Watching an arms race one lineage at a time

The work: High-resolution lineage tracking of phage–bacterial evolution. In preparation — I’ll link the preprint here when it’s out.

Who Wins the Early Race? Phage vs. Bacteria

During COVID, we all learned to watch a curve. Cases rose and fell, and then variants arrived with names like Alpha, Delta, and Omicron. Each name stood for a viral family line that outcompeted the others while the immunity of the people it infected kept shifting. It was an evolutionary arms race playing out in real time.

Even then, we mostly saw one side clearly. We could read the virus’s genetic code and spot new variants, but tracking the other side, the changing defenses of a whole population, lineage by lineage, was far harder.

Bacteria and the viruses that infect them, called phages, run the same kind of race, only faster and in a test tube. That lets us do something you can’t do in a human pandemic: give every player a name tag. We tagged the bacteria with about 5K unique DNA barcodes and the phages with about 60K. Because barcodes are inherited, each one lets us follow a single family line as it grows, shrinks, or vanishes.

Instead of two curves on a graph, we get a family tree of the whole fight, built as it happens rather than pieced together after the winners are known. So who wins the early race?

The arms race: steps and sweeps

A burst, then a crash

In the first few days, something surprising happened. The phages showed an incredible burst of diversity, with thousands of tiny genetic “tribes” popping up almost overnight, each finding its own clever way to thrive. But within days, most of them crashed and disappeared, leaving a handful of standout winners to take over the whole population.

The bacteria played a very different game. Instead of one dramatic burst, they showed a steady churn, with lineages rising and falling in a tug-of-war that lasted the entire month. The phages sprinted, and the bacteria settled in for a marathon.

A hidden demolition derby

On Day 2, it appeared that nearly every phage lineage had won the lottery. Tens of thousands of distinct lineages surged at once, each with a big fitness advantage. But this wasn’t tens of thousands of separate success stories. It was tens of thousands of lineages piling into the same narrow doorway at the same time, all trying to exploit the same opportunity, and only a tiny handful could fit through.

The rest of the story is coming soon…