Publications

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

Lab publications are printed in black; prior work of current lab members in gray.

2017

  • 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 preprint
  • P. Simões, I. Fragata, S.G. Seabra, G.S. Faria, M.A. Santos, M.R. Rose, M. Santos, and M. Matos. Predictable phenotypic, but not karyotypic, evolution of populations with contrasting initial history. Scientific Reports 7:913. 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 428: 538-553. link
  • I. Fragata, M. Lopes-Cunha, M. Bárbaro, B. Kellen, M. Lima, G.S. Faria, S.G. Seabra, M. Santos, P. Simões, and M. Matos. Keeping your options open: Maintenance of thermal plasticity during adaptation to a stable environment. Evolution 70: 195-206. link
  • J. Santos, M. Pascual, I. Fragata, P. Simões, M.A. Santos, M. Lima, A. Marques, M. Lopes-Cunha, B. Kellen, J. Balanyà, M.R. Rose, and M. Matos. Tracking changes in chromosomal arrangements and their genetic content during adaptation. Journal of Evolutionary Biology [epub ahead of print] link
  • A.-H. Ghenu, B.M. Bolker, D.J. Melnick, and B.J. Evans. Multicopy gene family evolution on primate Y chromosomes. BMC Genomics 17: 157. link
  • R.K. Schott, J. Müller, C.G.Y. Yang, N. Bhattacharyya, N. Chan, M. Xu, J.M. Morrow, A.-H. Ghenu, E.R. Loew, V. Tropepe, and B.S.W. Chang. Evolutionary transformation of rod photoreceptors in the all-cone retina of a diurnal garter snake. Proceedings of the National Academy of Sciences 113: 356-361. 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 32: 229-238. link
  • P. Simões*, I. Fragata*, M. Lopes-Cunha, M. Lima, B. Kellen, M. Bárbaro, M. Santos, and M. Matos. Wing trait-inversion associations in Drosophila subobscura can be generalized within continents, but may change through time. Journal of Evolutionary Biology 28: 2163-2174. link
  • M. Matos, P. Simões, M.A. Santos, S.G. Seabra, G.S. Faria, F. Vala, J. Santos, and I. Fragata. History, chance and selection during phenotypic and genomic experimental evolution: replaying the tape of life at different levels. Frontiers in Genetics 6: 71. link
  • M. Bárbaro, M.S. Mira, I. Fragata, P. Simões, M. Lima, M. Lopes-Cunha, B. Kellen, J. Santos, S.A.M. Varela, M. Matos, and S. Magalhaes. Evolution of mating behavior between two populations adapting to common environmental conditions. Ecology and Evolution 5: 1609-1617. link

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 30: 540-546. link
  • 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 196: 841-852. link

    In this publication, we present a statistical approach for estimating the fitness of engineered mutations in high-throughput bulk competitions, which we apply to a data set of the same 560 mutations in yeast Hsp90 under six environmental conditions. Analyzing the distribution of fitness effects across environments and between one-, two- and three-nucleotide step mutations, we find that larger step sizes harbor more potential for adaptation in challenging environments, but also tend to be more deleterious in the standard environment; an observation consistent with predictions from Fisher’s geometric model (which was proposed by Fisher in 1930). Furthermore, the shape of the beneficial tail of the fitness distribution becomes heavier under the most severe environmental challenge (here represented by a cold environment with high salinity), indicating a higher potential for rapid adaptation through mutations of unpredictably large size.

  • 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, 10(2): e1004185. 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 15: 176-192. link
  • D. Roze and A. Blanckaert. Epistasis, pleiotropy, and the mutation load in sexual and asexual populations. Evolution 68: 137-149. link
  • I. Fragata, M. Lopes-Cunha, M. Bárbaro, B. Kellen, M. Lima, M.A. Santos, G.S. Faria, M. Santos, M. Matos, and P. Simões. How much can history constrain adaptive evolution? A real-time evolutionary approach of inversion polymorphisms in Drosophila subobscura. Journal of Evolutionary Biology 27: 2727-2738. link
  • I. Fragata*, P. Simões*, M. Lopes-Cunha, M. Lima, B. Kellen, M. Bárbaro, J. Santos, M.R. Rose, M. Santos, and M. Matos. Laboratory selection quickly erases historical differentiation. PLOS ONE 9: e96227. link

2013

  • R.T. Hietpas*, C. Bank*, J.D. Jensen#, and D.N.A. Bolon#. Shifting fitness landscapes in response to altered environments. Evolution 67: 3512-3522. link
  • J. Santos, M. Pascual, P Simões, I. Fragata, M.R. Rose, and M. Matos. Fast evolutionary genetic differentiation during experimental colonizations. Journal of Genetics 92: 183-194. link

2012

  • C. Bank, R. Bürger, and J. Hermisson. The limits to parapatric speciation: Dobzhansky-Muller incompatibilities in a continent-island model. Genetics 191: 845-863. link

    Despite their deleterious effects on hybrids, epistatic genetic interactions in form of Dobzhansky-Muller incompatibilities (DMIs) seem to persist, and potentially even accumulate, in populations in the presence of gene flow. In this paper, we provide a rigorous theoretical framework to study this phenomenon. We determine the maximum amount of gene flow that allows for the accumulation or maintenance of DMIs, and interpret our results with respect to the relative importance of ecological and mutation-order speciation; two concepts that are controversially discussed in the field of speciation.

  • C. Bank, J. Hermisson, and M. Kirkpatrick. Can reinforcement complete speciation? Evolution 66: 229-239. link
  • J. Santos, M. Pascual, P. Simões, I. Fragata, M. Lima, B. Kellen, M. Santos, A. Marques, M.R. Rose, and M. Matos. From nature to the laboratory: the impact of founder effects on adaptation. Journal of Evolutionary Biology 25: 2607-2622. link

2010

  • I. Fragata, J. Balanyà, C. Rego, M. Matos, E.L. Rezende, and M. Santos. Contrasting patterns of phenotypic variation linked to chromosomal inversions in native and colonizing populations of Drosophila subobscura. Journal of Evolutionary Biology 23: 112-123. link
  • M. Santos, I. Fragata, J. Santos, P. Simões, A. Marques, M. Lima, and M. Matos. Playing Darwin. Part B. 20 years of domestication in Drosophila subobscura. Theory in Biosciences 129: 97-102. link
  • C. Rego, J. Balanyà, I. Fragata, M. Matos, E.L. Rezende, and M. Santos. Clinal patterns of chromosomal inversion polymorphisms in Drosophila subobscura are partly associated with thermal preferences and heat stress resistance. Evolution 64: 385-397. link
  • E.L. Rezende, J. Balanyà, F. Rodríguez-Trelles, C. Rego, I. Fragata, M. Matos, L. Serra, and M. Santos. Climate change and chromosomal inversions in Drosophila subobscura. Climate Research 43: 103. link

2008

  • P. Simões, J. Santos, I. Fragata, L.D. Mueller, M.R. Rose, and M. Matos. How repeatable is adaptive evolution? The role of geographical origin and founder effects in laboratory adaptation. Evolution 62: 1817-1829. link

*equal contribution; #co-corresponding authors