Redundancy, antiredundancy, and the robustnessof genomes
David C. Krakauer*†‡ and Joshua B. Plotkin†§*Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501; and §Institute for Advanced Study, Princeton, NJ 08540
Communicated by Simon A. Levin, Princeton University, Princeton, NJ, December 13, 2001 (received for review August 7, 2001)

genomic stability 兩 mutation selection 兩 canalization 兩 fitness
landscape 兩 quasispeciesT

he mutational instability of a genome undergoing replication
is both a source of evolutionary novelty and a cause ofdamage. The impact of deleterious mutations can be reduced
when several genes contribute toward a single function, or when
there are several copies of a single gene (1). In both cases theconsequence is genetic redundancy, also called genetic canalization (2). Redundancy has been found among homeotic genes(3), transcription factors (4), signal transduction proteins (5),metabolic pathway genes (6), and among the variable genes
encoding antibody peptides (7). It is thought that redundancy
promotes robustness by ‘‘backing-up’’ important functions. Redundancy can be preserved indefinitely only if there is someasymmetry in the contribution of genes to their shared function(8)—those genes making the larger contribution must experience higher rates of deleterious mutation than those making
smaller contributions. Without an asymmetry, the genes with thehigher mutation rates are lost by random drift.
Redundancy is rare in many organisms. In viruses and bacteria, for example, the need for genome compression leads tosmall genomes with no or few duplicate genes, a small numberof controlling elements, and overlapping reading frames. As aresult, a single mutation will often damage several distinct
functions simultaneously (9). Within multicellular eukaryotes,
checkpoint genes such as p53 respond to somatic mutations by
inducing apoptosis and removing damaged cells from a tissue(10). Similarly, the decline in telomerase enzyme during thedevelopment of a cell lineage ensures that cells do not propagate
mutations indefinitely (11). The loss of some error repair in
mitochondria increases the rate of mildly deleterious mutation
accumulation (12). In each of these cases, we observe theemergence of apparent antiredundancy—that is, mechanismsthat sensitize cells or individuals to genetic damage and thereby
eliminate them preemptively from a population.
www.pnas.org兾cgi兾doi兾10.1073兾pnas.032668599

We used a mathematical model to examine which generalconditions favor the evolution of redundancy and which favor
antiredundancy. We first derived the impact of fixed levels of
redundancy on the mean fitness of a population in mutationselection balance. Afterward, we allowed individual-level evolutionary variation in the level of redundancy. We do notdescribe explicitly how redundancy will have arisen or is encoded(13), nor do we estimate the time over which redundancy is
expected to be preserved (14). Instead, we investigated theimpact of genomic redundancy on mean fitness as a function of
the effective population size, the mutation rate, and the size ofthe genome.
A Quasispecies Model
We consider an extended form of the quasispecies equation,
which was originally introduced to describe selection and mutation among macromolecules (15). This equation provides avery general framework for exploring mutation and selection ina heterogenous population (16). We use this framework to
describe the evolution of L-bit genomes on a fitness landscape.
Instead of tracking the abundance of each individual genotype,
we tracked the abundance of each ‘‘hamming class’’—defined as
those genomes harboring an identical number of mutations froma central wild-type sequence. We assumed that fitness depends
only on the hamming distance of a mutant from the wild-typesequence. Thus, the fitness landscape is symmetric around thewild type; mutations to any part of the genome are equally
deleterious. If we let zk denote the total concentration of
genotypes with k deleterious mutations, we can express the time
evolution of the k-error mutants as a differential equation:

冘Lż k ⫽

z i f i P ki .

[1]

i⫽0

The value fi denotes the fitness of a genome with i mutations, and
Pki is the probability of mutation from an i-error genotype to a
k-error genotype during replication (see Appendix). L denotes
genome length.
We consider multiplicative fitness landscapes of the form fi ⬀(1 ⫺ s)i. The wild-type sequence, i ⫽ 0, is maximally fit, and eachdeleterious mutation reduces fitness by an amount (1 ⫺ s),independent of the other loci. The parameter s measures thedeleteriousness of each mutation; this selective value is usually
very small. By varying the magnitude of s we vary the steepnessof the landscape and hence the effective degree of redundancy
in the genome (Fig. 1).
To compare different mean fitness values for different levelsof redundancy (s), we normalize so that the sum of all fitnessclasses is unity:†D.C.K. and J.B.P. contributed equally to this work.
‡To whom reprint requests should be addressed. E-mail: krakauer@santafe.edu.

The publication costs of this article were defrayed in part by page charge payment. This
article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C.
§1734 solely to indicate this fact.

PNAS 兩 February 5, 2002 兩 vol. 99 兩 no. 3 兩 1405–1409

EVOLUTION

Genetic mutations that lead to undetectable or minimal changes inphenotypes are said to reveal redundant functions. Redundancy iscommon among phenotypes of higher organisms that experience
low mutation rates and small population sizes. Redundancy is lesscommon among organisms with high mutation rates and large
populations, or among the rapidly dividing cells of multicellularorganisms. In these cases, one even observes the opposite tendency: a hypersensitivity to mutation, which we refer to as antiredundancy. In this paper we analyze the evolutionary dynamics ofredundancy and antiredundancy. Assuming a cost of redundancy,
we find that large populations will evolve antiredundant mechanisms for removing mutants and thereby bolster the robustness ofwild-type genomes; whereas small populations will evolve redundancy to ensure that all individuals have a high chance of survival.
We propose that antiredundancy is as important for developmental robustness as redundancy, and is an essential mechanism forensuring tissue-level stability in complex multicellular organisms.
We suggest that antiredundancy deserves greater attention in
relation to cancer, mitochondrial disease, and virus infection.

Fig. 1. A schematic diagram of fitness landscapes with different degrees ofredundancy. The x–y plane denotes the space of genotypes and the x axis
denotes the corresponding fitness. High values of landscape steepness, s,correspond to antiredundant genomes (Lower Right) for which single mutations lead to considerable reductions in fitness. Smaller values of s correspondto shallower landscapes (Upper Left) and increasing degrees of redundancy.
All landscapes are normalized to have the same total volume (Eq. 2); shallower
landscapes have shorter wild-type peaks.

fi ⫽

冘

共1 ⫺ s兲 i.
Ljj ⫽ 0 共1 ⫺ s兲

[2]This normalization ensures that genotypes cannot evolve towardboth maximum fitness and maximum redundancy simultaneously. The normalization enforces a tradeoff between theabsolute height of the landscape and its steepness. The existenceof such a tradeoff follows from molecular considerations. Molecular mechanisms of redundancy impose fitness costs on thewild type, through increased genome size, increased metabolism,
or reduced binding specificity. Although the precise form of the
tradeoff curve is arbitrary and relatively unimportant (othernormalizations yield similar results), it is essential that we impose
some tradeoff between maximum fitness and redundancy.
Unlike most treatments of the quasispecies equation, we musthere allow for back mutations. According to two famous principles of population genetics, the neglect of back mutations
introduces pathologies into the equilibrium state of both infinite
and finite populations. If back mutations are neglected then,according the Haldane–Muller principle, the mean equilibrium
fitness of an infinite haploid population is independent of thelandscape’s steepness (19). If back mutations are ignored insmall populations, on the other hand, Muller’s ratchet implies
that mean fitness will tend always toward a minimum, regardlessof the landscape steepness. (The landscape steepness can affectthe speed, but not the eventual outcome, of Muller’s ratchet.) To
detect adaptive benefits or costs of redundancy, therefore, wecannot ignore back mutations.
We are assuming a form of redundancy produced by a genetic
network property with, on average, an equal contribution fromeach gene (20, 21). We do not model the explicit mechanism of
redundancy (see Table 1) but rather explore the generic consequences of redundancy on mean fitness. In the Appendix, wederive the average number of mutations, k៮ , for a genotype inmutation-selection equilibrium. This yields the following approximation for mean population fitness:៮៮f ⬇

s共1 ⫺ s兲 k.
1 ⫹ 共s ⫺ 1兲共1 ⫺ s兲 L

[3]

For small population sizes, the deterministic quasispecies
equation does not apply. In this case, however, moment equations (22) can be used to express the mean fitness as a function
1406 兩 www.pnas.org兾cgi兾doi兾10.1073兾pnas.032668599

Fig. 2. (a) The theoretical relationship between redundancy and equilibriummean fitness for populations of various sizes (N ⫽ 10, 100, 500, 1,000, 10,000,
and N infinite). Small populations benefit from redundant (i.e., flatter) landscapes, but large populations prefer antiredundant (i.e., steeper) landscapes.
The curves in the figure, given by Eqs. 3, 6, and 7, correspond to genome lengthL ⫽ 104 and mutation rate u ⫽ 5 䡠 10⫺5. (b) The relationship between redundancy and equilibrium mean fitness as observed from individual-based computer simulations of the quasispecies equation (L ⫽ 1,000, u ⫽ 5 䡠 10⫺4). Eachindividual is characterized by its hamming distance from wild type. The mean
population fitness is computed by averaging the last 20% of 10,000 generations with selection and mutation. In each discrete generation, N parents arechosen probabilistically from the previous generation according to theirrelative fitnesses. The offspring of a parent is mutated according to Eq. 5. The
numerical studies confirm the theoretical prediction: small populations prefershallow landscapes, whereas large populations prefer steep landscapes.

of the effective population size N (see Appendix). These equations determine the relationship between mean population
fitness, the strength of selection, the rate of mutation, thegenome length, and the size of the population. Recent studies(18) have emphasized the role of mutation in selecting for flatterlandscapes; we emphasize the role of population size.
The Influence of Population SizeFig. 2 shows the relationship between level of redundancy andexpected mean fitness for several different population sizes.
Both in theory (Fig. 2a) and in individual-based stochastic
simulations (Fig. 2b) we see that redundancy increases the mean
fitness in small populations, whereas it decreases fitness in large
populations. This central result has an intuitive explanation. In
small populations, mutational drift contributes disproportionately to the population fitness. There is a large temporal variancein the mean hamming class, and redundancy can effectively maskthese mutations. Small populations are thus better served byshallow landscapes—i.e., by slightly decreasing the fitness of thewild type, but increasing the fitness of its nearby neighbors.
Large populations, however, are not at risk of being ‘‘swept off’’
the fitness peak by the stochastic fluctuations that afflict small
populations; the temporal variance in the mean hamming class
Krakauer and Plotkin

Table 1. A summary of mechanisms responsible for creating redundancy and antiredundancy
at the cellular level

Gene duplication (14)Neutral codon usage (25)—
Polyploidy (28)Multiple regulatory elements for n genes (29)
Chaperone and heat shock proteins (30, 31)
Checkpoint genes promoting repair (32)
Telomerase induction (34)
Dominance (36, 37)
Autophagy (38, 39)mRNA surveillance (40, 41)
Bulk transmission (42, 43)
Molecular quality control (46)tRNA suppressor molecules (47)
Modularity (48)Multiple organelle copies (49)
Parallel metabolic pathways (6, 50)
Correlated gene expression (29, 51)
DNA error repair (52)

Antiredundancy
Overlapping reading frames (9)Nonconservative codon bias (26)Gene silencing (27)
Haploidy
Single regulatory element for n genes—
Checkpoint genes inducing apoptosis (33)
Loss of telomerase (35)
Incomplete dominance——
Bottlenecks in transmission (44, 45)———Single organelle copies
Serial metabolic pathways
Uncorrelated gene expression
Loss of error repair (53–55)

Redundant mechanisms mask the phenotypic effect of mutations, allowing the mutations to persist in
populations. We group together these mechanisms with a small s value. Antiredundant mechanisms increase theefficiency of local selection to remove damaged components, and are associated with large s values. These diverse
biological processes illustrate a range of mechanisms through which evolution can modify the redundancy of
genotypes. Reference numbers are given in parentheses.

is small. It is better, therefore, for large populations to amplify
the phenotypic penetrance of deleterious genes by means of
sharp landscapes.
Our results on equilibrium mean population fitness (Fig. 2)
constitute a population-based argument for the evolution of
redundancy in small populations and antiredundancy in large
populations. These results do not, in themselves, demonstratethat such strategies are evolutionarily stable or achievable. In
other words, we must yet demonstrate that individual replicators
subject to individual-level selection evolve degrees of redundancy consistent with the optimal population mean fitness. If weallow individuals to modify the heritable steepness of their own
individual landscapes through mutation, however, we find that
small populations do, indeed, evolve toward redundancy, andlarge populations evolve toward antiredundancy by means ofindividual-level selection (Fig. 3). For both population sizes, theevolution toward the preferred level of redundancy is punctuatedor episodic.
The evolutionary stability of these two strategies—sensitivity
in large populations and redundancy in small populations—has
an intuitive explanation. The stability rests on the fact that flatterlandscapes have lower fitness peaks. A large population on asteep landscape is highly localized near the wild type (low k៮ ).
Mutants with different s-values are thus most often generated
near the wild type—precisely where a more shallow landscapewould be disadvantageous to them. Conversely, small populations with shallow landscapes are delocalized (high k៮ ). In thiscase, landscape mutants tend to arise far from the wild type—precisely where a steeper landscape would decrease their fitness.
Thus, the landscape itself acts as a mechanism for ensuring therobustness of the incumbent strategy, in each population size.
Redundant and Antiredundant Mechanisms in Biology
We have shown how population size influences the degree of
redundancy expressed by a genome. In large populations ofviruses and bacteria, and in large populations of rapidly dividing
cells within multicellular organisms, we expect an evolution
toward antiredundant mechanisms. For small populations, on
Krakauer and Plotkin

the other hand, we expect a tendency toward redundancy. Table
1 lists a variety of molecular mechanisms capable of producing
redundancy and antiredundancy. Our quasispecies model provides a statistical treatment of the parameter s that is thedevelopmental end-point of each of these particular mechanisms. The mechanisms in Table 1 all influence development andsomatic processes by modifying the effective degree of deleteriousness, s, of mutations.
Antiredundant mechanisms (high s values) include overlapping reading frames, absence of tRNA suppressor genes, codon
bias, loss of DNA error repair, reduced number of promoters,
coordinated expression of genes, and checkpoint genes. All ofthese mechanisms remove mutant genomes from populations(either of individuals or cells). Redundant mechanisms (low s
values) include duplicated genes, correlated gene functions,tRNA suppressors, heat shock proteins, molecular quality control, and alternative metabolic pathways. These mechanisms,
which incur a cost (through increased genome size or greaterneed for resources), mask the effects of mutation. When available, both redundant and antiredundant strategies can be exploited, even simultaneously, by a single organism. Strategies
may also vary according to cell types.
Redundancy and Levels of Selection
The dynamics of redundancy and antiredundancy reveal an
intriguing interplay between the ‘‘levels of selection.’’ In multicellular organisms, rapidly dividing cells experience selection, in
effect, as members of a large quasispecies—much like viruses orbacteria. Large multicellular organisms often experience relatively small population sizes, though the cells of which they arecomposed experience huge population sizes. Hence there is apossible conflict between the organismal and cellular levels of
selection: the multicellular organism would benefit from aredundant (flatter) fitness landscape, whereas the cells of which
the organism is composed would benefit from an antiredundant(steeper) landscape. Interestingly, in some cases this conflict has
a synergistic resolution: antiredundancy at the cellular level is aneffective means of ensuring redundancy and robustness at the
PNAS 兩 February 5, 2002 兩 vol. 99 兩 no. 3 兩 1407

EVOLUTION

Redundancy

ismal level (for example, polyploidy); (ii) redundancy at thecellular level promoting antiredundancy at the organismal level(loss of molecular checkpoints); (iii) antiredundancy at thecellular level promoting redundancy at the organismal level(checkpoint genes inducing apoptosis); and (iv) antiredundancy
at the cellular level promoting antiredundancy at the organismallevel (bottlenecks in organelle transmission within and between
generations). The favored strategy depends on the local population size experienced by cell and organism. Because our model
does not separate germ line from soma, we cannot directly
address a true evolutionary conflict of interest between cells andorganism. Mammalian cancer provides such an example. Mutated cells strive to increase cellular redundancy to avoid the costof their mutations, thereby damaging the organism. The organism seeks to promote cellular antiredundancy so as to remove
mutant cells and increase organismal redundancy (case iii).
Antiredundancy at the cellular level should be viewed as a
victory for organismal selection.
Analogous to the cells of a complex organism, viruses, bacteria, and mitochondria often exhibit antiredundant mechanisms
as a consequence of their large populations and selection forcompressed genomes. Once again, antiredundant mechanisms at
the individual level can increase the mean fitness and stabilize
the quasispecies as a whole.

Fig. 3. The evolution of redundancy in a small population (Upper) and of
antiredundancy in a large population (Lower). We perform quasispecies simulations in which individuals are characterized both by their hamming class k
and their individual landscape steepness s. We choose genome size L ⫽ 500
and per-base mutation rate u ⫽ 0.001. On a slow time scale (probability 0.0005
per replication), an individual’s landscape is heritably mutated (uniformly
within [s ⫺ 0.005, s ⫹ 0.005]). For the small population, all individuals begin as
wild types with a fairly steep landscape, s ⫽ 0.05. For the large population, allindividuals begin as wild types with s ⫽ 0.025. After an initial transient, in bothcases the population’s mean landscape steepness s៮ evolves toward its preferred level. Simultaneously, the mean population fitness f៮ increases; although it increases less dramatically for the small population. Throughout theevolutionary time course, the within-population variance in redundancy (␴2)
is small. In addition, over time the small population becomes delocalized (k៮increases), whereas the large population becomes increasingly localized (datanot shown).

Redundancy and Cell Type
Finally, our theory predicts that, within a complex differentiatedorganism, the level or redundancy expressed within each cell
type will depend on the effective reproducing population size thecell type in question. For example, human brain cells seldom
regenerate and thus have an extremely small effective population
size. As a result, antiredundant mechanisms, such as apoptosis,
are strongly inhibited, whereas redundant mechanisms, including the chaperones, are highly expressed (23). The same logic
implies that the amount of redundancy found within genefamilies will depend on the effective population size of theselective unit at which those genes operate. Housekeeping genes
code for processes important at the single cell level. Because
individual cells are present in large population sizes, functionally
redundant copies of housekeeping genes should be rare. Conversely, genes involved in immune-system regulation encode
functions operating at the organismal level, where population
sizes are often much lower. We would expect that these genes
have many backup copies (7). The predicted level of redundancy
requires that we identify the effective population size at whichgenes come under strongest selection.
Appendix
Eigen’s quasispecies framework considers a large population of
L-bit genomes, xi, reproducing with imperfect fidelity according
to their fitnesses, wi, with fixed total concentration:冘j ⫽ 2Lẋ i ⫽

w j x j Q ij ⫺ x i W.

[4]

j⫽1

organismal level. Antiredundant mechanisms activated in mutant or damaged cells cause their removal, thereby ensuringstability (redundancy) against mutation in tissues.
Both the large cellular population within an individual and thesmaller population of individuals themselves can increase theirmean fitness by adopting these apparently conflicting strategies.
There are four combinations of strategies available: (i) redundancy at the cellular level promoting redundancy at the organ1408 兩 www.pnas.org兾cgi兾doi兾10.1073兾pnas.032668599

In this equation, W(t) ⫽ 兺w jx j(t) denotes the mean population
fitness. The mutation matrix Qij is determined by the per-basemutation rate, u, and the hamming distance H(i,j) between
genome i and j: Qij ⫽ uH(i,j)(1 ⫺ u)L⫺H(i,j).
When the fitness depends only on hamming class, the numberof equations is dramatically reduced (Eq. 1) by considering theevolution of all k-error mutants together: zk ⫽ 兺H(i) ⫽ kxi. The
chance of mutation from class l to class k is given by
Krakauer and Plotkinm ⫽ 兩k ⫺ l兩冉l共l ⫺ k ⫹ m兲兾2

冊冉L⫺l
共m ⫺ l ⫹ k兲兾2

u 共1 ⫺ u兲L ⫺ m,
m

冊
[5]

where we include only terms for which k ⫹ m ⬅ l (mod 2). In thisformulation, the forward and backward mutation rates are equal.
All of our qualitative results (Figs. 2b and 3) remain unchanged,
however, even if forward mutations occur at twice the rate of
backward mutations.
We consider multiplicative fitness landscapes of the form fk ⬀(1 ⫺ s)k (Eq. 2). For s small, this multiplicative formulation is the
prototypical example of a nonepistatic landscape (16, 17), which
has the advantage of analytic tractability. All of our qualitative
results (Figs. 2b and 3) remain essentially unchanged, however,
if landscapes containmoderate synergistic or antagonistic ep␣
istasis: fk ⬀ (1 ⫺ s)k , for 0.8 ⬍ ␣ ⬍ 1.2.
The dominant eigenvector of ( flPkl) provides the equilibrium
relative abundances of the hamming classes. Moreover, thecorresponding dominant eigenvalue equals the equilibriummean fitness. As suggested in ref. 24, we look for an eigenvectorof the binomial form zk ⫽ (kL)ak (1 ⫺ a)L⫺k, where a must yet be
determined. To compute a, we solve the discrete-time equivalentof Eq. 4, which reduces to the same eigensystem problem (24).
Given the current abundances of hamming classes (z0, z1, . . . , zL),
consider the random variable V defined by the hamming classafter mutation of an individual chosen from the populationaccording to its relative fitness. The generating function of V,冘⬁⌸ V 共x兲 ⫽prob共V ⫽ i兲xi,

i⫽0

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where x is a formal variable, is given by ⌸V(x) ⫽ 兺k zkfk 䡠 [u ⫹ (1 ⫺u)x]k 䡠 [(1 ⫺ u) ⫹ ux]L⫺k. In equilibrium we have ⌸V(x) ⫽ ␭ 兺zkxk, which, on the binomial substitution, determines the value ofa:a⫽1
共1 ⫺ u ⫹ 2u兾s ⫺ 冑共1 ⫺ u ⫹ 2u兾s兲 2 ⫺ 4u兾s兲.
2[6]

In equilibrium, the mean hamming distance from the wild typeis k៮ ⫽ aL.
According the moment equations of Woodcock and Higgs(24), when u is small the following expression approximates theequilibrium mean hamming class in a population of size N:k៮ 共N兲 ⫽

冉

2u
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⫹
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s
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⫺

冑冉

1⫹

1
2u
⫹
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2sN

冊

2

⫺

冊

1
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⫺
⫺ 2u .
ssN[7]

Substitution into Eq. 3 yields the equilibrium mean fitness.
We thank Jonathan Dushoff for many helpful conversations and forpointing out the application of generating functions in this setting. We
thank Walter Fontana, Lindi Wahl, and Gunter Wagner for theircomments and suggestions. We also thank the Alfred P. Sloan Foundation, The Ambrose Monell Foundation, The Florence Gould Foundation, and the J. Seward Johnson Trust. J.B.P. also acknowledges
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PNAS 兩 February 5, 2002 兩 vol. 99 兩 no. 3 兩 1409

EVOLUTION冘

min共l ⫹ k, 2L ⫺ l ⫺ k兲

P kl ⫽