The McDonald Lab
Laboratory for Microbial Experimental Evolution @ Monash University
Select Publications - see google scholar for full list
ANT Nguyen, R Gorrell, T Kwok, T Connallon, MJ McDonald
Nature Ecology and Evolution Jan. 4. 2024
AL Sezmis, LC Woods, AY Peleg, MJ McDonald
Molecular Biology and Evolution 40 (3), msad028. 2023
Bacteriophages evolve enhanced persistence to a mucosal surface
WH Chin, C Kett, O Cooper, D Müseler, Y Zhang, RS Bamert, R Patwa, ...
Proceedings of the National Academy of Sciences 119 (27), e2116197119. 2022
J Zhao, Y Zhu, YW Lin, H Yu, H Wickremasinghe, J Han, T Velkov, ...
Clinical Microbiology and Infection 28 (7), 1026. e1-1026. e5. 2022
Long-term experimental evolution decouples size and production costs in Escherichia coli
DJ Marshall, M Malerba, T Lines, AL Sezmis, CM Hasan, RE Lenski, ...
Proceedings of the National Academy of Sciences 119 (21), e2200713119. 2022
JN Barber, LC Nicholson, LC Woods, LM Judd, AL Sezmis, J Hawkey, ...
The ISME Journal 16 (5), 1442-1452. 2022
ANT Nguyen, LC Woods, R Gorrell, S Ramanan, T Kwok, MJ McDonald
Proceedings of the National Academy of Sciences 2022
Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations
MS Johnson, S Gopalakrishnan, J Goyal, ME Dillingham, CW Bakerlee, ...
Elife 10, e63910
Host Diversity slows bacteriophage adaptation by selecting generalists over specialists.
Duhita G Sant, Laura C Woods, Jeremy J Barr, Michael J McDonald
Nature Ecology & Evolution, January 2021
DOI: 10.1038/s41559-020-01364-1
Horizontal gene transfer potentiates adaptation by reducing selective constraints on the spread of genetic variation.
LC Woods, RJ Gorrell, F Taylor, T Connallon, T Kwok, MJ McDonald
PNAS, 2020 117 (43), 26868-26875
The evolution of coexistence from competition in experimental co-cultures of Escherichia coli and Saccharomyces cerevisiae
JN Barber, AL Sezmis, LC Woods, TD Anderson, JM Voss, MJ McDonald
ISME, 2020
DOI: 10.1038/s41396-020-00810-z
Sex alters molecular evolution in diploid experimental populations of S. cerevisiae
Jun-Yi Leu, Shang-Lin Chang, Jung-Chi Chao, Laura C. Woods & Michael J. McDonald
Nature of Ecology and Evolution, February 2020
DOI https://doi.org/10.1038/s41559-020-1101-1
Microbial Experimental Evolution – a proving ground for evolutionary theory and a tool for discovery
Michael J. McDonald
EMBO report 2019, July 27,
PMID: 31338963
DOI 10.15252/embr.201846992
Diverse hydrogen production and consumption pathways influence methane production in ruminants
Chris Greening, Renae Geier, Cecilia Wang, Laura C. Woods, Sergio E. Morales, Michael J. McDonald, Rowena Rushton-Green3, Xochitl C. Morgan, Satoshi Koike, Sinead C. Leahy, William J. Kelly, Isaac Cann, Graeme T. Attwood, Gregory M. Cook, Roderick I. Mackie2
The ISME Journal (2019), Published: 26 June 2019
PMID: 31243332
Adaptive evolution of genomically recoded Escherichia coli
Timothy M. Wannier, Aditya M. Kunjapur, Daniel P. Rice, Michael J. McDonald, Michael M. Desai, George M. Church
PNAS. 2018, Feb 13,
PMID: 29440500
Fitness cost of mcr-1mediated polymyxin resistance in Klebsiella pneumoniae
Nang, Sue; Morris, Faye; McDonald, Michael; Han, Mei-Ling; Wang, Jiping; Strugnell, Richard; Velkov, Tony; Li, Jian
Journal of Antimicrobial Chemotherapy. 2018
The dynamics of molecular evolution over 60,000 generations.
BH Good, MJ McDonald, JE Barrick, RE Lenski, Desai MM.
Nature. 2017, Nov 2
PMID: 29045390
Coevolution with bacteria drives the evolution of aerobic fermentation in Lachancea kluyveri
Nerve Zhou, Krishna BS Swamy, Jun-Yi Leu, Michael J McDonald, Silvia Galafassi, Concetta Compagno, Jure Piškur
PloS one. 2017 12 (3), e0173318
PMID: 28282411
Mutation at a distance caused by homopolymeric guanine repeats in Saccharomyces cerevisiae.
Michael J. McDonald, Yen-Hsin Yu, Jheng-Fen Guo, Shin Yen Chong, Cheng-Fu Kao and Jun-Yi Leu
Science Advances May 27 2016: E1501033 Free Open Access
Sex speeds adaptation by altering the dynamics of molecular evolution.
McDonald MJ, Rice DP, Desai MM.
Nature. 2016 Mar 10;531(7593):233-6. doi: 10.1038/nature17143. Epub 2016 Feb 24.
PMID: 26909573 PDF
The evolutionary dynamics of tRNA-gene copy number and codon-use in E. coli.
McDonald MJ, Chou CH, Swamy KB, Huang HD, Leu JY.
BMC Evolutionary Biology. 2015 Aug 19;15:163. doi: 10.1186/s12862-015-0441-y.
PMID: 26282127 PMC Open Access FullText
Crowded growth leads to the spontaneous evolution of semistable coexistence in laboratory yeast populations.
Frenkel EM, McDonald MJ, Van Dyken JD, Kosheleva K, Lang GI, Desai MM.
Proc Natl Acad Sci U S A. 2015 Sep 8;112(36):11306-11. doi: 10.1073/pnas.1506184112. Epub 2015 Aug 3.
PMID: 26240355 PMC Open Access FullText
The evolution of low mutation rates in experimental mutator populations of Saccharomyces cerevisiae.
McDonald MJ, Hsieh YY, Yu YH, Chang SL, Leu JY.
Current Biology. 2012 Jul 10;22(13):1235-40. doi: 10.1016/j.cub.2012.04.056. Epub 2012 Jun 21.
PMID: 22727704 PDF
Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences.
McDonald MJ, Wang WC, Huang HD, Leu JY.
PLoS Biology. 2011 Jun;9(6):e1000622. doi: 10.1371/journal.pbio.1000622. Epub 2011 Jun 14.
PMID: 21697975 Open Access Fulltext
The distribution of fitness effects of new beneficial mutations in Pseudomonas fluorescens.
McDonald MJ, Cooper TF, Beaumont HJ, Rainey PB.
Biology Letters. 2011 Feb 23;7(1):98-100. doi: 10.1098/rsbl.2010.0547. Epub 2010 Jul 21.
PMID: 20659918 PDF
Adaptive divergence in experimental populations of Pseudomonas fluorescens. IV. Genetic constraints guide evolutionary trajectories in a parallel adaptive radiation.
McDonald MJ, Gehrig SM, Meintjes PL, Zhang XX, Rainey PB.
Genetics. 2009 Nov;183(3):1041-53. doi: 10.1534/genetics.109.107110. Epub 2009 Aug 24.
PMID: 19704015 PMC Open Access FullText
Beneficial Mutations from Evolution Experiments Increase Rates of Growth and Fermentation
AL Sezmis, ME Malerba, DJ Marshall, MJ McDonald
Journal of Molecular Evolution, 1-7, 2018
PMID: 29349600