Bravery pays off, it seems.
So, based on my talks with Committee Member, things weren't going well. He wanted me to do analyses that my data didn't allow, and then do analyses with data from other studies that didn't even relate to my project. Specifically, to put my genus in the greater phylogenetic context, which I already knew had been well established.
After struggling with it for a while, I did what I should have done right off the bat...a literature review. Right away, I came up with two recent papers that did a phylogenetic analysis of the entire Alnus genus, and another for the entire Betulaceae family. So, here was proof. What he wanted me to do had already been done, far better than I could possibly do it.
And then I had an inspiration. I shared it with Jack the next day. Both of those studies were based on sequence data from the ITS 1 and ITS 2 regions, which are nuclear ribosomal. The sequences I'd been studying for my thesis are from chloroplast loci. How about I extract DNA from every alder species in this region (there's four, counting mine), sequence it at my chloroplast locus, analyze it, and see if I get the same trees as the nuclear data suggest.
And he paused, thought for a moment, and said okay.
So that's what I'm doing now...finishing the sequencing prep on Alnus incana, Alnus sinuata, and Alnus rhombifolia, and then I'll crunch the sequences with Alnus rubra, Alnus japonica, and Betula occidentalis and see how it measures up to nuclear findings. It'll be an interesting aside for my thesis, a good topic for my class project, and possibly an answer to whether nuclear and mitochondrial DNA tell the same story.