Marinov M, Bybee S, Doscher C, Kalfatakmolis D. 2019. Faunistic studies on Odonata of the Republic of Vanuatu (Insecta: Odonata) (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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) (opens in a new tab). 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 (opens in a new tab). 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) (opens in a new tab). 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) (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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) (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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) (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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) (opens in a new tab). 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) (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). 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) (opens in a new tab). Zootaxa. 1787:63–68.
Bybee SM. 2008. Phylogenetics (opens in a new tab). 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 (opens in a new tab). University of Florida.
Bybee SM, Branham MA. 2008. Scanning Rocks for Data (opens in a new tab). 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 (opens in a new tab). 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 (opens in a new tab). Zootaxa. 1270:1–17.
Bybee SM. (August 2005). Dragonflies and Damselflies (Insecta: Odonata) (opens in a new tab). 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 (opens in a new tab). Molecular Phylogenetics and Evolution. 30(3):789–797. doi:10.1016/S1055-7903(03)00253-7
