Papers

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Preprints

T Fu, RCT Wright, DR Gifford, CG Knight, MA Brockhurst (2024) Inflammation-like environments limit the loss of quorum sensing in Pseudomonas aeruginosa bioRxiv, doi:10.1101/2024.12.18.629113.

R Kettlewell, JH Forsyth, DR Gifford (2024) Evolutionary risk analysis of mutators for the development of nitrofurantoin resistance, bioRxiv, doi:10.1101/2024.10.07.616996.

Papers

T Ashfield, M Cooray, I Jimenez-Acha, Z Riaz, DR Gifford, M Lagator (2025) Reflecting on Fleming’s caveat: impact of stakeholder decision-making on antimicrobial resistance evolution, Microbiology (171), doi:10.1099/mic.0.001534.

MJ Jago, JK Soley, S Denisov, CJ Walsh, DR Gifford, BP Howden, M Lagator (2025) High-throughput method characterizes hundreds of previously unknown antibiotic resistance mutations, Nature Communications (16), doi:10.1038/s41467-025-56050-2

R Kettlewell*, C Jones*, TW Felton, M Lagator, DR Gifford (2024) Insights into durability against resistance from the antibiotic nitrofurantoin, npj Antimicrobials and Resistance 2(41), doi:10.1038/s44259-024-00056-1.

T Willmott, PP Kelly, L Jadaan, DR Gifford, SD Mercer, GJ Humphreys, CG Knight JR Lu, AJ McBain (2024) Investigations of microbial adaptation to singular, binary, and fully formulated quaternary ammonium compounds, Applied and Environmental Microbiology, doi:10.1128/aem.00666-24.

S Lindon, S Shah, DR Gifford, MA Gomis Font, D Kaur, A Oliver, RC MacLean, RM Wheatley (2024) Antibiotic resistance alters the ability of Pseudomonas aeruginosa to invade the respiratory microbiome, Evolution Letters, doi:10.1093/evlett/qrae030.

DR Gifford, A Bhattacharyya, A Geim*, E Marshall*, R Krašovec, CG Knight (2024) Environmental and genetic influence on rate and spectrum of spontaneous mutations in Escherichia coli, Microbiology 170(4), doi:10.1099/mic.0.001452.

Z Al-Baqsami, R Lowry Palmer, G Darwent, AJ McBain, CG Knight, DR Gifford (2024) Adaptation at the extremes of life: Experimental evolution with the extremophile archaeon Sulfolobus acidocaldarius. J Visualized Experiments (in production), doi:10.3791/66271.

AA Shahabuddin, R Clover, DR Gifford (2023) Coincidence analysis of efflux pumps in the Escherichia coli pangenome, Access Microbiology (under review).

T Fu, DR Gifford, CG Knight, MA Brockhurst (2023) Eco-evolutionary dynamics of experimental Pseudomonas aeruginosa populations under oxidative stress, Microbiology 169(11), doi:10.1099/mic.0.001396.

DR Gifford, E Berríos-Caro*, C Joerres*, M Suñé, JH Forsyth, A Bhattacharyya, T Galla, CG Knight (2023) Mutators can drive the evolution of multi-resistance to antibiotics, PLOS Genetics 19(6): e1010791. doi:10.1101/643585.

E Berríos-Caro, DR Gifford, T Galla (2021) Competition delays multi-drug resistance evolution during combination therapy, Journal of Theoretical Biology 509, doi: 10.1016/j.jtbi.2020.110524.

DR Gifford (2019) Life on the frontline reveals constraints, Nature Ecology & Evolution 3 (11), 1501-1502, doi:10.1038/s41559-019-1010-3.

GM Knight, NG Davies, C Colijn, F Coll, T Donker, DR Gifford, RE Glover, M Jit, E Klemm, S Lehtinen, JA Lindsay, M Lipsitch, MJ Llewelyn, ALP Mateus, JV Robothma, M Sharland, D Stekel, L Yakob, KE Atkins (2019) Mathematical modelling for antibiotic resistance control policy: do we know enough?, BMC Infectious Diseases 19, 1011, doi:10.1186/s12879-019-4630-y.

R Krašovec, H Richards, G Gomez, DR Gifford, A Mazoyer, CG Knight (2019) Measuring Microbial Mutation Rates with the Fluctuation Assay, Journal of Visualised Experiments, (153), e60406, doi: 10.3791/60406.

DR Gifford, R Krašovec, E Aston, RV Belavkin, A Channon, CG Knight (2018) Environmental pleiotropy and demographic history direct adaptation under antibiotic selection, Heredity, 121, 438-448, doi: 10.1038/s41437-018-0137-3.

DR Gifford*, V Furió*, A Papkou, T Vogwill, A Oliver, RC MacLean (2018) Identifying and exploiting genes that potentiate the evolution of antibiotic resistance, Nature Ecology & Evolution, doi: 10.1038/s41559-018-0547-x.

R Krašovec, H Richards, DR Gifford, RV Belavkin, A Channon, E Aston, AJ McBain, CG Knight (2018) Opposing effects of population density and stress on Escherichia coli mutation rate, ISME J, doi:10.1038/s41396-018-0237-3.

R Krašovec*, H Richards*, DR Gifford, C Hatcher, KJ Faulkner, RV Belavkin, A Channon, E Aston, AJ McBain, CG Knight (2017) Spontaneous mutation rate is a plastic trait associated with population density across domains of life, PLoS Biology, 15(8), e2002731, doi: 10.1371/journal.pbio.2002731.

E Aston, A Channon, RV Belavkin, DR Gifford, R Krašovec, CG Knight (2017) Critical mutation rate has an exponential dependence on population size for eukaryotic-length genomes with crossover, Scientific Reports, 7, 15519, doi: 10.1038/s41598-017-14628-x.

A San Millan, JA Escudero*, DR Gifford*, D Mazel, RC MacLean (2016) Multicopy plasmids potentiate the evolution of antibiotic resistance in bacteria, Nature Ecology & Evolution, 1(1), doi: 10.1038/s41559-016-0010.

DR Gifford*, E Moss*, RC MacLean (2016) Environmental variation alters the fitness effects of rifampicin resistance mutations in Pseudomonas aeruginosa, Evolution, 70(3), 725-730. doi: 10.1111/evo.12880.

DR Gifford, M Toll-Riera, RC MacLean (2016) Epistatic interactions between ancestral genotype and beneficial mutations shape evolvability in rifampicin resistant Pseudomonas aeruginosa, Evolution, 70(7), 1659-1666, doi: 10.1111/evo.12958.

T Vogwill*, RL Phillips*, DR Gifford*, RC MacLean (2016) Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution, Proceedings B, 283(1835), 20160749, doi: 10.1098/rspb.2016.0749.

A Betts, DR Gifford, RC MacLean, KC King (2016) Parasite diversity drives rapid host dynamics and evolution of resistance in a bacteria-phage system, Evolution, 70(5), 968-978. doi: 10.1111/evo.12909.

DR Gifford, M Toll-Riera, M Kojadinovic, RC MacLean (2015) Here’s to the losers: evolvable residents accelerate the evolution of high fitness invaders, The American Naturalist, 186(1), 41-49. doi: 10.1086/681598.

DR Gifford & RC MacLean (2013) Evolutionary reversals of antibiotic resistance in experimental populations of Pseudomonas aeruginosa, Evolution, 16(10), 2973-2981, doi: 10.1111/evo.12158.

DR Gifford & SE Schoustra (2013) Modelling colony population growth in the filamentous fungus Aspergillus nidulans, Journal of Theoretical Biology, 320, 124-30. doi: 10.1016/j.jtbi.2012.12.003.

DR Gifford, JAGM de Visser, LM Wahl (2012) Model and test in a fungus of the probability that beneficial mutations survive drift, Biology Letters, 9(1), doi: 10.1098/rsbl.2012.0310.

DR Gifford, SE Schoustra, R Kassen (2011) The length of adaptive walks is insensitive to starting fitness in Aspergillus nidulans, Evolution, 65(11), 3070-3078. doi: 10.1111/j.1558-5646.2011.01380.x.

SE Schoustra, T Bataillon, DR Gifford, R Kassen (2009) The properties of adaptive walks in evolving populations of fungus, PLoS Biology, 7(11), e1000250. doi: 10.1371/journal.pbio.1000250. (NSERC Impact Story)

* equal contributions