Calibrating the molecular clock for Oncorynchus clarki (cutthroat trout) in the Clearwater River, western Washington

Landscapes and the biota that inhabit them co-evolve. They both change over time, partly in response to one another. The primary forces driving landscape evolution are tectonics, climate, rock type and living organisms. Biological evolution is the result of more-or-less random genetic mutations (which influences an individuals traits) and non-random environmental selection processes (which determine whether or not those traits...and for that matter, those genes...are beneficial or detrimental to the survival of that organism).

Most of the genetic mutations that occur are a result of errors in copying DNA. Because this error rate is fairly constant for a given species, we can use the genetic disparity among populations to determine the length of time the populations have been isolated from one another.

In the Clearwater River basin, we have a special circumstance where we know the amount of time by which two small populations of Oncorynchus clarki (cutthroat trout) have been isolated from the main-stem population. The populations have been isolated in two tributaries to the Clearwater by waterfalls, as pictured to the left, for ~ 125,000 years. Knowing the time interval of physical isolation, we can calculate the rate at which genetic mutations accrue in this species. This can be used to calibrate the genetic mutation rate for this species, which allows us to study genetic divergence of isolated cutthroat trout species in other locations to constrain the time at which the population was isolated. This can be important for understanding the evolution of the species or constraining the age of the geologic feature that caused the isolation (e.g. a waterfall or landslide dam etc).

We are using two molecular techniques to constrain the mutation rate (AFLPs and mitochondrial DNA). Amplified Fragment Length Polymorphisms (AFLPs) assess the frequency of mutations that have occurred in genomic DNA. Analysis of mutations accrued in mitochondrial DNA provides an opportunity to replicate the experiment because the mitochondrial genome has a separate evolutionary origin and is directly passed down through the maternal line (so there is no inter-parental gene recombination like we observe in nuclear DNA).