Publications

NAU graduate students underlined. NAU undergraduate students are asterisked.

2024

Zachary T Compton, Valerie Harris, Walker Mellon, Shawn Rupp, Diego Mallo, Stefanie Kapsetaki, Mallory Wilmot, Ryan Kennington, Kathleen Noble, Cristina Baciu, Lucia Ramirez, Ashley Peraza, Brian Martins, Sushil Sudhakar, Selin Aksoy, Gabriela Furukawa, Orsolya Vincze, Mathieu T Giraudeau, Elizabeth Duke, Simon Spiro, Edmund Flach, Hannah Davidson, Ashley Zehnder, Trevor A Graham, Brigid Troan, Tara Harrison, Marc Tollis, Joshua Schiffman, Athena Aktipis, Lisa Abegglen, Carlo Maley, Amy Boddy (2024). Cancer Prevalence Across Vertebrates. Cancer Discovery, accepted August 2024. https://doi.org/10.1158/2159-8290.CD-24-0573.

Gable SM, Bushroe NA, Mendez JM, Wilson AA, Pinto BJ, Gamble T, Tollis M (2024). Differential conservation and loss of chicken repeat 1 (CR1) retrotransposons reveal lineage-specific genome dynamics across reptiles. Genome Biology and Evolution. 16(8). https://doi.org/10.1093/gbe/evae157.

Kapsetaki SE, Compton ZT, Dolan J, Harris VK, Mellon W, Rupp SM, Duke EG, Harrison TM, Aksoy S, Giraudeau M, Vincze O, McGraw KJ, Aktipis A, Tollis M, Boddy AM, Maley CM (2024). Life history traits and cancer prevalence in birds. Evolution, Medicine, and Public Health. eoae011, https://doi.org/10.1093/emph/eoae011.

Suárez-Menéndez M, Bérubé M, Bachmann L, Best P, Davison N, Heide-Jørgensen M, Lesage V, Oosting T, Prieto R, Ramp C, Robbins J, Sears R, Silva MA, ten Doeschate M, Tollis M, Vermeulen E, Víkingsson GA, Wiig Ø, Palsbøll PJ (2024). Baleen whale microsatellite panel for individual identification and parentage assignment in Mysticeti. Global Ecology and Conservation. 51: e02947. https://doi.org/10.1016/j.gecco.2024.e02947.

2023

Gable SM, Mendez JM*, Bushroe NA*, Wilson A*, Byars MI, Tollis M (2023). The state of squamate genomics: past, present, and future of genome research in the most speciose terrestrial vertebrate order. Genes. 14, 1387. https://doi.org/10.3390/genes14071387

Nguyen ED, Fard VN, Kim BY, Collins S, Galey M, Nelson BR, Wakenight P, Gable SM, McKenna A, Bammler TK, MacDonald J, Okamura DM, Shendure J, Beier DR, Ramirez JM, Majesky MW, Millen KJ, Tollis M, Miller DE (2023). Genome Report: chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus). G3:Genes|Genomes|Genetics. 13(10), jkad177. https://doi.org/10.1093/g3journal/jkad177

2022

Gable SM, Byars MI, Literman R, Tollis M (2022). A genomic perspective on the evolutionary diversification of turtles. Systematic Biology. 71(6):1331-1347. https://doi.org/10.1093/sysbio/syac019 (preprint: https://doi.org/10.1101/2021.10.14.464421)

Geneva AJ, Sungdae P, Bock D, de Mello P, Sarigol F, Tollis M, Donihue C, Reynolds RG, Feiner N, Rasys A, Lauderdale J, Minchey SG, Alcala AJ, Infante C, Kolbe JJ, Schluter D, Menke DB, Losos JB (2022). Chromosome-scale genome assembly of the brown anole (Anolis sagrei), a model species. Communications Biology. https://doi.org/10.1038/s42003-022-04074-5

2021

Westfall AK, Telemeco RS, Grizante MB, Waits DS, Clark AD, Simpson DY, Klabacka RL, Sullivan AP, Perry GH, Sears MW, Cox CL, Cox RM, Gifford ME, John-Alder HB, Langkilde T, Angilletta Jr. AJ, Leaché AD, Tollis M, Kusumi K, Schwartz TS (2021). A chromosome-level genome assembly for the Eastern Fence Lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology. GigaScience. 10:10. giab066. https://doi.org/10.1093/gigascience/giab066

Tollis M, Ferris E, Campbell MS, Harris VK, Rupp SM, Harrison TM, Kiso WK, Schmitt DL, Garner MM, Aktipis CA, Maley CC, Boddy AM, Yandell M, Gregg C, Schiffman JD, Abegglen LM (2021). Elephant genomes reveal accelerated evolution in mechanisms underlying disease defenses. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msab127

2020

Gemmell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey JR, Adelson DL, Suh A, Bertozzi T, Grau JH, Organ C, Gardner PP, Muffato M, Patricio M, Billis K, Martin FJ, Flicek P, Petersen B, Kang L, Michalak P, Buckley TR, Wilson M, Cheng Y, Miller H, Schott RK, Jordan M, Newcomb R, Arroyo JI, Valenzuela N, Hore TA, Renart J, Peona V, Peart CR, Warmuth VM, Zeng L, Kortschak RD, Raison JM, Zapata VV, Wu Z, Santesmasses D, Mariotti M, Guigó R, Rupp SM, Twort VG, Dussex N, Taylor H, Abe H, Paterson JM, Mulcahy DG, Gonzalez VL, Barbieri CG, DeMeo DP, Pabinger S, Ryder O, Edwards SV, Salzberg SL, Mickelson L, Nelson N, Stone C, Board NT (2020). The tuatara genome reveals ancient features of amniote evolution. Nature. https://doi.org/10.1038/s41586-020-2561-9.

Tollis M, Schneider-Utaka AK, Maley CC (2020). The evolution of human cancer gene duplications across mammals. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msaa125.

2019

Tollis M, Robbins J, Webb AE, Kuderna LFK Caulin AF, Garcia JD, Bèrubè M, Pourmand N, Marques-Bonet T, O’Connell MJ, Palsbøll PJ, Maley CC (2019). Return to the sea, get huge, beat cancer: an analysis of cetacean genomes including an assembly for the humpback whale (Megaptera novaeangliae). Molecular Biology and Evolution. 36:1746–1763. https://doi.org/10.1093/molbev/msz099

Schield DR, Card DC, Hales NR, Perry BW, Pasquesi GIM, Blackmon H, Adams RH, Corbin AB, Smith CF, Ramesh B, Demuth JP, Betrán E, Tollis M, Meik JM, Mackessy SP, and Castoe TA (2019). The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes. Genome Research. 29:590-601. http://www.genome.org/cgi/doi/10.1101/gr.240952.118.

2018

Tollis M, Hutchins ED, Stapley J, Rupp S, Eckalbar WL, Maayan I, Lasku E, Infante C, Dennis S, Roberston JA, May CM, Crusoe MR, Bermingham E, DeNardo DF, Hsieh ST, Kulathinal R, McMillan O, Menke DB, Pratt SC, Rawls A, Sanjur O, Wilson-Rawls J, Wilson-Sayres MA, Fisher RE, Kusumi K (2018). Comparative genomics reveals accelerated evolution in conserved pathways during the diversification of anole lizards. Genome Biology and Evolution. 10(2):489–506. https://doi.org/10.1093/gbe/evy013.

2017 and earlier

Tollis M, Boddy AM, Maley CC (2017). Peto’s Paradox: how has evolution solved the problem of cancer prevention? BMC Biology. 15:60. https://doi.org/10.1186/s12915-017-0401-7.

Tollis M, DeNardo DF, Cornelius JA, Dolby GA, Edwards T, Henen BT, Karl AE, Murphy BW, Kusumi K (2017). The Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species. PLoS ONE. 12(5): e0177708. https://doi.org/10.1371/journal.pone.0177708.

Tollis M, Schiffman JD, Boddy AM (2017). Evolution of cancer suppression as revealed by mammalian comparative genomics. Current Opinion in Genetics and Development. Feb 2; 42:40-47. http://dx.doi.org/10.1016/j.gde.2016.12.004.

Manthey JD, Tollis M, Lemmon AR, Lemmon EM, Boissinot S (2016). Diversification in wild populations of the model organism Anolis carolinensis: a genome-wide phylogeographic investigation. Ecology and Evolution. 6: 8115-8125. doi: 10.1002/ece3.2547

Chowell D, Boddy AM, Mallo D, Tollis M, Maley C (2016). When (distant) relatives stay too long: implications for cancer medicine. Genome Biology. 17:34. Doi: 10:1186/s13059-016-0906-3.

Edwards T, Tollis M, Hsieh P, Gutenkunst RN, Liu Z, Kusumi K, Culver M, Murphy RW (2016). Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses. Ecology and Evolution. 6(2):379-396. Doi: 10.1002/ece3.1865.

Pope WH, Bowman CA, Russell DA, Jacobs-Sera D, Asai DJ , Cresawn SG, Jacobs WR, Hendrix RW, Lawrence JG, Hatfull GF, Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science, Phage Hunters Integrating Research and Education, Mycobacterial Genetics Course (2015). Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. eLife 4: e06416. http://dx.doi.org/10.7554/eLife.06416.001.

Tollis M, Hutchins ED, Kusumi K (2014). Reptile genomes open the frontier for comparative analysis of amniote development and regeneration. International Journal of Developmental Biology. 58 (2014): 863-871.

Boissinot S, Alvarez L, Ramirez JG, Tollis M (2014). Neutral nuclear variation in baboons (genus Papio) provides insights into their evolutionary and demographic histories. American Journal of Physical Anthropology. 155: 621-634. doi: 10.1002/ajpa.22618.

Freilich X, Tollis M, Boissinot S (2014). Hiding in the highlands: evolution of a frog species complex of the genus Ptychadena in the Ethiopian highlands. Molecular Phylogenetics and Evolution. 71 (2014). 157-169. doi.org/10.1016/j.ympev.2013.11.015.

Tollis M and Boissinot S. (2014) Genetic variation in the green anole lizard (Anolis carolinensis) reveals island refugia and a fragmented Florida during the Quaternery. Genetica. 142: 59-72. doi.org/10.1007/s10709-013-9754-1.

Tollis M and Boissinot S. (2013). Lizards and LINEs: Selection and demography affect the fate of L1 retrotransposons in the genome of the green anole (Anolis carolinensis). Genome Biology and Evolution. 5(9): 1754-1768. doi: 10.1093/gbe/evt133.

Tollis M and Boissinot S (2012). The Evolutionary Dynamics of Transposable Elements in Eukaryote Genomes. (textbook chapter) Garrido-Ramos MA (ed). Repetitive DNA: Genome Dynamics, Volume 7. Karger, Basel. Pp 68–91. doi: 10.1159/000337126.

Tollis M, Ausubel G, Ghimire D, Boissinot S (2012). Multi-locus phylogeographic and population genetic analysis of Anolis carolinensis: Historical demography of a genomic model species. PLoS ONE. 7(6): e38474. doi:10.1371/journal.pone.0038474.

Hatfull GF, the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science Program, KwazaZulu-Natal Research Institute for Tuberculosis and HIV Mycobacterial Genetics Course Students, Phage Hunters Integrating Research and Education Program (2012). Complete genome sequences of 138 mycobacteriopahges. Journal of Virology. 86(4): 2382-2384. doi: 10.1128/JVI.06870-11.

Tollis M and Boissinot S (2011). The transposable element profile of the Anolis genome: How a lizard can provide insights into the evolution of vertebrate genome size and structure. Mobile Genetic Elements. 1:2; 107-111. doi.org/10.4161/mge.1.2.17733.