Publications

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

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

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

DOI:10.1038/s41396-019-0464-2