Literature DB >> 28509909

Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations.

Richard E Lenski1,2,3.   

Abstract

Evolution is an on-going process, and it can be studied experimentally in organisms with rapid generations. My team has maintained 12 populations of Escherichia coli in a simple laboratory environment for >25 years and 60 000 generations. We have quantified the dynamics of adaptation by natural selection, seen some of the populations diverge into stably coexisting ecotypes, described changes in the bacteria's mutation rate, observed the new ability to exploit a previously untapped carbon source, characterized the dynamics of genome evolution and used parallel evolution to identify the genetic targets of selection. I discuss what the future might hold for this particular experiment, briefly highlight some other microbial evolution experiments and suggest how the fields of experimental evolution and microbial ecology might intersect going forward.

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Year:  2017        PMID: 28509909      PMCID: PMC5607360          DOI: 10.1038/ismej.2017.69

Source DB:  PubMed          Journal:  ISME J        ISSN: 1751-7362            Impact factor:   10.302


  97 in total

1.  Experimental evolution recapitulates natural evolution.

Authors:  H A Wichman; L A Scott; C D Yarber; J J Bull
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2000-11-29       Impact factor: 6.237

2.  Long-Term Experimental Evolution in Escherichia coli. VIII. Dynamics of a Balanced Polymorphism.

Authors:  Daniel E Rozen; Richard E Lenski
Journal:  Am Nat       Date:  2000-01       Impact factor: 3.926

3.  Relative fitness can decrease in evolving asexual populations of S. cerevisiae.

Authors:  C E Paquin; J Adams
Journal:  Nature       Date:  1983 Nov 24-30       Impact factor: 49.962

4.  Local migration promotes competitive restraint in a host-pathogen 'tragedy of the commons'.

Authors:  Benjamin Kerr; Claudia Neuhauser; Brendan J M Bohannan; Antony M Dean
Journal:  Nature       Date:  2006-07-06       Impact factor: 49.962

5.  Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli.

Authors:  Ludovic Pelosi; Lauriane Kühn; Dorian Guetta; Jérôme Garin; Johannes Geiselmann; Richard E Lenski; Dominique Schneider
Journal:  Genetics       Date:  2006-05-15       Impact factor: 4.562

6.  Genome evolution and adaptation in a long-term experiment with Escherichia coli.

Authors:  Jeffrey E Barrick; Dong Su Yu; Sung Ho Yoon; Haeyoung Jeong; Tae Kwang Oh; Dominique Schneider; Richard E Lenski; Jihyun F Kim
Journal:  Nature       Date:  2009-10-18       Impact factor: 49.962

7.  Adaptive radiation in a heterogeneous environment.

Authors:  P B Rainey; M Travisano
Journal:  Nature       Date:  1998-07-02       Impact factor: 49.962

Review 8.  Genome dynamics during experimental evolution.

Authors:  Jeffrey E Barrick; Richard E Lenski
Journal:  Nat Rev Genet       Date:  2013-10-29       Impact factor: 53.242

9.  Recombination speeds adaptation by reducing competition between beneficial mutations in populations of Escherichia coli.

Authors:  Tim F Cooper
Journal:  PLoS Biol       Date:  2007-09       Impact factor: 8.029

Review 10.  Challenges in microbial ecology: building predictive understanding of community function and dynamics.

Authors:  Stefanie Widder; Rosalind J Allen; Thomas Pfeiffer; Thomas P Curtis; Carsten Wiuf; William T Sloan; Otto X Cordero; Sam P Brown; Babak Momeni; Wenying Shou; Helen Kettle; Harry J Flint; Andreas F Haas; Béatrice Laroche; Jan-Ulrich Kreft; Paul B Rainey; Shiri Freilich; Stefan Schuster; Kim Milferstedt; Jan R van der Meer; Tobias Groβkopf; Jef Huisman; Andrew Free; Cristian Picioreanu; Christopher Quince; Isaac Klapper; Simon Labarthe; Barth F Smets; Harris Wang; Orkun S Soyer
Journal:  ISME J       Date:  2016-03-29       Impact factor: 10.302

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  57 in total

1.  Soft sweep development of resistance in Escherichia coli under fluoroquinolone stress.

Authors:  Xianxing Xie; Ruichen Lv; Chao Yang; Yajun Song; Yanfeng Yan; Yujun Cui; Ruifu Yang
Journal:  J Microbiol       Date:  2019-09-25       Impact factor: 3.422

Review 2.  Co-evolution in the Jungle: From Leafcutter Ant Colonies to Chromosomal Ends.

Authors:  Ľubomír Tomáška; Jozef Nosek
Journal:  J Mol Evol       Date:  2020-03-10       Impact factor: 2.395

3.  The emergence of metabolic heterogeneity and diverse growth responses in isogenic bacterial cells.

Authors:  Emrah Şimşek; Minsu Kim
Journal:  ISME J       Date:  2018-01-15       Impact factor: 10.302

Review 4.  Public Microbial Resource Centers: Key Hubs for Findable, Accessible, Interoperable, and Reusable (FAIR) Microorganisms and Genetic Materials.

Authors:  P Becker; M Bosschaerts; P Chaerle; H-M Daniel; A Hellemans; A Olbrechts; L Rigouts; A Wilmotte; M Hendrickx
Journal:  Appl Environ Microbiol       Date:  2019-10-16       Impact factor: 4.792

5.  Emerging Frontiers in the Study of Molecular Evolution.

Authors:  David A Liberles; Belinda Chang; Kerry Geiler-Samerotte; Aaron Goldman; Jody Hey; Betül Kaçar; Michelle Meyer; William Murphy; David Posada; Andrew Storfer
Journal:  J Mol Evol       Date:  2020-04       Impact factor: 2.395

6.  Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris.

Authors:  Bo Wu; Feifei Liu; Aifen Zhou; Juan Li; Longfei Shu; Megan L Kempher; Xueqin Yang; Daliang Ning; Feiyan Pan; Grant M Zane; Judy D Wall; Joy D Van Nostrand; Philippe Juneau; Shouwen Chen; Qingyun Yan; Jizhong Zhou; Zhili He
Journal:  ISME J       Date:  2020-09-15       Impact factor: 10.302

7.  Adaptation reduces competitive dominance and alters community assembly.

Authors:  Christopher P Nadeau; Timothy E Farkas; Andrea M Makkay; R Thane Papke; Mark C Urban
Journal:  Proc Biol Sci       Date:  2021-02-17       Impact factor: 5.349

8.  Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations.

Authors:  Milo S Johnson; Shreyas Gopalakrishnan; Juhee Goyal; Megan E Dillingham; Christopher W Bakerlee; Parris T Humphrey; Tanush Jagdish; Elizabeth R Jerison; Katya Kosheleva; Katherine R Lawrence; Jiseon Min; Alief Moulana; Angela M Phillips; Julia C Piper; Ramya Purkanti; Artur Rego-Costa; Michael J McDonald; Alex N Nguyen Ba; Michael M Desai
Journal:  Elife       Date:  2021-01-19       Impact factor: 8.140

9.  Anion transport as a target of adaption to perchlorate in sulfate-reducing communities.

Authors:  Magdalena K Stoeva; Jennifer Kuehl; Alexey E Kazakov; Ouwei Wang; Rowena Rushton-Green; John D Coates
Journal:  ISME J       Date:  2019-10-28       Impact factor: 10.302

10.  Compensatory evolution of Pseudomonas aeruginosa's slow growth phenotype suggests mechanisms of adaptation in cystic fibrosis.

Authors:  Ruggero La Rosa; Elio Rossi; Adam M Feist; Helle Krogh Johansen; Søren Molin
Journal:  Nat Commun       Date:  2021-05-27       Impact factor: 14.919

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