Experimental evolution

Experimental evolution

In bacteria, yeast or viruses.[1][2] However, laboratory studies with foxes[3] and with rodents (see below) have shown that notable adaptations can occur within as few as 10-20 generations and experiments with wild guppies have observed adaptations within comparable numbers of generations.[4] More recently, using experimental evolution followed by whole genome pooled sequencing, an approach known as Evolve and Resequence (E&R) [5] is becoming popular in fruit flies.[6]

Contents

  • History 1
    • Domestication and breeding 1.1
    • Early experimental evolution 1.2
  • Modern experimental evolution 2
    • Fruit flies 2.1
    • Bacteria 2.2
    • Laboratory house mice 2.3
    • Other examples 2.4
  • Experimental evolution for teaching 3
  • See also 4
  • References 5
  • Further reading 6
  • External links 7

History

Domestication and breeding

This Chihuahua mix and Great Dane show the wide range of dog breed sizes created using artificial selection.

Unwittingly, humans have carried out evolution experiments for as long as they have been domesticating plants and animals. Selective breeding of plants and animals has led to varieties that differ dramatically from their original wild-type ancestors. Examples are the cabbage varieties, maize, or the large number of different dog breeds. The power of human breeding to create varieties with extreme differences from a single species was already recognized by Charles Darwin. In fact, he started out his book The Origin of Species with a chapter on variation in domestic animals. In this chapter, Darwin discussed in particular the pigeon.

Early experimental evolution

Drawing of the incubator used by Dallinger in his evolution experiments.

One of the first to carry out a controlled evolution experiment was Theodosius Dobzhansky. Like other experimental research in evolutionary biology during this period, much of this work lacked extensive replication and was carried out only for relatively short periods of evolutionary time.

Modern experimental evolution

Experimental evolution has been used in various formats to understand underlying evolutionary processes in a controlled system. Experimental evolution has been performed on multicellular[7] and unicellular[8] eukaryotes, prokaryotes,[9] viruses.[10] Similar works have also been performed by directed evolution of individual enzyme,[11][12] ribozyme[13] and replicator[14][15] genes.

Fruit flies

One of the first of a new wave of experiments using this strategy was the laboratory "evolutionary radiation" of Drosophila melanogaster populations that Michael R. Rose started in February, 1980.[16] This system started with ten populations, five cultured at later ages, and five cultured at early ages. Since then more than 200 different populations have been created in this laboratory radiation, with selection targeting multiple characters. Some of these highly differentiated populations have also been selected "backward" or "in reverse," by returning experimental populations to their ancestral culture regime. Hundreds of people have worked with these populations over the better part of three decades. Much of this work is summarized in the papers collected in the book Methuselah Flies, listed below.

The early experiments in flies were limited to studying phenotypes but the molecular mechanisms, i.e, changes in DNA that facilitated such changes, could not be identified. This changed with genomics technology.[17] Subsequently, Thomas Turner coined the term Evolve and Resequence (E&R) [5] and several studies used E&R approach with mixed success (reviewed in [18] and [19]). One of the coolest experimental evolution study was conduced by Gabriel Haddad's group at UC San Diego, where Haddad and colleagues evolved flies to adapt to low oxygen environment, also known as hypoxia.[20] After 200 generations, they used E&R approach to identify genomic regions that were selected by natural selection in the hypoxia adapted flies.[21] More recent experiments are have started following up E&R predictions with RNAseq[22] and genetic crosses.[6] Such efforts in combining E&R with experimental validations should be powerful in identifying genes that regulate adaptation in flies.

Bacteria

On February 15, 1988, Richard Lenski started a long-term evolution experiment with the bacterium E. coli. The experiment continues to this day, and is by now probably the largest controlled evolution experiment ever undertaken. Since the inception of the experiment, the bacteria have grown for more than 60,000 generations. Lenski and colleagues regularly publish updates on the status of the experiments.[23]

Laboratory house mice

Mouse from the Garland selection experiment with attached wheel (1.1 m circumference) and its photocell-based counter.

In 1998, Theodore Garland, Jr. and colleagues started a long-term experiment that involves selective breeding for high voluntary activity levels on running wheels.[24] This experiment also continues to this day (> 65 generations). Mice from the four replicate "High Runner" lines evolved to run almost 3 times as many running-wheel revolutions per day compared with the four unselected control lines of mice, mainly by running faster than the control mice rather than running for more minutes/day.

Female mouse with her litter, from the Garland selection experiment.

The HR mice exhibit an elevated maximal aerobic capacity when tested on a motorized treadmill and a variety of other traits that appear to be adaptations that facilitate high levels of sustained endurance running (e.g., larger hearts, more symmetrical hindlimb bones). They also exhibit alterations in motivation and the reward system of the brain. Pharmacological studies point to alterations in dopamine function and the endocannabinoid system.[25] The High Runner lines have been proposed as a model to study human attention-deficit hyperactivity disorder (ADHD), and administration of Ritalin reduces their wheel running approximately to the levels of Control mice. Click here for a mouse wheel running video.

Other examples

Stickleback fish have both marine and freshwater species, the freshwater species evolving since the last ice age. Fresh water species can survive colder temperatures. Scientists tested to see if they could reproduce this evolution of cold-tolerance by keeping marine sticklebacks in cold freshwater. It took the marine sticklebacks only three generations to evolve to match the 2.5 degree celsius improvement in cold-tolerance found in wild freshwater sticklebacks.[26]

Experimental evolution for teaching

Because of their rapid generation times microbes offer an opportunity to study microevolution in the classroom. A number of exercises involving bacteria and yeast teach concepts ranging from the evolution of resistance[27] to the evolution of multicellularity.[28] With the advent of next-generation sequencing technology it has become possible for students to conduct an evolutionary experiment, sequence the evolved genomes, and to analyze and interpret the results.[29]

See also

References

  1. ^ Buckling A, Craig Maclean R, Brockhurst MA, Colegrave N (February 2009). "The Beagle in a bottle". Nature 457 (7231): 824–9.  
  2. ^ Elena SF, Lenski RE (June 2003). "Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation". Nat. Rev. Genet. 4 (6): 457–69.  
  3. ^ Early Canid Domestication: The Fox Farm Experiment, p.2, by Lyudmila N. Trut, Ph.D., Retrieved February 19, 2011
  4. ^ Reznick, D. N.; F. H. Shaw; F. H. Rodd; R. G. Shaw (1997). "Evaluation of the rate of evolution in natural populations of guppies (Poecilia reticulata)". Science 275 (5308): 1934–1937.  
  5. ^ a b Turner TL, Stewart AD; et al. (March 2011). "Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster". PLoS. Genet.  
  6. ^ a b Jha AR, Miles CM, Lippert NR, Brown CD, White KP, Kreitman M (June 2015). "Whole-Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg-Size Variation in Drosophila melanogaster". Mol. Biol. Evol.  
  7. ^ Marden, JH; Wolf, MR; Weber, KE (November 1997). "Aerial performance of Drosophila melanogaster from populations selected for upwind flight ability.". The Journal of experimental biology 200 (Pt 21): 2747–55.  
  8. ^ Ratcliff, WC; Denison, RF; Borrello, M; Travisano, M (31 January 2012). "Experimental evolution of multicellularity.". Proceedings of the National Academy of Sciences of the United States of America 109 (5): 1595–600.  
  9. ^ Barrick, JE; Yu, DS; Yoon, SH; Jeong, H; Oh, TK; Schneider, D; Lenski, RE; Kim, JF (29 October 2009). "Genome evolution and adaptation in a long-term experiment with Escherichia coli.". Nature 461 (7268): 1243–7.  
  10. ^ Heineman, RH; Molineux, IJ; Bull, JJ (August 2005). "Evolutionary robustness of an optimal phenotype: re-evolution of lysis in a bacteriophage deleted for its lysin gene.". Journal of molecular evolution 61 (2): 181–91.  
  11. ^ Bloom, JD; Arnold, FH (16 June 2009). "In the light of directed evolution: pathways of adaptive protein evolution.". Proceedings of the National Academy of Sciences of the United States of America. 106 Suppl 1: 9995–10000.  
  12. ^ Moses, AM; Davidson, AR (17 May 2011). "In vitro evolution goes deep.". Proceedings of the National Academy of Sciences of the United States of America 108 (20): 8071–2.  
  13. ^ Salehi-Ashtiani, K; Szostak, JW (1 November 2001). "In vitro evolution suggests multiple origins for the hammerhead ribozyme.". Nature 414 (6859): 82–4.  
  14. ^ Sumper, M; Luce, R (January 1975). "Evidence for de novo production of self-replicating and environmentally adapted RNA structures by bacteriophage Qbeta replicase.". Proceedings of the National Academy of Sciences of the United States of America 72 (1): 162–6.  
  15. ^ Mills, DR; Peterson, RL; Spiegelman, S (July 1967). "An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule.". Proceedings of the National Academy of Sciences of the United States of America 58 (1): 217–24.  
  16. ^ Rose, M. R. (1984). "Artificial selection on a fitness component in Drosophila melanogaster". Evolution 38 (3): 516–526.  
  17. ^ Burke MK, Dunham JP; et al. (Sept 2015). "Genome-wide analysis of a long-term evolution experiment with Drosophila". Nature.  
  18. ^ Schlötterer C, Tobler R, Kofler R, Nolte V (Nov 2014). "Sequencing pools of individuals - mining genome-wide polymorphism data without big funding". Nat. Rev. Genet.  
  19. ^ Schlötterer C, Kofler R, Versace E, Tobler R, Franssen SU (Oct 2014). "Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation". Heredity.  
  20. ^ Zhou D, Xue J, Chen J, Morcillo P, Lambert JD, White KP, Haddad GG (May 2007). "Experimental selection for Drosophila survival in extremely low O(2) environment". PLoS One.  
  21. ^ Zhou D, Udpa N, Gersten M, Visk DW, Bashir A, Xue J, Frazer KA, Posakony JW, Subramaniam S, Bafna V, Haddad GG (Feb 2011). "Experimental selection of hypoxia-tolerant Drosophila melanogaster". Proc Natl Acad Sci.  
  22. ^ Remolina SC, Chang PL, Leips J, Nuzhdin SV, Hughes KA (Nov 2012). "Genomic basis of aging and life-history evolution in Drosophila melanogaster". Evolution.  
  23. ^ E. coli Long-term Experimental Evolution Project Site, Lenski, R. E.
  24. ^ Artificial Selection for Increased Wheel-Running Behavior in House Mice, John G. Swallow, Patrick A. Carter, and Theodore Garland, Jr., Behavior Genetics, Vol. 28, No. 3, 1998
  25. ^ Keeney, B. K.; D. A. Raichlen, T. H. Meek, R. S. Wijeratne, K. M. Middleton, G. L. Gerdeman, and T. Garland, Jr. (2008). "Differential response to a selective cannabinoid receptor antagonist (SR141716: rimonabant) in female mice from lines selectively bred for high voluntary wheel-running behavior" (PDF). Behavioural Pharmacology 19 (8): 812–820.  
  26. ^ Barrett, R. D. H.; Paccard, A.; Healy, T. M.; Bergek, S.; Schulte, P. M.; Schluter, D.; Rogers, S. M. (2010). "Rapid evolution of cold tolerance in stickleback". Proceedings of the Royal Society B: Biological Sciences 278 (1703): 233–238.  
  27. ^ Hyman, Paul (2014). "Bacteriophage as instructional organisms in introductory biology labs". Bacteriophage 4 (2): e27336.  
  28. ^ "A Novel Laboratory Activity for Teaching about the Evolution of Multicellularity". The American Biology Teacher 76 (2): 81–87. 2014.  
  29. ^ "Using experimental evolution and next-generation sequencing to teach bench and bioinformatic skills". PeerJ PrePrints (3): e1674. 2015.  

Further reading

  • Bennett, A. F. (2003). "Experimental evolution and the Krogh Principle: generating biological novelty for functional and genetic analyses" (PDF). Physiological and Biochemical Zoology 76 (1): 1–11.  
  • Dallinger, W. H. 1887. The president's address. J. Roy. Microscop. Soc., 185-199.
  • Elena, S. F.; Lenski, R. E. (2003). "Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation". Nature Reviews Genetics 4: 457–469.  
  • BIOS Scientific Publishers, Oxford, UK. PDF
  • Garland, T., Jr., and M. R. Rose, eds. 2009. Experimental evolution: concepts, methods, and applications of selection experiments. University of California Press, Berkeley, California. PDF of Table of Contents
  • Gibbs, A. G. (1999). "Laboratory selection for the comparative physiologist". Journal of Experimental Biology 202: 2709–2718. 
  • Lenski, R. E. (2004). "Phenotypic and genomic evolution during a 20,000-generation experiment with the bacterium Escherichia coli". Plant Breeding Reviews 24: 225–265.  
  • Lenski, R. E.; Rose, M. R.; Simpson, S. C.; Tadler, S. C. (1991). "Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations". American Naturalist 138: 1315–1341.  
  • McKenzie, J. A.; Batterham, P. (1994). "The genetic, molecular and phenotypic consequences of selection for insecticide resistance". Trends in Ecology and Evolution 9: 166–169.  
  • Reznick, D. N.; Bryant, M. J.; Roff, D.; Ghalambor, C. K.; Ghalambor, D. E. (2004). "Effect of extrinsic mortality on the evolution of senescence in guppies". Nature 431: 1095–1099.  
  • Rose, M. R., H. B. Passananti, and M. Matos, eds. 2004. Methuselah flies: A case study in the evolution of aging. World Scientific Publishing, Singapore.
  • Swallow, J. G.;  

External links

  • E. coli Long-term Experimental Evolution Project Site, Lenski lab, Michigan State University
  • A movie illustrating the dramatic differences in wheel-running behavior.
  • Experimental Evolution Publications by Ted Garland: Artificial Selection for High Voluntary Wheel-Running Behavior in House Mice — a detailed list of publications.
  • Experimental Evolution — a list of laboratories that study experimental evolution.
  • Network for Experimental Research on Evolution, University of California.
  • New Scientist article on domestication by selection
  • Inquiry-based middle school lesson plan: "Born to Run: Artificial Selection Lab"
  • Digital Evolution for Education software