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.

Contents

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 generations are required for adaptive mutation to occur, and experimental evolution via mutation is carried out in viruses or unicellular organisms with rapid generation times, such as bacteria and asexual clonal yeast. [1] [4] [5] Polymorphic populations of asexual or sexual yeast, [2] and multicellular eukaryotes like Drosophila, can adapt to new environments through allele frequency change in standing genetic variation. [3] Organisms with longer generations times, although costly, can be used in experimental evolution. Laboratory studies with foxes [6] 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. [7]

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

This Chihuahua mix and Great Dane show the wide range of dog breed sizes created using artificial selection. Big and little dog 1.jpg
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.

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

Drawing of the incubator used by Dallinger in his evolution experiments. Dallinger Incubator J.R.Microscop.Soc.1887p193.png
Drawing of the incubator used by Dallinger in his evolution experiments.

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

pokoleniia=generations, Smertnost'=mortality Dysaphis anthrisci majkopica.gif
поколения=generations, Смертность=mortality

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.

Much recently the experimental evolution in flies have taken the course to address the molecular mechanisms [32] [33] and in doing so it might pave way to understand physiology of an organism better and thus redefine disease therapeutics. [34]

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, [35] Pseudomonas aeruginosa, [36] Enterococcus faecalis [37] and E. coli (see below), while the Yeast S. cerevisiae has been used as a model for the study of eukaryotic evolution. [38]

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. [39] [40] When one of the populations evolved the ability to aerobically metabolize citrate from the growth medium and showed greatly increased growth, [41] 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.[ citation needed ] 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. [42]

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. [43]

Laboratory house mice

Mouse from the Garland selection experiment with attached running wheel and its rotation counter. Wheel Counter Box 1.jpg
Mouse from the Garland selection experiment with attached running wheel and its rotation counter.

In 1998, Theodore Garland, Jr. and colleagues started a long-term experiment that involves selective breeding of mice for high voluntary activity levels on running wheels. [44] This experiment also continues to this day (> 90 generations). 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.

Female mouse with her litter, from the Garland selection experiment. LitterMom1480.jpg
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. 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. [45] 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.

Multidirectional selection on bank voles

In 2005 Paweł Koteja with Edyta Sadowska and colleagues from the Jagiellonian University (Poland) started a multidirectional selection on a non-laboratory rodent, the bank vole Myodes (= Clethrionomys) glareolus. [46] The voles are selected for three distinct traits, which played important roles in the adaptive radiation 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; 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 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 basal metabolic rate and thermogenic capacity increased in the Aerobic lines. [47] [48] Thus, the results have provided some support for the “aerobic capacity model” for the evolution of endothermy 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”). [49]

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. [50] 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 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 [51] or the budding yeast Saccharomyces cerevisiae [52] degrade (lose function) during laboratory evolution. With appropriate selection, mechanisms underlying the evolutionary regain of lost biological function can be studied. [53] Experimental evolution of mammalian cells harboring synthetic gene circuits [54] reveals the role of cellular heterogeneity in the evolution of drug resistance, with implications for chemotherapy 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. [55]

Microbial cells [56] and recently mammalian cells [57] 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 [58] to the evolution of multicellularity. [59] 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. [60]

See also

Related Research Articles

<i>Drosophila</i> Genus of flies

Drosophila is a genus of flies, belonging to the family Drosophilidae, whose members are often called "small fruit flies" or pomace flies, vinegar flies, or wine flies, a reference to the characteristic of many species to linger around overripe or rotting fruit. They should not be confused with the Tephritidae, a related family, which are also called fruit flies ; tephritids feed primarily on unripe or ripe fruit, with many species being regarded as destructive agricultural pests, especially the Mediterranean fruit fly.

<span class="mw-page-title-main">Model organism</span> Organisms used to study biology across species

A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workings of other organisms. Model organisms are widely used to research human disease when human experimentation would be unfeasible or unethical. This strategy is made possible by the common descent of all living organisms, and the conservation of metabolic and developmental pathways and genetic material over the course of evolution.

<span class="mw-page-title-main">Transposable element</span> Semiparasitic DNA sequence

A transposable element is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Transposition often results in duplication of the same genetic material. In the human genome, L1 and Alu elements are two examples. Barbara McClintock's discovery of them earned her a Nobel Prize in 1983. Its importance in personalized medicine is becoming increasingly relevant, as well as gaining more attention in data analytics given the difficulty of analysis in very high dimensional spaces.

<i>Drosophila melanogaster</i> Species of fruit fly

Drosophila melanogaster is a species of fly in the family Drosophilidae. The species is often referred to as the fruit fly or lesser fruit fly, or less commonly the "vinegar fly", "pomace fly", or "banana fly". In the wild, D. melanogaster are attracted to rotting fruit and fermenting beverages, and are often found in orchards, kitchens and pubs.

Molecular evolution is the process of change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes. Major topics in molecular evolution concern the rates and impacts of single nucleotide changes, neutral evolution vs. natural selection, origins of new genes, the genetic nature of complex traits, the genetic basis of speciation, the evolution of development, and ways that evolutionary forces influence genomic and phenotypic changes.

Allopatric speciation – also referred to as geographic speciation, vicariant speciation, or its earlier name the dumbbell model – is a mode of speciation that occurs when biological populations become geographically isolated from each other to an extent that prevents or interferes with gene flow.

Evolvability is defined as the capacity of a system for adaptive evolution. Evolvability is the ability of a population of organisms to not merely generate genetic diversity, but to generate adaptive genetic diversity, and thereby evolve through natural selection.

Exaptation and the related term co-option describe a shift in the function of a trait during evolution. For example, a trait can evolve because it served one particular function, but subsequently it may come to serve another. Exaptations are common in both anatomy and behaviour.

<span class="mw-page-title-main">Mutation rate</span> Rate at which mutations occur during some unit of time

In genetics, the mutation rate is the frequency of new mutations in a single gene, nucleotide sequence, or organism over time. Mutation rates are not constant and are not limited to a single type of mutation; there are many different types of mutations. Mutation rates are given for specific classes of mutations. Point mutations are a class of mutations which are changes to a single base. Missense and Nonsense mutations are two subtypes of point mutations. The rate of these types of substitutions can be further subdivided into a mutation spectrum which describes the influence of the genetic context on the mutation rate.

<span class="mw-page-title-main">Richard Lenski</span> American evolutionary biologist

Richard Eimer Lenski is an American evolutionary biologist, a Hannah Distinguished Professor of Microbial Ecology, Genetics and Evolution, and Evolution of Pathogen Virulence at Michigan State University. He is a member of the National Academy of Sciences and a MacArthur Fellow. Lenski is best known for his still ongoing 36-year-old long-term E. coli evolution experiment, which has been instrumental in understanding the core processes of evolution, including mutation rates, clonal interference, antibiotic resistance, the evolution of novel traits, and speciation. He is also well known for his pioneering work in studying evolution digitally using self-replicating organisms called Avida.

<span class="mw-page-title-main">Directed evolution</span> Protein engineering method

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, selection and amplification. It can be performed in vivo, or in vitro. Directed evolution is used both for protein engineering as an alternative to rationally designing modified proteins, as well as for experimental evolution studies of fundamental evolutionary principles in a controlled, laboratory environment.

The Red Queen's hypothesis is a hypothesis in evolutionary biology proposed in 1973, that species must constantly adapt, evolve, and proliferate in order to survive while pitted against ever-evolving opposing species. The hypothesis was intended to explain the constant (age-independent) extinction probability as observed in the paleontological record caused by co-evolution between competing species; however, it has also been suggested that the Red Queen hypothesis explains the advantage of sexual reproduction at the level of individuals, and the positive correlation between speciation and extinction rates in most higher taxa.

<i>E. coli</i> long-term evolution experiment Scientific study

The E. coli long-term evolution experiment (LTEE) is an ongoing study in experimental evolution begun by Richard Lenski at the University of California, Irvine, carried on by Lenski and colleagues at Michigan State University, and currently overseen by Jeffrey E. Barrick at the University of Texas at Austin. It has been tracking genetic changes in 12 initially identical populations of asexual Escherichia coli bacteria since 24 February 1988. Lenski performed the 10,000th transfer of the experiment on March 13, 2017. The populations reached over 73,000 generations in early 2020, shortly before being frozen because of the COVID-19 pandemic. In September 2020, the LTEE experiment was resumed using the frozen stocks.

Host–parasite coevolution is a special case of coevolution, where a host and a parasite continually adapt to each other. This can create an evolutionary arms race between them. A more benign possibility is of an evolutionary trade-off between transmission and virulence in the parasite, as if it kills its host too quickly, the parasite will not be able to reproduce either. Another theory, the Red Queen hypothesis, proposes that since both host and parasite have to keep on evolving to keep up with each other, and since sexual reproduction continually creates new combinations of genes, parasitism favours sexual reproduction in the host.

<span class="mw-page-title-main">Robustness (evolution)</span> Persistence of a biological trait under uncertain conditions

In evolutionary biology, robustness of a biological system is the persistence of a certain characteristic or trait in a system under perturbations or conditions of uncertainty. Robustness in development is known as canalization. According to the kind of perturbation involved, robustness can be classified as mutational, environmental, recombinational, or behavioral robustness etc. Robustness is achieved through the combination of many genetic and molecular mechanisms and can evolve by either direct or indirect selection. Several model systems have been developed to experimentally study robustness and its evolutionary consequences.

<span class="mw-page-title-main">Evolving digital ecological network</span>

Evolving digital ecological networks are webs of interacting, self-replicating, and evolving computer programs that experience the same major ecological interactions as biological organisms. Despite being computational, these programs evolve quickly in an open-ended way, and starting from only one or two ancestral organisms, the formation of ecological networks can be observed in real-time by tracking interactions between the constantly evolving organism phenotypes. These phenotypes may be defined by combinations of logical computations that digital organisms perform and by expressed behaviors that have evolved. The types and outcomes of interactions between phenotypes are determined by task overlap for logic-defined phenotypes and by responses to encounters in the case of behavioral phenotypes. Biologists use these evolving networks to study active and fundamental topics within evolutionary ecology.

<span class="mw-page-title-main">Laboratory experiments of speciation</span> Biological experiments

Laboratory experiments of speciation have been conducted for all four modes of speciation: allopatric, peripatric, parapatric, and sympatric; and various other processes involving speciation: hybridization, reinforcement, founder effects, among others. Most of the experiments have been done on flies, in particular Drosophila fruit flies. However, more recent studies have tested yeasts, fungi, and even viruses.

<i>De novo</i> gene birth Evolution of novel genes from non-genic DNA sequence

De novo gene birth is the process by which new genes evolve from non-coding DNA. De novo genes represent a subset of novel genes, and may be protein-coding or instead act as RNA genes. The processes that govern de novo gene birth are not well understood, although several models exist that describe possible mechanisms by which de novo gene birth may occur.

<span class="mw-page-title-main">Michael Travisano</span>

Michael Travisano is an American evolutionary biologist, and a Distinguished McKnight University Professor at the University of Minnesota Twin Cities. In 2020, he started his position as Head Department in Ecology, Evolution & Behavior Department at the College of Biological Sciences.

Albert Farrell Bennett is an American zoologist, physiologist, evolutionary biologist, author, and academic. He is Dean Emeritus of the School of Biological Sciences at University of California, Irvine.

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