Publications

Marinov M, Bybee S, Doscher C, Kalfatakmolis D. 2019. Faunistic studies on Odonata of the Republic of Vanuatu (Insecta: Odonata). IDF Journal of the International Dragonfly Fund Faunistic Studies in Southeast Asian and Pacific Island Odonata. 26:1–46.

Toussaint EFA, Bybee SM, Erickson RJ, Condamine FL. 2019. Forest Giants on Different Evolutionary Branches: Ecomorphological Convergence in Helicopter Damselflies. Evolution. doi:10.1111/evo.13695

Büsse S, Heckmann S, Hörnschemeyer T, Bybee SM. 2018. The phylogenetic relevance of thoracic musculature: a case study including a description of the thorax anatomy of Zygoptera (Insecta: Odonata) larvae. Systematic Entomology. 43(1):31–42. doi:10.1111/syen.12246

Fallon TR, Lower SE, Chang CH, Bessho-Uehara M, Martin GJ, Bewick AJ, Behringer M, Debat HJ, Wong I, Day JC, et al. 2018. Firefly genomes illuminate parallel origins of bioluminescence in beetles. eLife. 7:e36495. doi:10.7554/eLife.36495

Bradshaw WS, Phillips AJ, Bybee SM, Gill RA, Peck SL, Jensen JL. 2018. A longitudinal study of attitudes toward evolution among undergraduates who are members of the church of jesus christ of latter-day saints. PLoS ONE. 13(11):e0205798. doi:10.1371/journal.pone.0205798

Manwaring KF, Jensen JL, Gill RA, Sudweeks RR, Davies RS, Bybee SM. 2018. Scientific reasoning ability does not predict scientific views on evolution among religious individuals. Evolution: Education and Outreach. 11(1):2. doi:10.1186/s12052-018-0076-8

Büsse S, Bybee SM. 2017. Larva, nymph and naiad – a response to the replies to Bybee et al. (2015) and the results of a survey within the entomological community. Systematic Entomology. 42(1):11–14. doi:10.1111/syen.12213

Lyman CA, Fujimoto MS, Suvorov A, Bodily PM, Snell Q, Crandall KA, Bybee SM, Clement MJ. 2017. Whole genome phylogenetic tree reconstruction using colored de bruijn graphs. In: Proceedings - 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE). p. 260–265. doi:10.1109/BIBE.2017.00-44

Sharkey CR, Fujimoto MS, Lord NP, Shin S, McKenna DD, Suvorov A, Martin GJ, Bybee SM. 2017. Overcoming the loss of blue sensitivity through opsin duplication in the largest animal group, beetles. Scientific Reports. 7(1):8. doi:10.1038/s41598-017-00061-7

Fujimoto MS, Lyman C, Suvorov A, Bodily P, Snell Q, Crandall K, Bybee S, Clement M. 2017. Genome polymorphism detection through relaxed de bruijn graph construction. In: Proceedings - 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE). p. 212–216. doi:10.1109/BIBE.2017.00-53

Suvorov A, Jensen NO, Sharkey CR, Fujimoto MS, Bodily P, Wightman HMC, Ogden TH, Clement MJ, Bybee SM. 2017. Opsins have evolved under the permanent heterozygote model: insights from phylotranscriptomics of Odonata. Molecular Ecology. 26(5):1306–1322. doi:10.1111/mec.13884

Martin GJ, Branham MA, Whiting MF, Bybee SM. 2017. Total evidence phylogeny and the evolution of adult bioluminescence in fireflies (Coleoptera: Lampyridae). Molecular Phylogenetics and Evolution. 107:564–575. doi:10.1016/j.ympev.2016.12.017

Arnold PR, Lord NP, Smith AN, Bybee SM. 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.

Naegle MA, Mugleston JD, Bybee SM, Whiting MF. 2016. Reassessing the phylogenetic position of the epizoic earwigs (Insecta: Dermaptera). Molecular Phylogenetics and Evolution. 100:382–390. doi:10.1016/j.ympev.2016.03.012

Lord NP, Plimpton RL, Sharkey CR, Suvorov A, Lelito JP, Willardson BM, Bybee SM. 2016. A cure for the blues: Opsin duplication and subfunctionalization for short-wavelength sensitivity in jewel beetles (Coleoptera: Buprestidae). BMC Evolutionary Biology. 16(1):107. doi:10.1186/s12862-016-0674-4

Fujimoto MS, Suvorov A, Jensen NO, Clement MJ, Bybee SM. 2016. Detecting false positive sequence homology: A machine learning approach. BMC Bioinformatics. 17(1):101. doi:10.1186/s12859-016-0955-3

Pacheco YM, Martin GJ, Bybee SM. 2016. On the Phototactic Response of Rwandan Diaphanes Motschulsky (Coleoptera: Lampyridae) to a Trap with a 630Nm Red Light. The Coleopterists Bulletin. 70(3):559–562. doi:10.1649/0010-065x-70.3.559

Mugleston J, Naegle M, Song H, Bybee SM, Ingley S, Suvorov A, Whiting MF. 2016. Reinventing the leaf: Multiple origins of leaf-like wings in katydids (Orthoptera:Tettigoniidae). Invertebrate Systematics. 30(4):335–352. doi:10.1071/IS15055

Manwaring KF, Whiting MF, Wilcox E, Bybee SM. 2016. A study of common scorpionfly (Mecoptera: Panorpidae) visual systems reveals the expression of a single opsin. Organisms Diversity and Evolution. 16(1):201–209. doi:10.1007/s13127-015-0241-7

Bybee S, Córdoba-Aguilar A, Duryea MC, Futahashi R, Hansson B, Lorenzo-carballa MO, Schilder R, Stoks R, Suvorov A, Svensson EI, et al. 2016. Odonata (dragonflies and damselflies) as a bridge between ecology and evolutionary genomics. Frontiers in Zoology. 13(46):1–20. doi:10.1186/s12983-016-0176-7

Fujimoto MS, Suvorov A, Jensen NO, Clement MJ, Snell Q, Bybee SM. 2016. The OGCleaner: filtering false-positive homology clusters. Bioinformatics. 33(1):125–127. doi:10.1093/bioinformatics/btw571

Aira M, Bybee SM, Pérez-Losada M, Domínguez J. 2015. Feeding on microbiomes: effects of detritivory on the taxonomic and phylogenetic bacterial composition of animal manures. FEMS Microbiology Ecology. 91(11): 117-122.

Aira M, Bybee SM, Dominquez J. 2015. Carnivory does not change the rhizosphere bacterial community of the plant Drosera intermedia. Applied Soil Ecology. 92: 14-17.

Martin GJ, Lord NP, Branham MA, Bybee SM. 2015. Review of the firefly visual system (Coleoptera: Lampyridae) and evolution of the opsin genes underlying color vision. Organisms Diversity and Evolution. 15(3):513–526. doi:10.1007/s13127-015-0212-z

Bybee SM, Hansen Q, Büsse S, Cahill Wightman HM, Branham MA. 2015. For consistency’s sake: The precise use of larva, nymph and naiad within Insecta. Systematic Entomology. 40(4):667–670. doi:10.1111/syen.12136

Houston DD, Mitchell KS, Clouse JW, Maughan PJ, Curtis Creighton J, Smith AN, Bybee SM, Belk MC. 2015. SNP development in North American burying beetles (Coleoptera: Silphidae): a tool to inform conservation decisions. Conservation Genetics Resources. 7(2):349–352. doi:10.1007/s12686-015-0438-2

Manwaring KF, Jensen JL, Gill RA, Bybee SM. 2015. Influencing highly religious undergraduate perceptions of evolution: Mormons as a case study. Evolution: Education and Outreach. 8(1):23. doi:10.1186/s12052-015-0051-6

Speiser DI, Pankey MS, Zaharoff AK, Battelle BA, Bracken-Grissom HD, Breinholt JW, Bybee SM, Cronin TW, Garm A, Lindgren AR, et al. 2014. Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms. BMC Bioinformatics. 15(1):350. doi:10.1186/s12859-014-0350-x

Dijkstra KDB, Bechly G, Bybee SM, Dow RA, Dumont HJ, Fleck G, Garrison RW, Hämäläinen M, Kalkman VJ, Karube H, et al. 2013. The classification and diversity of dragonflies and damselflies (Odonata). Zootaxa. 3703(1):36–45. doi:10.11646/zootaxa.3703.1.9

Bybee SM, Johnson KK, Gering EJ, Whiting MF, Crandall KA. 2012. All the better to see you with: A review of odonate color vision with transcriptomic insight into the odonate eye. Organisms Diversity and Evolution. doi:10.1007/s13127-012-0090-6

Bybee SM, Yuan F, Ramstetter MD, Llorente-Bousquets J, Reed RD, Osorio D, Briscoe AD. 2012. UV Photoreceptors and UV-Yellow Wing Pigments in Heliconius Butterflies Allow a Color Signal to Serve both Mimicry and Intraspecific Communication. The American Naturalist. 179(1):38–51. doi:10.1086/663192

Ingley SJ, Bybee SM, Tennessen KJ, Whiting MF, Branham MA. 2012. Life on the fly: Phylogenetics and evolution of the helicopter damselflies (Odonata, Pseudostigmatidae). Zoologica Scripta. 41(6):637–650. doi:10.1111/j.1463-6409.2012.00555.x

Bybee SM, Bracken-Grissom HD, Hermansen RA, Clement MJ, Crandall KA, Felder DL. 2011. Directed next generation sequencing for phylogenetics: An example using Decapoda (Crustacea). Zoologischer Anzeiger-A Journal of Comparitive Zoology. 250(4):497–506. doi:10.1016/j.jcz.2011.05.010

Bybee SM, Bracken-Grissom H, Haynes BD, Hermansen RA, Byers RL, Clement MJ, Udall JA, Wilcox ER, Crandall KA. 2011. Targeted amplicon sequencing (TAS): A scalable next-gen approach to multilocus, multitaxa phylogenetics. Genome Biology and Evolution. 3:1312–1323. doi:10.1093/gbe/evr106

Edwards TM, Smith BK, Watts DL, Germain-Aubrey CC, Roark AM, Bybee SM, Cox CE, Hamlin HJ, Guillette LJ. 2011. Group-Advantaged Training of Research (GATOR): A Metamorphosis of Mentorship. BioScience. 61(4):301–311. doi:10.1525/bio.2011.61.4.10

Capa M, Bybee DR, Bybee SM. 2010. Establishing species and species boundaries in Sabellastarte Krøyer, 1856 (Annelida: Sabellidae): An integrative approach. Organisms Diversity and Evolution. 10(5):351–371. doi:10.1007/s13127-010-0033-z

Briscoe AD, Bybee SM, Bernard GD, Yuan F, Sison-Mangus MP, Reed RD, Warren AD, Llorente-Bousquets J, Chiao C-C. 2010. Positive selection of a duplicated UV-sensitive visual pigment coincides with wing pigment evolution in Heliconius butterflies. Proceedings of the National Academy of Sciences. 107(8):3628–3633. doi:10.1073/pnas.0910085107

Briscoe AD, Bybee SM, Bernard GD, Yuan F, Sison-Mangus MP, Reed RD, Warren AD, Llorente-Bousquets J, Chiao C-C. 2010. Reply to Nozawa et al.: Complementary statistical methods support positive selection of a duplicated UV opsin gene in Heliconis. Proceedings of the National Academy of Sciences. USA 107:E97.

Bybee SM, Zaspel JM, Beucke KA, Scott CH, Smith BW, Branham MA. 2010. Are molecular data supplanting morphological data in modern phylogenetic studies? Systematic Entomology. 35(1):2–5. doi:10.1111/j.1365-3113.2009.00496.x

Nel A, Fleck G, Garrouste R, Gand G, Lapeyrie J, Bybee SM, Prokop J. 2009. Revision of Permo-Carboniferous griffenflies (Insecta: Odonatoptera: Meganisoptera) based upon new species and redescription of selected poorly known taxa from Eurasia. Palaeontographica Abteilung (A). 289:89–121. doi:10.1127/pala/289/2009/89

Bybee SM, Tennessen KJ. 2008. Description of the female and nymph of Philogenia mangosisa from southern Ecuador (Odonata: Megapodagrionidae). Zootaxa. 1787:63–68.

Bybee SM. 2008. Phylogenetics. In: Capinera J.L. (eds) Encyclopedia of Entomology. Springer, Dordrecht. 2863-2868

Bybee SM. 2008. Phylogenetics, evolution and systematics of Holodonata with special focus on wing structure evolution: Morphological, molecular and fossil evidence. University of Florida.

Bybee SM, Branham MA. 2008. Scanning Rocks for Data. American Entomologist. 52(2):214–217.

Bybee SM, Ogden TH, Branham MA, Whiting MF. 2008. Molecules, morphology and fossils: A comprehensive approach to odonate phylogeny and the evolution of the odonate wing. Cladistics. 24(4):477–514. doi:10.1111/j.1096-0031.2007.00191.x

Nearns EH, Branham MA, Bybee SM. 2006. Cerambycidae (Coleoptera) types of the Fernando de Zayas collection, Havana, Cuba. Zootaxa. 1270:1–17.

Bybee SM. (August 2005). Dragonflies and Damselflies (Insecta: Odonata). UF/IFAS Featured Creatures collection. EENY-355.

Bybee SM, Taylor SD, Riley Nelson C, Whiting MF. 2004. A phylogeny of robber flies (Diptera: Asilidae) at the subfamilial level: Molecular evidence. Molecular Phylogenetics and Evolution. 30(3):789–797. doi:10.1016/S1055-7903(03)00253-7