Experimental evolution is the use of laboratory experiments or controlled field manipulations to explore evolutionary dynamics.

Evolution Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...

may be observed in the laboratory as individuals/populations adapt to new environmental conditions by

natural selection Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is a key mechanism of evolution, the change in the heritable traits characteristic of a population over generations. Cha ...

. There are two different ways in which

adaptation In biology, adaptation has three related meanings. Firstly, it is the dynamic evolutionary process of natural selection that fits organisms to their environment, enhancing their evolutionary fitness. Secondly, it is a state reached by the po ...

can arise in experimental evolution. One is via an individual organism gaining a novel beneficial

mutation In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, m ...

. The other is from

allele An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution. ::"The chrom ...

frequency change in standing genetic variation already present in a population of organisms. 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 Genetic drift, also known as allelic drift or the Wright effect, is the change in the frequency of an existing gene variant (allele) in a population due to random chance. Genetic drift may cause gene variants to disappear completely and there ...

and

gene flow In population genetics, gene flow (also known as gene migration or geneflow and allele flow) is the transfer of genetic material from one population to another. If the rate of gene flow is high enough, then two populations will have equivalent a ...

. The organism used is decided by the experimenter, based on the hypothesis to be tested. Many

generation A generation refers to all of the people born and living at about the same time, regarded collectively. It can also be described as, "the average period, generally considered to be about 20–⁠30 years, during which children are born and gr ...

s are required for adaptive mutation to occur, and experimental evolution via mutation is carried out in

virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsk ...

es or unicellular organisms with rapid generation times, such as

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...

and asexual clonal

yeast Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The first yeast originated hundreds of millions of years ago, and at least 1,500 species are currently recognized. They are estimated to constit ...

. Polymorphic populations of asexual or sexual

, and

multicellular A multicellular organism is an organism that consists of more than one cell, in contrast to unicellular organism. All species of animals, land plants and most fungi are multicellular, as are many algae, whereas a few organisms are partially ...

eukaryote Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacter ...

s like

Drosophila ''Drosophila'' () is a genus of flies, belonging to the family Drosophilidae, whose members are often called "small fruit flies" or (less frequently) pomace flies, vinegar flies, or wine flies, a reference to the characteristic of many speci ...

, can adapt to new environments through allele frequency change in standing genetic variation. Organisms with longer generations times, although costly, can be used in experimental evolution. Laboratory studies with foxes and with

rodents Rodents (from Latin , 'to gnaw') are mammals of the order Rodentia (), which are characterized by a single pair of continuously growing incisors in each of the upper and lower jaws. About 40% of all mammal species are rodents. They are na ...

(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. More recently, experimentally evolved individuals or populations are often analyzed using

whole genome sequencing Whole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, is the process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism's genome at a ...

, an approach known as Evolve and Resequence (E&R). 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. 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. The nature of the adaptation and functional follow up studies can shed insight into what effect the mutation/allele has on

phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology (biology), morphology or physical form and structure, its Developmental biology, developmental proc ...

History

Domestication and breeding

Unwittingly, humans have carried out evolution experiments for as long as they have been domesticating plants and animals.

Selective breeding Selective breeding (also called artificial selection) is the process by which humans use animal breeding and plant breeding to selectively develop particular phenotypic traits (characteristics) by choosing which typically animal or plant ...

of plants and animals has led to varieties that differ dramatically from their original wild-type ancestors. Examples are the

cabbage Cabbage, comprising several cultivars of ''Brassica oleracea'', is a leafy green, red (purple), or white (pale green) biennial plant grown as an annual vegetable crop for its dense-leaved heads. It is descended from the wild cabbage ( ''B.&n ...

varieties,

maize Maize ( ; ''Zea mays'' subsp. ''mays'', from es, maíz after tnq, mahiz), also known as corn (North American English, North American and Australian English), is a cereal grain first domesticated by indigenous peoples of Mexico, indigenous ...

, 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 Charles Robert Darwin ( ; 12 February 1809 – 19 April 1882) was an English naturalist, geologist, and biologist, widely known for his contributions to evolutionary biology. His proposition that all species of life have descended ...

. 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

One of the first to carry out a controlled evolution experiment was William Dallinger. In the late 19th century, he cultivated small

unicellular organism A unicellular organism, also known as a single-celled organism, is an organism that consists of a single cell, unlike a multicellular organism that consists of multiple cells. Organisms fall into two general categories: prokaryotic organisms a ...

s 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. From the 1880s to 1980, experimental evolution was intermittently practiced by a variety of evolutionary biologists, including the highly influential

Theodosius Dobzhansky Theodosius Grigorievich Dobzhansky (russian: Феодо́сий Григо́рьевич Добржа́нский; uk, Теодо́сій Григо́рович Добржа́нський; January 25, 1900 – December 18, 1975) was a prominent ...

. 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 has been used in various formats to understand underlying evolutionary processes in a controlled system. Experimental evolution has been performed on multicellular and unicellular eukaryotes, prokaryotes, and viruses. Similar works have also been performed by

directed evolution Directed evolution (DE) is a method used in protein engineering that mimics the process of natural selection to steer proteins or nucleic acids toward a user-defined goal. It consists of subjecting a gene to iterative rounds of mutagenesis ...

of individual

enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products ...

ribozyme Ribozymes (ribonucleic acid enzymes) are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes. The 1982 discovery of ribozymes demons ...

and replicator 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.

Fruit flies

One of the first of a new wave of experiments using this strategy was the laboratory "evolutionary radiation" of ''

Drosophila melanogaster ''Drosophila melanogaster'' is a species of fly (the taxonomic order Diptera) in the family Drosophilidae. The species is often referred to as the fruit fly or lesser fruit fly, or less commonly the " vinegar fly" or "pomace fly". Starting with ...

'' populations that Michael R. Rose started in February, 1980. 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''. 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. Subsequently, Thomas Turner coined the term Evolve and Resequence (E&R) and several studies used E&R approach with mixed success. 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. After 200 generations, they used E&R approach to identify genomic regions that were selected by natural selection in the hypoxia adapted flies. More recent experiments are following up E&R predictions with RNAseq and genetic crosses. 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 time In population biology and demography, generation time is the average time between two consecutive generations in the lineages of a population. In human populations, generation time typically ranges from 22 to 33 years. Historians sometimes use this ...

s, 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'', ''Pseudomonas aeruginosa'', ''Enterococcus faecalis'' and ''E. coli'' (see below), while the Yeast ''S. cerevisiae'' has been used as a model for the study of eukaryotic evolution.

Lenski's ''E. coli'' experiment

One of the most widely known examples of laboratory bacterial evolution is the long-term ''E.coli'' experiment of Richard Lenski. On February 24, 1988, Lenski started growing twelve lineages of '' E. coli'' under identical growth conditions. When one of the populations evolved the ability to aerobically metabolize citrate from the growth medium and showed greatly increased growth, this provided a dramatic observation of evolution in action. The experiment continues to this day, and is now the longest-running (in terms of generations) 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.

Laboratory house mice

In 1998, Theodore Garland, Jr. and colleagues started a long-term experiment that involves selective breeding of

mice A mouse ( : mice) is a small rodent. Characteristically, mice are known to have a pointed snout, small rounded ears, a body-length scaly tail, and a high breeding rate. The best known mouse species is the common house mouse (''Mus musculus'' ...

for high voluntary activity levels on running wheels. This experiment also continues to this day (> 90

s). Mice from the four replicate "High Runner" lines evolved to run almost three 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. LitterMom1480

The HR mice exhibit an elevated maximal aerobic capacity when tested on a motorized treadmill. They also exhibit alterations in

motivation Motivation is the reason for which humans and other animals initiate, continue, or terminate a behavior at a given time. Motivational states are commonly understood as forces acting within the agent that create a disposition to engage in goal-dire ...

and the

reward system The reward system (the mesocorticolimbic circuit) is a group of neural structures responsible for incentive salience (i.e., "wanting"; desire or craving for a reward and motivation), associative learning (primarily positive reinforcement and cla ...

of the

brain A brain is an organ (biology), organ that serves as the center of the nervous system in all vertebrate and most invertebrate animals. It is located in the head, usually close to the sensory organs for senses such as Visual perception, vision. I ...

. Pharmacological studies point to alterations in

dopamine Dopamine (DA, a contraction of 3,4-dihydroxyphenethylamine) is a neuromodulatory molecule that plays several important roles in cells. It is an organic chemical of the catecholamine and phenethylamine families. Dopamine constitutes about 80% o ...

function and the

endocannabinoid system The endocannabinoid system (ECS) is a biological system composed of endocannabinoids, which are endogenous lipid-based retrograde neurotransmitters that bind to cannabinoid receptors (CBRs), and cannabinoid receptor proteins that are expressed ...

. The High Runner lines have been proposed as a model to study human attention-deficit hyperactivity disorder (

ADHD Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder characterised by excessive amounts of inattention, hyperactivity, and impulsivity that are pervasive, impairing in multiple contexts, and otherwise age-inap ...

), and administration of

Ritalin Methylphenidate, sold under the brand names Ritalin and Concerta among others, is the most widely prescribed central nervous system (CNS) stimulant medication used to treat attention deficit hyperactivity disorder (ADHD) and, to a lesser extent ...

reduces their wheel running approximately to the levels of control mice.

Multidirectional selection on bank voles

In 2005 Paweł Koteja with Edyta Sadowska and colleagues from the

Jagiellonian University The Jagiellonian University ( Polish: ''Uniwersytet Jagielloński'', UJ) is a public research university in Kraków, Poland. Founded in 1364 by King Casimir III the Great, it is the oldest university in Poland and the 13th oldest university in ...

(Poland) started a multidirectional selection on a non-laboratory rodent, the

bank vole The bank vole (''Myodes glareolus'') is a small vole with red-brown fur and some grey patches, with a tail about half as long as its body. A rodent, it lives in woodland areas and is around in length. The bank vole is found in much of Europe an ...

''Myodes (= Clethrionomys) glareolus''. The voles are selected for three distinct traits, which played important roles in the

adaptive radiation In evolutionary biology, adaptive radiation is a process in which organisms diversify rapidly from an ancestral species into a multitude of new forms, particularly when a change in the environment makes new resources available, alters biotic in ...

of terrestrial vertebrates: high maximum rate of aerobic metabolism, predatory propensity, and herbivorous capability. Aerobic lines are selected for the maximum rate of oxygen consumption achieved during swimming at 38°C; Predatory lines – for a short time to catch live

crickets Crickets are orthopteran insects which are related to bush crickets, and, more distantly, to grasshoppers. In older literature, such as Imms,Imms AD, rev. Richards OW & Davies RG (1970) ''A General Textbook of Entomology'' 9th Ed. Methuen 8 ...

; Herbivorous lines – for capability to maintain body mass when fed a low-quality diet “diluted” with dried, powdered grass. Four replicate lines are maintained for each of the three selection directions and another four as unselected Controls. After ~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

basal metabolic rate Basal metabolic rate (BMR) is the rate of energy expenditure per unit time by endothermic animals at rest. It is reported in energy units per unit time ranging from watt (joule/second) to ml O2/min or joule per hour per kg body mass J/(h·kg). P ...

and thermogenic capacity increased in the Aerobic lines. Thus, the results have provided some support for the “aerobic capacity model” for the evolution of

endothermy An endotherm (from Greek ἔνδον ''endon'' "within" and θέρμη ''thermē'' "heat") is an organism that maintains its body at a metabolically favorable temperature, largely by the use of heat released by its internal bodily functions inste ...

in mammals. 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 Personality is the characteristic sets of behaviors, cognitions, and emotional patterns that are formed from biological and environmental factors, and which change over time. While there is no generally agreed-upon definition of personality, ...

”). 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 microbiome in their

caecum The cecum or caecum is a pouch within the peritoneum that is considered to be the beginning of the large intestine. It is typically located on the right side of the body (the same side of the body as the appendix, to which it is joined). The wo ...

. Thus, the selection has resulted in evolution of the entire holobiome, and the experiment may offer a laboratory model of hologenome evolution.

Synthetic biology

Synthetic biology Synthetic biology (SynBio) is a multidisciplinary area of research that seeks to create new biological parts, devices, and systems, or to redesign systems that are already found in nature. It is a branch of science that encompasses a broad ran ...

offers unique opportunities for experimental evolution, facilitating the interpretation of evolutionary changes by inserting genetic modules into host genomes and applying selection specifically targeting such modules. Synthetic biological circuits inserted into the genome of

Escherichia coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Esc ...

or the budding yeast

Saccharomyces cerevisiae ''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have b ...

degrade (lose function) during laboratory evolution. With appropriate selection, mechanisms underlying the evolutionary regain of lost biological function can be studied. Experimental evolution of mammalian cells harboring synthetic gene circuits reveals the role of cellular heterogeneity in the evolution of drug resistance, with implications for

chemotherapy Chemotherapy (often abbreviated to chemo and sometimes CTX or CTx) is a type of cancer treatment that uses one or more anti-cancer drugs (chemotherapeutic agents or alkylating agents) as part of a standardized chemotherapy regimen. Chemother ...

resistance of cancer cells.

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. Microbial cells and recently mammalian cells 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 Microevolution is the change in allele frequencies that occurs over time within a population. This change is due to four different processes: mutation, selection ( natural and artificial), gene flow and genetic drift. This change happens over ...

in the classroom. A number of exercises involving bacteria and yeast teach concepts ranging from the evolution of resistance to the evolution of multicellularity. 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.

References

External links

E. coli Long-term Experimental Evolution Project Site
{{Webarchive, url=https://web.archive.org/web/20170727225642/http://myxo.css.msu.edu/ecoli/ , date=2017-07-27 , Lenski lab,

Michigan State University Michigan State University (Michigan State, MSU) is a public land-grant research university in East Lansing, Michigan. It was founded in 1855 as the Agricultural College of the State of Michigan, the first of its kind in the United States. It ...

*
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.

— a list of laboratories that study experimental evolution.
Network for Experimental Research on Evolution

University of California The University of California (UC) is a public land-grant research university system in the U.S. state of California. The system is composed of the campuses at Berkeley, Davis, University of California, Irvine, Irvine, University of Califor ...

.
New Scientist article on domestication by selection
* Inquiry-basedbr>middle school lesson plan: "Born to Run: Artificial Selection Lab"

Digital Evolution for Education software
Evolutionary biology Biology experiments