Reposted by Jake Barber
Pseudomonas aeruginosa lasR is a keystone gene in polymicrobial cultures https://www.biorxiv.org/content/10.1101/2025.10.06.680631v1
October 7, 2025 at 5:16 AM
Pseudomonas aeruginosa lasR is a keystone gene in polymicrobial cultures https://www.biorxiv.org/content/10.1101/2025.10.06.680631v1
Reposted by Jake Barber
#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
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
October 5, 2025 at 11:01 AM
#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
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
Reposted by Jake Barber
#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
🧬 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
October 2, 2025 at 8:38 AM
#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
🧬 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
Reposted by Jake Barber
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?"
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
September 30, 2025 at 3:30 PM
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?"
doi.org/10.1093/evol...
Reposted by Jake Barber
Now peer-reviewed, improved and published in @microbiologysociety.org Microbiology - thanks to editor and reviewers!
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
September 26, 2025 at 8:26 AM
Now peer-reviewed, improved and published in @microbiologysociety.org Microbiology - thanks to editor and reviewers!
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
Reposted by Jake Barber
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.
Thread 1/n
Thread 1/n
September 25, 2025 at 9:29 PM
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.
Thread 1/n
Thread 1/n
Reposted by Jake Barber
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
June 12, 2025 at 8:16 PM
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
Reposted by Jake Barber
Mutation bias is a key predictor of adaptation rate https://www.biorxiv.org/content/10.1101/2025.09.22.677663v1
September 24, 2025 at 7:33 AM
Mutation bias is a key predictor of adaptation rate https://www.biorxiv.org/content/10.1101/2025.09.22.677663v1
Reposted by Jake Barber
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/...
September 18, 2025 at 8:56 AM
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/...
Reposted by Jake Barber
New in Evolution:
Historical effects during experimental evolution of multicellularity in Saccharomyces cerevisiae,
by Joleen Khey and Mike Travisano
academic.oup.com/evolut/artic...
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
September 17, 2025 at 8:04 PM
New in Evolution:
Historical effects during experimental evolution of multicellularity in Saccharomyces cerevisiae,
by Joleen Khey and Mike Travisano
academic.oup.com/evolut/artic...
Historical effects during experimental evolution of multicellularity in Saccharomyces cerevisiae,
by Joleen Khey and Mike Travisano
academic.oup.com/evolut/artic...
Reposted by Jake Barber
Ecological diversification in rapidly evolving populations https://www.biorxiv.org/content/10.1101/2025.09.15.676408v1
September 17, 2025 at 6:32 AM
Ecological diversification in rapidly evolving populations https://www.biorxiv.org/content/10.1101/2025.09.15.676408v1
Reposted by Jake Barber
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
September 16, 2025 at 5:33 PM
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
Reposted by Jake Barber
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
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
September 10, 2025 at 4:17 PM
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
rdcu.be/eFrrc
Reposted by Jake Barber
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
September 12, 2025 at 3:32 PM
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
Reposted by Jake Barber
Nature research paper: Commensal yeast promotes Salmonella Typhimurium virulence
go.nature.com/4mTnRzG
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
September 5, 2025 at 3:19 PM
Nature research paper: Commensal yeast promotes Salmonella Typhimurium virulence
go.nature.com/4mTnRzG
go.nature.com/4mTnRzG