Experimental evolution

Experimental evolution is the use of laboratory experiments or controlled field manipulations to explore evolutionary dynamics. 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. The other is from allele 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 and gene flow. The organism used is decided by the experimenter, based on whether the hypothesis to be tested involves adaptation through mutation or allele frequency change. A large number of 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. Polymorphic populations of asexual or sexual yeast, and multicellular eukaryotes like Drosophila, 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 (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, 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.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. Experimental evolution is the use of laboratory experiments or controlled field manipulations to explore evolutionary dynamics. 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. The other is from allele 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 and gene flow. The organism used is decided by the experimenter, based on whether the hypothesis to be tested involves adaptation through mutation or allele frequency change. A large number of 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. Polymorphic populations of asexual or sexual yeast, and multicellular eukaryotes like Drosophila, 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 (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, 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. 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. 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. 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. 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 of individual enzyme, ribozyme and replicator genes. 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. 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. 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. Bacteria have short generation times, easily sequenced genomes, and well-understood biology. They are therefore commonly used for experimental evolution studies.