Co-amplification of Mitochondrial Pseudogenes

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Dr. Michael Whiting, Department of Biology

Funding was received from the BYU ORCA mentorship program during 2011 to support undergraduates performing research in my lab, under the mentorship of postdoctoral researchers, graduate students, and myself. During 2011, this funding provided direct support for 6 undergraduates who are in various stages of completing research projects. The following report focuses on undergraduate achievements, but also provides summary data for graduate students and other lab participants.

Review of Academic Objectives of the Proposal

Funding was received from ORCA in 2011 to provide students with the opportunity to work on five projects: (1) co-amplification of mitochondrial pseudogenes, (2) evolution of predation in katydids, (3) mitochondrial genome phylogeny for Orthoptera, (4) 454 sequencing for mt genome reconstruction, and (5) immature and adult associations of aquatic insects in Thailand via DNA bar coding techniques. The proposal submitted in 2011 described 5 team projects that included postdocs, graduate students, and undergraduates. We have already published on two of these projects, and the other projects are on track to be published in 2012. The overarching goal behind the research was to train students and mentor them all the way through the scientific process, from teaching basic lab and computer skills, to experimental design, data generation, analysis, and finally presentation at national meetings and publication in peer reviewed journals. As outlined below, the productivity of the lab as a whole in 2011 was very good (13 manuscripts and 10 presentations), and the productivity of the undergraduates was particularly excellent (authorship on 3 publications and 8 presentations). This past year we made major strides towards accomplishing the research as outlined in the proposal and finally completed the generation of the mt genomes for Orthoptera and made great strides in or 454 work. In addition, we used some of the MEG funds to generate preliminary data that formed the basis of two NSF proposals that were submitted in 2011 and are currently pending, and we plan to submit two more NSF proposals is 2012. If funded, these grants will provide additional research opportunities for undergraduate students.

Evaluation of the Mentoring Environment

In 2011, the mentoring environment of the lab consisted of 6 BYU undergraduates, three graduate students, and two postdocs. We met together in weekly lab meetings, read from the current literature, and reviewed each other’s manuscripts.

Whiting Lab Participants (2011)

  • Michael F. Whiting (PI)
  • Dr. Hojun Song (Postdoctoral Fellow)
  • Dr. Seth Bybee (Postdoctoral Fellow)
  • Joey Mugleston (graduate student)
  • Rebecca Buckmann (graduate student)
  • Katie Fager (graduate student)
  • Jessica Jensen (undergraduate)
  • Kelsy Johnson (undergraduate)
  • James Leavitt (undergraduate)
  • Michael Naegle (undergraduate)
  • Gavin Martin (undergraduate)
  • Matthew Moulton (undergraduate)

Specific Products of the MEG

Research Presentations

Over the past year, my lab group made 10 presentations at scientific meetings. Undergraduates participated as senior author or co-authors on 8 of the presentations, graduate students on 3 presentations. Undergraduates are indicated by blue; graduate students are indicated by red.

  • Leavitt, J. R., K. D. Hiatt, H. Song, and M. F. Whiting. Are past phallic phylogenies of Acridoidea fallacies? Annual Meeting of the Entomological Society of America, Reno, NV, Nov 13-15, 2011.
  • Mugleston, J. D., H. Song, and M. F. Whiting. A molecular phylogeny of the family Tettigoniidae. Annual Meeting of the Entomological Society of America, Reno, NV, Nov 13-15, 2011.
  • Buckman, R. S., and M. F. Whiting. Why thrips are thrilling: phylogenetic relationships among major groups and the evolution of the mitochondrial genome. Annual Meeting of the Entomological Society of America, Reno, NV, Nov 13-15, 2011.
  • Song, H., M. Moulton, and M. F. Whiting. A broad-scale survey of nuclear mitochondrial pseudogenes in Orthoptera (Insecta). Annual Meeting of the Entomological Society of America, Reno, NV, Nov 13-15, 2011.
  • Fager, K., S. M. Bybee, and M. F. Whiting. An investigation of the opsin gene complex in scorpionflies (Mecoptera: Panorpidae). Annual Meeting of the Entomological Society of America, Reno, NV, Nov 13-15, 2011.
  • Johnson, K. K., S. M. Bybee, and M. F. Whiting. The evolution of color vision in dragonflies and damselflies (Odonata). Annual Meeting of the Entomological Society of America, Reno, NV, Nov 13-15, 2011.
  • Naegle, M. A. and M. F. Whiting. Elucidating ectoparasitic earwig evolution. Annual Meeting of the Entomological Society of America, Reno, NV, Nov 13-15, 2011.
  • Martin, G. J., J. Zenger, S. M. Bybee, and M. F. Whiting. Molecular evolution of the visual system in the blind cave beetle (Glacicavicola basthysciodes). Annual Meeting of the Entomological Society of America, Reno, NV, Nov 13-15, 2011.
  • Leavitt, J. R., K. Hiatt, H. Song, and M. F. Whiting. Hopping towards a robust hypothesis: Phylogeny of Caelifera based on entire mitochondrial genomes. Utah Conference on Undergraduate Research, Ogden, UT, Feb 18, 2011.
  • Jensen, J., J. D. Mugleston, K. Hiatt, H. Song, and M. F. Whiting. Deep-level phylogeny of Ensifera (Orthoptera) based on molecular data. Utah Conference on Undergraduate Research, Ogden, UT, Feb 18, 2011.

Publications

During 2011, the Whiting lab group produced 13 manuscripts (5 published or in press; 5 in review; 3 to be submitted shortly). Of these, 3 manuscripts have undergraduate authors, and on 2 of these the undergraduate is the senior author. Six manuscripts have graduate student authors. One publication is particularly noteworthy: the Song et al. (2011) paper with two undergraduate authors is finally in press in Systematic Biology, which is considered a high-impact journal for the field (impact factor 10.77). Undergraduates are indicated by blue; graduate students are indicated by red.

  • Jones, J. R. and M. F. Whiting. 2011 A phylogeny of the panorpid scorpionflies (Mecoptera: Panorpidae) based on molecular evidence, with a comparison to species groups, the anal horn, and wing banding. Manuscript to be submitted to Molecular Phylogenetics and Evolution.
  • Leavitt, J. R. H. Song, and M. F. Whiting. 2011. Phylogeny of Orthoptera based on entire mitochondrial genomes. Manuscript to be submitted to Molecular Phylogenetics and Evolution.
  • Fogarty, F.M., S.M. Bybee, M.A. Branham, M.F. Whiting. 2011. Phylogenetic relationships of Central and South American flatwing damselfies (Odonata: Zygoptera: Megapodagrionidae): An examination of monophyly in a convoluted group. Molecular Evolution and Phylogenetics. Manuscript to be submitted to Zootaxa
  • Ingley, S.J., S. M. Bybee, K. J. Tennessen, M. F. Whiting, and M. A. Branham. 2011 Life on the fly: Evolution of Helicopter Damselflies (Odonata: Pseudostigmatidae). BMC Evolutionary Biology (in review).
  • Miller, K. B., C. Hayashi, M. F. Whiting, G. J. Svenson, and J. S. Edgerly. 2011. The phylogeny and classification of the Embioptera (Insecta). Systematic Entomology (in review)
  • Terry, M. D. and M. F. Whiting. 2011. Zorotypus novobritannicus, the first species of the order Zoraptera (Zorotypidae) from the Australasian Ecozone. Zootaxa (in review)
  • Legendre, F., C. D’Haese, P. Deleporte, R. Pellens, M. F. Whiting, and P. Grandcolas. 2011. Social behavior does not evolve only through adaptational leap when social systems or habitats change: phylogenetic evidence in Zetoborinae cockroaches (Blattaria: Blaberidae). Cladistics (in review).
  • Legendre, F., M. F. Whiting, and P. Grandcolas. 2011. Phylogenetic analysis of termite post-embryonic sequences illuminate caste and ontogenetic pathway evolution. Cladistics (in review)
  • Song, H., M. J. Moulton, K. D. Hiatt, M. F. Whiting. 2011. Uncovering historical signature of mitochondrial DNA hidden in the nuclear genome: The origin of the desert locust revisited. Systematic Biology (in press)
  • Sundberg, K., Q. Snell, M. Clement, K. Crandall, and M. F. Whiting. 2011. Partial Tree Mixing – a Novel Approach to Phylogenetic Search. BMC Bioinformatics (in press)
  • Cameron, S. L., K. Yoshizawa, A. Mizukoshi, M. F. Whiting, and K. P. Johnson. 2011. Mitochondrial genome deletions and minicircles are common in lice (Insecta: Phthiraptera). BMC Genomics 12:394- 409
  • Gontijo, A. M., V. Miguela, M. F. Whiting, R. C. Woodruff, and M. Dominguez. 2011. Intron retention in the Drosophila melanogaster Rieske iron sulphur protein gene generated a new protein. Nature Communications 2:323 (doi:10.1038/ncomms1328).
  • Beutel, R. G., F. Friedrich, T. Hörnschemeyer, H. Pohl, F. Hünefeld, F. Beckmann, R. Meier, B. Misof, M. F. Whiting, and L. B. Vilhelmsen, 2011. Morphological and molecular evidence converge upon a robust phylogeny for the megadiverse Holometabola. Cladistics 27:341-355.

External Grants

Data generated by my undergraduate students not only resulted in publications, but also form the preliminary data used in NSF grants proposals. There were two active NSF grants in my lab during 2011 that provided undergraduate support. During 2011, the Whiting lab also submitted 2 new NSF proposals that are currently pending. One proposal was submitted for the NSF RUI program, which is specifically focused on undergraduate research. The second was submitted to NSF Systematics and focuses on biodiscovery of aquatic insects in Thailand. In 2012 we plan to submit two additional NSF proposals: one that focuses on the evolution of visual pigments in dragonflies, and another one on the systematics of erotylid beetles. All of these proposals are based on undergraduate generated data and funding is specifically requested to provide continued support for undergraduate research activities.

Summary

This report provides a brief summary of undergraduate accomplishments based on ORCA mentoring support. Additional, specific information on the accomplishments of individual undergraduate students can be provided upon request. I feel a sense of gratitude for the opportunity to work with such high caliber students, and am grateful to ORCA for supporting the undergraduates in my lab. This mentored learning opportunity is directly blessing the lives of my students (and to the life of the PI), and I hope for continued support so that these sorts of experiences can be provided for additional students.