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...

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...

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 Are the Latest Sign of Our Spiritual Disintegration As 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...

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:

I am excited to share our latest paper, Uniform bacterial genetic diversity along the gut, now out in Nature Communications! www.nature.com/articles/s41.... (1/n)

Genotype-fitness mapping of adaptive mutants reveals shifting low-dimensional structure across divergent environments Predicting the effect of a genetic mutation on fitness is a major challenge in evolutionary biology. This study uses fitness effects of a large collection of adaptive yeast mutants in multiple lab env...

Really excited that this major work from my PhD is finally published in @plosbiology.org ! In it, we were trying to tackle a fundamental question in evolution - how do genetic mutations map onto evolutionary fitness? (1/n)
journals.plos.org/plosbiology/...

Selection-driven color variation in the aposematic strawberry poison frog, Oophaga pumilio Aguilar-Gómez et al. use exome sequencing of 347 strawberry poison frogs to uncover the genetic basis of color variation. They identify that kit, ttc39b, and bco1 underlie blue-red, yellow-red, and gr...

The last chapter of my PhD is finally out !!!! In the same species, on neighboring islands, we see radically different warning colors emerge. Evolution in action:
Selection-driven color variation in the aposematic strawberry poison frog, Oophaga pumilio: Current Biology www.cell.com/current-biol...

Congrats Diana!!

And guess what’s on the cover of Current Biology today 🐸

In the lab, antibiotics can make integrated viruses (prophages) pop out of bacterial genomes. In this (short!) preprint, we asked a simple question: how much does this happen outside the lab, in the human gut?

TLDR: Not much overall, in specific bacterial species.
🧵

www.biorxiv.org/content/10.6...

NEE Focus issue on "Evolution in medicine", including a comment article from @alisonfeder.bsky.social and me.

Capturing dynamic phage–pathogen coevolution by clinical surveillance @nature.com @ucberkeleyofficial.bsky.social
www.nature.com/articles/s41...

Amy Goldberg, PhD - Join The Goldberg lab is moving to UCLA summer 2025, and recruiting postdocs and graduate students. We are a computational lab with occasional wet lab or field collaborators. We will be located in the Depa...

The Goldberg lab at UCLA is hiring one or more postdocs. Flexible start date.

We develop methods to study population genetics of humans, our primate relatives, and our pathogens.

www.goldberglab.org/join

Parallel evolution of industrial melanism in the peppered moth: one locus, many alleles www.biorxiv.org/content/10.64898/2026.02...

Epistasis and co-adaptation in bacterial genome evolution Nature Reviews Genetics - Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic...

I’ve spent a lot of time over the past two years thinking about genome evolution and how recent research revealing complex gene-gene interactions has complicated traditional ‘gene-centric’ genomic approaches to evolution. So here is a review that consolidates these thoughts!

rdcu.be/e6pHY

Environmental exposure trains the immune system to dampen allergic responses Clean living conditions that lessen exposure to microorganisms are linked to an increase in allergies. Mouse data reveal how the environment affects allergic immune responses.

The most influential explanation of a recent surge in allergies is the hygiene hypothesis

go.nature.com/40woBkB

AI Keeps Failing at Microbiome Prediction Why simple models keep winning, where deep learning still shines, and where the field is headed

AI has huge promise for genomics -- but it has consistently failed at microbiome-based prediction.

My new post on why simple models keep winning, where deep learning actually earns its place, and where the field is headed

blekhman.substack.com/p/ai-keeps-f...

An historic black and white illustration of a paper nautilus floating on the ocean. There are boats, a city and hills in the background.

🎉 Huge news for BHL: The Field Museum is taking over the hosting of BHL’s website, servers & infrastructure, ensuring long-term stability and access for its 63+ million pages of open biodiversity literature. Learn more:
blog.biodiversitylibrary.org/2026/02/tran...
#BHLTransition #ILoveBHL 🌍 📚 🧪

Now published: our work using phylodynamics from surveillance data to quantify and experimentally validate the fitness impact of antibiotic resistance determinants & how this changes with patterns of antibiotic use: www.nature.com/articles/s41...

🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here:
www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)

Opinion | The Human Cost of Trump’s War on Science

Deep, well sourced, moving, and enraging story from the NYT

[Gift Link]

www.nytimes.com/2026/02/23/o...

Davis Summer Population Genomics Program Want to learn population genetics? Please fill out this form to indicate your potential interest in a 2-week intensive online summer population genetics course taught by Jeffrey Ross-Ibarra and Graham...

Fun news! @gcbias.bsky.social and I are teaching a 2-week online population genetics workshop this summer to raise money for the Center for Population Biology at UC Davis. We're trying to gauge interest -- please fill this out if you might be interested! And please share broadly!

Go to bed; tired is stupid.

Donate to Help bring 2-Year-Old Chloe and Her Father Home, organized by Jason Chavez-Cruz On January 22, 2026, Chloe who is 2 years of age, and Elvis who is h… Jason Chavez-Cruz needs your support for Help bring 2-Year-Old Chloe and Her Father Home

gofund.me/f20fd809d

Statement from Michael and Susan Pretti Parents of Alex Jeffrey Pretti “We are heartbroken but also very angry. Alex was a kindhearted soul who cared deeply for his family and friends and also the American veterans whom he cared for as an ICU nurse at the Minneapolis VA hospital. Alex wanted to make a difference in this world. Unfortunately, he will not be with us to see his impact. I do not throw around the ‘hero’ term lightly. However, his last thought and act was to protect a woman. The sickening lies told about our son by the administration are reprehensible and disgusting. Alex is clearly not holding a gun when attacked by Trump’s murdering and cowardly ICE thugs. He had his phone in his right hand and his empty left hand is raised above his head while trying to protect the woman ICE just pushed down, all while being pepper sprayed. Please get the truth out about our son. He was a good man. Thank you.

Kare 11 local news just read, in full, this statement from Michael and Susan Pretti, the parents of Alex Pretti.

"Please get the truth out about our son."

Genetic Data From Over 20,000 U.S. Children Misused for ‘Race Science’

An excellent, bone-chilling story about a cadre of online racists who stole genetic data from studies on children so they could make specious arguments for the innate inferiority of non-white people, it's embrace by Elon Musk/twitter & how the Trump administration might make it easier to do again.

Tomorrow's front page of the Minnesota Star Tribune: Jan. 24, 2026

A related study from Nandita’s group on gene-specific sweeps - a great idea to compare non-synonymous linkage disequilibrium (LD) vs synonymous LD! Gut microbiome show pervasive selective sweeps in carbohydrate metabolism - diet adaptation! #microsky #microbiomesky 🧪🦠
www.nature.com/articles/s41...

Representation in genetic studies affects inference about genetic architecture Knowledge of a trait's "genetic architecture," namely the joint distribution of allele frequencies of causal variants and the direction and magnitude of their effects, is essential to understanding it...

Excited to share our new preprint from the @arbelharpak.bsky.social Lab!

How do recruitment into genetic studies and study characteristics impact what we infer about the genetic bases of traits, and what are the consequences? (1/21)

www.biorxiv.org/content/10.6...

Rare variation in malaria parasites biases population-genetic inference Understanding how pathogens evolve is fundamental to disease control and is a basic question in evolutionary biology, yet pathogens with complex life cycles violate assumptions of classic evolutionary...

New preprint! and my first single-author paper, so bear with me.
www.biorxiv.org/content/10.6...

Malaria population genetic studies have found some puzzling patterns: Ne estimates spanning orders of magnitude, genome-wide negative Tajima's D, and over a quarter of genes with πN/πS >1

1/n