I’m excited to share our new preprint, where we ask: to what extent can evolution in fluctuating environments be predicted? Spoiler: far more than the strong history-dependence of fitness would suggest! www.biorxiv.org/content/10.6...

Order invariance of fitness makes evolution predictable despite strong history-dependent effects

Environmental change is ubiquitous in nature, yet understanding its effect on the predictability of evolution remains a challenge. Previous work in microbes has shown that growth and fitness in a part...

biorxiv.org

Comments due tomorrow (Oct. 13) on a proposed change to NIH procedures that would conceal expert reviewer scores on grant proposals from program officers & PIs and reduce the effectiveness of peer review, part of a larger project to sideline experts and politicize federal funding decisions. 👇

Joshua Weitz@joshuasweitz.bsky.social · last wk.

The NIH proposal to conceal reviewer scores from program officers, investigators, and advisory councils is ill-conceived, introduces disproportionate weight to small percentile differences, diminishes the role of scientific peer review, and should be withdrawn in its entirety. a 🧵

When is on-person evolution dominated by neutral vs adaptive forces? If you're looking for a postdoc position and this is a question that interests you, please see my lab website and reach out! [More info in next posts]

My final postdoc project is out today in Nature! We show microbes co-migrated with humans out of Africa; three independent methods agree, and timing matches archaeological / genetic evidence (Fig. 4c). Seeing Fig. 4c for 1st time was one of my most memorable "eureka" moments! doi.org/10.1038/s415...

Prehistoric global migration of vanishing gut microbes with humans - Nature

Microbial species disappearing from industrialized populations have evolved with humans over millennia and migrated worldwide with them—this may have consequences for human health.

doi.org

Fantastic outgoing third year Cambridge Genetics student Chris Leung has turned his prize-winning project on ARG methods for DNA viruses into a preprint www.biorxiv.org/content/10.6... @aylwyn-scally.bsky.social & I welcome your feedback.

Statistical inference of virus evolution using ancestral recombination graphs

Ancestral recombination graphs (ARGs) represent the coalescent history at every locus in the genome, subject to mutation and recombination. Modelling viruses using the coalescent with recombination re...

biorxiv.org

New Perspective w/ @petrovadmitri.bsky.social and Paul Schmidt! We ask what evolution-in-action studies tell us about an old question: what genetic variation matters for fitness, and what maintains it? ecoevorxiv.org/repository/v...

I am hiring a postdoc! Are you interested to work on population genetics/ drug resistance/ data? Want to work in Montpellier, France? Fastq files don't scare you? PhD required, start date hopefully Nov 1! (end date Sep 30 2028) Please share! abetterscientist.wordpress.com/2026/09/29/p...

Postdoc position on drug resistance evolution in Montpellier, France

I have some exciting news (again!). I got money from the region (Occitanie) to hire a postdoc (and later an engineer / technician) to work on drug resistance evolution in malaria (P. faciparum) and…

abetterscientist.wordpress.com

Four days ago, a scientist was surprised by the news that Anthropic discovered new virus genes for making DNA. He says he’s been studying them for years—and feeding his data to Anthropic’s AI as part of his own research. Coincidence? Here’s my story. nyti.ms/3VSWayc

Did Anthropic’s A.I. Really Make a Scientific Discovery on Its Own? (Gift Article)

An expert at the University of Copenhagen said his team had been sharing its research with the company’s A.I. model, Claude, and that its new finding matched their work.

nyti.ms

New paper with my postdoc advisor @wcratcliff.bsky.social. I love his creativity in putting together this video to summarize the work. Happy we had the chance to collaborate with each other!

Will Ratcliff@wcratcliff.bsky.social · 3w ago

New paper out with @kaylastoy.bsky.social: academic.oup.com/evlett/advan...

I’m looking to hire an NIH funded postdoc to join our lab here at Davis (please RT). Ongoing areas of interest include: 1) polygenic signals of selection from time series, ARGs, GWAS, etc 2) The interpretation of GWAS, polygenic scores, & sources of confounding

Here are 3 minutes of unedited sanderling joy from right before sunset tonight 🥹 🪶

Excited for @gabrielesgarlata.bsky.social’s new preprint on the Genome-Wide Effect of Drift and Selection over a Single Generation 1/n www.biorxiv.org/content/10.6...

The Genome-Wide Effect of Drift and Selection over a Single Generation

The relative importance of genetic drift versus selection to evolutionary change has long been debated. This debate has mainly focused over long-time-scales (e.g. hundreds of thousands of generations)...

biorxiv.org

The latent simplicity of microbial ecological interactions https://www.biorxiv.org/content/10.64898/2026.07.30.741683v1

A few months ago, @elena-romero.bsky.social published a paper showing that HIV escape from broadly neutralizing antibody 10-1074 is driven by very recurrent mutation. In her latest, she asks - just how soft are the signatures of these sweeps? www.biorxiv.org/content/10.6...

Haplotype and diversity signatures of ultra-soft selective sweeps in HIV-1

Many urgent medical and agricultural challenges are driven by resistance evolution via soft selective sweeps of multiple simultaneous mutations. Standard approaches to detect these mutations involve g...

biorxiv.org

Dear microbiome enthusiasts: I'm excited to be moving my lab to New York University this fall (& the NYU Institute for Engineering Health); with joint-appointment @isbscience.org I'm hiring a postdoc @ NYU to look at diet-driven evolution in the gut: apply.interfolio.com/189980 Please share! 🦠🤓

Interested in joining a growing lab in LA? We’re hiring a postdoc!! Please spread the word to folks in your network and feel free to get in touch with any questions recruit.apo.ucla.edu/JPF11142

Super excited to share new work with my advisor @nanditagarud.bsky.social! We re-examine the rapidity of adaptation in the human gut microbiome and begin to characterize the adaptive architecture of selective sweeps spreading across human guts. www.biorxiv.org/content/10... 1/n:

Complex adaptive architectures constrain the pace of adaptations sweeping across human gut microbiomes

Recent work has shown that commensal gut bacteria can evolve rapidly within hosts on short timescales of days to months, fueled by the enormous mutational input generated daily in the microbiome. Yet ...

biorxiv.org

We're excited to share our work on how prophages influence the evolution of resistance against DNA-damaging antibiotics! This has been a fun project with @sianowen.bsky.social, @baym.lol, @theshreyaspai.bsky.social, @kepatitis-c.bsky.social, & @fernpizza.bsky.social biorxiv.org/content/10.6... 1/

SOS-mediated prophage induction constrains resistance evolution to DNA-damaging antibiotics

Most naturally occurring bacteria are lysogens, encoding one or more temperate phages (prophages) integrated into their genome. As prophages are induced by the bacterial SOS response, DNA-damaging ant...

biorxiv.org

Spent the last two years developing a new Intro to Physics course for undergrad biology majors. It features tons of examples from biology (especially Ecology & Evolution!) and requires only middle school-level math. Lecture note here shorturl.at/0PiVp Any comments or feedback are highly welcome!

Just start writing. My new post: substack.com/home/post/p-...

New preprint from the last portion of my PhD! Despite low masked load, we found evidence for strong inbreeding depression in Devils Hole pupfish. The reason? A recessive lethal haplotype that causes a heart defect among developing embryos. www.biorxiv.org/content/10.6...

Long-term small effective population size, inbreeding, and a recessive lethal haplotype drive premature death in the endangered Devils Hole pupfish (Cyprinodon diabolis)

As anthropogenic habitat fragmentation and population decline accelerate globally, growing numbers of species face compounding demographic and genetic threats to long-term survival. Many populations a...

biorxiv.org

Our latest preprint, led by PhD student Jacob Cavon, is online: "Multivariate determinants of wearable-measured sleep quality across a large observational cohort: roles of physical activity, gut microbiome, blood analytes, and lifestyle factors." 🦠😴🏃⚕️ www.medrxiv.org/content/10.6... 🧵...

Multivariate determinants of wearable-measured sleep quality across a large observational cohort: roles of physical activity, gut microbiome, blood analytes, and lifestyle factors.

Emerging evidence links the gut microbiome to sleep quality, yet measuring sleep at scale remains challenging. Commercial wearables, such as Fitbit, capture objective sleep and activity data in natura...

medrxiv.org

First real post on the new blog! If you follow human genetics, you've likely of "missing heritability". If you look at twins to estimate heritability, you get values much larger than what molecular genomic methods produce. IQ, for example, goes from 50-80% heritability to 10-15%. Which is right?

Scoop: There has been a massive shakeup at the US National Institute of Allergy and Infectious Diseases (NIAID). Eight of the top ten officials have now been pushed out since President Donald Trump took office. In @nature.com www.nature.com/articles/d41...

Exclusive: NIH ousts infectious-disease leaders as COVID scientists face US charges

Eight of the top ten officials at the US National Institute of Allergy and Infectious Diseases have now been pushed out since President Donald Trump took office.

nature.com

📣 Our lab is recruiting postdocs to lead new fully funded projects on mechanisms of microbiome–gut–brain signaling & microbial regulation of brain–body interactions in disease, w supportive clinical collaborators. Expertise in gut–brain, systems neuro, or neuroimmunology preferred. Please email 📧

1/23 New preprint! Been thinking about the origin of cellular life. Specifically, how protocells (or *any* compartments) just aren't enough to support the evolution of increasingly complex cells. You gotta de-Darwinize the parts! The ribosome/genome do this. www.biorxiv.org/content/10.6...

Our paper entitled "The persistence and loss of hard selective sweeps amid admixture in ancient Eurasians" is now out in PNAS! www.pnas.org/doi/abs/10.1.... A really fun and informative collaboration with @mharris.bsky.social, Ziyi Mo and Adam Siepel. (1/n)

The persistence and loss of hard selective sweeps amid admixture in ancient Eurasians | PNAS

The extent to which human adaptations have persisted throughout history despite strong eroding demographic events such as admixture, genetic drift,...

pnas.org

Thrilled to have my first PhD paper with @mmdesai.bsky.social out! @science.org Link: www.science.org/doi/10.1126/... Thread below: #mevosky #evosky #evobio #popgen #evolsky #ecoevo #molevol

Sex decreases the pleiotropic costs of local adaptation by purging hitchhiking load

Understanding the evolutionary mechanisms that maintain sex despite its direct costs is a long-standing challenge. Previous work has shown that sexual recombination can accelerate adaptation, in part ...

science.org

Shreyas Pai@theshreyaspai.bsky.social · 2y ago

Why is sex so common if it's so costly? Super excited to share our new preprint “Sex decreases the pleiotropic costs of local adaptation”, where we bring a new angle to this age-old evolutionary question. Co-led by Parris Humphrey, in Michael Desai's lab. Short thread here: (1/n)

Transposable elements are driving rapid adaptation of Enterococcus faecium -in @nature.com from Ami Bhatt www.nature.com/articles/s41...

Transposable elements are driving rapid adaptation of Enterococcus faecium - Nature

Over three decades, rapid expansion of the transposable element ISL3 has reshaped Enterococcus faecium, which helps to explain this pathogen’s growing clinical threat.

nature.com

We've known the gut-brain axis is a key underpinning of Parkinson's disease. Today, for the 1st time, a gut microbiome signature denoting risk found in healthy individuals with genetic predisposition nature.com/articles/s41...

Microbiome signature of Parkinson’s disease in healthy and genetically at-risk individuals - Nature Medicine

Microbiome analysis suggests that gut microbial changes in Parkinson’s disease evolve progressively from healthy individuals to genetically at-risk individuals to clinically affected patients, with th...

nature.com