Профиль

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-1Many 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...www.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

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 antibioticsMost 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...www.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...www.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 chargesEight 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.www.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 | PNASThe extent to which human adaptations have persisted throughout history despite strong eroding demographic events such as admixture, genetic drift,...www.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 loadUnderstanding 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 ...www.science.org

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

1/25 New paper out in PNAS! We show that the fitness costs of reproductive specialization, where somatic cells give up reproduction, scale inversely with organism size. Larger organisms can afford far more soma, removing a key barrier to multicellular complexity.

New preprint! We sequenced 175 'Alalā (Hawaiian crow) genomes to understand why >50% of eggs fail to hatch in a species recovered from just 9 individuals. What we found was a both exciting and surprising. www.biorxiv.org/content/10.6...

Prediction markets aren't just corrupt. They are a sign of our nation's spiritual atrophy - as every moral question became commodified and wagering becomes a growing source of meaning and purpose. My latest substack:

Prediction Markets Are the Latest Sign of Our Spiritual DisintegrationAs I write this, hundreds of millions of dollars’ worth of bets have been placed on Polymarket, the massive prediction marketplace, regarding how many people will die in the Iran War over the next sev...www.chrismurphyct.com