Evolution of Genome Organization

Wolfgang Stephan, University of Rochester, NewYork, USA

Several features of chromosomes, such as chromosome number, polyploidy and the accumulation of repetitive DNA sequences near centromeres, reflect the evolutionary forces acting on eukaryotic genomes.

Secondary article
Article Contents
. Introduction . Evolutionary Forces Affecting Chromosome Number . Chromosome Architecture and Evolutionary Trends in Specific Chromosomal Regions . Evolution of Genome Size (Gene Number)

Introduction
The purpose of this article is to review the population processes that are likely to be most important in the evolution of genome organization and that have been explored theoretically by well-formulated models. The point of view consistently adopted here is that most evolutionary change at the genome level is the consequence of changes of gene and chromosome frequencies in natural populations, which result from the interaction of mutation, recombination, random genetic drift and natural selection. Some unconventional forces, such as meiotic drive and gene duplication, are also discussed. The role of recombination in determining certain features of the genome, such as chromosome number and the accumulation of repetitive DNA near centromeres and telomeres, is particularly emphasized. The question of why the genome is usually substructured into multiple chromosomes will be dealt with rst. Then the evolution of special regions of the eukaryotic chromosome (i.e. centromeres and telomeres) is discussed, followed by the evolution of genome size, with particular reference to gene duplication and polyploidization.

Which evolutionary forces inuence the spread of centric fusions and ssions?

The importance of recombination

It has been suggested that natural selection favouring a reduction in recombination will favour a centric fusion between two chromosomes, provided that there are suitable epistatic tness interactions between loci on the chromosomes concerned, suciently strong to generate linkage disequilibrium between unlinked genes (Charlesworth, 1985). On the other hand, selection for centric ssions could be generated by any mechanism leading to increased recombination (Charlesworth, 1985). To better understand these hypotheses, we will outline here the relevant parts of the theory of the evolution of recombination (reviewed in Otto and Michalakis, 1998) and then apply it to the evolution of chromosome number. There is a large body of literature dealing with the population genetics of systems in which a selection pressure exists for reducing the rate of recombination between loci. The case usually studied is that of a large, random-mating, diploid population segregating for a pair of loci with alleles A, a and B, b, respectively, which are under the control of natural selection. In a constant environment, lower recombination rates usually evolve when the population is near an equilibrium (with respect to selection) and there is linkage disequilibrium between these polymorphic loci. This is because parents who survive to reproduce have a genotype that works under local environmental conditions; tinkering with their osprings genotypes by recombination risks making the situation worse, with little chance of making it better. If epistatic tness interactions between polymorphic loci are a widespread phenomenon, it seems likely that the mechanism outlined above would favour genomes in which recombination is virtually absent. This is not the case, however. Consequently, a good deal of eort has been put into the investigation of theoretical models that generate selection for increased recombination. Increased recombination can evolve in a large population experiencing positive directional selection for benecial mutations (so that the population is far from equilibrium), but only if epistasis between loci is negative
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Evolutionary Forces Affecting Chromosome Number

The number of chromosomes in a cell changes by at least two processes: centric fusion and centric ssion (White, 1973). Centric fusion, in which two acrocentric chromosomes undergo a spontaneous translocation in the region of their centromere, reduces chromosome number. This process produces a metacentric chromosome with two large arms. Subsequent pericentric inversions can convert a large metacentric into an acrocentric chromosome. Evolutionary reduction in chromosome number due to centric fusions has been documented in both plants and animals (Stebbins, 1971; White, 1973). The converse process, centric ssion, increases chromosome number. This process is thought to be less common than centric fusion.

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Evolution of Genome Organization

(that is, when the tness eects of dierent loci contributing to a phenotypic trait are less than additive) and if this epistasis is not too strong. For increased recombination to evolve, relatively weak negative epistasis is also needed in the case of purifying (negative) selection against deleterious mutations. In smaller populations, in which random genetic drift plays an important role, recombination may be favoured in situations in which it protects rare benecial alleles from loss due to drift. Recent results on the eect of recombination on the fate of new benecial alleles are particularly important in this context. The average probability of xation of a new benecial allele is raised by recombination as long as there is genetic variance for tness at other loci. This occurs because, with tight linkage between tness loci, selection acts on the level of the haplotype and therefore the dynamics of a benecial allele will be governed more by the genomic background on which it arises and less by its own selective advantage. With loose linkage, however, selection at the locus itself becomes more important and drowns out the noise caused by selection at other loci. Furthermore, increased recombination rates may be favoured in temporally uctuating environments. If conditions change from time to time in such a way that the combinations of genes favoured by selection vary across generations, it is reasonable to suppose that increased recombination will facilitate the passage of the population into a new state when the environment changes. However, under uctuating selection, the conditions for increased recombination to evolve appear to be more restrictive than under directional selection. As the direction of selection changes, selection weakens relative to the strength of epistatic interactions, reducing the advantage of recombination. These models enable the strength of selection on chromosome number to be studied. A centric fusion between two chromosomes of equal length behaves formally as a dominant gene that reduces the frequency of crossing-over between pairs of loci that were formerly located on two dierent chromosomes; a ssion behaves like a recessive gene increasing recombination (Charlesworth, 1985). Calculations (based on models with negative epistasis) suggest that centric fusions are weakly selected against (Charlesworth, 1990), particularly in systems with large chromosome numbers, so that the eects of selection are probably overcome by random genetic drift. This may explain why centric fusions are a major mode of karyotypic evolution in a variety of taxonomic groups (White, 1973).

ments cause a loss of fertility when heterozygous, owing to the production of unbalanced gametes as a result of disturbances to normal segregation. Since a new mutation in a random-mating population is present predominantly in heterozygotes, the chance is small that a rearrangement associated with such fertility loss can rise to high frequency in a local population, except with very restricted population size. Migration between populations lowers the chance of establishment of new arrangements within a local population but increases the rate at which they can spread through the species. The most favourable population structure for rapid chromosomal evolution by this mechanism is when there is a high degree of subdivision into small, partially isolated populations, with a high rate of extinction and recolonization from adjacent areas. As a result of the recolonization process, there is a nite chance that, at some future date, each local population will be descended from just one of the populations present in a given generation, by analogy with the process of random xation of genes by drift in a single population. An alternative pathway is the origination of a new species from a small isolated population; if the isolate becomes xed for a new arrangement, this will obviously come to characterize the whole species (Charlesworth, 1985). It seems likely that this process of random xation of chromosomal rearrangements has played a major role in the alteration of chromosome number by centric fusions or ssions. The apparent preponderance of fusions over ssions in many taxonomic groups could be explained by the greater ease with which fusions originate by mutation (White, 1973). Inbreeding may play an important role in this process. Extreme inbreeding, such as self-fertilization, will accelerate this mode of chromosome evolution, since fewer heterozygotes occur. This may explain why derived, self-fertilizing plant taxa have generally smaller chromosome numbers than their more outcrossing ancestors (Charlesworth, 1985). However, it should be noted that selective factors inuencing recombination and chromosome numbers may also be aected by inbreeding. Associations between inbreeding and rapid karyotypic evolution do not, therefore, constitute strong evidence for the role of random genetic drift.

The effects of meiotic drive

A completely dierent mechanism that can promote the spread of chromosome rearrangements is meiotic drive. Examples of cytologically detectable chromosome changes that are associated with meiotic drive are known in a variety of plants and animals. It has been suggested that meiotic drive can x deleterious chromosome rearrangements in organisms with moderate population size (King, 1993), but the overall importance of this process in causing species dierences is not clear. Drive is, however, of major signicance in maintaining supernumerary chromosomes.

The effects of random genetic drift

In small populations, chromosome rearrangements, such as centric fusions or ssions, may rise in frequency and be subsequently xed by random genetic drift. The problem is complicated by the fact that most chromosome rearrange2

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Evolution of Genome Organization

These chromosomes are usually heterochromatic, with deleterious eects on the tness of their carriers, and are not homologous with members of the normal complement. They display a variety of drive mechanisms by which they can maintain their presence in populations despite counterselection at the individual level.

Chromosome Architecture and Evolutionary Trends in Specific Chromosomal Regions

In this section, we discuss some evolutionary hypotheses to account for two major features of the genetic and molecular evolution of the chromosomes of eukaryotes. The rst such feature is the reduced frequency of recombination in the neighbourhood of centromeres and telomeres. A lowered probability of genetic exchange in meiosis in the centromere region has been most clearly documented in Drosophila melanogaster, but a relative contraction of the genetic map near centromeres is observable also in several other well-studied organisms, such as tomatoes. The situation in the telomere regions is less clear, but a reduction of meiotic recombination has been found in many organisms. It has been suggested that this reduction in crossing-over frequencies is the consequence of natural selection for a lower frequency of unequal exchange between repeated sequences of functional signicance that are located in these chromosomal regions. The other phenomenon that we will discuss is the tendency for highly repeated DNA sequences of no apparent functional signicance (satellite DNA) and of transposable elements to accumulate in regions of restricted crossing-over (Charlesworth et al., 1986).

Restricted crossing-over near centromeres and telomeres

The structure of centromeres of eukaryotes with very small chromosomes, such as yeast, is apparently very simple. The yeast centromere lacks an identiable structure such as the kinetochore, and each chromosome is attached to a single microtubule. In contrast, the chromosomes of mammals and most other higher eukaryotes possess a highly dierentiated kinetochore, through which many microtubules attach to a large stretch of specialized chromatin. Although very small chromosomes often show dierentiated kinetochores, it is usually the case that chromosomes without dierentiated kinetochores are small (e.g. the chromosomes of Physarum, various yeasts, Neurospora and the microchromosomes of birds). It is likely that the disjunction of large chromosomes requires a greater force than is necessary for small chromosomes; hence, more microtubules per chromosomes are needed. The evolution

of larger chromosomes presumably led to the multitubule spindle bre and to multiple centromeric microtubulebinding sites (Charlesworth et al., 1986). Unequal exchange between these repeated sites would lead to variation in the number of binding sites per chromosome. Chromosomes with a number that deviates from the optimum may suer an imbalance of spindle forces at disjunction, leading to nondisjunction events and aneuploidy, with a consequent reduction in tness. Natural selection will therefore favour a reduction in crossing-over in the centromere region. If the kinetochore found at the centromere of most animal chromosomes is organized around an optimal number of microtubule-binding sites, then it is not surprising from the above considerations that crossing-over is restricted in these regions. The only optimum number of binding sites that would not favour the evolution of restricted recombination would be one. It is interesting to note that yeast has only one binding site and does not exhibit a centromeric reduction in crossingover comparable in magnitude to that of Drosophila. There is now clear molecular evidence for the presence of specialized tandemly repeated sequences in the telomere regions of most species. If there were an optimum number of repeats for ecient telomeric replication, the argument used above for centromeres would apply, and reduced recombination in the telomeric regions would be favoured by natural selection. There is, however, clear evidence that the size of the block of telomeric repeats is under the control of replicative mechanisms. This probably reduces any eect of unequal exchange on the number of copies of the repeats. In Drosophila, however, restricted recombination near telomeres may be favoured by selection. In contrast to most organisms, the proper replication of Drosophila telomeres is ensured by transposable elements that insert preferentially at the ends of chromosomes. Therefore, there may be selective pressure in favour of reduced rates of crossing-over in telomeric regions to protect these elements from removal by ectopic exchange (see below for more details).

Accumulation of repetitive DNA sequences in regions of restricted recombination

It has been suggested that the association between highly repeated DNA sequences, such as satellite arrays, and regions of restricted crossing-over may be a consequence of evolution rather than an inherent functional property of these sequences (Charlesworth et al., 1986). This hypothesis is based on a population genetic model that incorporates the following processes: amplication, describing a sudden increase in array length by one or more repeat units; unequal exchange between tandem arrays on homologous chromosomes; random genetic drift; and natural selection against too high copy numbers. Analysis of this model shows that mean array size will be very large
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Evolution of Genome Organization

when Ng ! 1 and selection against total array length is weak (where N is the population size and g is the recombination rate per array). Thus, in regions with restricted recombination and very weak selection pressure against array size, such as in the centromere region, which is devoid of functional genes, highly repeated sequences may accumulate. In contrast, in more distant regions where the functional genes are located and recombination rates are generally higher, highly repeated sequences, such as satellite sequences, are only rarely found. The tandem arrays that are usually located in these latter regions have much smaller sizes, and are accordingly called microsatellites or minisatellites. Several other properties of tandem arrays of noncoding DNA sequences, including repeat length and higher-order structure of arrays, seem to correlate with rates of recombination along chromosomes. Models accounting for these characteristics have been discussed elsewhere (Stephan, 1997). A similar model has been proposed to account for the accumulation of transposable elements in regions of reduced recombination. Recombination between elements at nonhomologous insertion sites (ectopic exchange) can cause deletions and duplications of genetic material, which are expected to have dominant deleterious eects in many cases. This can oppose increase in transposable elements by reducing the fertility of individuals with high element copy numbers. There is direct evidence for the occurrence of ectopic exchange between element sequences in Drosophila melanogaster (Montgomery et al., 1991) and in other species including humans. Survey data from D. melanogaster indeed show that transposable elements are signicantly overabundant in chromosomal regions in which the rate of recombination is reduced, as expected if ectopic exchange is reduced parallel with regular meiotic recombination.

not clear. Articially produced autopolyploids (polyploidization of homologous chromosomes) are generally inferior to their diploid ancestors. The inferiority is expressed in lower fertility and a lower ability to compete with diploids. These experimental results and the fact that the performance of induced polyploids as agricultural crops has consistently fallen short of expectations have led most researchers to believe that genome duplication per se is selectively disadvantageous. The widespread success of polyploidy in owering plants has therefore been attributed to hybridization between individuals from dierent populations (allopolyploidy). Hybridization increases genetic diversity and may enable the polyploids to compete with their progenitors or to colonize new habitats. In contrast, polyploidy is extremely rare in bisexually reproducing animals, presumably because the two sexes are strongly dierentiated with regard to the mechanism of chromosome segregation and combination, and polyploidy invariably disturbs this process. In amphibians and sh, however, many tetraploid species have been found. In these species, genome duplication does not result in sexual imbalance because the chromosomal determinants of the opposite sexes are still in a rather early state of dierentiation so that the sex chromosomes (usually labelled as X and Y, or Z and W) can substitute for each other (Li, 1997).

Chromosome duplication
The duplication of a chromosome or part of a chromosome is likely to cause a severe imbalance in gene product. Its chance of being xed in a population and its evolutionary signicance are thus very small. For example, in Drosophila the viability of terminal triploids declines with the amount of the triplicated material, generally becoming lethal when more than one-half of an autosomal arm is present in three doses. In humans, trisomies can be lethal or can cause sterility. Well-known examples are the Down syndrome (trisomy 21) and trisomy of chromosome 18 (Li, 1997).

Evolution of Genome Size (Gene Number)

The mechanisms discussed earlier contribute to changes in the arrangement of the genetic material as opposed to changes in its quantity. Alterations of quantity can proceed by the processes of duplication of entire genomes (polyploidization), complete and partial duplication of chromosomes, and gene duplication. These will be discussed in turn.

Gene duplication
Gene duplication seems to play a very important role in increasing genome size. The evolutionary signicance of gene duplication was already recognized in the 1930s, when Haldane and Muller suggested that a redundant duplicate of a gene may acquire divergent mutations and eventually emerge as a new gene. Once a duplication has become xed in a population, the way is open for evolutionary divergence of the two duplicates, if an advantageous mutation conferring a new function becomes xed in one of the two copies. Duplicated genes can be divided into two types: variant and invariant repeats. Invariant repeats are (nearly) identical in sequence to one another. In several cases, the repetition of identical sequences can be shown to be

Genome duplication
Genome duplication occurs as a consequence of lack of disjunction between the daughter chromosomes following DNA replication. Polyploidy is a widespread phenomenon in plants, in particular in owering plants (Stebbins, 1971). The reasons for the prevalence of polyploidy in plants are
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Evolution of Genome Organization

correlated with the synthesis of increased quantitites of a gene product that is required for the normal function of the organism (dosage repetition). Representative examples include the genes for tRNAs and rRNAs required for translation. Other examples are the amplication of an esterase gene in a Californian Culex mosquito, leading to insecticide resistance, and the tandem duplication of the D. melanogaster metallothionein gene involved in heavy metal detoxication. Variant gene copies dier in their sequence to various degrees. Depending on their degree of divergence, they form multigene families (with weakly to intermediately divergent members) or superfamilies (with very divergent members). The members of a multigene family, such as various types of isozymes, may dier to some extent in function or regulation, so that they can contribute to the ne-tuning of physiological processes of an organism. Members of a superfamily have, however, diverged a long time ago and may have quite distinct functions. A well-known example is that of trypsin and chymotrypsin, which diverged about 1500 million years ago. These two digestive enzymes have acquired distinct functions: trypsin cleaves polypeptide chains at arginine and lysine residues, whereas chymotrypsin cleaves at phenylalanine, tryptophan, and tyrosine residues (Li, 1997). A much more likely fate for a redundant duplicate gene than evolution into a new gene is that it accumulates deleterious mutations and becomes nonfunctional. This is because deleterious mutations occur far more often than advantageous ones. This process produces so-called pseudogenes. Most multigene families or superfamilies, such as the globin superfamily, contain a rather high percentage of pseudogenes.

References
Charlesworth B (1985) Recombination, genome size and chromosome number. In: Cavalier-Smith T (ed.) Natural Selection and Genome Size, pp. 489513. Chichester, UK: Wiley. Charlesworth B (1990) Mutationselection balance and the evolutionary advantage of sex and recombination. Genetical Research 55: 199221. Charlesworth B, Langley CH and Stephan W (1986) The evolution of restricted recombination and the accumulation of repeated DNA sequences. Genetics 112: 947962. King M (1993) Species Evolution: The Role of Chromosome Change. Cambridge, UK: Cambridge University Press. Li W-H (1997) Molecular Evolution. Sunderland, MA: Sinauer Associates. Montgomery EA, Huang S-M, Langley CH and Judd BH (1991) Chromosome rearrangement by ectopic recombination in Drosophila melanogaster: genome structure and evolution. Genetics 129: 1085 1098. Otto SP and Michalakis Y (1998) The evolution of recombination in changing environments. Trends in Ecology and Evolution 13: 145151. Stebbins GL (1971) Chromosomal Evolution in Higher Plants. London: Edward Arnold. Stephan W (1997) Tandem-repetitive noncoding DNA sequences. In: Meyers RA (ed.) Encyclopedia of Molecular Biology and Molecular Medicine, vol. 6, pp. 110. Weinheim, Germany: Verlagsgesellschaft. White MJD (1973) Animal Cytology and Evolution, 3rd edn. Cambridge, UK: Cambridge University Press.

Further Reading
Cavalier-Smith T (ed.) (1985) The Evolution of Genome Size. Chichester, UK: Wiley. Charlesworth B, Sniegowski P and Stephan W (1994) The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371: 215220. John B and Miklos GLG (1988) The Eukaryote Genome in Development and Evolution. London: Allen and Unwin. Ohno S (1970) Evolution by Gene Duplication. Berlin: Springer-Verlag.

ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net