PI: Seth M. Bybee
Evaluation of how well the academic objectives of the proposal were met
The proposal had three main aims: 1). Examine the evolution of opsins across dragonflies and damselflies (Odonata) using transcriptomics. 2). CT-scan the internal morphology of extant and fossil taxa and 3). Build expertise in bioinformatics and create computational tools from data generated in aims I & II.
Goals one and three were both very successful (more below), however goal two became bogged down and was ultimately abandoned. CT-scanning is a process that requires hundreds or even thousands of fine x-rays through an organism in cross-section to be “stacked” together. Stacking the x-rays together allows researchers to literally explore the internal and external anatomy of organisms in ways never before possible. The most successful scans are those produced when tissues are discrete and have different attributes in terms of pattern, hardness, etc. We focused heavily on fossil specimens embedded in amber. Unfortunately, the cuticle of these specimens were not sufficiently different in hardness, etc. from the amber they were embedded in and the result was not usable for our goals. Additionally, the expertise to run the programs to trace the scans was difficult for students to learn who worked only a few hours in the lab. We had not anticipated this problem prior to MEG funding since we had had good luck with it in the past. It may have been a mismatch in student interests and project. We will try this goal again in the future when we have a student more passionate about internal anatomy and CT-scans of multiple specimens so that there will be a more comparative option. Still, we were able to publish a paper involving goal two, but it did not include any BYU undergraduates as co-authors.
As mentioned goals one and three were quite successful! We also changed goal two to focus on smaller phylogenetic questions in three genera of Odonata (Hetaerina, Anax, and Ischnura) to benefit students. Each goal has been met at the highest level with publication and/or national meeting attendance resulting from the MEG funding.
Goal 1: We recently saw our first publication from this research (Suvorov et al., 2016). The research demonstrated how opsins, the proteins in the eye of all animals including humans that detect color, have evolved. It included three graduate co-authors and one undergraduate student that was heavily mentored by the graduate students and Bybee.
Goal 2: As mentioned we changed this goal to focus on the phylogeny of several odonate genera using both molecular and morphological data. Phylogenies for Hetaerina and Anax were presented at national meetings and are approaching publication. The Hetaerina project in particular has become an international effort with institutions from Columbia and Mexico as well as others from the US such as UCLA and Rutgers getting involved. The phylogeny of Ischnura is also progressing toward publication but to date has yet to be presented at any meetings. That should change this coming year.
Goal 3: As part of the analyses required to support Goals 1 and 2, my lab has written several programs. Each of these was published in peer-reviewed journals in the past two years and included BYU students, both undergraduates and graduate students.
Evaluation of the mentoring environment
I measure the success of the mentored environment on student success in terms of academic products (meeting attendance, grants, publications, etc.). Each student below has achieved at a high level, showing that the mentoring environment is working well. Further, something that is less measurable is the impact that this research has on aspects of the BYU student experience (spiritually strengthening, character building and service). Several of my students have gone onto serve mission, one even choosing a mission over a fellowship to graduate school. The research we do in our lab helps students confront touchy topics such as the relationship of science and religion. Specifically, students in my lab are constantly working in the field of Evolutionary Biology. As they work and see the evidence for evolution in the organisms they work with, at both the molecular and the anatomical levels, it is a natural way for them to consider how to reconcile their research with LDS doctrine on religion. It is also an excellent chance for me as a mentor to discuss the neutrality of LDS doctrine towards evolution. Character building is one of the aspects that I think my research develops most in students. As they take on their own research project they are required to push if forward. This requires them to read, write and develop ownership of the project. It is fun to watch students develop from timid, uncertain scientists into actual scholars of the subject matter. The service portion is harder to measure however each of my students is part of a team and it is satisfying to see them each use their strengths to push each others’ projects forward.
List of students who participated & academic deliverable
In addition to the tree main goals listed above, there was a goal to include six total students in this research and produce some sort of academic outcome. We have exceeded this goal in every way.
Preston Arnold – Senior author on publication, 4 meeting presentations, now on a fellowship for MD/PhD program at Texas A&M
Nick Jensen – Co-Authored three publications (see below), now serving Mission in England 3
Taylor King – Two presentations at national meetings, one publication in prep. Recently accepted to the University of Utah medical school.
Rebecca Clement – Two presentations at national meetings, currently applying to for graduate work in insect evolution.
Samantha Smith – One presentation at national meetings, currently applying to for graduate work in insect evolution.
David Morris – Presented at two national meetings, now in a masters program at LSU
Mitchel Young – Contributed to tools developed as part of objective 3. Will present results of research this coming year.
Owen “Bryn” Decker – Contributed to tools developed as part of objective 3, transferred to UVU.
Tiffany Blake – Worked briefly on data generation before leaving for a mission to the Philippines.
Description of the results/findings of the project
For all citations below, U = Undergraduate, G = Gradaute student and P = Postdoc co-authors mentored at least in part in the Bybee lab.
GSuvorov, A., N.O. JensenU, M.S. FujimotoG, P. Bodily, H.M. Cahill WightmanG, C.R. SharkeyP, T.H. Ogden, M.J. Clement, S.M. Bybee. Opsins have evolved under the permanent heterozygote model: insights from phylotranscriptomics of Odonata Molecular Ecology. Published online early
GFujimoto, S.M., A. SuvorovG, N.O. JensenU, M.J. Clement, Q. Snell and S.M. Bybee. 2016. The OGCleaner: filtering false-positive homology clusters. Bioinformatics. Published online early
UArnold, P.R., N.P. LordP, A.N. SmithG, S.M. Bybee. 2016. The effects of non-ideal temperature regimes on RNA quality from samples stored in RNAlater: an attempt to replicate field conditions. Journal of Analytical and Molecular Techniques. 2(1). 8
GFujimoto, M.S. A. SuvorovG, N.O. JensenU, M.J. Clement, S.M. Bybee. 2016. Detecting false positive sequence homology: a machine learning approach. BMC Bioinformatics. 17: 101
Bybee, S.M., K.D. Dijkstra, V. Kalkman, H. WightmanG, D. MorrisU, K. K. JohnsonU. An Updated Phylogeny of Odonata: Thinking forward to define, approach, and solve the current problems in odonate higher-level phylogeny. Molecular Phylogenetics & Evolution. Manuscript form
UClement, R., UP. Arnold, S.M. Bybee. (July 2016). Phylogeny of Anax, a preliminary attempt. Dragonfly Society of America Meetings, Provo, UT.
USmith, S. UClement, R., S.M. Bybee. (July 2016). Discovering the phylogeny of rubyspot damselflies. Dragonfly Society of America Meetings, Provo, UT.
UArnold, P., T. KingU, S.M. Bybee. (Nov. 2015) Phylogeny of Anax with special attention to the common green darner (Anax junius). Annual Meeting of the Entomological Society of America, Minneapolis, MN.
UKing, T., P. ArnoldU, Y. PachecoU, P. Pessacq, S.M. Bybee. (Nov. 2015) A population-level study of Cyanallagma (Odonata: Coenagrionidae) in Patagonia utilizing EPIC DNA sequence markers. Annual Meeting of the Entomological Society of America, Minneapolis, MN.
UArnold, P.R., N.P. LordP, S.M. Bybee. (Nov. 2014) Jewels in the rough: A first molecular phylogeny of the charismatic beetle family Buprestidae. Annual Meeting of the Entomological Society of America, Portland, OR.
GWightman, H.C., A. SuvorovG, S.M. Bybee. (Nov. 2014). The phylogeny of Odonata: An update. Annual Meeting of the Entomological Society of America, Portland, OR.
Description of how the budget was spent
The funding provided by ORCA was combined with NSF funds to support lab supplies, travel, and student salaries.