Every fall, salmon swim into Issaquah Creek, lay their eggs, and die. The water carries away their molecular traces: fragments of DNA, short-lived RNA, and chemical marks that change with age, like tree rings. Every week, scientists collected a liter of water and read these traces with a portable device.
At first everything was clear. RNA showed that the fish were alive and active. Marks on the DNA said these were adults. Disease-causing organisms appeared on schedule: first a bacterium, a week after the spawning peak, then a fungus that multiplied on the carcasses.
But then the traces began to spoil. RNA disappeared a few days after the fish died, because it's a fragile molecule. Age marks lasted longer, but they too faded, and then the device started mistaking old fish for young ones. The water seemed to forget how old the salmon had been.
That's why it matters to sample in the first weeks of spawning, while the Freshness Gate is open. Then a single water sample will tell you the species, the age, and the health of the fish. And if you're late, the data will start lying, and no one will notice.
At the peak of salmon carcass decomposition, the oomycete Saprolegnia parasitica accounted for 51.5% of all reads in the water sample. That is, more than half of the DNA in the stream belonged not to fish but to the fungus eating their remains.
Not published on arXiv. Here are its page, the PDF and the formalization: you can check it yourself, not only read our account.