Experimental evolution
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Experimental evolution is the use of laboratory experiments or controlled field manipulations to explore evolutionary dynamics.[1] Evolution may be observed in the laboratory as individuals/populations adapt to new environmental conditions by natural selection.
There are two different ways in which adaptation can arise in experimental evolution. One is via an individual organism gaining a novel beneficial mutation.[2] The other is from allele frequency change in standing genetic variation already present in a population of organisms.[2] Other evolutionary forces outside of mutation and natural selection can also play a role or be incorporated into experimental evolution studies, such as genetic drift and gene flow.[3]
The organism used is decided by the experimenter, based on the hypothesis to be tested. Many
More recently, experimentally evolved individuals or populations are often analyzed using whole genome sequencing,[8][9] an approach known as Evolve and Resequence (E&R).[10] E&R can identify mutations that lead to adaptation in clonal individuals or identify alleles that changed in frequency in polymorphic populations, by comparing the sequences of individuals/populations before and after adaptation.[2] The sequence data makes it possible to pinpoint the site in a DNA sequence that a mutation/allele frequency change occurred to bring about adaptation.[10][9][2] The nature of the adaptation and functional follow up studies can shed insight into what effect the mutation/allele has on phenotype.
History
Domestication and breeding
Unwittingly, humans have carried out evolution experiments for as long as they have been
Altogether at least a score of pigeons might be chosen, which if shown to an ornithologist, and he were told that they were wild birds, would certainly, I think, be ranked by him as well-defined species. Moreover, I do not believe that any ornithologist would place the English carrier, the short-faced tumbler, the runt, the barb, pouter, and fantail in the same genus; more especially as in each of these breeds several truly-inherited sub-breeds, or species as he might have called them, could be shown him. (...) I am fully convinced that the common opinion of naturalists is correct, namely, that all have descended from the rock-pigeon (Columba livia), including under this term several geographical races or sub-species, which differ from each other in the most trifling respects.
— Charles Darwin, The Origin of Species
Early
One of the first to carry out a controlled evolution experiment was William Dallinger. In the late 19th century, he cultivated small unicellular organisms in a custom-built incubator over a time period of seven years (1880–1886). Dallinger slowly increased the temperature of the incubator from an initial 60 °F up to 158 °F. The early cultures had shown clear signs of distress at a temperature of 73 °F, and were certainly not capable of surviving at 158 °F. The organisms Dallinger had in his incubator at the end of the experiment, on the other hand, were perfectly fine at 158 °F. However, these organisms would no longer grow at the initial 60 °F. Dallinger concluded that he had found evidence for Darwinian adaptation in his incubator, and that the organisms had adapted to live in a high-temperature environment. Dallinger's incubator was accidentally destroyed in 1886, and Dallinger could not continue this line of research.[11][12]
From the 1880s to 1980, experimental evolution was intermittently practiced by a variety of evolutionary biologists, including the highly influential 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.[13]
Modern
Experimental evolution has been used in various formats to understand underlying evolutionary processes in a controlled system. Experimental evolution has been performed on multicellular[14] and unicellular[15] eukaryotes, prokaryotes,[16] and viruses.[17] Similar works have also been performed by directed evolution of individual enzyme,[18][19] ribozyme[20] and replicator[21][22] genes.
Aphids
In the 1950s, the Soviet biologist Georgy Shaposhnikov conducted experiments on aphids of the Dysaphis genus. By transferring them to plants normally nearly or completely unsuitable for them, he had forced populations of parthenogenetic descendants to adapt to the new food source to the point of reproductive isolation from the regular populations of the same species.[23]
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.[24] 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.[25]
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.[26] Subsequently, Thomas Turner coined the term Evolve and Resequence (E&R)[10] and several studies used E&R approach with mixed success.[27][28] One of the more interesting experimental evolution studies was conducted by Gabriel Haddad's group at UC San Diego, where Haddad and colleagues evolved flies to adapt to low oxygen environments, also known as hypoxia.[29] After 200 generations, they used E&R approach to identify genomic regions that were selected by natural selection in the hypoxia adapted flies.[30] More recent experiments are following up E&R predictions with RNAseq[31] and genetic crosses.[9] Such efforts in combining E&R with experimental validations should be powerful in identifying genes that regulate adaptation in flies.
Microbes
Many microbial species have short generation times, easily sequenced genomes, and well-understood biology. They are therefore commonly used for experimental evolution studies. The bacterial species most commonly used for experimental evolution include P. fluorescens,[32] Pseudomonas aeruginosa,[33] Enterococcus faecalis [34] and E. coli (see below), while the Yeast S. cerevisiae has been used as a model for the study of eukaryotic evolution.[35]
Lenski's E. coli experiment
One of the most widely known examples of laboratory bacterial evolution is the
Leishmania donovani
Bussotti and collaborators isolated amastigotes from Leishmania donovani and cultured them in vitro for 3800 generations (36 weeks). The culture of these parasites showed how they adapted to in vitro conditions by compensating for the loss of a NIMA-related kinase, important for the correct progression of mitosis, by increasing the expression of another orthologous kinase as the culture generations progressed. Furthermore, it was observed how L. donovani has been adapted to in vitro culture by reducing the expression of 23 transcripts related to flagellar biogenesis and increasing the expression of ribosomal protein clusters and non-coding RNAs such as nucleolar small RNAs. Flagella are considered less necessary by the parasite in in vitro culture and therefore the progression of generations leads to their elimination, causing an energy saving due to lower motility so that proliferation and growth rate in culture is higher. The amplified snoRNAs also lead to increased ribosomal biosynthesis, increased protein biosynthesis and thus increased growth rate of the culture. These adaptations observed over generations of parasites are governed by copy number variations (CNV) and epistatic interactions between affected genes, and allow us to justify Leishmania genomic instability through its post-transcriptional regulation of gene expression.[40]
Laboratory house mice
In 1998,
The HR mice exhibit an elevated
Multidirectional selection on bank voles
In 2005 Paweł Koteja with Edyta Sadowska and colleagues from the
After approximately 20 generations of selective breeding, voles from the Aerobic lines evolved a 60% higher swim-induced metabolic rate than voles from the unselected Control lines. Although the selection protocol does not impose a thermoregulatory burden, both the
More than 85% of the Predatory voles capture the crickets, compared to only about 15% of unselected Control voles, and they catch the crickets faster. The increased predatory behavior is associated with a more proactive coping style (“personality”).[46]
During the test with low-quality diet, the Herbivorous voles lose approximately 2 grams less mass (approximately 10% of the original body mass) than the Control ones. The Herbivorous voles have an altered composition of the bacterial
Synthetic biology
Other examples
Stickleback fish have both marine and freshwater species, the freshwater species evolving since the last ice age. Freshwater 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.[52]
Microbial cells [53] and recently mammalian cells [54] are evolved under nutrient limiting conditions to study their metabolic response and engineer cells for useful characteristics.
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[55] to the evolution of multicellularity.[56] 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.[57]
See also
- Artificial selection
- Bacteriophage experimental evolution
- Directed evolution
- Domestication
- Evolutionary biology
- Evolutionary physiology
- Genetics
- Genomics of domestication
- Laboratory experiments of speciation
- Quantitative genetics
- Selective breeding
- Tame Silver Fox
References
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- ^ Shaposhnikov GK (1966). "Origin and breakdown of reproductive isolation and the criterion of the species" (PDF). Entomological Review. 45: 1–8. Archived from the original (PDF) on 2013-09-08.
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- ^ Lenski RE. "E. coli Long-term Experimental Evolution Project Site". Michigan State University. Archived from the original on 2017-07-27. Retrieved 2004-07-08.
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Further reading
- Bennett AF (2003). "Experimental evolution and the Krogh principle: generating biological novelty for functional and genetic analyses". Physiological and Biochemical Zoology. 76 (1): 1–11. S2CID 9032244.
- Dallinger WH (April 1887). "The president's address". Journal of the Royal Microscopical Society. 7 (2): 185–99. .
- Garland Jr T (2003). "Selection experiments: an under-utilized tool in biomechanics and organismal biology." (PDF). In Bels VL, Gasc JP, Casinos A (eds.). Vertebrate biomechanics and evolution. Oxford, UK: BIOS Scientific Publishers. pp. 23–56. Archived from the original(PDF) on 2015-09-23. Retrieved 2007-02-10.
- Garland Jr T, Rose MR, eds. (2009). Experimental evolution: concepts, methods, and applications of selection experiments. Berkeley, California: University of California Press. ISBN 978-0-520-26180-8.
- Gibbs AG (October 1999). "Laboratory selection for the comparative physiologist". The Journal of Experimental Biology. 202 (Pt 20): 2709–2718. PMID 10504307.
- Lenski RE (2004). "Phenotypic and Genomic Evolution during a 20,000-Generation Experiment with the Bacterium Escherichia coli". Phenotypic and genomic evolution during a 20,000-generation experiment with the bacterium Escherichia coli. Vol. 24. pp. 225–265. )
- Lenski RE, Rose MR, Simpson SC, Tadler SC (1991). "Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations". American Naturalist. 138 (6): 1315–1341. S2CID 83996233.
- McKenzie JA, Batterham P (May 1994). "The genetic, molecular and phenotypic consequences of selection for insecticide resistance". Trends in Ecology & Evolution. 9 (5): 166–169. PMID 21236810.
- Reznick DN, Bryant MJ, Roff D, Ghalambor CK, Ghalambor DE (October 2004). "Effect of extrinsic mortality on the evolution of senescence in guppies". Nature. 431 (7012): 1095–1099. S2CID 205210169.
- Rose MR, Passananti HB, Matos M, eds. (2004). Methuselah flies: A case study in the evolution of aging. Singapore: World Scientific Publishing.
- Swallow JG, S2CID 2305227.
External links
- E. coli Long-term Experimental Evolution Project Site Archived 2017-07-27 at the Wayback Machine, 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