So, my research question basically asks if the north-coastal red alders (normal distribution north of central Oregon) are genetically distinct from south-coastal red alders (normal distribution south of central Oregon), and if so, which of the two groups parented the scattered red alder colonies far away in Idaho. We already thought that there would be some difference between the coastal alders because of a study in the 1990's that found some differences using restriction enzymes, but our methods are much more sophisticated now.
When going through my sequences last week and correcting some of the error the computer sometimes makes in gaps, I made an interesting discovery; roughly half of my samples had an absolutely enormous insertion; 15 nucleotides long, which is a huge mutation. I sat there and marked which ones had it and which didn't, and drew a crude map to better visualize it. Here's what I found.
The ancestral condition (without the mutation) is found in my two California groups I've sequences so far: Fort Bragg and the redwoods. The derived state (with the mutation) is north of that. It's in Cannon Beach, Long Beach, Shoreline, Bellingham, Port Hardy, and Haida Gwaii. However, the samples from Forks were ancestral. That part of the state was not covered by glaciers during the last glacial maximum and must have been a refugium. I don't know why it wasn't recolonized with the new mutation as the red alders moved back north, following the glacial retreat. Maybe because they're wind-pollenated and wind-dispersed, and it's hard to move against a prevailing west wind from the ocean.
But here's the other interesting thing: when looking at the Idaho samples to see if they had the ancestral or derived condition (thereby telling if they were part of an ancient pre-Cascadian inland forest, or had colonized from the north or south coast), I found that they were both. Half my Clearwater samples were derived and half ancestral, and 1 of my 4 samples from Lake Pend Orielle were ancestral.
This means one of two things. Either Idaho was colonized twice...once from the south over the central Oregon Highlands, and once from the north over the Okanagan Highlands, or Idaho has had red alders since before the Cascades rose and created a rain shadow (ancestral state), and the new breed of red alders migrated over from the coast more recently, and they're still mixing.
I am fascinated. I'm very excited to add more information from my other sample sites. I haven't sequenced my central Oregon samples yet (where the division will be), nor the Jenner samples (near San Fran) or the Nanaimo or Prince Rupert samples. I also have samples from the Lochsa River and the Umatilla National Forest (went there yesterday with Tyler), so there's still much to do...but the early results are very very good.