Abstract
LONG BEFORE it was given such a name, experimental evolution took place during the serial passages of pathogenic viruses and bacteria necessary to develop live attenuated vaccines (Kawecki et al. 2012). The field of experimental evolution as we know it now, however, has developed rapidly and dramatically during the past three decades. Probably the best known experimental evolution study is Richard Lenski’s long-term evolution experiment (LTEE) at Michigan State University. Starting with twelve replicate E. coli cultures in February 1988, the experiment reached an astonishing 66,000 generations in November 2016, and (of course) continues. Using a strain that lacks a mechanism for genetic exchange, any changes seen in the twelve lines is a reflection of mutations alone, under the action of selection.
Keep your eyes peeeled for a small black iron door.
David Mitchell
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Notes
- 1.
Lenski’s lab typically freezes samples of every 500th generation at −80 °C. Unfrozen “fossil” samples are allowed one day to thaw and acclimate to experimental conditions before being used for comparisons of fitness, cell size, or other assays.
- 2.
In clonal interference, competition occurs among organisms with different beneficial mutations, which makes it more difficult for the beneficial mutations to spread throughout the population; this is a particular issue in asexual populations, which do not undergo genetic recombination, rendering the beneficial mutations incapable of “joining forces”.
- 3.
In diminishing-returns epistasis, “the marginal improvement from a beneficial mutation declines with increasing fitness” (Wiser et al. 2013).
- 4.
The DM25 medium contained 139 μM glucose, serving as a carbon source for non-Cit+ E. coli.
- 5.
When establishing the LTEE in 1988, Lenski and colleagues used twelve E. coli strains derived from a single clone, identical except for their ability to utilize arabinose. Six strains had a mutation that allowed them to utilize arabinose (strains Ara+1, Ara+2, etc.…), and six did not (Ara-1, Ara-2, etc.…) This mutation had no effect on the strains under the conditions of the LTEE, which did not include arabinose in the DM25 medium, but did allow the strains to be distinguished from each other when grown on tetrazolium-arabinose plates, where the Ara− cells make red colonies and the Ara+ cells make colonies that appear white.
- 6.
Cit+ cells never completely dominated the population; about 1% of the population retained the Cit− phenotype when Cit+ and Cit− cells were grown together. As Blount et al. (2008) observed, “[a]lthough the Cit+ cells continued to use glucose, they did not drive the Cit− subpopulation extinct because the Cit− cells were superior competitors for glucose. Thus, the overall diversity increased as one population gave rise evolutionarily to an ecological community with two members, one a resource specialist and the other a generalist.”
- 7.
Ara-3 was not one of the populations that had evolved a hypermutator phenotype!
- 8.
Note that “older” means later in the lineage, not “more ancestral”.
- 9.
Blount et al. note that “[c]omparative studies have shown that gene duplications have an important creative role in evolution by generating redundancies that allow neo-functionalization… Our findings highlight the less-appreciated capacity of duplications to produce new functions by promoter capture events that change gene regulatory networks.”
- 10.
Relative fitness was measured as the ratio of doublings of the competing genotypes, using a method described by Lenski and colleagues in the context of the LTEE (Lenski et al. 1991).
- 11.
Even colonies without cheaters collapse eventually, when the mat becomes too heavy to remain at the air-broth interface and sinks below the surface, where all the cells perish due to lack of oxygen. Colonies with cheaters collapse faster than purely cooperative colonies.
- 12.
Gregory Velicer was a graduate student, and later a postdoc, in Lenski’s laboratory before moving to Indiana University and later leading his own research laboratories at the Max Planck Institute in Tübingen and at the ETH in Zurich.
- 13.
Note how this essentially mimics a reverse of ZoBell’s “bottle effect” (Chap. 9).
- 14.
Recall from Chap. 11 that C. reinhardtii reproduces by multiple fission, and offspring do not break out from the parent immediately.
- 15.
See Chap. 11.
- 16.
A similar process appears to be at work in higher-level collectivities. In eusocial insects, there can be several orders of magnitude difference in the lifetime of workers compared to queens, and this has been suggested to result from oxidative stress on the workers’ metabolism (Corona et al. 2005; Remolina and Hughes 2008; Goldsby et al. 2014a). Young and Robinson (1983) suggested that the increased metabolic load imposed by foraging behavior in workers increases oxidative stress. The relative roles of RNA and DNA, which have significantly different levels of stability with respect to mutation, may represent a molecular division of labor “ensuring both high fidelity transmission of hereditary information and the execution of critical chemical work” (Goldsby et al. 2014a).
- 17.
In these experiments, colonies could only perform up to a total of five tasks.
References
Bendich AJ (2010) Mitochondrial DNA, chloroplast DNA and the origins of development in eukaryotic organisms. Biol Direct 5:42
Blount ZD, Borland CZ, Lenski RE (2008) Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci U S A 105(23):7899–7906
Blount ZD, Barrick JE, Davidson CJ, Lenski RE (2012) Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489:513–518
Boraas ME, Seale DB, Boxhorn JE (1998) Phagotrophy by a flagellate selects for colonial prey: a possible origin of multicellularity. Ecol Evol 12(2):153–164
Buss LW (1987) The Evolution of Individuality. Princeton University Press, Princeton
Celiker H, Gore J (2014) Clustering in community structure across replicate ecosystems following a long-term bacterial evolution experiment. Nat Commun 5:4643
Chow SS, Wilke CO, Ofria C, Lenski RE, Adami C (2004) Adaptive radiation from resource competition in digital organisms. Science 305:84–86
Corona M, Hughes KA, Weaver DB, Robinson GE (2005) Gene expression patterns associated with queen honey bee longevity. Mech Ageing Dev 126(11):1230–1238
de Aguiar MA, Baranger M, Baptestini EM, Kaufman L, Bar-Yam Y (2009) Global patterns of speciation and diversity. Nature 460(7253):384–387
Dees ND, Bahar S (2010) Mutation size optimizes speciation in an evolutionary model. PLoS ONE 5(8):e11952
Elena SF, Cooper VS, Lenski RE (1996) Punctuated evolution caused by selection of rare beneficial mutations. Science 272:1802–1804
Fiegna F, Yu YT, Kadam SV, Velicer GJ (2006) Evolution of an obligate social cheater to a superior cooperator. Nature 441(7091):310–314
Fox JW, Lenski RE (2015) From here to eternity—the theory and practice of a really long experiment. PLoS Biol 13(6):e1002185
Goldsby HJ, Dornhaus A, Kerr B, Ofria C (2012) Task-switching costs promote the evolution of division of labor and shifts in individuality. Proc Natl Acad Sci U S A 109(34):13686–13691
Goldsby HJ, Knoester DB, Ofria C, Kerr B (2014a) The evolutionary origin of somatic cells under the dirty work hypothesis. PLoS Biol 12(5):e1001858
Goldsby HJ, Knoester DB, Kerr B, Ofria C (2014b) The effect of conflicting pressures on the evolution of division of labor. PLoS ONE 9(8):e102713
González C, Ray JC, Manhart M, Adams RM, Nevozhay D, Morozov AV, Balázsi G (2015) Stress-response balance drives the evolution of a network module and its host genome. Mol Syst Biol 11(8):827
Gorelick R, Bertram SM, Killeen PR, Fewell JH (2004) Normalized mutual entropy in biology: quantifying division of labor. Am Nat 164(5):677–682
Gould SJ (1989) Wonderful Life: The Burgess Shale and the Nature of History. W. W. Norton and Company, New York/London
Gould SJ (2002) The Structure of Evolutionary Theory. The Belknap Press of Harvard University Press, Cambridge, MA/London
Hofstadter D (1979) Gödel Escher Bach: An Eternal Golden Braid. Basic Books, New York
Kauffman SA (1993) The Origins of Order: Self-Organization and Selection in Evolution. Oxford University Press, Oxford
Kawecki TJ, Lenski RE, Ebert D, Hollis B, Olivieri I, Whitlock MC (2012) Experimental evolution. Trends Ecol Evol 27(10):547–560
Kim W, Levy SB, Foster KR (2016) Rapid radiation in bacteria leads to a division of labour. Nat Commun 7:10508
King DM (2015) Evolutionary Dynamics of Speciation and Extinction. PhD Dissertation, University of Missouri at St. Louis
King DM, Scott AD, Bahar S (2017) Multiple phase transitions in an agent-based evolutionary model with neutral fitness. R Soc Open Sci 4(4):170005
Koschwanez JH, Foster KR, Murray AW (2011) Sucrose utilization in budding yeast as a model for the origin of undifferentiated multicellularity. PLoS Biol 9:e1001122
Leiby N, Marx CJ (2014) Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli. PLoS Biol 12(2):e1001789
Leiby N, Harcombe WR, Marx CJ (2012) Multiple long-term, experimentally-evolved populations of Escherichia coli acquire dependence upon citrate as an iron chelator for optimal growth on glucose. BMC Evol Biol 12:151
Lenski RE, Travisano M (1994) Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proc Natl Acad Sci U S A 91:6808–6814
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(6):1315–1341
Michod RE (1996) Cooperation and conflict in the evolution of individuality. II. Conflict mediation. Proc R Soc B 263(1372):813–822
Michod RE, Nedelcu AM, Roze D (2003) Cooperation and conflict in the evolution of individuality. IV. Conflict ediation and evolvability in Volvox carteri. BioSystems 69:95–114
Nevozhay D, Adams RM, Van Itallie E, Bennett MR, Balázsi G (2012) Mapping the environmental fitness landscape of a synthetic gene circuit. PLoS Comput Biol 8(4):e1002480
Ofria C, Wilke CO (2004) Avida: a software platform for research in computational evolutionary biology. Artif Life 10(2):191–229
Oud B, Guadalupe-Medina V, Nijkamp JF, de Ridder D, Pronk JT, van Maris AJ, Daran JM (2013) Genome duplication and mutations in ACE2 cause multicellular, fast-sedimenting phenotypes in evolved Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 110(45):E4223–E4231
Quandt EM, Gollihar J, Blount ZD, Ellington AD, Georgiou G, Barrick JE (2015) Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment. eLIFE 4:e09696
Rainey PB, Rainey K (2003) Evolution of cooperation and conflict in experimental bacterial populations. Nature 425:72–74
Ratcliff WC, Denison RF, Borello M, Travisano M (2012) Experimental evolution of multicellularity. Proc Natl Acad Sci U S A 109(5):1595–1600
Ratcliff WC, Pentz JT, Travisano M (2013a) Tempo and mode of multicellular adaptation in experimentally evolved Saccharomyces cerevisiae. Evolution 67(6):1573–1581
Ratcliff WC, Herron MD, Howell K, Pentz JT, Rosenzweig F, Travisano M (2013b) Experimental evolution of an alternating uni- and multicellular life cycle in Chlamydomonas reinhardtii. Nat Commun 4:2742
Ratcliff WC, Fankhauser JD, Rogers DW, Greig D, Travisano M (2015) Origins of multicellular evolvability in snowflake yeast. Nat Commun 6:6102
Remolina SC, Hughes KA (2008) Evolution and mechanisms of long life and high fertility in queen honey bees. Age (Dordr) 30(2–3):177–185
Scott AD (2014) Speciation Dynamics of an Agent-Based Evolution Model in Phenotype Space. PhD Dissertation, University of Missouri at St. Louis
Scott AD, King DM, Marić N, Bahar S (2013) Clustering and phase transitions on a neutral landscape. Europhys Lett 102(6):68003
Spiers AJ, Kahn SG, Bohannon J, Travisano M, Rainey PB (2002) Adaptive divergence in experimental populations of Pseudomonas fluorescens. I. Genetic and phenotypic bases of wrinkly spreader fitness. Genetics 161(1):33–46
Spiers AJ, Bohannon J, Gehrig SM, Rainey PB (2003) Biofilm formation at the air-liquid interface by the Pseudomonas fluorescens SBW25 wrinkly spreader requires an acetylated form of cellulose. Mol Microbiol 50(1):15–27
Turner CB, Blount ZD, Lenski RE (2015) Replaying evolution to test the cause of extinction of one ecotype in an experimentally evolved population. PLoS ONE 10(11):e0142050
Velicer GJ, Stredwick KL (2002) Experimental social evolution with Myxococcus xanthus. Antonie Van Leeuwenhoek 81(1–4):155–164
Velicer GJ, Yu YT (2003) Evolution of novel cooperative swarming in the bacterium Myxococcus xanthus. Nature 425(6953):75–78
Velicer GJ, Kroos L, Lenski RE (1998) Loss of social behaviors by Myxococcus xanthus during evolution in an unstructured habitat. Proc Natl Acad Sci U S A 95:12376–12380
Velicer GJ, Kroos L, Lenski RE (2000) Developmental cheating in the social bacterium Myxococcus xanthus. Nature 404(6778):598–601
Velicer GJ, Lenski R, Kroos L (2002) Rescue of social motility lost during evolution of Myxococcus xanthus in an asocial environment. J Bacteriol 184:2719–2727
Willensdorfer M (2009) On the evolution of differentiated multicellularity. Evolution 63:306–323
Wiser MJ, Ribeck N, Lenski RE (2013) Long-term dynamics of adaptation in asexual populations. Science 352:1364–1367
Young RG, Robinson G (1983) Age and oxygen toxicity related fluorescence in the honey bee thorax. Exp Gerontol 18(6):471–475
Author information
Authors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media B.V.
About this chapter
Cite this chapter
Bahar, S. (2018). Experimental Evolution. In: The Essential Tension. The Frontiers Collection. Springer, Dordrecht. https://doi.org/10.1007/978-94-024-1054-9_12
Download citation
DOI: https://doi.org/10.1007/978-94-024-1054-9_12
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-024-1052-5
Online ISBN: 978-94-024-1054-9
eBook Packages: Physics and AstronomyPhysics and Astronomy (R0)