Publications

  1. de Visser, J.A.G.M., S.F. Elena, I. Fragata and S. Matuszewski. 2018. The utility of fitness landscapes and big data for predicting evolution. (Editorial for special issue). Heredity 121: 401-405.
  2. de Vos, M.G.J., S.E. Schoustra and J.A.G.M. de Visser. 2018. Ecology dictates evolution? About the importance of genetic and ecological constraints in adaptation. Europhysics Letters 122: 58002.
  3. Zwart, M.P., M.F. Schenk, S. Hwang, B. Koopmanschap, N. de Lange, L. van de Pol, T. Thi Thuy Nga, I.G. Szendro, J. Krug and J.A.G.M. de Visser. 2018. Unraveling the causes of adaptive benefits of synonymous mutations in TEM-1 β-lactamase. Heredity 121: 406-421.
  4. de Vos, M.G.J., J.A.G.M. de Visser, J.W.A. Rossen and B.J. Zwaan. 2018. Polymicrobiële infecties: ecosystemen met bijzondere eigenschappen (in Dutch). Nederlands Tijdschrift voor Geneeskunde 162: D2224.
  5. Gorter, F.A., J. Bobula, M.G.M. Aarts, B.J. Zwaan, R. Korona and J.A.G.M. de Visser. 2018. Local Fitness Landscapes Predict Yeast Evolutionary Dynamics in Directionally Changing Environments. Genetics 208: 307-322. DOI: doi.org/10.1534/genetics.117.300519
  6. Salverda, M.L.M., J. Koomen, B. Koopmanschap, M.P. Zwart and J.A.G.M. de Visser. 2017. Adaptive benefits from small mutation supplies in an antibiotic resistance enzyme. Proceedings of the National Academy of Sciences USA 114: 12773-12778. Doi:10.1073/pnas.1712999114
  7. Ibarlucea, B., R. Taiuk Rim, B. Chang-Ki, J.A.G.M. de Visser, L. Baraban and G. Cuniberti. 2017. Nanowire sensors monitor bacterial growth kinetics and response to antibiotics. Lab on a Chip, DOI: 10.1039/c7lc00807d.
  8. van Dijk, T., S. Hwang, J. Krug, J.A.G.M. de Visser and M.P. Zwart. 2017. Mutation supply and the repeatability of selection for antibiotic resistance. Physical Biology 14: 055005. DOI: 10.1088/1478-3975/aa7f36
  9. Gorter, F.A., M.F.L. Derks, J. van den Heuvel, M.G.M. Aarts, B.J. Zwaan, D. de Ridder and J.A.G.M. de Visser. 2017. Genomics of adaptation depends on the rate of environmental change in experimental yeast populations. Molecular Biology and Evolution 34: 2613-2626. DOI: 1093/molbev/msx185
  10. Plech, M., K. Tomala, H. Tutaj, D.E. Piwcewicz, J.A.G.M. de Visser and R. Korona. 2017. Power provides protection: Genetic robustness in yeast depends on the capacity to generate energy. PLoS Genetics 13: e1006768. DOI: 1371/journal.pgen.1006768
  11. Pieczynska, M.D., R. Korona and J.A.G.M. de Visser. 2017. Experimental tests of host-virus coevolution in natural killer yeast strains. Journal of Evolutionary Biology 30: 773-781. DOI: 1111/jeb.13044
  12. Rozen, D. and A. de Visser. 2017. A poster child for experimental evolution. Peer Community in Evolutionary Biology. DOI: 10.24072/pci.evolbiol.100011
  13. Pesce, D., N. Lehman and J.A.G.M. de Visser. 2016. Sex in a test tube: benefits of in vitro recombination. Philosophical Transactions of the Royal Society 371: 20150529. DOI: 10.1098/rstb.2015.0529.
  14. Schoustra, S.E., S. Hwang, J. Krug and J.A.G.M. de Visser. 2016. Diminishing-returns epistasis among random beneficial mutations in a multicellular fungus. Proceedings of the Royal Society London B 283: 20161376. DOI: 10.1098/rspb.2016.1376.
  15. Pieczynska, M., D. Wloch-Salamon, R. Korona and J.A.G.M. de Visser. 2016. Rapid multiple-level coevolutionary dynamics in experimental populations of yeast killer and non-killer strains. Evolution 70: 1342-1353. DOI: 1111/evo.12945
  16. Cottinet, D., F. Condamine, N. Bremond, A.D. Griffiths, P.B. Rainey, J.A.G.M. de Visser, J. Baudry and J. Bibette. 2016. Lineage tracking for probing heritable phenotypes at single-cell resolution. PLoS One, 11: e0152395. DOI: 10.1371/journal.pone.o152395.
  17. Gorter, F.A., M.G.M. Aarts, B.J. Zwaan and J.A.G.M. de Visser. 2016. Dynamics of adaptation in experimental yeast populations exposed to gradual and abrupt change in heavy metal concentration. The American Naturalist 187: 110-119. DOI: 10.1086/684104
  18. De Visser, J.A.G.M. 2015. Evolution of coexistence in a crowded microplate well (Commentary). Proceedings of the National Academy of Sciences USA 112: 11148-11149. DOI: 1073/pnas.1514399112
  19. Karnaushenko, D., L. Baraban, D. Ye, I. Uguz, R.G. Mendes, M.H. Rümmeli, J.A.G.M. de Visser, O.G. Schmidt, G. Cuniberti and D. Makarov. 2015. Monitoring microbial metabolites using an inductively coupled resonance circuit. Scientific Reports 5: 12878, DOI: 10.1038/srep12878.
  20. Dellus-Gur, E., M. Elias, E. Caselli, F. Prati, M.L.M. Salverda, J.A.G.M. de Visser, J.S. Fraser and D.S. Tawfik. 2015. Negative epistasis and evolability in TEM-1 β-lactamase – The thin line between an ezyme’s conformational freedom and disorder. Journal of Molecular Biology 427: 2396-2409. DOI: 10.1016/j.jmb.2015.05.011
  21. Schenk, M.F., S. Witte, M.L.M. Salverda, B. Koopmanschap, J. Krug and J.A.G.M. de Visser. 2015. Role of pleiotropy during adaptation of TEM-1 β-lactamase to two novel antibiotics. Evolutionary Applications 8: 248-260. DOI: 10.1111/eva.12200
  22. De Visser, J.A.G.M. and J. Krug. 2014. Empirical fitness landscapes and the predictability of evolution. Nature Reviews Genetics 15: 480-490. DOI: 10.1038/nrg3744
  23. Plech, M., J.A.G.M. de Visser and R. Korona. 2014. Heterosis is prevalent among domesticated but not wild strains of Saccharomyces cerevisiae. G3: Genes, Genomes, Genetics 4: 315-323. DOI: 10.1534/g3.113.009381
  24. Pieczynska, M.D., J.A.G.M. de Visser and R. Korona. 2013. Incidence of symbiotic dsRNA ‘killer’ viruses in wild and domesticated yeast. FEMS Yeast Research 13: 856-859. DOI: 10.1111/1567-1364.12086
  25. Schenk, M.F., I.G. Szendro, M.L.M. Salverda, J. Krug and J.A.G.M. de Visser. 2013. Patterns of epistasis between beneficial mutations in an antibiotic resistance enzyme. Molecular Biology and Evolution 30: 1779-1787. DOI: 10.1093/molbev/mst096
  26. Schenk, M.F. and J.A.G.M. de Visser. 2013. Predicting the evolution of antibiotic resistance. BMC Biology 11: 14. DOI: 10.1186/1741-7007-11-14
  27. Gifford, D.R., J.A.G.M. de Visser and L.M. Wahl. 2013. Model and test in a fungus of the probability that beneficial mutations survive drift. Biology Letters 9: 20120310. DOI: 10.1098/rsbl.2012.0310
  28. Szendro, I.G., J. Franke, J.A.G.M. de Visser and J. Krug. 2013. Predictability of evolution depends non-monotonically on population size. Proceedings of the National Academy of Sciences USA 110: 571-576. DOI: 1073/pnas.1213613110
  29. Szendro, I.G., M.F. Schenk, J. Franke, J. Krug and J.A.G.M. de Visser. 2013. Quantitative analyses of empirical fitness landscapes. Journal of Statistical Mechanics P01005. DOI: 10.1088/1742-5468/2013/01/P01005
  30. Schenk, M.F., I.G. Szendro, J. Krug and J.A.G.M. de Visser. 2012. Quantifying the adaptive potential of an antibiotic resistance enzyme. PLoS Genetics 8: e1002783. DOI: 10.1371/journal.pgen.1002783
  31. de Visser, J.A.G.M., T.F. Cooper and S.F. Elena. 2011. The causes of epistasis. Proceedings of the Royal Society London B 278: 3617-3624. DOI: 10.1098/rspb.2011.1537
  32. Franke, J., A. Klözer, J.A.G.M. de Visser and J. Krug. 2011. Evolutionary accessibility of mutational pathways. PLoS Computational Biology 7: e1002134. DOI: 10.1371/journal.pcbi.1002134
  33. Baraban, L., F. Bertholle, M.L.M. Salverda, N. Bremond, P. Panizza, J. Baudry, J.A.G.M. de Visser and J. Bibette. 2011. Millifluidic droplet analyser for microbiology. Lab on a Chip 11: 4057. DOI: 10.1039/c1lc20545e
  34. Salverda, M.L.M. and J.A.G.M. de Visser. 2011. Evolution with foresight (Dispatch). Current Biology 21: R398-R400. DOI: 10.1016/j.cub.2011.04.023
  35. Salverda, M.L.M., E. Dellus, F.A. Gorter, A.J.M. Debets, J. van der Oost, R.F. Hoekstra, D.S. Tawfik and J.A.G.M. de Visser. 2011. Initial mutations direct alternative pathways of protein evolution. PLoS Genetics 7: e1001321. DOI: 10.1371/journal.pgen.1001321
  36. Salverda, M.L.M., J.A.G.M. de Visser and M. Barlow. 2010. Natural evolution of TEM-1 beta-lactamase: experimental reconstruction and clinical relevance. FEMS Microbiology Reviews 34: 1015-1036. DOI: 10.1111/j.1574-6976.2010.00222.x
  37. Zwart, M.P., L. Hemerik, J.S. Cory, J.A.G.M. de Visser, F.J.J.A. Bianchi, M.M. van Oers, J.M. Vlak, R.F. Hoekstra and W. van der Werf. 2009. An experimental test of the independent action hypothesis in virus-insect pathosystems. Proceedings of the Royal Society London B 276: 2233-2242. DOI: 10.1098/rspb.2009.0064
  38. Rozen, D.E., N. Philippe, J.A. de Visser, R.E. Lenski and D. Schneider. 2009. Death and cannibalism in a seasonal environment facilitate bacterial coexistence. Ecology Letters 12: 34-44. DOI: 10.1111/j.1461-0248.2008.01257.x
  39. Zwart, M.P., W. van der Werf, M.M. van Oers, L. Hemerik, J.M.V. van Lent, J.A.G.M. de Visser, J.M. Vlak, and J.S. Cory. 2009. Mixed infections and the competitive fitness of faster-acting genetically modified viruses. Evolutionary Applications 2: 209-221. DOI: 10.1111/j.1752-4571.2008.00058.x
  40. de Visser, J.A.G.M., S.-C. Park and J. Krug. 2009. Exploring the effect of sex on empirical fitness landscapes. The American Naturalist 174: S15-S30. DOI: 1086/599081
  41. Aanen, D.K., A.J.M. Debets, J.A.G.M. de Visser and R.F. Hoekstra. 2008. The social evolution of somatic fusion. BioEssays 30: 1193-1203. DOI: 10.1002/bies.20840
  42. Zwart, M.P., E. Erro, M. van Oers, J.A.G.M. de Visser and J.M. Vlak. 2008. Low multiplicities of infection in vivo result in purfying selection against baculovirus deletion mutants originating from tissue cultures. Journal of General Virololgy 89: 1220-1224. DOI: 10.1099/vir.0.83645-0
  43. Rozen, D.E., M.G.J.L. Habets, A. Handel and J.A.G.M. de Visser. Heterogeneous adaptive trajectories of small populations on complex fitness landscapes. PLoS One 3: e1715. DOI: 10.1371/journal.pone.0001715
  44. Wloch-Salamon, D.M., D. Gerla, R.F. Hoekstra and J.A.G.M. de Visser. 2008. Effect of dispersal and nutrient availability on the competitive ability of toxin producing yeast. Proceedings of the Royal Society London B 275: 535-541. DOI: 10.1098/rspb.2007.1461
  45. Ter Maat, A., C. Zonneveld, J.A.G.M. de Visser, R.F. Jansen, C. Montagne-Wajer and J.M. Koene. 2007. Food intake, growth and reproduction as affected by day length and food availability in the pond snail Lymnaea stagnalis. American Malacological Bulletin 23: 113-120. DOI: 10.4003/0740-2783-23.1.113
  46. Habets, M.G.L.M., T. Czárán, R.F. Hoekstra and J.A.G.M. de Visser. 2007. Spatial structure inhibits the rate of invasion of beneficial mutations in asexual populations. Proceedings of the Royal Society London B 274: 2139-2143. DOI: 10.1098/rspb.2007.0529
  47. De Visser, J.A.G.M. 2007. Bacterial solutions to the problem of sex. PLoS Biology 5 (9): 1844-1846. DOI: 10.1371/journal.pbio.0050245
  48. De Visser, J.A.G.M. and S.F. Elena. 2007. The evolution of sex: empirical insights into the roles of epistasis and drift. Nature Reviews Genetics 8: 139-149. DOI: 10.1038/nrg1985
  49. Habets, M.G.J.L., D.E. Rozen, R.F. Hoekstra and J.A.G.M. de Visser. 2006. The effect of population structure on the adaptive radiation of microbial populations evolving in spatially structured environments. Ecology Letters 9: 1041-1048. DOI: 10.1111/j.1461-0248.2006.00955.x
  50. De Visser, J.A.G.M. and D.E. Rozen. 2006. Clonal interference and the periodic selection of new beneficial mutations in Escherichia coli. Genetics 172: 2093-2100. DOI: 10.1534/genetics.105.052373
  51. De Visser, J.A.G.M. and D.E. Rozen. 2005. Limits to adaptation in asexual populations. Journal of Evolutionary Biology 18: 779-788. DOI: 10.1111/j.1420-9101.2005.00879.x
  52. De Visser, J.A.G.M., A.D.L. Akkermans, R.F. Hoekstra and W.M. de Vos. 2004. Insertion sequence-mediated mutations isolated during adaptation to growth and starvation in Lactococcus lactis. Genetics 168: 1145-1157. DOI: 10.1534/genetics.104.032136
  53. De Visser, J.A.G.M. and D.E. Rozen. 2004. Comment on “High deleterious genomic mutation rate in stationary phase of Escherichia coli”. Science 304: 518. DOI: 10.1126/science.1094911
  54. De Visser, J.A.G.M., J. Hermisson, G.P. Wagner, L. Ancel Meyers, H. Bagheri-Chaichian, J.L. Blanchard, L. Chao, J.M. Cheverud, S.F. Elena, W. Fontana, G. Gibson, T.F. Hansen, D. Krakauer, R.C. Lewontin, C. Ofria, S.H. Rice, G. von Dassow, A. Wagner and M.C. Whitlock. 2003. Evolution and detection of genetic robustness (Perspective). Evolution 57: 1959-1972. DOI: 1111/j.0014-3820.2003.tb00377.x
  55. Bruggeman, J., A.J.M. Debets, P.J. Wijngaarden, J.A.G.M. de Visser and R.F. Hoekstra. 2003. Sex slows down the accumulation of deleterious mutations in the homothallic fungus Aspergillus nidulans. Genetics 164: 479-485. URL: http://www.genetics.org/content/164/2/479
  56. Elena, S.F. and J.A.G.M. de Visser. 2003. Environmental stress and mutational effects (Minireview). Journal of Biology 2:12. URL: jbiol.com/content/2/2/12
  57. De Visser, J.A.G.M. and R.E. Lenski. 2002. Long-term experimental evolution in Escherichia coli. XI. Rejection of non-transitive interactions as cause of declining rate of adaptation. BMC Evolutionary Biology 2: 19. DOI: 10.1186/1471-2148-2-19
  58. Rozen, D.E., J.A.G.M. de Visser and P.J. Gerrish. 2002. Fitness effects of fixed beneficial mutations in microbial populations. Current Biology 12: 1040-1045. DOI: 10.1016/S0960-9822(02)00896-5
  59. De Visser, J.A.G.M. 2002. The fate of microbial mutators. Microbiology 148: 1247-1252. DOI: 1099/00221287-148-5-1247
  60. Zoetendal, E.G., A.D.L. Akkermans, W.M. Akkermans-van Vliet, J.A.G.M. de Visser and W.M. de Vos. 2001. The host genotype affects the bacterial community in the human gastrointestinal tract. Microbial Ecology in Health and Disease 13: 129-134. DOI: 10.3402/mehd.v13i3.8013
  61. Van Belkum, A., M. Struelens, A. de Visser, H. Verbrugh and M. Tibayrenc. 2001. Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology. Clinical Microbiology Reviews 14: 547-560. DOI: 10.1128/CMR.14.3.547-560.2001
  62. Zeyl, C., M. Mizesko and J.A.G.M. de Visser. 2001. Mutational meltdown in laboratory yeast populations. Evolution 55: 909-917. DOI: 10.1111/j.0014-3820.2001.tb00608.x
  63. Zeyl, C. and J.A.G.M. de Visser. 2001. Estimates of the rate and distribution of fitness effects of spontaneous mutation in Saccharomyces cerevisiae. Genetics 157: 53-61. URL: http://www.genetics.org/content/157/1/53
  64. De Visser, J.A.G.M., C.W. Zeyl, P.J. Gerrish, J.L. Blanchard and R.E. Lenski. 1999. Diminishing returns from mutation supply rate in asexual populations. Science 283: 404-406. DOI: 1126/science.283.5400.404
  65. De Visser, J.A.G.M. and R.F. Hoekstra. 1998. Synergistic epistasis between loci affecting fitness: evidence in plants and fungi. Genetical Research, Camb. 71: 39-49. DOI: 10.1017/S0016672397003091
  66. De Visser, J.A.G.M., R.F. Hoekstra and H. van den Ende. 1997. Test of interaction between genetic markers that affect fitness in Aspergillus niger. Evolution 51: 1499-1505. DOI: 2307/2411202
  67. De Visser, J.A.G.M., R.F. Hoekstra and H. van den Ende. 1997. An experimental test for synergistic epistasis and its application in Chlamydomonas. Genetics 145: 815-819. URL: genetics.org/content/145/3/815
  68. Hoekstra, R.F., J.A.G.M. de Visser and A.J.M. Debets. 1997. The role of sexual reproduction in the elimination of deleterious mutations. Journal of Reproductive Development 43: Suppl., 7-8.
  69. De Visser, J.A.G.M., R.F. Hoekstra and H. van den Ende. 1996. The effect of sex and deleterious mutations on fitness in Chlamydomonas. Proceedings of the Royal Society London B 263: 193-200. DOI: 1098/rspb.1996.0031
  70. De Visser, J.A.G.M., A. ter Maat and C. Zonneveld. 1994. Energy budgets and reproductive allocation in the simultaneous hermaphrodite pond snail, Lymnea stagnalis (L.): a trade-off between male and female function. The American Naturalist 144: 861-867. DOI: 10.1086/285712
  71. Van Schaik, C.P. and J.A.G.M. de Visser. 1990. Fragile sons or harassed daughters? Sex differences in mortality among juvenile primates. Folia Primatologica 55: 10-23. DOI: 10.1159/000156493