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Horizontal gene transfer facilitates the molecular reverse-evolution of antibiotic sensitivity in experimental populations of H. pylori

ANT Nguyen, R Gorrell, T Kwok, T Connallon, MJ McDonald

Nature Ecology and Evolution Jan. 4. 2024

Horizontal Gene Transfer, Fitness Costs and Mobility Shape the Spread of Antibiotic Resistance Genes into Experimental Populations of Acinetobacter Baylyi

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

Polymyxin dose tunes the evolutionary dynamics of resistance in multidrug-resistant Acinetobacter baumannii

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

Species interactions constrain adaptation and preserve ecological stability in an experimental microbial community

JN Barber, LC Nicholson, LC Woods, LM Judd, AL Sezmis, J Hawkey, ...

The ISME Journal 16 (5), 1442-1452. 2022

Recombination resolves the cost of horizontal gene transfer in experimental populations of Helicobacter pylori

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

DOI: 10.1073/pnas.2005331117


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 LeuShang-Lin ChangJung-Chi ChaoLaura C. Woods & Michael J. McDonald 

Nature of Ecology and Evolution, February 2020


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

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