Education SOCI331 Week 5 - Assignment: Comparing Quantitative Designs
Feature Review
Experimental evolution Tadeusz J. Kawecki1, Richard E. Lenski2, Dieter Ebert3, Brian Hollis1, Isabelle Olivieri4, and Michael C. Whitlock5
1 Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland 2 BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA 3 University of Basel, Zoological Institute, Vesalgasse 1, 4051 Basel, Switzerland 4 Université Montpelier 2, CNRS, Institut des Sciences de l’Evolution, UMR 5554, 34095 Montpelier cedex 05, France 5 Department of Zoology, University of British Columbia, Vancouver, V6T 1Z4, Canada
Review
Experimental evolution is the study of evolutionary pro- cesses occurring in experimental populations in re- sponse to conditions imposed by the experimenter. This research approach is increasingly used to study adaptation, estimate evolutionary parameters, and test diverse evolutionary hypotheses. Long applied in vac- cine development, experimental evolution also finds new applications in biotechnology. Recent technological developments provide a path towards detailed under- standing of the genomic and molecular basis of experi- mental evolutionary change, while new findings raise new questions that can be addressed with this approach. However, experimental evolution has important limita- tions, and the interpretation of results is subject to caveats resulting from small population sizes, limited timescales, the simplified nature of laboratory environ- ments, and, in some cases, the potential to misinterpret the selective forces and other processes at work.
Experimental evolution as a research tool Evolutionary theories are usually inspired and tested by studying patterns of, for example, phylogeny, divergence between species or populations, variation within popula- tions, genome structure, and genome sequence, which all reflect past evolution. Experimental evolution is an alter- native research framework that offers the opportunity to study evolutionary processes experimentally in real time. The past decade has seen the fast growth of studies that tap into this potential, fuelled both by an increasing awareness of the power of this approach and by technolog- ical advances that facilitate analysis of the genetic and molecular basis of experimental evolution.
We define experimental evolution as the study of evolu- tionary changes occurring in experimental populations as a consequence of conditions (environmental, demographic, genetic, social, and so forth) imposed by the experimenter (Figure 1). Thus, we do not consider cases of evolution in action that do not result from a planned and designed experiment. The above definition also excludes artificial selection (see [1]), where breeding individuals are chosen explicitly by the investigator based on phenotypic values of defined traits or genotypes (e.g., at specific marker loci), thus enforcing a predetermined relation between those
Corresponding author: Kawecki, T.J. (tadeusz.kawecki@unil.ch)
0169-5347/$ – see front matter � 2012 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j
traits or genotypes and fitness. By contrast, in experimen- tal evolution, selection can act on any and all traits and genes relevant to fitness under the environmental regimes of interest. Experimental evolution is sometimes called ‘laboratory natural selection’; however, some experimental evolution studies have been conducted in the field [2–4] and, moreover, others have explicitly focused on other evolutionary forces, including mutation, genetic drift, and gene flow (e.g., [5,6]). Indeed, these other forces almost invariably act along with selection during experimental evolution, just as they do in nature.
Here, we provide an introduction to experimental evo- lution as a research approach, not only illustrating its power and versatility, but also highlighting its limitations and caveats. We discuss major aspects of study systems and experimental design, and we summarize recent tech- nological advances that are revolutionizing the study of the genetic and molecular basis of experimental evolutionary change.
Applications Experimental evolution has been used to address diverse questions in many areas of evolutionary biology. Here, we discuss several major types of question, keeping in mind that different questions are often addressed in a single experiment. We also address the advantages of long-term experiments and some practical applications of experimen- tal evolution.
Adaptation to specific environments
Many evolution experiments seek to understand how populations adapt to particular environmental conditions, usually defined in terms of a particular factor, such as temperature [7], nutrition [8], other environmental stress- ors [9], parasites [3], or competition [10,11]. A few of these studies are specifically designed to test hypothetical links between particular polymorphisms and fitness: they start from a gene pool constructed to be polymorphic at the focal locus or loci and then measure the response in terms of changes in allele frequency (e.g., [12,13]). By contrast, most studies rely on natural (i.e., uncontrolled) genetic variation sampled from a base population or generated de novo by random mutations. Although these studies are often motivated by specific hypotheses about traits pre- sumed to be relevant for adaptation (inspired, e.g., by
.tree.2012.06.001 Trends in Ecology and Evolution, October 2012, Vol. 27, No. 10 547
(a)
(b)
(c) (d)
WT
A
E
A
E
Introduction site
Ancestral site
10 mm0.1 mm
25 µm
TRENDS in Ecology & Evolution
Figure 1. Examples of experimentally evolved phenotypic changes. (a) Cells of the social bacterium Myxococcus xanthus cooperate to swarm across solid surfaces in
search of food and to form multicellular fruiting bodies. Strains initially unable to swarm due to loss of a necessary gene (A) evolved alternative swarming mechanisms,
leading to novel swarm morphologies (E) that are markedly different from the ancestral form (WT) [223]. Each swarm contains many millions of cells. (b) Multicellular
‘snowflake’ yeast (right) experimentally evolved from a single-celled ancestor (left) under conditions favoring large size. (c) Two male morphs in Rhizoglyphus mites;
‘fighter’ males (top) use their modified third pair of legs (arrow) to kill rival males, but are less mobile than ‘scrambler’ males (bottom). Ten generations of evolution in a
complex environment shifted the underlying reaction norm, leading to a substantial decrease in the frequency of the fighter morph [224]. (d) Populations of the guppy
(Poecilia reticulata) introduced to sites free of the main predator (bottom) evolved brighter male coloration (here, blue dorsolateral spots and stronger blue-green
iridescence on posterior body) compared with their ancestors (top), which evolved with visual predators [201]. Reproduced, with permission, from [223] (a), Jacek Radwan
(c) and Darrell J. Kemp (d); adapted, with permission, from [164] (b).
Review Trends in Ecology and Evolution October 2012, Vol. 27, No. 10
patterns of interpopulation variation in nature), other traits may evolve and provide additional and unexpected insights. Therefore, what one can learn from experimental evolution is relatively unconstrained by preconceptions about what traits and evolutionary processes are most important. The traditional focus on phenotypic aspects of adaptation has been increasingly combined with genomic data, facilitated by technological advances (Box 1).
Study of evolutionary trade-offs and constraints
It is widely assumed that many or most adaptations are associated with trade-offs, such that changes in traits that increase fitness in some environments or situations are deleterious in some other environments or situations. Experimental evolution provides ample evidence for wide- spread (although not universal) trade-offs in general and insights into their mechanisms in specific cases (e.g., [14]); the evidence has been reviewed elsewhere [15,16]. As one example, experimental populations of Drosophila melano- gaster that evolved postponed aging showed a decline in their early fecundity relative to populations that were allowed to breed immediately after emerging as adults [17]. This experiment and several similar ones were pivotal in the broader acceptance of an evolutionary explanation for aging [18,19]. Experimental evolution has also been used to study constraints imposed by a lack of standing genetic variation for specific adaptation [20] and to address the notion that certain adaptations are unattainable by
548
mutation. In this latter category, evolution experiments have falsified the hypotheses that bacteria cannot evolve resistance to amphipathic antimicrobial peptides [21] and that Escherichia coli cannot evolve to feed on citrate under oxic conditions [22]. The study of citrate use also throws light on the nature of the constraint: the appear- ance of the crucial mutation was contingent on earlier evolutionary changes. This contingency explains why this new function only evolved after 31 000 generations of experimental evolution and only in one of 12 replicate populations [22].
Estimating population genetic parameters
Mutation accumulation experiments, in which very small and initially isogenic populations evolve under conditions designed to minimize selection, are one important source of information about the statistical properties of spontaneous mutations affecting fitness and other quantitative traits. These statistics include the rate at which such mutations occur per genome, the distribution of their effects, the way they interact within (dominance) and between (epistasis) loci, and the variance and covariance they contribute to phenotypic variation per generation (reviewed in [6]). Laboratory adaptation experiments with bacteria, coupled with new population-genetic theory, have been devised to estimate the rates and effect sizes of beneficial mutations [23–25]. In particular, one can estimate these parameters by following the dynamics of a neutral genetic marker
Box 1. Genomics and experimental evolution
The first complete genome sequence was for the phage FX174, and
its 5375-bp sequence appeared in 1982. A draft of the approximately
3000-Mb human genome was published in 2001. These achieve-
ments were remarkable in their day but now, thanks to technical
advances, whole-genome resequencing is accessible for experi-
mental evolution studies. In 1997, Bull et al. [104] sequenced nine
FX174 isolates that had evolved on two hosts. In 2007, Velicer and
colleagues [105] sequenced the genome of a Myxococcus xanthus
derivative that had evolved from socially cooperative to cheating
and back to cooperative. In 2009, Barrick and Lenski [49] deeply
sequenced seven whole-population samples that spanned 40 000
generations from an evolving Escherichia coli population to find
genetic polymorphisms. In 2010, genomics was extended to
experimentally evolved eukaryotes: Saccharomyces cerevisiae
[106] and Drosophila melanogaster [54]. The application of geno-
mics to experimental evolution may soon be limited only by the
imagination of the investigator and the quality of the study design.
Other high-throughput approaches are also increasingly useful for
experimental evolution, including characterizing the capacity of an
organism to use diverse resources (e.g., [43]) as well as proteomic
(e.g., [107]), transcriptional (e.g., [40]), and metabolic profiling (e.g.,
[108]).
To date, studies at the interface of genomics and experimental
evolution have ranged from descriptive ones that demonstrate new
technologies [109,110] or find genes of interest [105,106,111] to
quantitative analyses of diverse conceptual issues. How repeatable
is evolution at the levels of nucleotides, genes, and pathways
[27,51,104,112,113]? How do epistatic interactions and the order of
mutations affect evolvability, marginal fitness effects, and the origin
of new functions [26,27,113–115]? What are genomic mutation rates
and the spectrum of mutational types, and how do they evolve
[49,51,116–118]? What are the dynamics of genome evolution in
relation to phenotypic change and in terms of hard versus soft
selective sweeps [49,51,54,104,111,113]?
Although these high-throughput methods provide new opportu-
nities, they can also be difficult to analyze and interpret. In
particular, demonstrating causal links between specific changes at
the genomic or transcriptional level with divergence in morphology,
physiology, behavior, or life history remains challenging, especially
in non-microbial systems. These methods often identify divergence
in allele frequencies at hundreds of loci [54,111] or in expression of
hundreds of transcripts [119]. Owing to linkage, drift, and statistical
false-positives, not all of these differences will have been caused by
adaptation. Therefore, such data must be interpreted with caution.
Review Trends in Ecology and Evolution October 2012, Vol. 27, No. 10
seeded into a set of asexual populations, even without identifying the beneficial mutations themselves. Also, by constructing isogenic strains with specific combinations of evolved mutations, the extent and form of epistatic inter- actions among the beneficial mutations can be measured [26,27]. Experimental evolution has also been used to estimate genetic variance in fitness within populations [28], as well as between replicate evolving lines [29,30]. Finally, selection coefficients acting on alleles can some- times be directly estimated from their frequency dynamics under the experimental conditions [29,31].
Testing evolutionary theories
The versatility of experimental evolution as a research framework is apparent in its applications to test predic- tions from evolutionary theory. It has been used, for exam- ple, to address controversies as to whether particular evolutionary processes, postulated on theoretical grounds, are plausible. Such ‘proof of principle’ studies have dem- onstrated, for example, that bacteria can evolve a new phenotypic switch (bet hedging) [32], that natural selection may favor male traits that directly reduce the fitness of
their mates [33], and that some degree of reproductive isolation can evolve as a byproduct of divergent natural selection in different environments [34–36] or as a conse- quence of selection against hybrids [37,38]. Conversely, no unequivocal evidence for founder-effect speciation has emerged from several experiments designed to test this model (e.g., [5,39] and references therein); although these failed attempts do not prove that the process cannot occur, they do suggest that it is rare or requires more time than the experiments allowed to yield a discernible signal.
More often, experimental evolution has been used to test specific predictions concerning the effect of general properties of the environment (e.g., spatial or temporal variability), demography (e.g., population size or structure, extrinsic mortality patterns, and transmission rate and mode for parasites), social factors (e.g., relatedness) or other attributes of the population (e.g., mode of reproduc- tion or mating system) on evolutionary processes and out- comes. Some of those hypotheses are listed in Table 1. We emphasize that this is not a comprehensive list and the studies cited are examples, chosen to cover the broad array of research topics to which experimental evolution has contributed. A comprehensive review of evidence for each hypothesis is beyond the scope of this paper.
Long-term experiments
Most evolution experiments start with one specific aim in mind, but, as observations accrue, new questions arise. A long-term experiment with E. coli (now past 55 000 gen- erations) provides a case in point. The initial focus was on the dynamics of adaptation and divergence in 12 replicate populations, with mean fitness in the selection environ- ment being the response of interest [29,30]. In time, anal- yses expanded to examine parallelism from morphological [29] to genetic levels [40,41]; correlated responses, pleio- tropy, and specialization [42–44]; the evolution of mutation rates [45,46]; forces maintaining diversity [47–49]; histor- ical contingency [50] and the origin of a new function [22]; evolvability [30] and epistasis [26]; and the coupling be- tween genomic and phenotypic evolution [51]. Long-term evolution experiments in Drosophila (some of which have been running for over 600 generations) have also yielded important insights into reversals of correlated evolution- ary responses [52], the causes of aging and late-age mor- tality plateaus [53], and the relative importance of standing versus mutational variance in adaptation [54]. One of the longest-running ecological experiments (started in 1856), which was designed to study the effects of fertili- zation and soil pH on plant community and ecosystem processes, led to insights into local adaptation and the evolution of reproductive isolation [55,56]. Sufficiently long experiments might also probe the limits of adaptive evolu- tion, at least for simple environments. Many evolution experiments show declining rates of phenotypic change, but does adaptive evolution eventually cease in the ab- sence of environmental change?
Experimental evolution in medicine and technology
For decades, experimental evolution has been the method of choice for the development of live attenuated vaccines against viral and bacterial diseases, such as
549
Table 1. Examples of evolutionary hypotheses with references to selected studies that have tested (but not necessarily supported) those hypotheses using evolution experimentsa
Hypothesis Organism Refs
Mutation and adaptation
Adaptation occurs mostly via many mutations of small effect Bacteriophage w6 [191]
Escherichia coli [23–25]
Fitness effects of beneficial mutations show negative epistatic
interactions
Bacteriophage T7 [192]
E. coli [26]
Methylobacterium extorquens [115]
Mutators (strains with elevated mutation rates) may evolve during
adaptation to a novel environment
E. coli [45]
Mutators may enhance rates of adaptive evolution E. coli [46]
Genetic drift and inbreeding
Genetic drift reshapes genetic variance–covariance matrices Drosophila melanogaster [193]
Bottlenecks do not reduce and may increase additive genetic variance Musca domestica [194]
Tribolium castaneum [195]
D. melanogaster [196]
Offspring of immigrants have high fitness in small inbred populations Daphnia magna (F) [2]
Environmental variability
Spatial heterogeneity with restricted gene flow favors local adaptation
in metapopulations
Arabidopsis thaliana [75]
Spatial environmental heterogeneity drives adaptive radiation Pseudomonas fluorescens [153]
Fluctuating environments favor generalist genotypes, and constant
environments favor specialist genotypes
Chlamydomonas reinhardtii [197]
Vesicular stomatitis virus [198]
E. coli [43]
Digital organisms [132]
Fluctuating environments maintain genetic variation D. melanogaster [76,199]
Sexual selection and conflict
Intensity of sexual signals increases under strong sexual selection Drosophila pseudoobscura [200]
Saccharomyces cerevisiae [154]
Intensity of sexual signals increases when predation pressure is relaxed Poecilia reticulata (F) [201]
Sexual selection facilitates elimination of deleterious alleles D. melanogaster [31]
Sexual selection leads to reduction (–) or increase (+) in non-sexual
fitness components
Callosobruchus maculatus (+) [202]
D. melanogaster (+) [203]
D. melanogaster (–) [204]
Drosophila serrata (–) [205]
Polygamy favors male traits that reduce fitness of their mates
(interlocus sexual conflict)
D. melanogaster [33]
Rhizoglyphus robini (mite) [206]
Sepsis cynipseaii (fly) [207]
Life history and sex allocation
High extrinsic mortality leads to the evolution of shorter intrinsic lifespan D. melanogaster [208]
High predation favors high reproductive effort P. reticulata (F) [95]
Antagonistic pleiotropy contributes to late-life mortality plateau D. melanogaster [53]
Sex allocation in hermaphrodites evolves towards the Fisherian ratio Mercurialis annua (plant) [68]
Local mate competition favors female-biased sex ratio Tetranychus urticae (mite) [209]
Sexual reproduction and mating systems
Fitness declines in asexual populations by Muller’s ratchet Bacteriophage w6 [210]
Sex and recombination accelerate adaptation to a novel environment C. reinhardtii [162]
S. cerevisiae [83]
E. coli [156]
Incidence of sex increases in heterogeneous environments (in species
with facultative sex)
Brachionus calyciflorus (rotifer) [82]
Self-fertilization evolves under pollinator limitation Mimulus guttatus (plant) [69]
Sexual reproduction favors altered gene interactions and modularity Bacteriophage T4 [155]
Digital organisms [131]
Kin selection and cooperation
Relatedness favors restraint from cannibalism Tribolium confusum [211]
Limited migration and local extinction promote competitive restraint Bacteriophage T4 [212]
Cooperators evolve to suppress social cheaters Myxococcus xanthus [213]
Parasitic mitochondria evolve when among-cell selection is weak S. cerevisiae [214]
Single-cell bottlenecks promote cooperation among cells in
multicellular organisms
Dictyostelium discoideum [215]
Conditions favoring large size may lead to evolution of multicellularity S. cerevisiae [164]
Review Trends in Ecology and Evolution October 2012, Vol. 27, No. 10
550
Table 1 (Continued )
Hypothesis Organism Refs
Behavior and cognition
Variation in foraging behavior is maintained by negative
frequency-dependent selection
D. melanogaster [12]
Opportunity to learn may accelerate genetically-based
adaptation (Baldwin effect)
D. melanogaster [216]
Host–parasite interactions
Parasites or predators select for host or prey resistance,
and resistance is costly
Daphnia magna and microsporidian
parasite (F)
[3]
E. coli and various bacteriophages [14,27,44,217]
Chlorella vulgaris (algae) and
Brachionus calyciflorus (rotifer)
[218]
Parasites impose negative frequency-dependent selection
on the host
Potamopyrgus antipodarum (gastropod)
and Microphallus sp. (trematode)
[74]
Host–parasite coevolution drives divergence and local
adaptation
E. coli and bacteriophage w6 [139,149]
Vertical transmission and lower virulence evolve under
conditions of high host population growth
Paramecium caudatum and Holospora
undulate
[219]
Speciation
Divergent selection leads to premating isolation D. pseudoobscura [35]
D. serrata [34]
Divergent selection leads to postmating isolation Neurospora sp. [36]
Hybrid inferiority leads to reinforcement of prezygotic
reproductive isolation
Drosophila yakuba [38]
Repeated bottlenecks lead to reproductive isolation D. pseudoobscura [5,39]
M. domestica [220]
Repeatability of evolution
Adaptation in independent populations occurs via parallel
changes in gene expression, parallel mutations, or parallel
enrichment of pre-existing alleles
E. coli [40]
S. cerevisiae [221]
Various bacteriophages [27,104,222]
D. melanogaster [54]
Traits less correlated with fitness are more influenced by
chance and history
E. coli [50]
Ontogeny recapitulates phylogeny Digital organisms [130]
aF indicates an evolution experiment in the field.
Review Trends in Ecology and Evolution October 2012, Vol. 27, No. 10
polio, tuberculosis, yellow fever, measles, mumps, and rubella. For this purpose, the pathogens were serially passaged in other host species or artificial media until their pathogenic effects in humans had attenuated as a correlated response to selection for improved growth in the new environment [57,58]. Thus, experimental evolu- tion has contributed to saving millions of human lives, beginning even before it was understood that this method of vaccine production involves Darwinian evolution.
More recently, experimental evolution combined with genome sequencing and genetic mapping has been used to identify mutations that confer drug resistance to patho- gens, before such mutations appear in nature (e.g., [59]). This approach might facilitate the rapid diagnosis of resis- tant infections if they appear in patients, allowing appro- priate public-health measures, including the development in advance of new drugs that target the resistant mutants.
Experimental evolution also has great potential in other areas of biotechnology. Serial passage of a pathogen on a particular host often leads to increased specialization and higher virulence on that host [57], and this principle has been used to produce more virulent strains of microbial [60] and metazoan [61] agents of biological pest control. Experimental evolution has also been used to produce biocatalysts and biocontrol agents with other desired prop- erties, such as high thermal tolerance [62]. For some
microbial systems, this process can be fully automated [60,62]. From an engineering perspective, experimental evolution will undoubtedly be used as a ‘bottom-up’ com- plement or supplement to ‘top-down’ genetic engineering methods to generate organisms for the production of bio- fuels [63] and for carbon sequestration.
Experimental evolution can even be extended to artifi- cial living systems, including some that are based on molecular processes and others that are computational in nature (Box 2). These artificial systems are being used not only to test basic hypotheses, but also to evolve useful new products, from protein catalysts to software and even robots [64–66].
Designing evolution experiments Study system
Many questions in evolutionary biology apply to a broad range of organisms or even to all. Thus, the choice of the study system becomes largely a matter of convenience. As a result, most evolutionary experiments have used one of several favorites, in particular E. coli, Pseudomonas, yeast, and Drosophila (Table 1). Several phage-bacteria systems and Daphnia with its pathogens have been widely used to address questions about coevolution (Box 3). The relative paucity of evolution experiments on vascular plants [67– 69] reflects, in part, their long generation times (even for
551
Box 2. Experimental evolution with artificial life
One of the goals of experimental evolution, as a field, is to test
general hypotheses about evolutionary processes, in contrast to
many comparative studies that seek to understand the evolution of a
particular trait in a given phylogenetic context. Yet, all of life on
Earth derives from the same primordial ancestors, so how general
can evolutionary tests be? As Maynard Smith put it [120]: ‘So far, we
have been able to study only one evolving system, and we cannot
wait for interstellar flight to provide us with a second. If we want to
discover generalizations about evolving systems, we will have to
look at artificial ones.’
Artificial evolving systems include synthetic replicators built from
organic molecules [121,122] and digital organisms living in virtual
worlds [123,124]. As Dennett states [125]: ‘The process of natural
selection is substrate-neutral. . .evolution will occur whenever and
wherever three conditions are met: replication, variation (mutation),
and differential fitness (competition).’ The Avida system is a
computational platform developed for this research, in which digital
organisms are programs that replicate, mutate, and compete
[124,126]. (Both research and educational versions of Avida are
freely available on the web.) The organisms can manipulate bit-
strings and, if they perform an operation appropriate to their
environment, they obtain additional energy to run their genetic
programs. Starting from a simple ancestor that can replicate but not
perform other functions, populations can evolve a complex
computational metabolism [127]. Because in nature, selection acts
on the phenotypes of digital organisms, not on their genetic
encoding.
Digital systems offer short generations, controllable environ-
ments, and automated analyses including, for example, lines of
descent (showing every intermediate from the ancestor to an
evolved state of interest) and genotype–phenotype maps (showing
the effect of mutating each genomic position on every phenotype).
To date, experiments with digital organisms have addressed diverse
issues, including the origin of parasites [123], effect of mutation rate
on robustness [128], historical contingency [129], origin of complex
functions [127], ontogeny and phylogeny [130], evolution of sex
[131], role of pleiotropy in ecological specialization [132], recovery
from extinctions [133], and selection for altruism [134]. One can
even extend this approach to embodied robots by evolving their
morphology, behavior, or both in a virtual world constrained by
physical laws, then building the computationally evolved robots
[64]. In this way, robots can evolve to pursue or evade other robots
as predators or prey [135], cooperate [136], and communicate with
one another [137,138].
Box 3. Experimental coevolution
The term ‘coevolution’ refers to two phenomena: (i) the evolution of
interacting species, whereby evolutionary change in one species
induces evolutionary change in another species and vice versa; and
(ii) a similar process occurring between genes and traits of the same
population but expressed in different classes of individual (e.g.,
sexes or mother versus offspring) or with different modes of
transmission (e.g., selfish genetic elements and their suppressors).
Most evolution experiments have concentrated on antagonistic
coevolution, where the fitness of both parties cannot be simulta-
neously maximized. Rather than being externally controlled, a
crucial aspect of the environment in coevolutionary experiments is
the coevolving party and, thus, a moving target.
Disentangling co- from evolution
Identifying evolved changes that result from the coevolutionary
feedback often requires comparing coevolutionary regimes (where
the interacting species evolve together) with ‘unilateral’ regimes
where only one species is allowed to evolve and the other is kept static
[139–141]. An analogous approach to coevolution between the sexes
is challenging because the sexes share a gene pool, but inroads have
been made using sophisticated breeding designs [142].
Dynamics of coevolution
Antagonistic coevolution proceeds by two fundamentally different
modes [143]. (i) Time-lagged negatively frequency-dependent
selection, which favors phenotypes that were rare or absent a few
generations ago; this mode often leads to unstable dynamics, such
as an arms race. (ii) Selective sweep coevolution, which occurs
when beneficial mutations arise and spread to fixation. Coevolution
experiments have been performed to investigate by which mode
coevolution proceeds and to test how coevolutionary dynamics are
affected by, and in turn influence, genetic and demographic factors
[139,144,145]. Systems in which samples of coevolving populations
can be preserved and revived allow time-shift-experiments [146].
These experiments involve reciprocal transplants in time, where
populations of one antagonist (e.g., host) sampled at time t1 are
confronted with the other antagonist (e.g., parasite) sampled at
times t0 (past), t1 (contemporary), and t2 (future). Parasites from the
future are expected to be more infective to hosts from time t1 under
a selective sweep model, but not under negative frequency-
dependent selection models [147,148].
Coevolution-driven divergence
In a coevolving system, stochastic changes in one antagonist may
change selection on the other antagonist, and the resulting
evolutionary change may feed back on the evolution of the first
species and so on. Thus, coevolution will magnify stochastic effects
and accelerate divergence between isolated populations, as seen in
a several experiments with phage and bacteria [27,139,149].
Review Trends in Ecology and Evolution October 2012, Vol. 27, No. 10
Arabidopsis this is 2 months, compared with 2 weeks in Drosophila and Daphnia, 3–4 days in Caenorhabditis ele- gans, and hours in microbes). Concentrating on model systems has obvious advantages, such as integration of results from different fields and the availability of genomic information and tools. However, even if the questions an experimenter asks are general in nature, the answers obtained might nevertheless be specific to the taxon under study. Microbes differ from multicellular eukaryotes in many fundamental ways (Box 4), and so extrapolating between these domains must be done with care and may sometimes be problematic. Even closely related species may differ in ways relevant for evolution. For example, populations of D. melanogaster are often polymorphic for large chromosomal inversions, which effectively suppress recombination over large regions of the genome; but such inversion polymorphisms are rare in the closely related Drosophila simulans [70]. Thus, the evolution of the former species is more likely to be affected by linkage disequilib- rium, which may produce more pronounced correlated responses in the absence of pleiotropy. Over time, the differences between general principles and idiosyncratic
552
features of particular systems should emerge if the com- munity of researchers uses a wide range of study systems.
More generally, the common model systems may also be more similar to one another, and unrepresentative of nature, precisely in the ways that make them so easy to study. These species have been chosen because they have short generation times. They all tolerate human-influ- enced environments, in some cases (e.g., D. melanogaster) because they are human commensals. Some of them have recently increased in population size and adapted to the human-modulated environment, perhaps selecting for higher recombination rates and mutation rates than those in their sister taxa. Compared with their wild counter- parts, the strains used in these studies have often already adapted to some laboratory conditions. They may prefer more constant abiotic conditions (e.g., temperature), use a narrower spectrum of resources that require little effort to locate, undergo little or no dispersal, have little need to react to stresses, have reduced capacity to interact with
Box 4. Microbes versus macrobes
Microbes were largely ignored by evolutionary biologists for many
decades. Eventually, however, the utility of microbes for experi-
mental evolution became clear. Their obvious advantages include
short generations, large populations, and the ease with which
environments can be controlled and manipulated. Another impor-
tant feature is that most microbes can be stored frozen in a non-
evolving state and later revived (this is also possible for some
animals and plant seeds). This property effectively enables travel in
time: the experimenter can directly compare organisms from
different generations, for example, by competing derived and
ancestral genotypes to measure their relative fitness [30,150].
Indeed, by performing simultaneous assays with organisms from
many different generations, one minimizes the effects of uncon-
trolled fluctuations in conditions that might confound interpretation
of data collected at different times. One can also perform ‘replays’,
where evolution is restarted from intermediate generations to test
whether an outcome of interest, such as the origin of a new
function, was contingent on earlier changes [22,27,113].
Evolutionary experiments with microbes and other organisms
differ in several ways, the importance of which may depend on the
question of interest. Most experiments with microbes start with a
single clone and depend on new mutations to generate variation.
Evolution often occurs by consecutive selective sweeps, although
frequency-dependent interactions and clonal interference (competi-
tion between beneficial mutations) also can be important [48,151–
153]. By contrast, experimental evolution in non-microbial experi-
ments is mostly fuelled by genetic variation already present in the
initial population, and alleles are regularly recombined by sex. As a
consequence, microbial populations may evolve more slowly, at
least on a generational basis. Furthermore, some phenomena
central to the evolution of many plants and animals, such as sex,
sexual selection, parental care, and speciation, are either absent or
involve very different mechanisms in microbes (particularly bacteria
or viruses), limiting the utility of the latter as model systems for
those phenomena in the former. By contrast, eukaryotic microbes
have been used to study the evolution of reproductive isolation
[36,37] and sexual selection [154]. Furthermore, factors such as
mutation rates [46], recombination [83,155–157], and genetic
relatedness [158–162] can be manipulated in some microbes to
examine their evolutionary effects.
Finally, microbes are less familiar than the larger organisms we
see all around us. As a consequence, most evolutionary biologists
have better intuition about what phenotypic traits and environ-
mental factors matter for animals and plants, for example, beak size
and seed hardness, than for the physiological traits and physico-
chemical factors that determine the fitness of microbes. The
potential for microbes to exhibit complex life histories
[161,163,164] and social behaviors [160,161,165] has only recently
become appreciated. Thus, microbes are now being used as model
systems to study the evolution of traits that biologists traditionally
ascribed only to multicellular organisms.
Review Trends in Ecology and Evolution October 2012, Vol. 27, No. 10
other species, and so forth. Whether these differences between the typical organisms used in experimental evo- lution and those more broadly representative of nature are important may depend on the goals of a particular study. For example, experimental evolution is often well suited to asking whether some particular process or factor (e.g., population size) can be important in evolution, but this approach may not be appropriate to extrapolating param- eter estimates (e.g., selection coefficients) to nature with- out appropriate caveats.
Regimes and controls
Hypothesis testing in evolution experiments typically involves comparisons between sets of populations evolving under different regimes, but originally derived from the same base population or the same ancestral genotype
(Figure 1c,d). Such comparisons quantify the differences in evolutionary response under the various regimes. Some- times, a distinction can be made between ‘selection’ (or ‘treatment’) and ‘control’ (or ‘unselected’) regimes, perhaps suggesting that the ‘control’ conditions mimic the ancestral conditions to which the base population or ancestral strain was adapted before the start of the experiment (e.g., [8,71]). However, this assumption is rarely fulfilled, because most of the evolutionary history of any lineage occurred outside the laboratory. In any case, the contribution of the different regimes to the observed divergence can be best evaluated if the ancestral population is included in the comparison. The phenotype of evolved populations can be compared in contemporaneous assays with that of the ancestral popu- lation if the latter can be preserved alive but prevented from evolving (Figure 1a,b), for example, by freezing or in resting stages, such as seeds. At the genetic level, once candidate polymorphisms that may contribute to pheno- typic evolution have been identified, allele frequencies in the various evolved populations can be compared with the ancestral population if a sample of genetic material for the latter is available (even if the ancestral organisms are no longer viable). Also, it should be kept in mind that a difference between evolved and ancestral populations might reflect greater inbreeding of the former (for sexually reproducing organisms: see below) or adaptation to aspects of the selection regime other than the factor being tested.
Experimental replicates
Isolated populations derived from the same gene pool will diverge with time even if they are maintained under the same environmental conditions. Such divergence will be driven by random genetic drift affecting pre-existing poly- morphisms and the establishment of new mutations, by the order in which mutations appear, and by any uncontrolled environmental variation that affects the direction and intensity of selection. Divergence generated by these sto- chastic mechanisms can be further amplified by selection if the resulting differences in genetic background influence the fitness effects of alleles [72]. Therefore, genetic diver- gence between populations cannot be attributed with con- fidence to different regimes unless this divergence is shown to be greater than that which occurs in the absence of the imposed differences in regime. Rather, divergence between experimental regimes should be tested relative to variation among independently evolving replicate populations sub- jected to the same regime. In other words, experimental populations are the units of replication for testing evolu- tionary hypotheses.
Base population or ancestral genotype
Replicate populations are usually derived from a single base population or ancestral strain. In other cases, experi- mental populations may be paired or blocked based on their origin, before evolving under different experimental regimes. Evolutionary change is contingent on the initial gene pool, so starting from different ancestors may reduce the statistical power (because the different starting popu- lations may respond differently); by contrast, having mul- tiple starting populations increases the generality of any conclusions.
553
Box 5. Effects of population size in experimental evolution
By necessity, experimental populations are orders of magnitude
smaller than in nature. Therefore, many fewer alleles are available to
respond to selection, for two reasons. First, some alleles are lost due
to drift in small populations, with the loss rate inversely propor-
tional to the effective population size (Ne). Effective sizes for
eukaryotes are usually thought to be up to an order of magnitude
smaller than census sizes (N) [166]; factors that reduce Ne compared
with N include selection at other loci, random variation in
reproductive output, biased sex ratio, and fluctuations in population
sizes. In microbial populations propagated by serial transfer (e.g.,
[30,167]), the effective size depends strongly on the transfer size, not
the maximum population size [30,168]. For diploid organisms, the
loss of genetic diversity can also lead to inbreeding depression,
which lowers fitness in subsequent generations. Deleterious alleles
can fix by random drift if the population is small enough (Ne less
than the reciprocal of the selection coefficient); in fact mutation-
accumulation experiments rely on this process [6]. The loss of
diversity and inbreeding are unlikely to matter too much over the
first ten generations or so, provided Ne is a few dozen or more.
Second, the number of new mutations per generation is propor-
tional to the number of genomes in the population, that is N or 2N
depending on ploidy. The relative importance of standing variation
and new mutations depends on the size of the population and the
length of the experiment. Hill [169] estimates that, in long-term
experimental selection studies, many fixed alleles arise as new
mutations and, of course, many experimental populations are
started from a genetically uniform stock, making new mutations
all-important. Responses to selection can be significantly limited by
population size [46,167,170,171].
Small population sizes can affect the progress of evolution in
several ways. For multicellular sexual organisms, the rate of
adaptation in a laboratory population is likely to be mutation limited
only after it exhausts (through selection or drift) the starting genetic
variation. Such species typically have long generation times, and
few alleles have time to reach fixation during a typical experiment.
By contrast, it may be possible to have much larger populations of
single-celled organisms. Indeed, in some cases, all one-step point
mutations are estimated to have arisen multiple times [22]. Still, in
such cases, the rate of adaptive evolution may be limited by small
population sizes because some adaptations may require two or
more mutations, and the order in which they occur and their
epistatic interactions may constrain evolution [22,26,113]. Simulta-
neous double mutations are rare, and exploring the space of all
possible double mutations would require very large populations.
Review Trends in Ecology and Evolution October 2012, Vol. 27, No. 10
Evolution experiments that rely on pre-existing genetic variation (i.e., most non-microbial studies) start with a base population. That base population was itself typically founded with some dozens to thousands of individuals sampled from nature, then allowed to adapt to the labo- ratory environment for many generations while being maintained at a large size (e.g., [71,73]). Such base popu- lations will probably harbor more polymorphisms, includ- ing rare alleles, than will typical laboratory stocks. An experimenter could also mix individuals from different natural populations or laboratory stocks to increase ge- netic variation, but doing so would generate linkage dis- equilibrium, which might be problematic depending on the question of interest.
Experimental population size and number of
generations
Whereas evolving microbial populations are usually main- tained at sizes of millions, experimental populations in non-microbial systems are limited by practical consider- ations to thousands, hundreds or even dozens of breeding individuals. Small population sizes have important con- sequences for several aspects of evolution (Box 5). Of the studies cited in Table 1, many that started from outbred populations have detected divergence in mean trait values or fitness within 10–20, and sometimes as few as 3–8, generations (e.g., [68,74,75]). However, experiments that fail to produce an evolutionary response are often not published, and so these numbers should be viewed as optimistic. In microbial experiments, responses may occur within a single day (5–10 generations) when strong selec- tive agents, such as viruses and antibiotics, are used. With more subtle selection for improved competitive ability, 200 or more generations might be needed before the first beneficial mutations rise to fixation [30]. Experiments designed to detect changes in variance [30,76], or to ob- serve second-order effects on traits such as mutation rate [45], typically require more generations.
Controlling for maternal effects
Different experimental evolution regimes often involve different environmental, demographic, or social conditions. Conditions experienced by the parents often affect the phenotypes of their offspring (or even grand-offspring) via nongenetic maternal and paternal effects. Such effects can be mediated by egg or seed provisioning, signaling molecules in the cytoplasm, chromatin modification, and other epigenetic mechanisms [77]. Most evolution experi- ments focus on genetically based changes. To eliminate effects caused by different parental environments, samples of populations from all regimes (and the revived ancestor, where applicable) should be reared in a common environ- ment for one or more generations before their divergence is assessed. However, the choice of this common parental environment can be complicated if there is an interaction between genotypic and maternal–environment effects [78].
Controlling for differential inbreeding
Even if populations under different regimes are main- tained at the same census size, the regime with stronger selection will have a smaller effective population size [79],
554
leading to a greater degree of inbreeding in sexually repro- ducing organisms. Greater inbreeding could, in turn, lead to a reduction in fitness components (inbreeding depres- sion), which might be misinterpreted as a correlated re- sponse to selection (reflecting pleiotropy or linkage disequilibrium). Crossing replicate populations within se- lection regimes should restore heterozygosity and, thus, largely eliminate the inbreeding depression. If crosses between replicate populations within regimes exhibit the same pattern of phenotypic differences between regimes as the original populations, then the differences can be more safely interpreted as resulting from selection (e.g., [8]). However, such crosses may also show complex patterns if the phenotypically similar responses of replicate popula- tions reflect different genetic mechanisms that interact in a nonadditive way (e.g., [80]).
Caveats and limitations Timescale and serendipity
Numerous success stories notwithstanding, experimental evolution has some limitations as a research approach, and
Review Trends in Ecology and Evolution October 2012, Vol. 27, No. 10
the conclusions from evolutionary experiments are subject to caveats. Although experimental evolution can be ex- tremely fast, some evolutionary processes may be too slow to be seen within the span of a research grant or even a researcher’s professional lifetime. Limited insight from experimental evolution into speciation is a case in point; although a measurable degree of reproductive isolation has evolved in several experiments, it has never reached the degree of isolation expected between biological species [72] (except for the special mechanism of speciation via poly- ploidization of hybrids in plants [81]). Other processes, such as the origin of morphological novelty, may depend on rare sequences of mutational events or improbable outcomes of drift, such that the likelihood of them happen- ing in an experiment is too low to justify the undertaking, especially if other approaches can provide empirical sup- port. Still other questions have been difficult to address with experimental evolution for want of an appropriate study system. In particular, despite some progress (e.g., [82,83]), efforts to test hypotheses about the short-term advantages of sex have been hampered by the fact that, in species capable of both modes of reproduction, sexual and asexual offspring are usually physiologically or ecologically distinct.
Technical difficulties and laboratory artifacts
Evolution experiments can be compromised by contamina- tion, that is, inadvertent introduction of ‘immigrants’ into experimental populations [84]. Other unexpected factors may confound the intended regimes. For example, in a study to test the effect of extrinsic host mortality on para- site virulence, the host mortality regime became unexpect- edly confounded with multiplicity of infection, completely altering the selective forces on the parasite [85]. Finally, populations may evolve to obviate the intended regimes; for example, a study concerning the effect of ploidy on adaptation in yeast was thwarted when the initially hap- loid and tetraploid populations all evolved diploidy [86].
In studies aimed at understanding adaptation to a par- ticular environmental factor, the results may depend on the way in which that factor is implemented. For example, selection for acute starvation resistance in Drosophila led to reduced locomotor activity [87]. This behavior was adap- tive under the laboratory regime, where flies were deprived of food for a certain time and the survivors were given food later, because reduced locomotion conserves energy. How- ever, food shortages in nature may often favor increased mobility to find new food sources. Indeed, as a plastic (phenotypic) response, flies become highly active when de- prived of food [87]. Laboratory environments often confine mobile animals to small space, changing the context of social and sexual interactions; for example, in contrast to nature, female Drosophila cannot escape aggressive sexual inter- actions, which inflates mating frequency and may amplify sexual conflict [88,89]. Such considerations indicate the need for caution in extrapolating particular adaptive out- comes from the laboratory to the field.
Population genetics of laboratory evolution
The population genetics of laboratory evolution may differ in important ways from evolution in nature. One reason is
the small effective population size in experiments relative to nature, which has manifold consequences for evolution (Box 5). Also, in experiments with outbred populations, evolutionary responses will depend largely on the standing genetic variation present in the base population, at least over the first 100 or so generations [90]. From a population genetic view, such experiments mimic evolution following abrupt environmental changes. The genetics of such responses are expected to differ from evolution that depends on new mutations in several ways; in particular, adaptations to abrupt changes are more likely to involve recessive alleles and alleles with smaller effects (reviewed in [91]).
Finally, owing to the simple environments and strong selection, laboratory evolution may involve alleles with different patterns of pleiotropy from those typical in na- ture. Many fitness-related traits are presumably affected by many alleles with diverse pleiotropic effects. In nature, selection will usually act simultaneously on many aspects of the phenotype of the organism; hence, selection on any particular function or trait will often be weak. Thus, adap- tation in nature is more likely to involve alleles that show few or no adverse pleiotropic effects (if such alleles exist). By contrast, experiments often impose strong selection on a single focal factor. Other sources of selection (e.g., sub- optimal conditions, pathogens, locomotion, and so on) are often absent or minimized. As a consequence, pleiotropic effects that would be deleterious in nature may be neutral or nearly so in the laboratory; as a case in point, approxi- mately 60% of single-gene deletions in yeast are effectively neutral under optimal laboratory conditions [92]. Further- more, the availability of alleles with small or no antago- nistic pleiotropic effects may be limited by the small sizes of laboratory populations. Thus, laboratory selection may involve alleles with strong adverse pleiotropic effects more often than does evolution in nature. Therefore, experimen- tal evolution studies may tend to overstate the importance of evolutionary trade-offs.
Experimental evolution in the field Some of the concerns discussed above can be circumvented by performing evolution experiments in natural environ- ments. A pioneering evolution experiment in the field was initiated in 1976 by transferring a guppy (Poecilia reticu- lata) population between environments with different predation regimes, leading to seminal insights into the evolution of life histories, sexual signaling, mate prefer- ences, and predator–prey coevolution [4,93–95]. Despite this early and successful start, there have been few exper- imental evolution studies in the field. Such studies involve moving populations, manipulating natural environments, or both, and these actions impose logistical challenges and may also raise legal, ethical, or conservation issues. An- other difficulty is the need to confine experimental popu- lations, which limits the approach to island-like habitats [2,3,96–98]. Finally, the environment as a whole is not controlled, making the experiments more likely to fail if, for example, populations become locally extinct. Many of the hypotheses in Table 1 concern general demographic, genetic, social, or other factors, and their predictions are unrelated to a specific environment and its complexity, so
555
Box 6. New opportunities, new challenges
Automation
Experimental evolution requires a substantial investment of time
and labor to maintain the populations under their intended regimes,
while the return on this investment, in terms of results and
publications, takes months, years, or even decades, and is
uncertain. The problem may be alleviated to some extent by
progress in automation of population maintenance under particular
regimes (e.g., www.ksepdx.com/live_transferring.htm and [62]) and
of assays of physiological [43], morphological [172], and life-history
phenotypes [173].
Use of transgenics to verify genetic basis of adaptation
Advances in genetic manipulation techniques offer increasing
possibilities to examine the causal links between genomic
changes, phenotypes, and fitness. For example, specific point
mutations can now be introduced or recombined in several model
systems [174,175]. In Drosophila melanogaster, the GAL4-UAS
dual technique is now routinely used to express any exogenous
transcript in specific tissues or cells [176] or, in combination with
RNA interference techniques, to downregulate endogenous tran-
scripts [177]. Such techniques permit independent tests of the
phenotypic and fitness effects of particular mutations or changes
in gene expression observed in the course of experimental
evolution.
Very long projects
Some ecological experiments (e.g., [55]) and artificial selection
projects (e.g., [178]) have now been running for over a century,
spanning multiple generations of researchers. Comparable efforts
in experimental evolution (already proposed in 1892 [100]) would
offer insights into rare events and slow processes, such as the
origin of morphological novelties, the functional differentiation of
duplicated genes, and perhaps even the speciation process taken to
completion.
Epigenetic inheritance
The past decade provided evidence that some quasi-hereditary
information can be encoded in patterns of chromatin modification
(e.g., DNA methylation). Evidence for such epigenetic inheritance is
pervasive in plants [179], but has also been reported to affect
longevity in Caenorhabditis elegans [180] as well as wing develop-
ment and possibly reproductive mode in aphids [181]. Epigenetic
inheritance is only beginning to be incorporated into evolutionary
theory [182] and experimental evolution may contribute to this
development.
Protein-coding or regulatory bases of adaptation
Experimental evolution can contribute new data about the relative
contributions of mutations in protein-coding versus regulatory
regions to adaptive evolution, at least those changes occurring
between closely related taxa [183,184].
Experimental evolution and anthropogenic change
There is growing awareness that evolutionary processes can
sometimes be rapid enough to have implications for conservation
of species and ecosystems [185–187]. Experimental evolution can
contribute to understanding of processes such as species invasions
[188] and evolutionary rescue from local extinction [189]. Experi-
mental evolution studies may also shed light on the scenarios of
biotic responses to global change, such as evolutionary responses
of algae to elevated CO2 levels [190].
Review Trends in Ecology and Evolution October 2012, Vol. 27, No. 10
it can be argued that field tests in such cases are not worth the additional effort. By contrast, for reasons discussed in the preceding section, where the question concerns adaptation to specific environmental factors, laboratory environments may introduce artifacts. Furthermore, populations in the field can be much larger. Some experi- ments are impractical in the laboratory; for example, by introducing predators to islands, Losos et al. [96] showed that predation drives the evolution of an arboreal lifestyle in Anolis lizards. Finally, field experiments enable one to study the direct and indirect effects of evolutionary change on ecosystem processes [94].
Mesocosms (e.g., artificial ponds) offer an intermediate between laboratory and field studies. Experiments per- formed in parallel in natural habitats and in mesocosms produced reassuringly similar effects of predation on the evolution of color pattern evolution in guppies [93] and on the advantage of immigrant alleles in genetically depau- perate populations of Daphnia [2].
Finally, in some cases, one can verify the relevance of laboratory-evolved adaptations to fitness in nature by assaying experimentally derived organisms under field conditions. For example, compared with Drosophila from control populations, Drosophila from populations selected for cold tolerance were more likely to be recaptured at food sources hours after their release into the field in cold weather, but not at mild temperatures [99]. This finding indicates that the experimental adaptation to cold under laboratory conditions translated into improved ability to survive and find food under cold conditions in the field.
Concluding remarks The potential value of experimental evolution as a research approach has long been recognized; a book published in 1892 and entitled Experimental Evolution proposed using this methodology to resolve the controversy between the Darwinian and Lamarckian theories of evolution [100]. The past decade has seen increasing application of experi- mental evolution to an expanding range of questions, while advances in genomic technology are beginning to provide unprecedented insights into the genetic and molecular bases of evolutionary change. These and other technologi- cal advances open new avenues, while discoveries in fields including genetics, developmental biology, and global change pose new questions that can be tackled with exper- imental evolution (Box 6).
Experimental evolution also offers a unique opportuni- ty to improve science education. Although paleontology and comparative studies provide ample evidence for evo- lution, the fact that scientists can observe evolution in action through manipulative experiments is an eye-open- er to people for whom ‘seeing is believing’. Also, many organisms used for research in experimental evolution can be readily deployed in teaching laboratories. For example, a class can quickly evolve bacteria to resist antibiotics [101]. If time permits, students could then compete the evolved and ancestral strains in the absence of antibiotic to test for trade-offs. Using Drosophila, students can, over a semester, observe selection against alleles that are readily scored, such as those that disrupt wing morpholo- gy [102]. (Of course, such experiments in classrooms
556
require suitable facilities and appropriately trained teach- ers, and they must comply with institutional policies and local regulations on biological experiments.) Using digital organisms (computer programs that self-replicate, mu- tate, and compete in a virtual world), students can watch evolution before their eyes as they vary environments and other factors, and observe their effects on the emergence of new phenotypes [103]. As the use of experimental evolu- tion continues to expand in the research community, we hope that it will also have a growing impact on science education.
Review Trends in Ecology and Evolution October 2012, Vol. 27, No. 10
Acknowledgments T.J.K. and D.E. are supported by the Swiss National Science Foundation. R.E.L.’s research is supported by the US National Science Foundation (DEB-1019989 and Cooperative Agreement DBI-0939454). I.O. is supported by CNRS (PICS to IO and Sara Magalhães), Institut Universitaire de France, and French National Research Agency (ANR, project GENEVOLSPE); M.C.W. is supported by Natural Sciences and Engineering Research Council (Canada). We thank two anonymous reviewers for comments, and D.J. Kemp, M. Travisano, J. Radwan, and G.J. Velicer for sharing photographs.
References 1 Garland, T. and Rose, M.R., eds (2009) Experimental Evolution,
University of California Press 2 Ebert, D. et al. (2002) A selective advantage to immigrant genes in a
Daphnia metapopulation. Science 295, 485–488 3 Zbinden, M. et al. (2008) Experimental evolution of field populations of
Daphnia magna in response to parasite treatment. J. Evol. Biol. 21, 1068–1078
4 Reznick, D.A. et al. (1990) Experimentally induced life-history evolution in a natural population. Nature 346, 357–359
5 Rundle, H.D. (2003) Divergent environments and population bottlenecks fail to generate premating isolation in Drosophila pseudoobscura. Evolution 57, 2557–2565
6 Halligan, D.L. and Keightley, P.D. (2009) Spontaneous mutation accumulation studies in evolutionary genetics. Annu. Rev. Ecol. Evol. Syst. 40, 151–172
7 Bennett, A.F. and Lenski, R.E. (1993) Evolutionary adaptation to temperature. II. Thermal niches of experimental lines of Escherichia coli. Evolution 47, 1–12
8 Kolss, M. et al. (2009) Life history consequences of adaptation to larval nutritional stress in Drosophila. Evolution 63, 2389–2401
9 Dhar, R. et al. (2011) Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution. J. Evol. Biol. 24, 1135–1153
10 terHorst, C.P. (2011) Experimental evolution of protozoan traits in response to interspecific competition. J. Evol. Biol. 24, 36–46
11 Santos, M. et al. (1997) Density-dependent natural selection in Drosophila: evolution of growth rate and body size. Evolution 51, 420–432
12 Fitzpatrick, M.J. et al. (2007) Maintaining a behaviour polymorphism by frequency-dependent selection on a single gene. Nature 447, 210– 212
13 Murray, R.L. and Cutter, A.D. (2011) Experimental evolution of sperm count in protandrous self-fertilizing hermaphrodites. J. Exp. Biol. 214, 1740–1747
14 Lenski, R.E. (1988) Experimental studies of pleiotropy and epistasis in Escherichia coli. I. Variation in competitive fitness among mutants resistant to virus T4. Evolution 42, 425–432
15 Fry, J.D. (2003) Detecting ecological trade-offs using selection experiments. Ecology 84, 1672–1678
16 Roff, D.A. and Fairbairn, D.J. (2007) The evolution of trade-offs: where are we? J. Evol. Biol. 20, 433–447
17 Rose, M.R. (1984) Laboratory evolution of postponed senescence in Drosophila melanogaster. Evolution 38, 1004–1010
18 Williams, G.C. (1957) Pleiotropy, natural selection and the evolution of senescence. Evolution 11, 398–411
19 Hamilton, W.D. (1966) The moulding of senescence by natural selection. J. Theor. Biol. 12, 12–45
20 Hoffmann, A.A. et al. (2003) Low potential for climatic stress adaptation in a rainforest Drosophila species. Science 301, 100–102
21 Perron, G.G. et al. (2006) Experimental evolution of resistance to an antimicrobial peptide. Proc. R. Soc. B 273, 251–256
22 Blount, Z.D. et al. (2008) Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 105, 7899–7906
23 Hegreness, M. et al. (2006) An equivalence principle for the incorporation of favorable mutations in asexual populations. Science 311, 1615–1617
24 Perfeito, L. et al. (2007) Adaptive mutations in bacteria: high rate and small effects. Science 317, 813–815
25 Rozen, D.E. et al. (2002) Fitness effects of fixed beneficial mutations in microbial populations. Curr. Biol. 12, 1040–1045
26 Khan, A.I. et al. (2011) Negative epistasis between beneficial mutations in an evolving bacterial population. Science 332, 1193– 1196
27 Meyer, J.R. et al. (2012) Repeatability and contingency in the evolution of a key innovation in phage Lambda. Science 335, 428–432
28 Fowler, K. et al. (1997) Genetic variation for total fitness in Drosophila melanogaster. Proc. R. Soc. B 264, 191–199
29 Lenski, R.E. and Travisano, M. (1994) Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proc. Natl. Acad. Sci. U.S.A. 91, 6808–6814
30 Lenski, R.E. et al. (1991) Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. Am. Nat. 138, 1315–1341
31 Hollis, B. et al. (2009) Sexual selection accelerates the elimination of a deleterious mutant in Drosophila melanogaster. Evolution 63, 324– 333
32 Beaumont, H.J.E. et al. (2009) Experimental evolution of bet hedging. Nature 462, 90–93
33 Rice, W.R. (1996) Sexually antagonistic male adaptation triggered by experimental arrest of female evolution. Nature 381, 232–234
34 Rundle, H.D. et al. (2005) Divergent selection and the evolution of signal traits and mating preferences. PLoS Biol. 3, 1988–1995
35 Dodd, D.M.B. (1989) Reproductive isolation as a consequence of adaptive divergence in Drosophila pseudoobscura. Evolution 43, 1308–1311
36 Dettman, J.R. et al. (2008) Divergent adaptation promotes reproductive isolation among experimental populations of the filamentous fungus Neurospora. BMC Evol. Biol. 8, 35
37 Leu, J.Y. and Murray, A.W. (2006) Experimental evolution of mating discrimination in budding yeast. Curr. Biol. 16, 280–286
38 Matute, D.R. (2010) Reinforcement can overcome gene flow during speciation in Drosophila. Curr. Biol. 20, 2229–2233
39 Moya, A. et al. (1995) Founder effect speciation theory: failure of experimental corroboration. Proc. Natl. Acad. Sci. U.S.A. 92, 3983– 3986
40 Cooper, T.F. et al. (2003) Parallel changes in qene expression after 20,000 generations of evolution in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 100, 1072–1077
41 Woods, R. et al. (2006) Tests of parallel molecular evolution in a long- term experiment with Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 103, 9107–9112
42 Travisano, M. and Lenski, R.E. (1996) Long-term experimental evolution in Escherichia coli. IV. Targets of selection and the specificity of adaptation. Genetics 143, 15–26
43 Cooper, V.S. and Lenski, R.E. (2000) The population genetics of ecological specialization in evolving Escherichia coli populations. Nature 407, 736–739
44 Meyer, J.R. et al. (2010) Parallel changes in host resistance to viral infection during 45,000 generations of relaxed selection. Evolution 64, 3024–3034
45 Sniegowski, P.D. et al. (1997) Evolution of high mutation rates in experimental populations of E. coli. Nature 387, 703–705
46 de Visser, J. et al. (1999) Diminishing returns from mutation supply rate in asexual populations. Science 283, 404–406
47 Elena, S.F. and Lenski, R.E. (1997) Long-term experimental evolution in Escherichia coli. VII. Mechanisms maintaining genetic variability within populations. Evolution 51, 1058–1067
48 Rozen, D.E. et al. (2009) Death and cannibalism in a seasonal environment facilitate bacterial coexistence. Ecol. Lett. 12, 34–44
49 Barrick, J.E. and Lenski, R.E. (2009) Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harb. Symp. Quant. Biol. 74, 119–129
50 Travisano, M. et al. (1995) Experimental tests of the roles of adaptation, chance, and history in evolution. Science 267, 87–90
51 Barrick, J.E. et al. (2009) Genome evolution and adaptation in a long- term experiment with Escherichia coli. Nature 461, 1243–1247
52 Archer, M.A. et al. (2003) Breakdown in correlations during laboratory evolution. II. Selection on stress resistance in Drosophila populations. Evolution 57, 536–543
53 Rose, M.R. et al. (2002) Evolution of late-life mortality in Drosophila melanogaster. Evolution 56, 1982–1991
54 Burke, M.K. et al. (2010) Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature 467, 587–590
557
Review Trends in Ecology and Evolution October 2012, Vol. 27, No. 10
55 Silvertown, J. et al. (2006) The Park Grass Experiment 1856-2006: its contribution to ecology. J. Ecol. 94, 801–814
56 Silvertown, J. et al. (2005) Reinforcement of reproductive isolation between adjacent populations in the Park Grass Experiment. Heredity 95, 198–205
57 Ebert, D. (1998) Experimental evolution of parasites. Science 282, 1432–1435
58 Plotkin, S.A. and Plotkin, S.L. (2011) The development of vaccines: how the past led to the future. Nat. Rev. Microbiol. 9, 889–893
59 Hunt, P. et al. (2010) Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites. BMC Genomics 11, 499
60 Kolodny-Hirsch, D.M. and VanBeek, N.A.M. (1997) Selection of a morphological variant of Autographa californica nuclear polyhedrosis virus with increased virulence following serial passage in Plutella xylostella. J. Invertebr. Pathol. 69, 205–211
61 Dion, E. et al. (2011) Rapid evolution of parasitoids when faced with the symbiont-mediated resistance of their hosts. J. Evol. Biol. 24, 741–750
62 de Crecy, E. et al. (2009) Directed evolution of a filamentous fungus for thermotolerance. BMC Biotechnol. 9, 74
63 Arnold, F.H. (2008) The race for new biofuels. Eng. Sci. 2, 12–19 64 Lipson, H. and Pollack, J.B. (2000) Automatic design and
manufacture of robotic lifeforms. Nature 406, 974–978 65 Brustad, E.M. and Arnold, F.H. (2011) Optimizing non-natural
protein function with directed evolution. Curr. Opin. Chem. Biol. 15, 201–210
66 Koza, J.R. (1992) Genetic Programming: On the Programming of Computers by Means of Natural Selection, MIT Press
67 Goldringer, I. et al. (2006) Rapid differentiation of experimental populations of wheat for heading time in response to local climatic conditions. Ann. Bot. 98, 805–817
68 Dorken, M.E. and Pannell, J.R. (2009) Hermaphroditic sex allocation evolves when mating opportunities change. Curr. Biol. 19, 514–517
69 Roels, S.A.B. and Kelly, J.K. (2011) Rapid evolution caused by pollinator loss in Mimulus guttatus. Evolution 65, 2541–2552
70 Capy, P. and Gibert, P. (2004) Drosophila melanogaster, Drosophila simulans: so similar yet so different. Genetica 120, 5–16
71 Magalhäes, S. et al. (2007) Adaptation in a spider mite population after long-term evolution on a single host plant. J. Evol. Biol. 20, 2016–2027
72 Coyne, J.A. and Orr, H.A. (2004) Speciation, Sinauer Associates 73 Rice, W.R. et al. (2005) Inter-locus antagonistic coevolution as an
engine of speciation: assessment with hemiclonal analysis. Proc. Natl. Acad. Sci. U.S.A. 102, 6527–6534
74 Koskella, B. and Lively, C.M. (2009) Evidence for negative frequency- dependent selection during experimental coevolution of a freshwater snail and a sterilizing trematode. Evolution 63, 2213–2221
75 Porcher, E. et al. (2006) Genetic differentiation of neutral markers and quantitative traits in predominantly selfing metapopulations: confronting theory and experiments with Arabidopsis thaliana. Genet. Res. Camb. 87, 1–12
76 Yeaman, S. et al. (2010) No effect of environmental heterogeneity on the maintenance of genetic variation in wing shape in Drosophila melanogaster. Evolution 64, 3398–3408
77 Mousseau, T.A. et al. (2009) Evolution of maternal effects: past and present. Philos. Trans. R. Soc. B. 364, 1035–1038
78 Magalhäes, S. et al. (2011) Environmental effects on the detection of adaptation. J. Evol. Biol. 24, 2653–2662
79 Santiago, E. and Caballero, A. (1998) Effective size and polymorphism of linked neutral loci in populations under directional selection. Genetics 149, 2105–2117
80 Kawecki, T.J. and Mery, F. (2006) Genetically idiosyncratic responses of Drosophila melanogaster populations to selection for improved learning ability. J. Evol. Biol. 19, 1265–1274
81 Soltis, P.S. and Soltis, D.E. (2009) The role of hybridization in plant speciation. Annu. Rev. Plant Biol. 60, 561–588
82 Becks, L. and Agrawal, A.F. (2010) Higher rates of sex evolve in spatially heterogeneous environments. Nature 468, 89–92
83 Goddard, M.R. et al. (2005) Sex increases the efficacy of natural selection in experimental yeast populations. Nature 434, 636–640
84 Houle, D. et al. (1994) Erratum: The genomic mutation rate for fitness in Drosophila (vol 359, pg 58, 1992). Nature 371, 358
558
85 Ebert, D. and Mangin, K.L. (1997) The influence of host demography on the evolution of virulence of a microsporidian gut parasite. Evolution 51, 1828–1837
86 Gerstein, A.C. et al. (2006) Genomic convergence toward diploidy in Saccharomyces cerevisiae. PLoS Genetics 2, 1396–1401
87 Williams, A.E. et al. (2004) The respiratory pattern in Drosophila melanogaster selected for desiccation resistance is not associated with the observed evolution of decreased locomotory activity. Physiol. Biochem. Zool. 77, 10–17
88 Stewart, A.D. et al. (2005) Assessing putative interlocus sexual conflict in Drosophila melanogaster using experimental evolution. Proc. R. Soc. B 272, 2029–2035
89 Gromko, M.H. and Markow, T.A. (1993) Courtship and remating in field populations of Drosophila. Anim. Behav. 45, 253–262
90 Hermisson, J. and Pennings, P.S. (2005) Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169, 2335–2352
91 Barrett, R.D.H. and Schluter, D. (2008) Adaptation from standing genetic variation. Trends Ecol. Evol. 23, 38–44
92 Hillenmeyer, M.E. et al. (2008) The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science 320, 362–365
93 Endler, J.A. (1980) Natural selection on color patterns in Poecilia reticulata. Evolution 34, 76–91
94 Palkovacs, E.P. et al. (2009) Experimental evaluation of evolution and coevolution as agents of ecosystem change in Trinidadian streams. Philos. Trans. R. Soc. B. 364, 1617–1628
95 Reznick, D.N. et al. (1997) Evaluation of the rate of evolution in natural populations of guppies (Poecilia reticulata). Science 275, 1934–1937
96 Losos, J.B. et al. (2004) Predator-induced behaviour shifts and natural selection in field-experimental lizard populations. Nature 432, 505– 508
97 Losos, J.B. et al. (1997) Adaptive differentiation following experimental island colonization in Anolis lizards. Nature 387, 70–73
98 Barrett, R.D.H. et al. (2011) Rapid evolution of cold tolerance in stickleback. Proc. R. Soc. B 278, 233–238
99 Kristensen, T.N. et al. (2007) Can artificially selected phenotypes influence a component of field fitness? Thermal selection and fly performance under thermal extremes. Proc. R. Soc. B 274, 771–778
100 de Varigny, H. (1892) Experimental Evolution, MacMillan 101 Krist, A.C. and Showsh, S.A. (2007) Experimental evolution of
antibiotic resistance in bacteria. Am. Biol. Teach. 69, 94–97 102 Plunkett, A.D. and Yampolsky, L.Y. (2010) When a fly has to fly to
reproduce: selection against conditional recessive lethals in Drosophila. Am. Biol. Teach. 72, 12–15
103 Speth, E.B. et al. (2009) Using Avida-ED for teaching and learning about evolution in undergraduate introductory biology courses. Evol. Educ. Outreach 2, 415–428
104 Bull, J.J. et al. (1997) Exceptional convergent evolution in a virus. Genetics 147, 1497–1507
105 Velicer, G.J. et al. (2006) Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor. Proc. Natl. Acad. Sci. U.S.A. 103, 8107–8112
106 Araya, C.L. et al. (2010) Whole-genome sequencing of a laboratory- evolved yeast strain. BMC Genomics 11, 88
107 Knight, C.G. et al. (2006) Unraveling adaptive evolution: how a single point mutation affects the protein coregulation network. Nat. Genet. 38, 1015–1022
108 Ibarra, R.U. et al. (2002) Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420, 186–189
109 Albert, T.J. et al. (2005) Mutation discovery in bacterial genomes: metronidazole resistance in Helicobacter pylori. Nat. Methods 2, 951– 953
110 Shendure, J. et al. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728–1732
111 Turner, T.L. et al. (2011) Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster. PLoS Genet. 7, e1001336
112 Herring, C.D. et al. (2006) Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat. Genet. 38, 1406–1412
Review Trends in Ecology and Evolution October 2012, Vol. 27, No. 10
113 Woods, R.J. et al. (2011) Second-order selection for evolvability in a large Escherichia coli population. Science 331, 1433–1436
114 Lee, D.H. and Palsson, B.O. (2010) Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a nonnative carbon cource, L-1,2- propanediol. Appl. Environ. Microbiol. 76, 4158–4168
115 Chou, H.H. et al. (2011) Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 332, 1190–1192
116 Wielgoss, S. et al. (2011) Mutation rate inferred from synonymous substitutions in a long-term evolution experiment with Escherichia coli. G3 (Bethesda) 1, 183–186
117 Haag-Liautard, C. et al. (2007) Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila. Nature 445, 82–85
118 Denver, D.R. et al. (2009) A genome-wide view of Caenorhabditis elegans base-substitution mutation processes. Proc. Natl. Acad. Sci. U.S.A. 106, 16310–16314
119 Sorensen, J.G. et al. (2007) Gene expression profile analysis of Drosophila melanogaster selected for resistance to environmental stressors. J. Evol. Biol. 20, 1624–1636
120 Maynard Smith, J. (1992) Byte-sized evolution. Nature 355, 772–773 121 Bartel, D.P. and Szostak, J.W. (1993) Isolation of new ribozymes from
a large pool of random sequences. Science 261, 1411–1418 122 Joyce, G.F. (2009) Evolution in an RNA world. Cold Spring Harb.
Symp. Quant. Biol. 74, 17–23 123 Ray, T.S. (1992) An approach to the synthesis of life. In Artificial Life
II (Langton, C.G. et al., eds), pp. 371–408, Springer 124 Adami, C. (1998) Introduction to Artificial Life, Springer 125 Dennett, D. (2002) The new replicators. In Encyclopedia of Evolution
(Pagel, M.D., ed.), pp. E83–E92, Oxford University Press 126 Ofria, C. and Wilke, C.O. (2004) Avida: a software platform for
research in computational evolutionary biology. Artif. Life 10, 191– 229
127 Lenski, R.E. et al. (2003) The evolutionary origin of complex features. Nature 423, 139–144
128 Wilke, C.O. et al. (2001) Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature 412, 331–333
129 Yedid, G. and Bell, G. (2002) Macroevolution simulated with autonomously replicating computer programs. Nature 420, 810–812
130 Clune, J. et al. (2012) Ontogeny tends to recapitulate phylogeny in digital organisms. Am. Nat. http://www.jstor.org/stable/full/10.1086/ 666984
131 Misevic, D. et al. (2006) Sexual reproduction reshapes the genetic architecture of digital organisms. Proc. R. Soc. B 273, 457–464
132 Ostrowski, E.A. et al. (2007) Ecological specialization and adaptive decay in digital organisms. Am. Nat. 169, E1–E20
133 Yedid, G. et al. (2009) Selective press extinctions, but not random pulse extinctions, cause delayed ecological recovery in communities of digital organisms. Am. Nat. 173, E139–E154
134 Clune, J. et al. (2011) Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory. Proc. R. Soc. B 278, 666–674
135 Floreano, D. and Keller, L. (2010) Evolution of adaptive behaviour in robots by means of Darwinian selection. PLoS Biol. 8, e1000292
136 Waibel, M. et al. (2011) A quantitative test of Hamilton’s rule for the evolution of altruism. PLoS Biol. 9, e1000615
137 Floreano, D. et al. (2007) Evolutionary conditions for the emergence of communication in robots. Curr. Biol. 17, 514–519
138 Mitri, S. et al. (2011) Relatedness influences signal reliability in evolving robots. Proc. R. Soc. B 278, 378–383
139 Buckling, A. and Rainey, P.B. (2002) The role of parasites in sympatric and allopatric host diversification. Nature 420, 496–499
140 Schulte, R.D. et al. (2010) Multiple reciprocal adaptations and rapid genetic change upon experimental coevolution of an animal host and its microbial parasite. Proc. Natl. Acad. Sci. U.S.A. 107, 7359–7364
141 Hollis, B. (2012) Rapid antagonistic coevolution between strains of the social amoeba Dictyostelium discoideum. Proc. R. Soc. B 279, 3565–3571
142 Rice, W.R. (1998) Male fitness increases when females are eliminated from gene pool: Implications for the Y chromosome. Proc. Natl. Acad. Sci. U.S.A. 95, 6217–6221
143 Ebert, D. (2008) Host–parasite coevolution: insights from the Daphnia–parasite model system. Curr. Opin. Microbiol. 11, 290–301
144 Vogwill, T. et al. (2011) Coevolving parasites enhance the diversity- decreasing effect of dispersal. Biol. Lett. 7, 578–580
145 Yoshida, T. et al. (2007) Cryptic population dynamics: rapid evolution masks trophic interactions. PLoS Biol. 5, 1868–1879
146 Gaba, S. and Ebert, D. (2009) Time-shift experiments as a tool to study antagonistic coevolution. Trends Ecol. Evol. 24, 226–232
147 Decaestecker, E. et al. (2007) Host–parasite ‘Red Queen’ dynamics archived in pond sediment. Nature 450, 870–873
148 Hall, A.R. et al. (2011) Host–parasite coevolutionary arms races give way to fluctuating selection. G3 (Bethesda) 14, 635–642
149 Morgan, A.D. et al. (2005) The effect of migration on local adaptation in a coevolving host–parasite system. Nature 437, 253–256
150 Dykhuizen, D.E. and Hartl, D.L. (1983) Selection in chemostats. Microbiol. Rev. 47, 150–168
151 Gerrish, P.J. and Lenski, R.E. (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102–3, 127–144
152 Treves, D.S. et al. (1998) Repeated evolution of an acetate- crossfeeding polymorphism in long-term populations of Escherichia coli. Mol. Biol. Evol. 15, 789–797
153 Rainey, P.B. and Travisano, M. (1998) Adaptive radiation in a heterogeneous environment. Nature 394, 69–72
154 Rogers, D.W. and Greig, D. (2009) Experimental evolution of a sexually selected display in yeast. Proc. R. Soc. B 276, 543–549
155 Malmberg, R.L. (1977) Evolution of epistasis and advantage of recombination in populations of bacteriophage T4. Genetics 86, 607–621
156 Cooper, T.F. (2007) Recombination speeds adaptation by reducing competition between beneficial mutations in populations of Escherichia coli. PLoS Biol. 5, 1899–1905
157 Schoustra, S. et al. (2010) Fitness-associated sexual reproduction in a filamentous fungus. Curr. Biol. 20, 1350–1355
158 Turner, P.E. and Chao, L. (1999) Prisoner’s dilemma in an RNA virus. Nature 398, 441–443
159 Chao, L. and Levin, B.R. (1981) Structured habitats and the evolution of anticompetitor toxins in bacteria. Proc. Natl. Acad. Sci. U.S.A. 78, 6324–6328
160 Velicer, G.J. et al. (2000) Developmental cheating in the social bacterium Myxococcus xanthus. Nature 404, 598–601
161 Khare, A. et al. (2009) Cheater-resistance is not futile. Nature 461, 980–982
162 Kaltz, O. and Bell, G. (2002) The ecology and genetics of fitness in Chlamydomonas. XII. Repeated sexual episodes increase rates of adaptation to novel environments. Evolution 56, 1743–1753
163 Ackermann, M. et al. (2003) Senescence in a bacterium with asymmetric division. Science 300, 1920
164 Ratcliff, W.C. et al. (2012) Experimental evolution of multicellularity. Proc. Natl. Acad. Sci. U.S.A. 109, 1595–1600
165 Griffin, A.S. et al. (2004) Cooperation and competition in pathogenic bacteria. Nature 430, 1024–1027
166 Frankham, R. (1995) Effective population size adult population size ratios in wildlife: a review. Genet. Res. Camb. 66, 95–107
167 Samani, P. and Bell, G. (2010) Adaptation of experimental yeast populations to stressful conditions in relation to population size. J. Evol. Biol. 23, 791–796
168 Wahl, L.M. and Gerrish, P.J. (2001) The probability that beneficial mutations are lost in populations with periodic bottlenecks. Evolution 55, 2606–2610
169 Hill, W.G. (1982) Rates of change in quantitative traits from fixation of new mutations. Proc. Natl. Acad. Sci. U.S.A. Biol. Sci. 79, 142–145
170 Weber, K.E. (1990) Increased selection response in larger populations. I. Selection for wing-tip height in Drosophila melanogaster at three population sizes. Genetics 125, 579–584
171 Weber, K.E. and Diggins, L.T. (1990) Increased selection response in larger populations. II. Selection for ethanol vapor resistance in Drosophila melanogaster at two population sizes. Genetics 125, 585–597
172 Houle, D. et al. (2003) Automated measurement of Drosophila wings. BMC Evol. Biol. 3, 25
173 Stearns, S.C. et al. (1987) A device for collecting flies of precisely determined post-hatching age. Dros. Inf. Serv. 66, 167–179
174 Storici, F. et al. (2001) In vivo site-directed mutagenesis using oligonucleotides. Nat. Biotechnol. 19, 773–776
175 Wesolowska, N. and Rong, Y.K.S. (2010) The past, present and future of gene targeting in Drosophila. Fly 4, 53–59
559
Review Trends in Ecology and Evolution October 2012, Vol. 27, No. 10
176 Brand, A.H. and Perrimon, N. (1993) Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118, 401–415
177 Dietzl, G. et al. (2007) A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila. Nature 448, 151–156
178 Dudley, J.W. and Lambert, R.J. (2004) 100 generations of selection for oil and protein in corn. Plant Breed. Rev. 24, 79–110
179 Hauser, M-T. et al. (2011) Transgenerational epigenetic inheritance in plants. Biochim. Biophys. Acta Gene Regul. Mech. 1809, 459–468
180 Greer, E.L. et al. (2011) Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans. Nature 479, 365–371
181 Walsh, T.K. et al. (2010) A functional DNA methylation system in the pea aphid, Acyrthosiphon pisum. Insect Mol. Biol. 19, 215–228
182 Day, T. and Bonduriansky, R. (2011) A unified approach to the evolutionary consequences of genetic and nongenetic inheritance. Am. Nat. 178, E18–E36
183 Hoekstra, H.E. and Coyne, J.A. (2007) The locus of evolution: evo devo and the genetics of adaptation. Evolution 61, 995–1016
184 Haag, E.S. and Lenski, R.E. (2011) L’enfant terrible at 30: the maturation of evolutionary developmental biology. Development 138, 2633–2637
185 Lankau, R. et al. (2011) Incorporating evolutionary principles into environmental management and policy. Evol. Appl. 4, 315–325
186 Lavergne, S. et al. (2010) Biodiversity and climate change: integrating evolutionary and ecological responses of species and communities. Annu. Rev. Ecol. Evol. Syst. 41, 321–350
187 Bell, G. and Collins, S. (2008) Adaptation, extinction and global change. Evol. Appl. 1, 3–16
188 Lee, C.E. et al. (2007) Response to selection and evolvability of invasive populations. Genetica 129, 179–192
189 Bell, G. and Gonzalez, A. (2011) Adaptation and evolutionary rescue in metapopulations experiencing environmental deterioration. Science 332, 1327–1330
190 Collins, S. et al. (2006) Changes in C uptake in populations of Chlamydomonas reinhardtii selected at high CO2. Plant Cell Environ. 29, 1812–1819
191 Burch, C.L. and Chao, L. (1999) Evolution by small steps and rugged landscapes in the RNA virus w6. Genetics 151, 921–927
192 Bull, J.J. et al. (2003) Experimental evolution yields hundreds of mutations in a functional viral genome. J. Mol. Evol. 57, 241–248
193 Whitlock, M.C. et al. (2002) Persistence of changes in the genetic covariance matrix after a bottleneck. Evolution 56, 1968–1975
194 Bryant, E.H. and Meffert, L.M. (1993) The effect of serial founder- flush cycles on quantitative genetic variation in the housefly. Heredity 70, 122–129
195 Wade, M.J. et al. (1996) Inbreeding: its effect on response to selection for pupal weight and the heritable variance in fitness in the flour beetle, Tribolium castaneum. Evolution 50, 723–733
196 Swindell, W.R. and Bouzat, J.L. (2005) Modeling the adaptive potential of isolated populations: experimental simulations using Drosophila. Evolution 59, 2159–2169
197 Reboud, X. and Bell, G. (1997) Experimental evolution in Chlamydomonas. III. Evolution of specialist and generalist types in environments that vary in space and time. Heredity 78, 507–514
198 Turner, P.E. and Elena, S.F. (2000) Cost of host radiation in an RNA virus. Genetics 156, 1465–1470
199 Mackay, T.F.C. (1980) Genetic variance, fitness, and homeostasis in varying environments: an experimental check of the theory. Evolution 34, 1219–1222
200 Snook, R.R. et al. (2005) Experimental manipulation of sexual selection and the evolution of courtship song in Drosophila pseudoobscura. Behav. Genet. 35, 245–255
560
201 Kemp, D.J. et al. (2009) Predicting the direction of ornament evolution in Trinidadian guppies (Poecilia reticulata). Proc. R. Soc. B 276, 4335– 4343
202 Fricke, C. and Arnqvist, G. (2007) Rapid adaptation to a novel host in a seed beetle (Callosobruchus maculatus): the role of sexual selection. Evolution 61, 440–454
203 Promislow, D.E.L. et al. (1998) Adult fitness consequences of sexual selection in Drosophila melanogaster. Proc. Natl. Acad. Sci. U.S.A. 95, 10687–10692
204 Hollis, B. and Houle, D. (2011) Populations with elevated mutation load do not benefit from the operation of sexual selection. J. Evol. Biol. 24, 1918–1926
205 Rundle, H.D. et al. (2006) The roles of natural and sexual selection during adaptation to a novel environment. Evolution 60, 2218–2225
206 Tilszer, M. et al. (2006) Evolution under relaxed sexual conflict in the bulb mite Rhizoglyphus robini. Evolution 60, 1868–1873
207 Martin, O.Y. and Hosken, D.J. (2003) Costs and benefits of evolving under experimentally enforced polyandry or monogamy. Evolution 57, 2765–2772
208 Stearns, S.C. et al. (2000) Experimental evolution of aging, growth, and reproduction in fruitflies. Proc. Natl. Acad. Sci. U.S.A. 97, 3309–3313
209 Macke, E. et al. (2011) Experimental evolution of reduced sex ratio adjustment under local mate competition. Science 334, 1127–1129
210 Chao, L. et al. (1992) Muller’s ratchet and the advantage of sex in the RNA virus w6. Evolution 46, 289–299
211 Wade, M.J. (1980) An experimental study of kin selection. Evolution 34, 844–855
212 Kerr, B. et al. (2006) Local migration promotes competitive restraint in a host-pathogen ‘tragedy of the commons’. Nature 442, 75–78
213 Manhes, P. and Velicer, G.J. (2011) Experimental evolution of selfish policing in social bacteria. Proc. Natl. Acad. Sci. U.S.A. 108, 8357– 8362
214 Taylor, D.R. et al. (2002) Conflicting levels of selection in the accumulation of mitochondrial defects in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 99, 3690–3694
215 Kuzdzal-Fick, J.J. et al. (2011) High relatedness is necessary and sufficient to maintain multicellularity in Dictyostelium. Science 334, 1548–1551
216 Mery, F. and Kawecki, T.J. (2004) The effect of learning on experimental evolution of resource preference in Drosophila melanogaster. Evolution 58, 757–767
217 Chao, L. et al. (1977) Complex community in a simple habitat: experimental study with bacteria and phage. Ecology 58, 369–378
218 Meyer, J.R. et al. (2006) Prey evolution on the time scale of predator– prey dynamics revealed by allele-specific quantitative PCR. Proc. Natl. Acad. Sci. USA 103, 10690–10695
219 Magalon, H. et al. (2010) Host growth conditions influence experimental evolution of life history and virulence of a parasite with vertical and horizontal transmission. Evolution 64, 2126–2138
220 Meffert, L.M. and Bryant, E.H. (1991) Mating propensity and courtship behavior in serially bottlenecked lines of the housefly. Evolution 45, 293–306
221 Ferea, T.L. et al. (1999) Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. USA 96, 9721–9726
222 Wichman, H.A. et al. (1999) Different trajectories of parallel evolution during viral adaptation. Science 285, 422–424
223 Velicer, G.J. and Yu, Y.T.N. (2003) Evolution of novel cooperative swarming in the bacterium Myxococcus xanthus. Nature 425, 75–78
224 Tomkins, J.L. et al. (2011) Habitat complexity drives experimental evolution of a conditionally expressed secondary sexual trait. Current Biology 21, 569–573
- Experimental evolution
- Experimental evolution as a research tool
- Applications
- Adaptation to specific environments
- Study of evolutionary trade-offs and constraints
- Estimating population genetic parameters
- Testing evolutionary theories
- Long-term experiments
- Experimental evolution in medicine and technology
- Designing evolution experiments
- Study system
- Regimes and controls
- Experimental replicates
- Base population or ancestral genotype
- Experimental population size and number of generations
- Controlling for maternal effects
- Controlling for differential inbreeding
- Caveats and limitations
- Timescale and serendipity
- Technical difficulties and laboratory artifacts
- Population genetics of laboratory evolution
- Experimental evolution in the field
- Concluding remarks
- Acknowledgments
- References