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

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...

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…

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.

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)...

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...

The extent to which adaptation to environmental change occurs via single or multiple advantageous mutations remains an open question, which we examined by studying the spread of melanic forms of the p...

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...

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 ...

Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...

Bacteria acquire adaptive mutations during infections, but the role of mutations in the gut microbiome is unknown. Zhao and Lieberman et al. report that Bacteroides fragilis adapts via mutation within...

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 ...

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...

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...

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...

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.

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

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 ...

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

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...

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...

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...

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...

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

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...