PERSPECTIVESEVOLUTION

In Evolution, the Sum Is Less
than Its Parts

Laboratory experiments with bacteria shedlight on how epistatic interactions inﬂuence
the pace of evolution.

Sergey Kryazhimskiy,1,2 Jeremy A. Draghi,1 Joshua B. Plotkin11160

3 JUNE 2011 VOL 332 SCIENCE www.sciencemag.org
Published by AAASCREDIT: ADAPTED BY P. HUEY/SCIENCE

Fitness

Downloaded from www.sciencemag.org on June 2, 2011P

ropagating bacteria in a lab
for thousands of generations may seem tedious, orAncestor strain
even irrelevant, to most evolutionAdapted strainary biologists. Nonetheless, such
Evolves in lab
experiments provide an opportunity
to deduce quantitative principles ofFitness Wabevolution and directly test them incontrolled environments. Combinedwith modern sequencing technologies, as well as theory, recent microbial experiments have suggested a
critical role for genetic interactions
Fitness Waamong mutations, called epistasis,Reconstruct intermediates
Diminishing returns
in determining the pace of evolution.
Two papers in this issue, by Khan etal. on page 1193 (1) and Chou et al.
(2) on page 1190, present preciseAntagonistic epistasis
experimental measurements of these
Fitness Wb
Wab < Wa • Wb
epistatic interactions.
1st
2nd
3rd
Microbial evolution experiments
mutation mutation mutation
in a simple, constant environment
reveal a characteristic pattern: At Antagonistic epistasis. Bacteria adapt to a laboratory environment by acquiring beneﬁcial mutations. Khan et al.
ﬁrst, a population rapidly acquires and Chou et al. identiﬁed the mutations that accrued in an adapted strain, and measured their ﬁtness beneﬁts (growth
benef icial mutations, but then advantage relative to the ancestor). The mutations conferred smaller marginal beneﬁts in combination than they did
adaptation progressively slows so individually. This antagonistic epistasis causes progressively slower rates of adaptation over time.
that thousands of generations passbetween subsequent beneﬁcial substitutions late predictive evolutionary models or to infer tions, individually and in combination, the(3). Unexpected outcomes, however, can and such interactions from empirical data. Nev- researchers were able to directly quantify thedo occur even in these simple experimental ertheless, epistasis is at the heart of classi- extent and form of epistasis (see the ﬁgure).
conditions. Populations evolve a dramatically cal theories, such as the evolution of sex (8),Both studies found a predominance ofelevated mutation rate (4), discover rare phe- and also of modern concepts such as robust- antagonistic epistasis, which impeded thenotypic innovations (5), or diverge into dis- ness and evolvability (a population’s ability rate of ongoing adaptation relative to a nulltinct lineages that either coexist (6) or com- to evolve) (9). Moreover, recent theoretical model of independent mutational effects.
pete vigorously as each strain races to acquire work (10) suggests that the overall dynami- Chou et al. further interpreted the prevalence
more adaptive mutations (7). Recent theory cal pattern of adaptation observed in long- of antagonistic epistasis in terms of metasuggests that a common cause underlies all term microbial experiments can be explained bolic costs and beneﬁts. The concordance of
these phenomena: the structure of epistatic by a prevalence of what is called antagonistic results from the two studies is noteworthy,
interactions among mutations.
epistasis, in which beneﬁcial mutations con- especially because Khan et al. analyzed EschEpistasis describes how the ﬁtness conse- fer less beneﬁt in combination than they do erichia coli populations [from the long-term
quence of a mutation depends on the status of individually.
experiments of Lenski (3)], whereas Chou etthe rest of the genome. In one extreme examTo quantify epistasis among beneficial al. studied an engineered strain of Methylople, called sign epistasis, a mutation may be mutations and to test these theoretical predic- bacterium extorquens. The remarkable precibeneﬁcial if it arises on one genetic back- tions, both Khan et al. and Chou et al. exam- sion with which both studies quantiﬁed episground, but detrimental on another. Although ined the initial substitutions that occurred in tasis among beneﬁcial mutations was madeinteractions among genes may seem an obvi- populations of bacteria adapting in the labo- possible only by leveraging whole-genome
ous fact of biology, the myriad possible forms ratory. The researchers identiﬁed the hand- sequencing combined with the ability toof epistasis have made it difﬁcult to formu- ful of mutations across the genome that had reconstruct mutational combinations andsubstituted in an evolved strain, and then con- assay them in the same environment in which1
Department of Biology, University of Pennsylvania, Philastructed intermediate strains containing com- the mutations ﬁrst arose.
2delphia, PA 19103, USA. Department of Organismic andbinations of these mutations. By measuring
The view of epistasis across a genome that
Evolutionary Biology, Harvard University, Cambridge, MA
the ﬁtness beneﬁts conferred by these muta- emerges from this work contrasts sharply
02138, USA. E-mail: jplotkin@sas.upenn.edu

PERSPECTIVES
whether experiments in simple environments,
with only one or a few niches for coexistingstrains, will reﬂect the pattern of adaptation in
more complex ecologies, such as Pseudomonas ﬂuorescens in structured environments(6). Nonetheless, the compelling consistency
between these two studies should inspire
efforts to test the generality of their ﬁndings,
by measuring epistasis in a wide range ofexperimental and even natural systems.
These studies, and the long-term laboratory evolution experiments from which they
derive, represent a resounding achievement
for the reductionist approach to studying
biology. The mechanistic picture they paintof evolution is complex but not incomprehensible; although epistatic interactions leadto surprising phenomena, the advantagesof a frozen “fossil record” of laboratoryraised isolates, and the ease of manipulating—and, now, fully sequencing—evolved
strains enables researchers to tease apart andexamine the underlying causes of these phenomena. Moreover, the theory and concepts
developed to explain these simple experiments may have broad payoffs. Already,epistasis has been implicated in the evolution of drug resistance in inﬂuenza viruses(12) and in bacterial pathogens (13). Ultimately, populations of bacteria tediously
propagated in the lab may be key to predicting the next moves of the most mutable anddangerous human pathogens.

Behavior and the Dynamic Genome

Does behavior evolve through gene expression
changes in the brain in response to theenvironment?

References

1. A. I. Khan, D. M. Dinh, D. Schneider, R. E. Lenski, T. F.
Cooper, Science 332, 1193 (2011).
2. H.-H. Chou, H.-C. Chiu, N. F. Delaney, D. Segrè, C. J.
Marx, Science 332, 1190 (2011).
3. S. F. Elena, R. E. Lenski, Nat. Rev. Genet. 4, 457 (2003).
4. P. D. Sniegowski, P. J. Gerrish, R. E. Lenski, Nature 387,703 (1997).
5. Z. D. Blount, C. Z. Borland, R. E. Lenski, Proc. Natl. Acad.
Sci. U.S.A. 105, 7899 (2008).
6. P. B. Rainey, M. Travisano, Nature 394, 69 (1998).
7. R. J. Woods et al., Science 331, 1433 (2011).
8. A. S. Kondrashov, Nature 336, 435 (1988).
9. G. P. Wagner, L. Altenberg, Evolution 50, 967 (1996).
10. S. Kryazhimskiy, G. Tkačik, J. B. Plotkin, Proc. Natl. Acad.
Sci. U.S.A. 106, 18638 (2009).
11. D. M. Weinreich, N. F. Delaney, M. A. Depristo, D. L.
Hartl, Science 312, 111 (2006).
12. J. D. Bloom, L. I. Gong, D. Baltimore, Science 328, 1272
(2010).
13. S. Trindade et al., PLoS Genet. 5, e1000578 (2009).
10.1126/science.1208072

GENOMICS

Alison M. Bell1,3 and Gene E. Robinson2,3

W

hen circumstances change, anorganism’s ﬁrst response is often
behavioral. But how does adaptive behavior evolve, given that it requires
constant and often instantaneous interactions between an individual and its environment? The dominant view emphasizes new
random DNA mutation as the starting point.
This may lead to behavioral variation. If
the resulting variants have different ﬁtness
values, then natural selection could result
in behavioral evolution through changes inallele frequencies across generations. An
alternative theory proposes environmentallyinduced change in an organism’s behavior asthe starting point (1), and “phenotypic plasticity” that is inherited across generations
through an unspeciﬁed process of “geneticassimilation” (2). Despite numerous examDepartment of Animal Biology, University of Illinois,Urbana-Champaign, IL 61801, USA. 2Department of Entomology, University of Illinois, Urbana-Champaign, IL 61801,
USA. 3Neuroscience Program, Program in Ecology, Evolutionary Biology and Conservation, Institute for Genomic Biology,
University of Illinois, Urbana-Champaign, IL 61801, USA.
E-mail: generobi@life.uiuc.edu
1ples (3), the latter as a driver of behavioral
evolution has never been widely accepted,
perhaps as a reaction against Lamarckianism—the idea that characteristics acquiredby habit, use, or disuse can be passed on
across generations. However, behavioral
genetics and genomics, especially for animals in natural populations, lend some plausibility to the phenotypic plasticity view.
The ability to analyze genome-wide gene
expression through “transcriptomics” hasshown that the genome responds dynamically to stimuli (4). One illustrative example is the honey bee. The African honey bee(Apis mellifera scutellata) responds much
more ﬁercely when its hive is attacked thando other subspecies of honey bee. Evolutionary changes in brain gene expression
may have resulted in an increase in responsiveness to alarm pheromone (the chemicalbees use to alert each other to danger) for
African honey bees (5). About 10% of thesame genes regulated in the brain by alarm
pheromone are also differentially expressed
between African and the less aggressive
European honey bees. These genes, acting

over both physiological and evolutionary
time scales, provide a possible mechanism
for how behavioral plasticity might drive
rapid behavioral evolution through changes
in gene regulation. In an environment withmore predators, colonies producing morebees with lower thresholds for responding
to alarm pheromone would have fared better, which would then result in a population with patterns of gene expression whose
output was an “aroused” behavior, even in
the absence of alarm pheromone. Although
this view does not rule out the possibility
that these differences in aggression arose
through new mutation, the transcriptomics
agrees with the idea of “genetic accommodation” (3), the modern, more inclusive version of genetic assimilation, which could
involve either evolutionary increases ordecreases in plasticity. In certain environments, plastic genotypes might be favored,
but in other environments, nonplastic genotypes might be preferred instead. Futurestudies will determine whether differencesin honey bee aggression can be explainedby selection on regulatory regions of thewww.sciencemag.org SCIENCE VOL 332 3 JUNE 2011
Published by AAAS1161Downloaded from www.sciencemag.org on June 2, 2011

with the type of epistasis found among adaptive mutations within a single protein (11).
Notably, Weinreich et al. studied mutationsin an antibiotic resistance gene, β-lactamase,and found a prevalence of sign epistasis,
which limits the number of genetic paths
that evolution can follow (11). In contrast,
the epistasis documented by Khan et al. andChou et al. exerts less constraint on the orderof substitutions that increase ﬁtness, so thatthe speciﬁc path that evolution will take isless predictable. At the same time, the prevalence of antagonistic epistasis measured by
the two groups ensures a predictable tempoof adaptation characterized by diminishingmarginal returns (10).
Although these new experiments suggest
a consistent principle of how epistasis shapes
the pattern of adaptation, many questions
must be answered before their results canbe extended to evolution outside the laboratory. It remains unclear, for instance, whether
these results would be altered by changing
fundamental evolutionary parameters, suchas population size, rate of mutation, and rateof recombination. Likewise, it is unclear