Theoretical Ecology and Evolution

The Bank lab @ Universität Bern & the Gulbenkian Institute

Publications

Please email us for pdf copies of lab papers hidden behind a paywall.

This list shows publications of lab members during their time in the lab. For additional publications of individual lab members, see their personal pages.

*equal contribution; #co-corresponding authors

2021

D. Stajic#, C. Bank, and I. Gordo#. Epigenetic switching outcompetes genetic mutations during adaptation to fluctuating environments. Submitted. preprint

M.A.D. Louro, M. Bettencourt-Dias, and C. Bank. Patterns of selection against centrosome amplification in human cell lines. Plos Computational Biology, in press. bioRxiv, doi: 10.1101/2020.01.24.918615 preprint

R.K. Butlin, M.R. Servedio, C.M. Smadja, C. Bank, N.H. Barton, S.M. Flaxman, T. Giraud, R. Hopkins, E.L. Larson, M.E. Maan, J. Meier, R. Merrill, M.A.F. Noor, D. Ortiz‐Barrientos, A. Qvarnström. Homage to Felsenstein 1981, or why are there so few/many species? Evolution, doi:10.1111/evo.14235 link

E. Berdan*#, A. Blanckaert*#, R.K. Butlin, and C. Bank. Deleterious mutation accumulation and the long-term fate of chromosomal inversions. Plos Genetics, doi: 10.1371/journal.pgen.1009411 link or preprint

P.A. Cote-Hammarlof*, I. Fragata*, J.M. Flynn, K.B. Zeldovich, C. Bank#, and D.N.A. Bolon#. The Adaptive Potential of the Middle Domain of Yeast Hsp90. Molecular Biology and Evolution, doi: 10.1093/molbev/msaa211 link or preprint

2020

C. Bank. Defining Theories in Evolution. Trends in Ecology & Evolution, doi: 10.1016/j.tree.2020.05.009 (A book review of The Theory of Evolution: Principles, Concepts, and Assumptions.) link or pdf

C. Bank. Reconciling the upsides and downsides of migration for evolutionary rescue. Peer Community in Evolutionary Biology, doi: 10.24072/pci.evolbiol.100098 (A preprint recommendation of Tomasini et al., 2020, Evolution.) link

D. Stajic, and C. Bank. Phenotypic switching and its evolutionary consequences. Book Chapter in Phenotypic Switching: Implications in Biology and Medicine. Preprint version: Evolutionary consequences of epigenetically induced phenotypic switching, EcoEvoRxiv, doi: 10.32942/osf.io/6yf4u preprint

A. Blanckaert, C. Bank, and J. Hermisson. The limits to parapatric speciation III: Fast reproductive isolation in the presence of gene flow despite limited ecological differentiation. Philosophical Transactions of The Royal Society B, doi: 10.1098/rstb.2019.0532 link

J.M. Flynn, A. Rossouw, P.A. Cote-Hammarlof, I. Fragata, D. Mavor, C. Hollins III, C. Bank, and D.N.A. Bolon. Comprehensive fitness maps of Hsp90 show widespread environmental dependence. eLife, doi: DOI: 10.7554/eLife.53810 link or preprint

R.S. Ramiro#, P. Durão, C. Bank, and I. Gordo#. Low mutational load allows for high mutation rate variation in gut commensal bacteria. Plos Biology, doi: 10.1371/journal.pbio.3000617. link or preprint

2019

P. Nouhaud, A. Blanckaert, C. Bank, and J. Kulmuni. Understanding admixture: haplodiploidy to the rescue. Trends in Ecology and Evolution, doi: 10.1016/j.tree.2019.08.013 link

A.E. Hall, K. Kakare, V.S. Cooper, C. Bank, T.F. Cooper#, and F.B.G. Moore#. Environment changes epistasis to alter trade-offs along alternative evolutionary paths. Evolution, doi: 10.1111/evo.13825 link

S. Ramos, A.R. Carlos, B. Sundaram, V. Jeney, A. Ribeiro, R. Gozzelino, C. Bank, E. Gjini, F. Braza, R. Martins, T.W. Ademolue, B. Blankenhaus, Z. Licínia, P. Faisca, D. Trujillo, S. Cardoso, S. Rebelo, L. del Barrio, A. Zarjou, S. Bolisetty, A. Agarwal, and M.P. Soares. Renal control of disease tolerance to malaria. Proceedings of the National Academy of Sciences, doi: 10.1073/pnas.1822024116 link

I. Fragata, A. Blanckaert, M.A.D. Louro, D.A. Liberles, and C. Bank. Evolution in the light of fitness landscape theory. Trends in Ecology and Evolution, doi: 10.1016/j.tree.2018.10.009 link or preprint

2018

A. Blanckaert, and C. Bank. In search of the Goldilocks zone for hybrid speciation. PLOS Genetics, doi: 10.1371/journal.pgen.1007613 link or preprint

J.A.G.M. de Visser#, S.F. Elena#, I. Fragata# and S. Matuszewski#. The utility of fitness landscapes and big data for predicting evolution. Heredity, doi: 10.1038/s41437-018-0128-4 link

I. Fragata, P. Simôes, M. Matos, E. Szathmáry, and M. Santos. Playing evolution in the laboratory: from the first major evolutionary transition to global warming. EPL (Europhysics Letters), doi: 10.1209/0295-5075/122/38001 link

I. Fragata, and C. Bank. Let’s move beyond costs of resistance! Peer Community In Evolutionary Biology, 100052 doi: 10.24072/pci.evolbiol.100052 (A preprint recommendation of Lenormand et al., 2018, bioRxiv.) link

A. Blanckaert, and J. Hermisson. The limits to parapatric speciation II: strengthening a preexisting genetic barrier to gene flow in parapatry. Genetics, doi: 10.1534/genetics.117.300652 link or preprint

I. Fragata*#, S. Matuszewski*#, M.A. Schmitz, T. Bataillon, J.D. Jensen, and C. Bank. The fitness landscape of the codon space across environments. Heredity, doi: 10.1038/s41437-018-0125-7 link or preprint

A.-H. Ghenu*, A. Blanckaert*, R.K. Butlin, J. Kulmuni, and C. Bank. Conflict between heterozygote advantage and hybrid incompatibility in haplodiploids (and sex chromosomes). Molecular Ecology, doi: 10.1111/mec.14482 link or preprint. Read our summary of this article here.

2017

I. Fragata, and C. Bank. What doesn’t kill us makes us stronger: can Fisher’s Geometric model predict antibiotic resistance evolution? Peer Community in Evolutionary Biology, doi:10.24072/pci.evolbiol.100028 (A post-print recommendation of Harmand et al., 2016, Evolution.) link

L. Ormond, P. Liu, S. Matuszewski, N. Renzette, C. Bank, K.B. Zeldovich, D.N.A. Bolon, T.F. Kowalik, R.W. Finberg, J.D. Jensen#, and J.P. Wang#. The combined effect of oseltamivir and favipiravir on influenza A virus evolution. Genome Biology and Evolution, doi:10.1093/gbe/evx138 link

S. Matuszewski, L. Ormond, C. Bank, and J.D. Jensen. Two sides of the same coin: a population genetics perspective on lethal mutagenesis and mutational meltdown. Virus Evolution, doi:10.1093/ve/vex004 link or direct pdf link

2016

C. Bank*, S. Matuszewski*, R.T. Hietpas, and J.D. Jensen. On the (un)predictability of a large intragenic fitness landscape. Proceedings of the National Academy of Sciences, doi:10.1073/pnas.1612676113 link or preprint. Read our summary of this article here.

C. Bank, N. Renzette, P. Liu, S. Matuszewski, H. Shim, M. Foll, D.N.A. Bolon, K.B. Zeldovich, T.F. Kowalik, R.W. Finberg, J.P. Wang#, and J.D. Jensen#. An experimental evaluation of drug-induced mutational meltdown as an antiviral treatment strategy. Evolution, doi:10.1111/evo.13041 link or preprint. Read our summary of this article here.

K.K. Irwin, S. Laurent, S. Matuszewski, S. Vuilleumier, L. Ormond, H. Shim, C. Bank, and J.D. Jensen. On the importance of skewed offspring distributions and background selection in viral population genetics. Heredity, doi:10.1038/hdy.2016.58 link or preprint. Read our summary of this article here.

S. Matuszewski*#, M.E. Hildebrandt*, A.-H. Ghenu, J.D. Jensen, and C. Bank#. A statistical guide to the design of deep mutational scanning experiments. Genetics, doi:10.1534/genetics.116.190462 link or preprint. Read our summary of this article here.

L. Jiang, P. Liu, C. Bank, N. Renzette, K. Prachanronarong, L.S. Yilmaz, D.R. Caffrey, K.B. Zeldovich, C.A. Schiffer, T.F. Kowalik, J.D. Jensen, R.W. Finberg, J.P. Wang#, and D.N.A. Bolon#. A balance between inhibitor binding and substrate processing confers influenza drug resistance. Journal of Molecular Biology, doi:10.1016/j.jmb.2015.11.027 link

2015

C. Bank, R.T. Hietpas, J.D. Jensen, and D.N.A. Bolon. A systematic survey of an intragenic epistatic landscape. Molecular Biology and Evolution, doi:10.1093/molbev/msu301 link or preprint

2014

C. Bank, G. Ewing, A. Ferrer-Admetlla, M. Foll, and J.D. Jensen. Thinking too positive? Revisiting current methods of population-genetic selection inference. Trends in Genetics, doi:10.1016/j.tig.2014.09.010 link or preprint

C. Bank, R.T. Hietpas, A. Wong, D.N.A. Bolon#, and J.D. Jensen#. A Bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments. Genetics, doi:10.1534/genetics.113.156190 link. Read our summary of this article here.

M. Foll*, Y.-P. Poh*, N. Renzette, A. Ferrer-Admetlla, C. Bank, H. Shim, A.-S. Malaspinas, G. Ewing, D. Wegmann, D.R. Caffrey, K.B. Zeldovich, D.N. Bolon, J. Wang, T.F. Kowalik, C.A. Schiffer, R.W. Finberg, and J.D. Jensen. Influenza virus drug resistance: a time-sampled population-genetics perspective. PLOS Genetics, doi:10.1371/journal.pgen.1004185 link

O. Seehausen, R.K. Butlin, I. Keller, C. Wagner, J. Boughman, P. Hohenlohe, C. Peichel, G.-P. Saetre, C. Bank, A. Brännström, A. Brelsford, C. Clarkson, F. Eroukhmanoff, J.L. Feder, M.C. Fischer, A.D. Foote, P. Franchini, C.D. Jiggins, F.C. Jones, A.K. Lindholm, K. Lucek, M.E. Maan, D.A. Marques, S.H. Martin, B. Matthews, J.I. Meier, M. Möst, M.W. Nachman, E. Nonaka, C.L. Peichel, D.J. Rennison, G.-P. Saetre, J. Schwarzer, C.E. Wagner, E.T. Watson, A.M. Westram, and A. Widmer. Genomics and the origin of species. Nature Reviews Genetics, doi:10.1038/nrg3644 link

2013

R.T. Hietpas*, C. Bank*, J.D. Jensen#, and D.N.A. Bolon#. Shifting fitness landscapes in response to altered environments. Evolution, doi:10.1111/evo.12207 link or direct pdf link

2012

C. Bank, R. Bürger, and J. Hermisson. The limits to parapatric speciation: Dobzhansky-Muller incompatibilities in a continent-island model. Genetics, doi:10.1534/genetics.111.137513 link. Read our summary of this article here.

C. Bank, J. Hermisson, and M. Kirkpatrick. Can reinforcement complete speciation? Evolution, doi: 10.1111/j.1558-5646.2011.01423.x link or direct pdf link