Theoretical Ecology and Evolution

The Bank lab @ Universität Bern

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; &co-last authors

2024

M.A.D. Louro*#, C. Peneda*#, C. Bank, and M. Bettencourt-Dias#. Adaptation of human cell populations to different levels of centriole amplification involves a two-step response. In review. preprint

A. Hinz, A. Amado, R. Kassen, C. Bank, and A. Wong. Unpredictability of the fitness effects of antimicrobial resistance mutations across environments in Escherichia coli. Molecular Biology and Evolution, accepted pending revision. preprint

A. Amado, and C. Bank. Ecological tradeoffs lead to complex evolutionary trajectories and sustained diversity on dynamic fitness landscapes. Journal of Physics A, accepted. preprint

K. Höcketstaller, I.A. Marti, C. Bank, B. Yilmaz, and J. Becker. Antimicrobial Resistance in Wildlife across Switzerland and the Principality of Liechtenstein: Associations with Environmental Factors and Taxonomic Variation. In review.

A.-H. Ghenu*#, L. Marrec*#, and C. Bank. Challenges and pitfalls of inferring microbial growth rates from lab cultures. Frontiers in Ecology and Evolution, doi: 10.3389/fevo.2023.1313500. link or preprint

2023

L. Marrec. Quantifying the impact of genotype-dependent gene flow on mutation fixation in subdivided populations. preprint

D. McLeod, C. Bank&, and S. Gandon&. A multilocus perspective on the evolutionary dynamics of multistrain pathogens. preprint

I. Fragata*, Y. Anciaux*, P. Cote-Hammarlof, T. Bataillon&, and C. Bank&. Distributions of fitness effects along the protein sequence of Hsp90 reveal variable costs of adaptation across protein domains and environments. In review.

J. Li, and C. Bank. Dominance and multi-locus interaction. Trends in Genetics, in press. preprint

L. Marrec, C. Bank, and T. Bertrand. Solving the stochastic dynamics of population growth. Ecology and Evolution, doi: 10.1002/ece3.10295. link or preprint

D. Grbin, S. Geček, A. Miljanović, D. Pavić, S. Hudina, J. Žučko, J. Rieder, S.R.R. Pisano, I. Adrian-Kalchhauser, A. Bielen. Comparison of exoskeleton microbial communities of co-occurring native and invasive crayfish species. Journal of Invertebrate Pathology, doi: j.jip.2023.107996. link

A. Blanckaert, V. Sriram, and C. Bank. In search of the Goldilocks zone for hybrid speciation II: hard times for hybrid speciation? Evolution, doi: 10.1093/evolut/qpad125. link or preprint

L. Marrec, and C. Bank. Evolutionary rescue in a fluctuating environment: periodic versus quasi-periodic environmental changes. Proceedings of the Royal Society B, doi: 10.1098/rspb.2023.0770. link or preprint

A. Amado*#, J. Li*#, and C. Bank. STUN: forward-time Simulation on TUnable fitNess landscapes in recombining populations. Bioinformatics Advances, doi:10.1093/bioadv/vbad164. link or preprint

J. Li*#, A. Amado*#, and C. Bank. Rapid adaptation of recombining populations on tunable fitness landscapes. Molecular Ecology, doi: 10.1111/mec.16900. link or preprint

A.-H. Ghenu, A. Amado, I. Gordo, and C. Bank. Epistasis decreases with increasing antibiotic pressure but not temperature. Philosophical Transactions B, doi: 10.1098/rstb.2022.0058. link or preprint

J. Li, and C.-R. Lee. The role of gene presence–absence variations on genetic incompatibility in Asian rice. New Phytologist, doi: 10.1111/nph.18969. link

J. Rieder, A. Kapopoulou, C. Bank, and I. Adrian-Kalchhauser. Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems. Environmental Microbiome, doi: 10.1186/s40793-023-00459-z. link or preprint

M.T. Wortel, D. Agashe, S.F. Bailey, C. Bank, K. Bisschop, T. Blankers, J. Cairns, E.S. Colizzi, D. Cusseddu, M.M. Desai, B. van Dijk, M. Egas, J. Ellers, A.T. Groot, D.G. Heckel, M.L. Johnson, K. Kraaijeveld, J. Krug, L. Laan, M. Lässig, P.A. Lind, J. Meijer, L.M. Noble, S. Okasha, P.B. Rainey, D.E. Rozen, S. Shitut, S.J. Tans, O. Tenaillon, H. Teotónio, J.A.G.M. de Visser, M.E. Visser, R.M.A. Vroomans, G.D.A. Werner, B. Wertheim, and P.S. Pennings. Towards evolutionary predictions: Current promises and challenges. Evolutionary Applications, doi: 10.1111/eva.13513. link or earlier preprint

2022

C. Bank. Epistasis and adaptation on fitness landscapes. Annual Review in Ecology, Evolution, and Systematics, doi: 10.1146/annurev-ecolsys-102320-112153. link or preprint

J. Rieder, P. M. Martin-Sanchez, O. A. Osman, I. Adrian-Kalchhauser, A. Eiler. Detecting aquatic pathogens with field-compatible dried qPCR assays. Journal of Microbiological Methods, doi: 10.1016/j.mimet.2022.106594. link

C. Bank, M.A. Schmitz, and A.Y. Morales-Arce. Evolutionary models predict potential mechanisms of escape from mutational meltdown. Frontiers in Virology, doi: 10.3389/fviro.2022.886655. link or preprint

L. Lansch-Justen, D. Cusseddu, M.A. Schmitz, and C. Bank. The extinction time under mutational meltdown driven by high mutation rates. Ecology and Evolution, doi: 10.1002/ece3.9046. link or preprint

D. Stajic#, C. Bank, and I. Gordo#. Adaptive Potential of Epigenetic Switching During Adaptation to Fluctuating Environments. Genome Biology and Evolution, doi: 10.1093/gbe/evac065. link or preprint

D.V. McLeod, S. Gandon. Effects of epistasis and recombination between vaccine-escape and virulence alleles on the dynamics of pathogen adaptation. Nature Ecology & Evolution, doi: 10.1038/s41559-022-01709-y. link

J. Li#, M. Schumer, and C. Bank#. Imbalanced segregation of recombinant haplotypes in hybrid populations reveals inter- and intrachromosomal Dobzhansky-Muller incompatibilities. Plos Genetics, doi: 10.1371/journal.pgen.1010120. link or preprint

2021

M.A.D. Louro, M. Bettencourt-Dias, and Jorge Carneiro. A first-takes-all model of centriole copy number control based on cartwheel elongation. Plos Computational Biology, doi: 10.1371/journal.pcbi.1008359. link

M.S. Joshi, A. Kapopoulou, and S. Laurent. Impact of genetic variation in gene regulatory sequences: a population genomics perspective. Frontiers in Genetics, doi: 10.3389/fgene.2021.660899. link

M.A.D. Louro, M. Bettencourt-Dias, and C. Bank. Patterns of selection against centrosome amplification in human cell lines. Plos Computational Biology, doi: 10.1371/journal.pcbi.1008765. link or 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: 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

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

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

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

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

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

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

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.

C. Bank, J. Hermisson, and M. Kirkpatrick. Can reinforcement complete speciation? Evolution, doi: 10.1111/j.1558-5646.2011.01423.x. link This paper was listed in a Perspective on Recent work in speciation research by women authors in the journal Evolution, which appeared in 2022.