We previously attempted to sequence the B. vosnesenskii genome using Oxford Nanopore technology...didn't work out so good. Turns out we didn't know what we were doing! So we are trying again, thanks to Janna Fierst's intrepid grad student John Sutton and a few other students in the department who got some actual training on the thing. Things looking MUCH better so far, very good output, nice read length distribution etc! Turns out there are a few useful tricks for DNA isolation quality, etc. that aren't as important for sequencing with Illumina. Hopefully the data turn out to be useful for assembly, as we very much want to be able to align our population genetics data directly to a reference genome for our target species, as opposed to cross-species alignments against available genomes (e.g., Bombus impatiens) which works ok but has some challenges.
Whoa something not about bees! Relatively recent lab alumnus Peter Scott (now a postdoc at UCLA) just published part of his dissertation in Molecular Phylogenetics and Evolution: Resolving taxonomic turbulence and uncovering cryptic diversity in the musk turtles (Sternotherus) using robust demographic modeling. He was also interviewed by NPR's Morning Edition! Take a listen here. Cool! Congrats Peter.
The Lozier, Dillon, and Strange labs are well represented at ESA this year! We will be presenting a number of things over the next week.
Undergrad Clare Ols received an Undergraduate Research and Creative Activity award from the UA College of Arts and Sciences to help fund her sequencing (well, her's, and Charles', and Vanessa's) of COI from our UA Arboretum Bee Biodiversity Survey. Clare has done a lot of work, not only to come out and put out the bee bowls, but processing specimens, sorting, and IDing, so the grant is well-deserved!
Congratulations to Jason, who won best poster at the UA Department of Biology Biofest research poster competition. Gets a nice chunk of change for research or meeting travel!
The bee game also made its debut! Was a pretty big hit, lots of people interested in playing and learning how hard it is to fly at high elevations (including some professors!)
Now, who didn't wake up this morning and think: "I wonder what it would be like to be a bumble bee?". OK, maybe just me. Nonetheless, now you can find out! As part of our NSF mountain bees grant Broader Impacts, my collaborator Michael Dillon and folks at the U Wyoming Biodiversity Institute (thanks Brian Barber and Kyle Summerfield, especially!) devised "Flight of the Bombus" an especially creative interactive video game that illustrates some of the interesting aspects of insect flight, especially the challenges of flight at altitude. I wrote a small grant to the European Society for Evolutionary Biology and got some additional outreach funds to build a version of the game here. Pretty neat eh! We are not entirely sure where this will go long-term, but we intend to bring it out for various events, take it to local schools etc. A pretty creative endeavor! Go Team!
Our collaborator in the Dept, Dr. Janna Fierst, recently purchased a starter kit for the Oxford Nanopore MinION mini-sequencer (the "flash drive" sequencer). She had a flowcell that needed to be used, and we happen to have a bee-nome we want sequenced, so it all worked out! So we'll be collaborating on assembling a new bumble bee genome, put the sample on the sequencer today! This method is great because it can sequence nice long reads and has a super easy library preparation. Once the long reads are done we can then layer on some shotgun sequencing data to increase coverage, correct errors, etc. If this works well, it'll be a game changer for assembling draft genomes. Fingers crossed!
Undergraduate researcher Clare Ols and I have been surveying the University of Alabama Arboretum using bee bowl pan traps for the past 8 months. We have uncovered a remarkable amount of native bee diversity in such a small area. We're currently going through and trying to ID everything, but we're estimating at least 60 species collected thus far.
As the semester starts winding down, we've been having a busy week in the lab.
1) Riley successfully defended her M.S. Thesis!
Congrats Riley! Riley did a great job on her defense talk and committee grilling session to finish up her Master's work on "The Influence of Space, Sex, and Temperature on Morphology of the Kudzu Bug, Megacopta cribraria (Hemiptera:Plataspidae), a Rapidly Expanding Invasive Species". Riley will be continuing on to get a PhD with Jennifer Howeth in the department.
2) Jason got a teaching award
Jason received a teaching excellence award this week at the UA Honor's Week Graduate Honors Convocation for his teaching work in the Biological Sciences! Congratulations to Jason as well!
3) Meaghan, Jason, and I published a new paper on bumble bee color pattern evolution
Meaghan got her first first-authored post doc paper out, and some more of Jason's PhD work contributed to a follow-up paper on Bombus bifarius color pattern population genomics. We use RNAseq (and some RADseq) SNPs to detect signs of selection and identify a possible player in color pattern polymorphism for one of the B. bifarius lineages B. bifarius nearcticus.
Pimsler et al. 2017. Population genomics reveals a candidate gene involved in bumble bee pigmentation. Ecology & Evolution doi:10.1002/ece3.2935
4) I will get to call myself an Associate Professor!
Nature just published my short article reviewing a recent paper by Carvell et al. (2017) that evaluated how habitat quality impacted bumble bee colony survival across the generations. Check it out here!
Lozier, J. Nature http://dx.doi.org/10.1038/nature21897 (2017).
Carvell, C. et al. Nature http://dx.doi.org/10.1038/nature21709 (2017).
The lab threw me a surprise b-day party yesterday at lab meeting, and made me a cake. A bumble-log! All made with bee themed ingredients like almonds, honey, and bee pollinated berries. They also made me a cool personalized calendar with pictures of our field sites! Very nice! Thanks guys!
Lee Roop wrote up a very nice article about our bumble bee research on AL.com. The article also does a nice job of highlighting all the great opportunities for research here at UA. I believe he is planning on doing similar stories about other Alabama scientists as a regular article series, so keep an eye out!
Lozier Lab News
Dispatches from the lab and field!