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

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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

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

physics_for_biologists.pdf

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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

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

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

biorxiv.org

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

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

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

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

The fitness costs of reproductive specialization scale inversely with organismal size

pnas.org

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...

chrismurphyct.com

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...

journals.plos.org

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...

cell.com

Species-specific prophage induction by ciprofloxacin in human gut metagenomes

Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction and whether it is associated with antibiotic exposure. Across two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in specific bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut. Importance Bacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses its host to release new viral particles. In the lysogenic cycle, the phage, now called a prophage, integrates its genome into that of its host without killing it. Prophages can switch to the lytic cycle in a process called induction, in which the viral genome is replicated, the host cell is lysed, and viral particles are released. The most immediate consequence of induction is host cell death which can impact bacterial populations and communities. Since prophages are mobile genetic elements that can move between bacteria, they are also an important vehicle for horizontal gene transfer. While induction has been well studied in vitro , whether and how induction occurs within the complex microbial ecosystem in humans is less well characterized. Understanding prophage induction in vivo is therefore critical in corroborating in vitro observations. ### Competing Interest Statement The authors have declared no competing interest. NIH Common Fund, https://ror.org/001d55x84 Natural Sciences and Engineering Research Council

biorxiv.org

Context dependency is essential for predicting intrahost evolution - Nature Ecology & Evolution

The ability to predict rapid evolutionary processes within our bodies would advance both medical science and evolutionary biology. We discuss technologies that move us towards intrahost evolutionary p...

nature.com

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...

goldberglab.org