My latest in @plosbiology.org Look I get it, it seems really dark, but there are opportunities. My paper explores some ideas and tries to guide ways of thinking through the anticipated challenges. An emphasis on America’s “biohubs” and entrepreneurship journals.plos.org/plosbiology/...

A recent study of an mRNA vaccine in a mouse model of 𝘊𝘭𝘰𝘴𝘵𝘳𝘪𝘥𝘪𝘰𝘪𝘥𝘦𝘴 𝘥𝘪𝘧𝘧𝘪𝘤𝘪𝘭𝘦 infection provided proof of concept of a protective effect. Learn more: nej.md/4kS8x5X @umich.edu #MedSky #IDSky

Here's my interview with @stevenstrogatz.com on @quantamagazine.bsky.social's Joy of Why podcast. This was *so much fun*. I was nervous going into it (I really look up to Steve!), but I had a blast and I think this is the best interview I have ever done. Thanks for having me on, folks!

Quanta Magazine@quantamagazine.org · last yr.

In the history of evolution, multicellularity has evolved independently at least 50 times. But we’ve only figured that out in the past few decades. Listen to the first episode of the new season of “The Joy of Why” with hosts @stevenstrogatz.com and Janna Levin. www.quantamagazine.org/how-did-mult...

I’m thrilled to share my first ever publication, now published in PNAS! www.pnas.org/doi/10.1073/... With mentorship from the amazing @ksxue.bsky.social, I looked at how the outcomes of species introductions to microbial communities are influenced by the number of introduced microbes.

Delighted to share a major update on our work investigating age-related deceleration in clonal haematopoiesis. Takehome: Widespread and substantial deceleration in fitness with age! Amazing effort by PhD student Hamish MacGregor 💪 www.biorxiv.org/content/10.1...

I am glad to see this work in print & on the cover! Read more at academic.oup.com/genetics/article/228/3/iyae145/7747749

Fascinating work showing genome-wide DNA packaging into phage capsids in "normie" gut bacteria!

@colinhillucc.bsky.social · 2y ago

First post on a lovely story from the lab that shows that Faecalibacterium prausnitzii can package its own genome in bite-size segments in phage-like capsids www.biorxiv.org/content/10.1...

We usually think of genetic drift as the predominant stochastic force in evolving populations. But working with some model microbial populations, we found a distinct source of demographic stochasticity that scales (and behaves) differently than drift Learn more in our new paper 👉 rdcu.be/d07Np

Asynchronous abundance fluctuations can drive giant genotype frequency fluctuations

Nature Ecology & Evolution - Based on a combination of experiments and modelling, this study shows large stochastic fluctuations in genotype frequencies caused by intrinsic and extrinsic...

rdcu.be

Hi friends new and old! I study how microbes interact and evolve in complex communities like the human gut microbiome.🦠🧬💩 I'm thrilled to share that I'm starting a lab at UC Irvine in April 2025 and am recruiting at all levels - please spread the word! kxuelab.com More about my work below...🧵1/n

Xue lab at UC Irvine

Ecology and evolution in the human gut microbiome

kxuelab.com

Our paper on allele frequency transitions under polygenic selection, with a focus on evolve & resequence experiments, is up at Genetics. Led by grad student Nathan Anderson: urldefense.com/v3/__https:/...

A path integral approach for allele frequency dynamics under polygenic selection

Abstract. Many phenotypic traits have a polygenic genetic basis, making it challenging to learn their genetic architectures and predict individual phenotyp

urldefense.com

Just posting this to #popgen Here's a link to my notes on population & quantitative genetics: github.com/cooplab/popg... Hoping to extend it more after the winter holidays, as I'm just finishing up teaching the undergrad version of class.

Releases · cooplab/popgen-notes

Population genetics notes. Contribute to cooplab/popgen-notes development by creating an account on GitHub.

github.com

Resharing here a recent X post. In this preprint, we introduce an improved version of NanoSeq, a duplex sequencing protocol with <5 errors per billion bp in single DNA molecules, and use it to study the somatic mutation landscape of oral epithelium in >1000 people. 1/ www.medrxiv.org/content/10.1...

Somatic mutation and selection at epidemiological scale

As we age, many tissues become colonised by microscopic clones carrying somatic driver mutations ([1][1]–[10][2]. Some of these clones represent a first step towards cancer whereas others may contribu...

medrxiv.org

My first theory project! I've really enjoyed how we could decompose complex dynamics into those of individual lineages. This approach is quite flexible, and we're hoping to extend it to more complex scenarios, including N(t) and certain forms of positive selection!

Nastia Lyulina@alyulina.github.io · 2y ago

How do we predict the statistical associations between mutations that spontaneously emerge in an evolving population? Excited to share some new work w/ @zzzhiru.bsky.social and @benjaminhgood.bsky.social that approaches this question!

High-resolution lineage tracking of within-host evolution and strain transmission in a human gut symbiont across ecological scales https://www.biorxiv.org/content/10.1101/2024.02.17.580834v1

High-resolution lineage tracking of within-host evolution and strain transmission in a human gut symbiont across ecological scales https://www.biorxiv.org/content/10.1101/2024.02.17.580834v1

Gut bacteria rapidly evolve in vivo, but their long-term success requires dispersal across hosts. He

biorxiv.org

Excited (and relieved!) to share that my 1st paper in grad school finally came out in PLOS Biology! We were motivated by a very basic question: how fast, really, do bacteria exchange DNA in the human gut? (1/n)

Dynamics of bacterial recombination in the human gut microbiome

Recombination is a ubiquitous force in bacterial evolution, but its dynamics are poorly characterized in many natural populations. This study presents a metagenomic approach for quantifying the landsc...

t.co

Been dreaming of this paper for a decade. 1 PhD and 1 postdoc later, here it is! What do ecology and evolution look like in a 20-year microbiome time series? They blur together @quendi.bsky.social @archaeal.bsky.social @uslter.bsky.social @sarilog.bsky.social 🧪🖥️🧬 www.biorxiv.org/content/10.1...

Bacterial ecology and evolution converge on seasonal and decadal scales

Ecology and evolution are distinct theories, but the short lifespans and large population sizes of microbes allow evolution to unfold along contemporary ecological time scales. To document this in a natural system, we collected a two-decade, 471-metagenome time series from a single site in a freshwater lake, which we refer to as the TYMEFLIES dataset. This massive sampling and sequencing effort resulted in the reconstruction of 30,389 metagenomic-assembled genomes (MAGs) over 50% complete, which dereplicated into 2,855 distinct genomes (>96% nucleotide sequence identity). We found both ecological and evolutionary processes occurred at seasonal time scales. There were recurring annual patterns at the species level in abundances, nucleotide diversities (π), and single nucleotide variant (SNV) profiles for the majority of all taxa. During annual blooms, we observed both higher and lower nucleotide diversity, indicating that both ecological differentiation and competition drove evolutionary dynamics. Overlayed upon seasonal patterns, we observed long-term change in 20% of the species' SNV profiles including gradual changes, step changes, and disturbances followed by resilience. Most abrupt changes occurred in a single species, suggesting evolutionary drivers are highly specific. Nevertheless, seven members of the abundant Nanopelagicaceae family experienced abrupt change in 2012, an unusually hot and dry year. This shift coincided with increased numbers of genes under selection involved in amino acid and nucleic acid metabolism, suggesting fundamental organic nitrogen compounds drive strain differentiation in the most globally abundant freshwater family. Overall, we observed seasonal and decadal trends in both interspecific ecological and intraspecific evolutionary processes. The convergence of microbial ecology and evolution on the same time scales demonstrates that understanding microbiomes requires a new unified approach that views ecology and evolution as a single continuum. ### Competing Interest Statement The authors have declared no competing interest.

biorxiv.org

How stable are bacterial genomes as they adapt to an environment? My collaboration with Anurag Limdi, Alex Couce, @relenski.bsky.social, and Olivier Tenaillon exploring this over 50,000 generations of evolution is out today! 1/ (cross-post from the other place) www.science.org/doi/10.1126/...

Changing fitness effects of mutations through long-term bacterial evolution

Predictable and parallel changes occur in the fitness effects of mutations in Escherichia coli over 50,000 generations.

science.org

Journal fees for open access are becoming obscene. But what are we, scientists, paying for? I made a simple plot with journals in my research area(s). Clearly, we are paying for prestige: a shockingly clean correlation between the impact factor and journal fees

I wanted to highlight this pre-print by David Ho’s group on the neutralizing antibody response to new (XBB.1.5-based) COVID vaccine booster, as it illustrates some points related to paradigm of updating SARS-CoV-2 vaccines to keep pace w viral evolution. www.biorxiv.org/content/10.1...

XBB.1.5 monovalent mRNA vaccine booster elicits robust neutralizing antibodies against emerging SARS...

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

biorxiv.org

New accessibility pilot on bioRxiv pilot: AI-generated paper summaries at 3 levels (general -> expert). Click Automated Services in the dashboard to view these. We welcome feedback. connect.biorxiv.org/news/2023/11...

Seems population immunity should be useful for forecasting flu, right? Using cross-sectional, age-representative neutralizing titers measured in the summer of 2017 in Philly, we find that the clade to which we infer the greatest susceptibility dominated the next season. Even more, we found...

medRxivpreprint@medrxivpreprint.bsky.social · 3y ago

Measures of population immunity can predict the dominant clade of influenza A (H3N2) and reveal age-associated differences in susceptibility and specificity https://www.medrxiv.org/content/10.1101/2023.10.26.23297569v1

Did you think hermit crabs always live in snail shells? 🧪🦀 Some deep sea hermit species live symbiotically with anemones that DISSOLVE the shell and SECRETE a new one ("carcinoecium") made of chitin! The carcinoecium has evolved at least 3 times! Photo credits in alt text. @megdaly.bsky.social

1. Imagine we land a space probe on one of Jupiters’ moons, take up a sample of material, and find it is full of organic molecules. How can we tell whether those molecules are just randomly assembled goo or the outcome of some evolutionary process taking place there? 🧪

Hello world! I have nothing to say yet, but check out these Karman vortices (I think?) in my pour over coffee