By Angela, Jan 31 2017 04:22PM
I have inadvertently neglected this blog a bit, but I'm alive and doing well! It's been a crazy couple of months since I last posted. I've been in a flurry of analyzing data and writing my dissertation and applying for jobs. Everything is coming along and I'm excited about my work and looking forward to finding a job and taking on whatever the future holds. I thought I would post a quick list of updates and some news. I have an enormous list of things on my to-do list before I defend in April (and a big pile of coffee at home to match it!), but here are a few things that have been going on since my last post.
In November I presented my findings about a new species Mark and I named last year, Matelea hirtelliflora, at the annual Oklahoma Academy of Sciences technical meeting. It was a fun meeting and a good place to share 'local' work. Matelea hirtelliflora is apparently endemic to NE Texas, so it's not been found in Oklahoma (yet!). The talk was well-received and even won an award, so that really fun and I was happy to spread the "milkeed gospel".
I (finally) submitted a manuscript about Gonolobinae systematics that includes data from four chloroplast and three nuclear regions. It was kind of a beast of a paper for me since it represents a tremendous amount of work but not a ton of data (relatively speaking!). The paper includes lots of topology tests using the estimated gene trees to see what support for critical nodes there is in the data and also makes comments about how this affects taxonomy of the lineage. I also included a species tree estimated for Gonolobinae as well as a supertree estimate of Apocynaceae and a reconstruction of growth form evolution on both the species tree of Gonolobinae as well as the supertree estimate of Apocynaceae.
My friend Wyatt came to visit our lab over the holiday break and I helped him prepare 48 libraries for his dissertation research on Ayenia (Malvaceae). It went well and was a great success! I hear the libraries are pooled and will likely be sequenced any day now.
Finally, I'd like to note here that plastome finishing is a non-trivial task. I thought assembly and analysis of the hundreds of nuclear regions I gathered data for would surely be the most difficult to sort through and assemble. The good news is that the nuclear data isn't so bad to make sense of (thanks, HybPiper!). However, I have been surprised by the plastome data. Reference-guided assembly seems to misassemble or miss completely regions that are divergent while de novo assembly methods can spit out an entire plastome that is all kinds of out of order (thanks, circular molecules with repeats!) and requires a bunch of editing.
Off to finish a few more plastomes!