Experimental evolution as a high-throughput screen for genetic adaptations

mSphere

Volumn 3, Issue 3, 2018, Pages

  Cooper, Vaughn S ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

Evolutionary biology; Genomics; Population genetics

Indexed keywords

ADAPTATION; BIOLOGICAL MODEL; GENETIC SELECTION; MICROBIAL GENETICS; MOLECULAR EVOLUTION; POPULATION GENETICS; PROCEDURES;

ADAPTATION, BIOLOGICAL; EVOLUTION, MOLECULAR; GENETICS, MICROBIAL; GENETICS, POPULATION; MODELS, BIOLOGICAL; SELECTION, GENETIC;

EID: 85048240131     PISSN: None     EISSN: 23795042     Source Type: Journal    
DOI: 10.1128/mSphere.00121-18     Document Type: Note

References (44)

1. Good BH, McDonald MJ, Barrick JE, Lenski RE, Desai MM. 2017. The dynamics of molecular evolution over 60,000 generations. Nature 551: 45-50. https://doi.org/10.1038/nature24287
2. Levy SF, Blundell JR, Venkataram S, Petrov DA, Fisher DS, Sherlock G. 2015 Quantitative evolutionary dynamics using high-resolution lineage tracking. Nature 519:181-186. https://doi.org/10.1038/nature14279
3. O'Malley MA, Travisano M, Velicer GJ, Bolker JA. 2015. How do microbial populations and communities function as model systems? Q Rev Biol 90:269-293. https://doi.org/10.1086/682588
4. Bull JJ. 2015. Evolutionary reversion of live viral vaccines: can genetic engineering subdue it? Virus Evol 1:vev005. https://doi.org/10.1093/ve/ vev005
5. Lenski RE. 2017. Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations. ISME J 11:2181-2194. https://doi.org/10.1038/ismej.2017.69
6. Cooper VS, Schneider D, Blot M, Lenski RE. 2001. Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B. J Bacteriol 183:2834-2841. https://doi.org/10.1128/JB .183.9.2834-2841.2001
7. Cooper TF, Rozen DE, Lenski RE. 2003. Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proc Natl Acad Sci U S A 100:1072-1077. https://doi.org/10.1073/pnas .0334340100
8. Schneider D, Duperchy E, Coursange E, Lenski RE, Blot M. 2000. Longterm experimental evolution in Escherichia coli. IX. Characterization of insertion sequence-mediated mutations and rearrangements. Genetics 156:477-488
9. Pankey MS, Foxall RL, Ster IM, Perry LA, Schuster BM, Donner RA, Coyle M, Cooper VS, Whistler CA. 2017. Host-selected mutations converging on a global regulator drive an adaptive leap by bacteria to symbiosis. Elife 6:e24414. https://doi.org/10.7554/eLife.24414
10. Gerrish PJ, Lenski RE. 1998. The fate of competing beneficial mutations in an asexual population. Genetica 102-103:127-144. https://doi.org/10 .1007/978-94-011-5210-5_12
11. Dillon MM, Sung W, Sebra R, Lynch M, Cooper VS. 2017. Genome-wide biases in the rate and molecular spectrum of spontaneous mutations in Vibrio cholerae and Vibrio fischeri. Mol Biol Evol 34:93-109. https://doi .org/10.1093/molbev/msw224
12. Lee H, Popodi E, Tang HX, Foster PL. 2012. Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proc Natl Acad Sci U S A 109: E2774-E2783. https://doi.org/10.1073/pnas.1210309109
13. Cottinet D, Condamine F, Bremond N, Griffiths AD, Rainey PB, de Visser JAGM, Baudry J, Bibette J. 2016. Lineage tracking for probing heritable phenotypes at single-cell resolution. PLoS One 11:e0152395. https://doi .org/10.1371/journal.pone.0152395
14. van der Woude MW, Bäumler AJ. 2004. Phase and antigenic variation in bacteria. Clin Microbiol Rev 17:581-611. https://doi.org/10.1128/CMR.17 .3.581-611.2004
15. Cooper VS, Staples RK, Traverse CC, Ellis CN. 2014. Parallel evolution of small colony variants in Burkholderia cenocepacia biofilms. Genomics 104:447-452. https://doi.org/10.1016/j.ygeno.2014.09.007
16. Luria SE, Delbrück M. 1943. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28:491-511
17. Martin P, van de Ven T, Mouchel N, Jeffries AC, Hood DW, Moxon ER. 2003 Experimentally revised repertoire of putative contingency loci in Neisseria meningitidis strain MC58: evidence for a novel mechanism of phase variation. Mol Microbiol 50:245-257. https://doi.org/10.1046/j .1365-2958.2003.03678.x
18. Gallie J, Libby E, Bertels F, Remigi P, Jendresen CB, Ferguson GC, Desprat N, Buffing MF, Sauer U, Beaumont HJE, Martinussen J, Kilstrup M, Rainey PB. 2015. Bistability in a metabolic network underpins the de novo evolution of colony switching in Pseudomonas fluorescens. PLoS Biol 13:e1002109. https://doi.org/10.1371/journal.pbio.1002109
19. Dillon MM, Rouillard NP, Van Dam B, Gallet R, Cooper VS. 2016. Diverse phenotypic and genetic responses to short-term selection in evolving Escherichia coli populations. Evolution 70:586-599. https://doi.org/10 .1111/evo.12868
20. Peng F, Widmann S, Wünsche A, Duan K, Donovan KA, Dobson RCJ, Lenski RE, Cooper TF. 2018. Effects of beneficial mutations in pykF gene vary over time and across replicate populations in a long-term experiment with bacteria. Mol Biol Evol 35:202-210. https://doi.org/10.1093/ molbev/msx279
21. Patwa Z, Wahl LM. 2008. The fixation probability of beneficial mutations. J R Soc Interface 5:1279-1289. https://doi.org/10.1098/rsif.2008.0248
22. Lenski RE, Rose MR, Simpson SC, Tadler SC. 1991. Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. Am Nat 138:1315-1341. https://doi.org/10.1086/ 285289
23. Lind PA, Farr AD, Rainey PB. 2017. Evolutionary convergence in experimental Pseudomonas populations. ISME J 11:589-600. https://doi.org/ 10.1038/ismej.2016.157
24. O'Rourke D, Fitzgerald CE, Traverse CC, Cooper VS. 2015. There and back again: consequences of biofilm specialization under selection for dispersal. Front Genet 6:18. https://doi.org/10.3389/fgene.2015.00018
25. Lind PA, Farr AD, Rainey PB. 2015. Experimental evolution reveals hidden diversity in evolutionary pathways. Elife 4:e07074. https://doi.org/10 .7554/eLife.07074
26. McDonald MJ, Gehrig SM, Meintjes PL, Zhang X-X, Rainey PB. 2009. Adaptive divergence in experimental populations of Pseudomonas fluorescens. IV. Genetic constraints guide evolutionary trajectories in a parallel adaptive radiation. Genetics 183:1041-1053. https://doi.org/10 .1534/genetics.109.107110
27. Marchetti M, Capela D, Glew M, Cruveiller S, Chane-Woon-Ming B, Gris C, Timmers T, Poinsot V, Gilbert LB, Heeb P, Médigue C, Batut J, Masson-Boivin C. 2010. Experimental evolution of a plant pathogen into a legume symbiont. PLoS Biol 8:e1000280. https://doi.org/10.1371/journal .pbio.1000280
28. O'Connor JR, Kuwada NJ, Huangyutitham V, Wiggins PA, Harwood CS. 2012 Surface sensing and lateral subcellular localization of WspA, the receptor in a chemosensory-like system leading to c-di-GMP production. Mol Microbiol 86:720-729. https://doi.org/10.1111/mmi.12013
29. Toprak E, Veres A, Michel J-B, Chait R, Hartl DL, Kishony R. 2011. Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat Genet 44:101-105. https://doi.org/10.1038/ng.1034
30. Barbosa C, Trebosc V, Kemmer C, Rosenstiel P, Beardmore R, Schulenburg H, Jansen G. 2017. Alternative evolutionary paths to bacterial antibiotic resistance cause distinct collateral effects. Mol Biol Evol 34: 2229-2244. https://doi.org/10.1093/molbev/msx158
31. Zhou A, Lau R, Baran R, Ma J, von Netzer F, Shi W, Gorman-Lewis D, Kempher ML, He Z, Qin Y, Shi Z, Zane GM, Wu L, Bowen BP, Northen TR, Hillesland KL, Stahl DA, Wall JD, Arkin AP, Zhou J. 2017. Key metabolites and mechanistic changes for salt tolerance in an experimentally evolved sulfate-reducing bacterium, Desulfovibrio vulgaris. mBio 8:e01780-17. https://doi.org/10.1128/mBio.01780-17
32. McCully LM, Bitzer AS, Seaton SC, Smith LM, Silby MW. 2018. Social motility: interaction between two sessile soil bacteria leads to emergence of surface motility. bioRxiv https://doi.org/10.1101/296814
33. Martin M, Hölscher T, Dragoš A, Cooper VS, Kovács áT. 2016. Laboratory evolution of microbial interactions in bacterial biofilms. J Bacteriol 198: 2564-2571. https://doi.org/10.1128/JB.01018-15
34. Martin M, Dragoš A, Hölscher T, Maróti G, Bálint B, Westermann M, Kovács áT. 2017. De novo evolved interference competition promotes the spread of biofilm defectors. Nat Commun 8:15127. https://doi.org/ 10.1038/ncomms15127
35. Hillesland KL, Stahl DA. 2010. Rapid evolution of stability and productivity at the origin of a microbial mutualism. Proc Natl Acad Sci U S A 107:2124-2129. https://doi.org/10.1073/pnas.0908456107
36. Burmeister AR, Lenski RE, Meyer JR. 2016. Host coevolution alters the adaptive landscape of a virus. Proc Biol Sci 283:20161528. https://doi .org/10.1098/rspb.2016.1528
37. Shapiro JW, Turner PE. 2018. Evolution of mutualism from parasitism in experimental virus populations. Evolution 72:707-712. https://doi.org/ 10.1111/evo.13440
38. Guidot A, Jiang W, Ferdy J-B, Thébaud C, Barberis P, Gouzy J, Genin S. 2014 Multihost experimental evolution of the pathogen Ralstonia solanacearum unveils genes involved in adaptation to plants. Mol Biol Evol 31:2913-2928. https://doi.org/10.1093/molbev/msu229
39. King KC, Brockhurst MA, Vasieva O, Paterson S, Betts A, Ford SA, Frost CL, Horsburgh MJ, Haldenby S, Hurst GD. 2016. Rapid evolution of microbemediated protection against pathogens in a worm host. ISME J 10: 1915-1924. https://doi.org/10.1038/ismej.2015.259
40. Zanini F, Neher RA. 2012. FFPopSim: an efficient forward simulation package for the evolution of large populations. Bioinformatics 28: 3332-3333. https://doi.org/10.1093/bioinformatics/bts633
41. Hill WG, Robertson A. 1966. The effect of linkage on limits to artificial selection. Genet Res 8:269-294. https://doi.org/10.1017/S0016672300010156
42. Dillon MM, Cooper VS. 2016. The fitness effects of spontaneous mutations nearly unseen by selection in a bacterium with multiple chromosomes. Genetics 204:1225-1238. https://doi.org/10.1534/genetics.116 .193060
43. Desai MM, Fisher DS. 2007. Beneficial mutation selection balance and the effect of linkage on positive selection. Genetics 176:1759-1798. https://doi.org/10.1534/genetics.106.067678
44. Kim W, Levy SB, Foster KR. 2016. Rapid radiation in bacteria leads to a division of labour. Nat Commun 7:10508. https://doi.org/10.1038/ ncomms10508