Publications

2020

Genome-wide analysis of cis-regulatory changes in the metabolic adaptation of cavefish
Krishnan J, Seidel C, Zhang N, VanCampen J, Peuß R, Xiong S, Kenzior A, Li H, Conaway JW, Rohner N. bioRxiv 2020.08.27.270371; doi: https://doi.org/10.1101/2020.08.27.270371
Pleiotropic function of the oca2 gene underlies the evolution of sleep loss and albinism in cavefish
O'Gorman, M., Thakur, S., Imrie, G., Moran, R., Duboue, E. R., Rohner, N., McGaugh, S. E., Keene, A. C., Kowalko, J. E. bioRxiv 2020.09.27.314278; doi: https://doi.org/10.1101/2020.09.27.314278
Repeated evolution of circadian clock dysregulation in cavefish populations
Mack KL, Jaggard JB, Persons JL, Passow CN, Stanhope BA, Ferrufino E, Tsuchiya D, Smith SE, Slaughter BD, Kowalko J, Rohner N, Keene AC, McGaugh SE bioRxiv 2020.01.14.906628; doi: https://doi.org/10.1101/2020.01.14.906628
A chromosome level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution
Warren W, Boggs T, Borowsky R, Carlson B, Ferrufino E, Gross J, Hillier L, Hu Z, Keene A, Kenzior A, Kowalko J, Tomlinson C, Kremitzki M, Lemieux M, Graves-Lindsay T, McGaugh S, Miller J, Mommersteeg M, Moran R, Peuß R, Rice E, Riddle M, Sifuentes-Romero I, Stanhope B, Tabin C, Thakur S, Yamamoto Y, Rohner N. bioRxiv 2020.07.06.189654; doi: https://doi.org/10.1101/2020.07.06.189654
Adaptation to low parasite abundance affects immune investment and immunopathological responses of cavefish.
Peuß R, Box AC, Chen S, WangY, Tsuchiya D, Persons JL, Kenzior A, Maldonado E, Krishnan J, Scharsack JP,Slaughter BD, Rohner N. Nat Ecol Evol. 2020 Jul 20. doi:10.1038/s41559-020-1234-2. Online ahead of print.PMID: 32690906
Dark world rises: The emergence of cavefish as a model for the study of evolution, development,behavior, and disease.
McGaugh SE, Kowalko JE,Duboué E, Lewis P, Franz-Odendaal TA, Rohner N, Gross JB, KeeneAC. J Exp Zool B Mol Dev Evol. 2020 Jul 7. doi: 10.1002/jez.b.22978. Online ahead of print. PMID: 32638529
Comparative transcriptome analysis of wild and lab populations of Astyanax mexicanus uncovers differential effects of environment and morphotype on gene expression [published online ahead of print, 2020 Feb 4].
Krishnan J, Persons JL, Peuss R, Hassan H, Kenzior A, Xiong S, Olsen L, Maldonado E, Kowalko JE, Rohner N.  J Exp Zool B Mol Dev Evol. 2020;10.1002/jez.b.22933. doi:10.1002/jez.b.22933

2019

Label-independent flow cytometry and unsupervised neural network method for de novo clustering of cell populations
Peuß R, Box AC, Accorsi A, Wood C, Alvarado AS, Rohner N. bioRxiv 603035; doi: https://doi.org/10.1101/603035
Diet-induced loss of adipose Hexokinase 2 triggers hyperglycemia
Shimobayashi M, Shetty S, Frei IC, Wölnerhanssen BK, Weissenberger D, Dietz N, Thomas A, Ritz D, Meyer-Gerspach AC, Maier T, Hay N, Peterli R, Rohner N, Hall MN bioRxiv 2019.12.28.887794; doi: https://doi.org/10.1101/2019.12.28.887794
An Adult Brain Atlas Reveals Broad Neuroanatomical Changes in Independently Evolved Populations of Mexican Cavefish.
Loomis C, Peuss R, Jaggard JB, Wang Y, McKinney S, Raftopoulos A, Raftopoulos S, Whu D, Green MR, McGaugh SE, Rohner NE, Keene AC, Duboue ER. Front Neuroanat. 2019;13:88. Published 2019 Oct 4. doi:10.3389/fnana.2019.00088
Sweet fish: Fish models for the study of hyperglycemia and diabetes.
Krishnan J, Rohner N. J Diabetes. 2019;11(3):193–203. doi:10.1111/1753-0407.12860
Stable transgenesis in Astyanax mexicanus using the Tol2 transposase system.
Stahl BA, Peuss R, McDole B, Kenzior A, Jaggard JB, Gaudenz K, Krishnan J, McGaugh SE, Duboue ER, Keene AC, Rohner N. Dev Dyn. 2019;248(8):679–687. doi:10.1002/dvdy.32
Gamete Collection and In Vitro Fertilization of Astyanax mexicanus.
Peuß R, Zakibe Z, Krishnan J, Merryman MS, Baumann DP, Rohner N.  J Vis Exp. 2019;(147):10.3791/59334. Published 2019 May 25. doi:10.3791/59334

2018

Insulin resistance in cavefish as an adaptation to a nutrient-limited environment.
Biddle MR, Aspiras AC, Gaudenz K, Peuss R, Sung JY, Martineau B, Peavey M, Box AC, Tabin JA, McGaugh S, Borowsky R, Tabin CJ, Rohner N. Nature. 2018;555(7698):647–651. doi:10.1038/nature26136
Cavefish as an evolutionary mutant model system for human disease.
Rohner N. Dev Biol. 2018;441(2):355–357. doi:10.1016/j.ydbio.2018.04.013
Seeing a bright future for a blind fish.
Gore AV, Rohner N, Rétaux S, Jeffery WR. Dev Biol. 2018;441(2):207–208. doi:10.1016/j.ydbio.2018.08.004
Evolution: A Dark Past.
Rohner N. Curr Biol. 2018;28(20):R1190–R1192. doi:10.1016/j.cub.2018.08.045
Temperature preference of cave and surface populations of Astyanax mexicanus.
Tabin JA, Aspiras A, Martineau B, Riddle M, Kowalko J, Borowsky R, Rohner N, Tabin CJ. Dev Biol. 2018;441(2):338–344. doi:10.1016/j.ydbio.2018.04.017
CRISPR mutagenesis confirms the role of oca2 in melanin pigmentation in Astyanax mexicanus.
Klaassen H, Wang Y, Adamski K, Rohner N, Kowalko JE. Dev Biol. 2018;441(2):313–318. doi:10.1016/j.ydbio.2018.03.014
Early adipogenesis contributes to excess fat accumulation in cave populations of Astyanax mexicanus.
Xiong S, Krishnan J, Peuß R, Rohner N. Dev Biol. 2018;441(2):297–304. doi:10.1016/j.ydbio.2018.06.003
The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra, Astyanax mexicanus.
Herman A, Brandvain Y, Weagley J, Jeffery WR, Keene AC, Kono TJY, Bilandzija H, Borowsky R, Espinasa L, O'Quin K, Ornelas-Garcia CP, Yoshizawa M, Carlson B, Maldonado E, Gross JB, Cartwright RA, Rohner N, Warren WC, McGaugh SE. Mol Ecol. 2018;27(22):4397–4416. doi:10.1111/mec.14877

2017

Cavefish and the basis for eye loss.
Krishnan J, Rohner N. Philos Trans R Soc Lond B Biol Sci. 2017;372(1713):20150487. doi:10.1098/rstb.2015.0487

2016

Parallelism and Epistasis in Skeletal Evolution Identified through Use of Phylogenomic Mapping Strategies.
Daane JM, Rohner N, Konstantinidis P, Djuranovic S, Harris MP. Mol Biol Evol. 2016;33(1):162–173. doi:10.1093/molbev/msv208

2015

Melanocortin 4 receptor mutations contribute to the adaptation of cavefish to nutrient-poor conditions.
Aspiras AC, Rohner N, Martineau B, Borowsky RL, Tabin CJ. Proc Natl Acad Sci U S A. 2015;112(31):9668–9673. doi:10.1073/pnas.1510802112

2014

The cavefish genome reveals candidate genes for eye loss.
McGaugh SE, Gross JB, Aken B, Blin M, Borowsky R, Chalopin D, Hinaux H, Jeffery WR, Keene A, Ma L, Minx P, Murphy D, O'Quin KE, Rétaux S, Rohner N, Searle SM, Stahl BA, Tabin C, Volff JN, Yoshizawa M, Warren WC. Nat Commun. 2014;5:5307. Published 2014 Oct 20. doi:10.1038/ncomms6307
Development: facial makeup enhancing our looks.
Rohner N, Tschopp P, Tabin C. Curr Biol. 2014;24(1):R36–R38. doi:10.1016/j.cub.2013.11.026

2013

Loss of schooling behavior in cavefish through sight-dependent and sight-independent mechanisms.
Kowalko JE, Rohner N, Rompani SB, Peterson BK, Linden TA, Yoshizawa M, Kay EH, Weber J, Hoekstra HE, Jeffery WR, Borowsky R, Tabin CJ. Curr Biol. 2013;23(19):1874–1883. doi:10.1016/j.cub.2013.07.056
The African coelacanth genome provides insights into tetrapod evolution.
Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K. Nature. 2013;496(7445):311–316. doi:10.1038/nature12027
Cryptic variation in morphological evolution: HSP90 as a capacitor for loss of eyes in cavefish.
Rohner N, Jarosz DF, Kowalko JE, Yoshizawa M, Jeffery WR, Borowsky RL, Lindquist S, Tabin CJ. Science. 2013;342(6164):1372–1375. doi:10.1126/science.1240276
Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.
Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SM, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson YW, Nanlohy KG, Libants SV, Yeh CY, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner ME, Warren WC, Clifton SW, Wilson RK, Li W. Nat Genet. 2013;45(4):415–421e4212. doi:10.1038/ng.2568
Convergence in feeding posture occurs through different genetic loci in independently evolved cave populations of Astyanax mexicanus.
Kowalko JE, Rohner N, Linden TA, Rompani SB, Warren WC, Borowsky R, Tabin CJ, Jeffery WR, Yoshizawa M. Proc Natl Acad Sci U S A. 2013;110(42):16933–16938. doi:10.1073/pnas.1317192110

2008-2011

Modulation of Fgfr1a signaling in zebrafish reveals a genetic basis for the aggression-boldness syndrome.
Norton WH, Stumpenhorst K, Faus-Kessler T, Folchert A, Rohner N, Harris MP, Callebert J, Bally-Cuif L. J Neurosci. 2011;31(39):13796–13807. doi:10.1523/JNEUROSCI.2892-11.2011
Enhancing the efficiency of N-ethyl-N-nitrosourea-induced mutagenesis in the zebrafish.
Rohner N, Perathoner S, Frohnhöfer HG, Harris MP. Zebrafish. 2011;8(3):119–123. doi:10.1089/zeb.2011.0703
Duplication of fgfr1 permits Fgf signaling to serve as a target for selection during domestication.
Rohner N, Bercsényi M, Orbán L, Kolanczyk ME, Linke D, Brand M, Nüsslein-Volhard C, Harris MP. Curr Biol. 2009;19(19):1642–1647. doi:10.1016/j.cub.2009.07.065
Zebrafish eda and edar mutants reveal conserved and ancestral roles of ectodysplasin signaling in vertebrates.
Harris MP, Rohner N, Schwarz H, Perathoner S, Konstantinidis P, Nüsslein-Volhard C. PLoS Genet. 2008;4(10):e1000206. Published 2008 Oct 3. doi:10.1371/journal.pgen.1000206
Adaptation to low parasite abundance affects immune investment and immunopathological responses of cavefish.
Peuß R, Box AC, Chen S, WangY, Tsuchiya D, Persons JL, Kenzior A, Maldonado E, Krishnan J, Scharsack JP,Slaughter BD, Rohner N. Nat Ecol Evol. 2020 Jul 20. doi:10.1038/s41559-020-1234-2. Online ahead of print.PMID: 32690906