How selfish is DNA?

C-value paradox: Genesis in misconception that natural selection follows anthropocentric parameters of 'economy' and 'optimum'

C-value paradox refers to the lack of correlation between biological complexity and the intuitively expected protein-coding genomic information or DNA content. Here I discuss five questions about this paradox: i) Do biologically complex organisms carry more protein-coding genes? ii) Does variable accumulation of selfish/ junk/ parasitic DNA underlie the c-value paradox? iii) Can nucleoskeletal or nucleotypic function of DNA explain the enigma of orders of magnitude high levels of DNA in some 'lower' taxa or in taxonomically related species? iv) Can the newly understood noncoding but functional DNA explain the c-value paradox? and, v) Does natural selection uniformly apply the anthropocentric parameters for 'optimum' and 'economy'? Answers to Q.1-5 are largely negative. Biology presents numerous 'anomalous' examples where the same end function/ phenotype is attained in different organisms through astoundingly diverse ways that appear 'illogical' in our perceptions. Such evolutionary oddities exist because natural selection, unlike a designer, exploits random and stochastic events to modulate the existing system. Consequently, persistence of the new-found 'solution/s' often appear bizarre, uneconomic, and therefore, paradoxical to human logic. The unexpectedly high c-values in diverse organisms are irreversible evolutionary accidents that persisted, and the additional DNA often got repurposed over the evolutionary time scale. Therefore, the c-value paradox is a redundant issue. Future integrative biological studies should address evolutionary mechanisms and processes underlying sporadic DNA expansions/ contractions, and how the newly acquired DNA content has been repurposed in diverse groups.

The impact of transposable elements on tomato diversity

Tomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. Here, we leverage whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of transposable elements (TEs) to tomato diversity. We identify 6,906 TE insertions polymorphisms (TIPs), which result from the mobilization of 337 distinct TE families. Most TIPs are low frequency variants and TIPs are disproportionately located within or adjacent to genes involved in environmental responses. In addition, genic TE insertions tend to have strong transcriptional effects and they can notably lead to the generation of multiple transcript isoforms. Using genome-wide association studies (GWAS), we identify at least 40 TIPs robustly associated with extreme variation in major agronomic traits or secondary metabolites and in most cases, no SNP tags the TE insertion allele. Collectively, these findings highlight the unique role of TE mobilization in tomato diversification, with important implications for breeding.

Transposable element insertion polymorphisms (TIPs) are a potential source of large effect alleles. Here, the authors use genome resequencing data for 602 tomato accessions together with transcriptomic and extensive phenotypic information to investigate the contribution of TIPs to tomato diversity.

A century of bias in genetics and evolution

Mendel proposed that the heritable material is particulate and that transmission of alleles is unbiased. An assumption of unbiased transmission was necessary to show how variation can be preserved in the absence of selection, so overturning an early objection to Darwinism. In the second half of the twentieth century, it was widely recognised that even strongly deleterious alleles can invade if they have strongly biased transmission (i.e. strong segregation distortion). The spread of alleles with distorted segregation can explain many curiosities. More recently, the selectionist-neutralist duopoly was broken by the realisation that biased gene conversion can explain phenomena such as mammalian isochore structures. An initial focus on unbiased transmission in 1919, has thus given way to an interest in biased transmission in 2019. A focus on very weak bias is now possible owing to technological advances, although technical biases may put a limit on resolving power. To understand the relevance of weak bias we could profit from having the concept of the effectively Mendelian allele, a companion to the effectively neutral allele. Understanding the implications of unbiased and biased transmission may, I suggest, be a good way to teach evolution so as to avoid psychological biases.

Selfish genetic elements

Selfish genetic elements (historically also referred to as selfish genes, ultra-selfish genes, selfish DNA, parasitic DNA, genomic outlaws) are genetic segments that can enhance their own transmission at the expense of other genes in the genome, even if this has no or a negative effect on organismal fitness. [1-6] Genomes have traditionally been viewed as cohesive units, with genes acting together to improve the fitness of the organism. However, when genes have some control over their own transmission, the rules can change, and so just like all social groups, genomes are vulnerable to selfish behaviour by their parts. Early observations of selfish genetic elements were made almost a century ago, but the topic did not get widespread attention until several decades later. Inspired by the gene-centred views of evolution popularized by George Williams[7] and Richard Dawkins,[8] two papers were published back-to-back in Nature in 1980-by Leslie Orgel and Francis Crick[9] and Ford Doolittle and Carmen Sapienza[10] respectively-introducing the concept of selfish genetic elements (at the time called "selfish DNA") to the wider scientific community. Both papers emphasized that genes can spread in a population regardless of their effect on organismal fitness as long as they have a transmission advantage. Selfish genetic elements have now been described in most groups of organisms, and they demonstrate a remarkable diversity in the ways by which they promote their own transmission.[11] Though long dismissed as genetic curiosities, with little relevance for evolution, they are now recognized to affect a wide swath of biological processes, ranging from genome size and architecture to speciation.[12].

Selfish genetic elements and the gene's-eye view of evolution

During the last few decades, we have seen an explosion in the influx of details about the biology of selfish genetic elements. Ever since the early days of the field, the gene's-eye view of Richard Dawkins, George Williams, and others, has been instrumental to make sense of new empirical observations and to the generation of new hypotheses. However, the close association between selfish genetic elements and the gene's-eye view has not been without critics and several other conceptual frameworks have been suggested. In particular, proponents of multilevel selection models have used selfish genetic elements to criticize the gene's-eye view. In this paper, I first trace the intertwined histories of the study of selfish genetic elements and the gene's-eye view and then discuss how their association holds up when compared with other proposed frameworks. Next, using examples from transposable elements and the major transitions, I argue that different models highlight separate aspects of the evolution of selfish genetic elements and that the productive way forward is to maintain a plurality of perspectives. Finally, I discuss how the empirical study of selfish genetic elements has implications for other conceptual issues associated with the gene's-eye view, such as agential thinking, adaptationism, and the role of fitness maximizing models in evolution.

Mating system shifts and transposable element evolution in the plant genus Capsella

Background

Despite having predominately deleterious fitness effects, transposable elements (TEs) are major constituents of eukaryote genomes in general and of plant genomes in particular. Although the proportion of the genome made up of TEs varies at least four-fold across plants, the relative importance of the evolutionary forces shaping variation in TE abundance and distributions across taxa remains unclear. Under several theoretical models, mating system plays an important role in governing the evolutionary dynamics of TEs. Here, we use the recently sequenced Capsella rubella reference genome and short-read whole genome sequencing of multiple individuals to quantify abundance, genome distributions, and population frequencies of TEs in three recently diverged species of differing mating system, two self-compatible species (C. rubella and C. orientalis) and their self-incompatible outcrossing relative, C. grandiflora.

Results

We detect different dynamics of TE evolution in our two self-compatible species; C. rubella shows a small increase in transposon copy number, while C. orientalis shows a substantial decrease relative to C. grandiflora. The direction of this change in copy number is genome wide and consistent across transposon classes. For insertions near genes, however, we detect the highest abundances in C. grandiflora. Finally, we also find differences in the population frequency distributions across the three species.

Conclusion

Overall, our results suggest that the evolution of selfing may have different effects on TE evolution on a short and on a long timescale. Moreover, cross-species comparisons of transposon abundance are sensitive to reference genome bias, and efforts to control for this bias are key when making comparisons across species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-602) contains supplementary material, which is available to authorized users.

Myonuclei acquired by overload exercise precede hypertrophy and are not lost on detraining

Effects of previous strength training can be long-lived, even after prolonged subsequent inactivity, and retraining is facilitated by a previous training episode. Traditionally, such "muscle memory" has been attributed to neural factors in the absence of any identified local memory mechanism in the muscle tissue. We have used in vivo imaging techniques to study live myonuclei belonging to distinct muscle fibers and observe that new myonuclei are added before any major increase in size during overload. The old and newly acquired nuclei are retained during severe atrophy caused by subsequent denervation lasting for a considerable period of the animal's lifespan. The myonuclei seem to be protected from the high apoptotic activity found in inactive muscle tissue. A hypertrophy episode leading to a lasting elevated number of myonuclei retarded disuse atrophy, and the nuclei could serve as a cell biological substrate for such memory. Because the ability to create myonuclei is impaired in the elderly, individuals may benefit from strength training at an early age, and because anabolic steroids facilitate more myonuclei, nuclear permanency may also have implications for exclusion periods after a doping offense.

Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution

BACKGROUND

The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long-standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis.

RESULTS

I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation advantages. These successive changes took place in naked growing cells, probably as indirect consequences of the origin of phagotrophy. The first eukaryote had 1-2 cilia and also walled resting cysts; I outline how encystation may have promoted the origin of meiotic sex. I also explain why many alternative ideas are inadequate.

CONCLUSION

Nuclear pore complexes are evolutionary chimaeras of endomembrane- and mitosis-related chromatin-associated proteins. The keys to understanding eukaryogenesis are a proper phylogenetic context and understanding organelle coevolution: how innovations in one cell component caused repercussions on others.

The problem of the eukaryotic genome size

The current state of knowledge concerning the unsolved problem of the huge interspecific eukaryotic genome size variations not correlating with the species phenotypic complexity (C-value enigma also known as C-value paradox) is reviewed. Characteristic features of eukaryotic genome structure and molecular mechanisms that are the basis of genome size changes are examined in connection with the C-value enigma. It is emphasized that endogenous mutagens, including reactive oxygen species, create a constant nuclear environment where any genome evolves. An original quantitative model and general conception are proposed to explain the C-value enigma. In accordance with the theory, the noncoding sequences of the eukaryotic genome provide genes with global and differential protection against chemical mutagens and (in addition to the anti-mutagenesis and DNA repair systems) form a new, third system that protects eukaryotic genetic information. The joint action of these systems controls the spontaneous mutation rate in coding sequences of the eukaryotic genome. It is hypothesized that the genome size is inversely proportional to functional efficiency of the anti-mutagenesis and/or DNA repair systems in a particular biological species. In this connection, a model of eukaryotic genome evolution is proposed.

Nuclear domains during muscle atrophy: nuclei lost or paradigm lost?

According to the current paradigm, muscle nuclei serve a certain cytoplasmic domain. To preserve the domain size, it is believed that nuclei are injected from satellite cells fusing to fibres undergoing hypertrophy, and lost by apoptosis during atrophy. Based on single fibre observations in and ex vivo we suggest that nuclear domains are not as constant as is often indicated. Moreover, recent time lapse in vivo imaging of single fibres suggests that at least for the first few weeks, atrophy is not accompanied by any loss of nuclei. Apoptosis is abundant in muscle tissue during atrophy conditions, but in our opinion it has not been unequivocally demonstrated that such nuclei are myonuclei. As we see it, the preponderance of current evidence suggests that disuse atrophy is not accompanied by loss of nuclei, at least not for the first 2 months. Moreover, it has not been proven that myonuclear apoptosis does occur in permanent fibres undergoing atrophy; it seems more likely that it is confined to stromal cells and satellite cells. If muscle atrophy is not related to loss of nuclei, design of intervention therapies should focus on protein metabolism rather than regeneration from stem cells.

Origins and Evolution of Spliceosomal Introns

Research into the origins of introns is at a critical juncture in the resolution of theories on the evolution of early life (which came first, RNA or DNA?), the identity of LUCA (the last universal common ancestor, was it prokaryotic- or eukaryotic-like?), and the significance of noncoding nucleotide variation. One early notion was that introns would have evolved as a component of an efficient mechanism for the origin of genes. But alternative theories emerged as well. From the debate between the "introns-early" and "introns-late" theories came the proposal that introns arose before the origin of genetically encoded proteins and DNA, and the more recent "introns-first" theory, which postulates the presence of introns at that early evolutionary stage from a reconstruction of the "RNA world." Here we review seminal and recent ideas about intron origins. Recent discoveries about the patterns and causes of intron evolution make this one of the most hotly debated and exciting topics in molecular evolutionary biology today.

Number and spatial distribution of nuclei in the muscle fibres of normal mice studied in vivo

We present here a new technique with which to visualize nuclei in living muscle fibres in the intact animal, involving injection of labelled DNA into single cells. This approach allowed us to determine the position of all of nuclei within a sarcolemma without labelling satellite cells. In contrast to what has been reported in tissue culture, we found that the nuclei were immobile, even when observed over several days. Nucleic density was uniform along the fibre except for the endplate and some myotendinous junctions, where the density was higher. The perijunctional region had the same number of nuclei as the rest of the fibre. In the extensor digitorum longus (EDL) muscle, the extrajunctional nuclei were elongated and precisely aligned to the long axis of the fibre. In the soleus, the nuclei were rounder and not well aligned. When comparing small and large fibres in the soleus, the number of nuclei varied approximately in proportion to cytoplasmic volume, while in the EDL the number was proportional to surface area. Statistical analysis revealed that the nuclei were not randomly distributed in either the EDL or the soleus. For each fibre, actual distributions were compared with computer simulations in which nuclei were assumed to repel each other, which optimizes the distribution of nuclei with respect to minimizing transport distances. The simulated patterns were regular, with clear row-like structures when the density of nuclei was low. The non-random and often row-like distribution of nuclei observed in muscle fibres may thus reflect regulatory mechanisms whereby nuclei repel each other in order to minimize transport distances.

Transiently beneficial insertions could maintain mobile DNA sequences in variable environments

The maintenance of mobile DNA sequences in clonal organisms has been seen as a paradox. If selfish mobile sequences spread through genomes only by overreplication in transposition, then sexuality is necessary for their spread through populations. The persistence of bacterial transposable elements without obvious dominant selectable markers has previously been explained by horizontal transfer. However, advantageous insertions of mobile DNAs are known in bacteria. Here we model maintenance of an otherwise selfish mobile DNA element in a clonal species in which selection for null mutations occurs during one of two temporally alternating environments. Large areas of parameter space permit maintenance of mobile DNAs where, without selection, they would have gone extinct. Horizontal transfer diminishes, rather than enhances, mean copy number. In finite populations, effective population sizes are greatly reduced by selective sweeps, and mean copy number can be increased as the reduced variance in copy number results in reduced selection.

The Modulation of DNA Content: Proximate Causes and Ultimate Consequences

The forces responsible for modulating the large-scale features of the genome remain one of the most difficult issues confronting evolutionary biology. Although diversity in chromosomal architecture, nucleotide composition, and genome size has been well documented, there is little understanding of either the evolutionary origins or impact of much of this variation. The 80,000-fold divergence in genome sizes among eukaryotes represents perhaps the greatest challenge for genomic holists. Although some researchers continue to characterize much variation in genome size as a mere by-product of an intragenomic selfish DNA “free-for-all” there is increasing evidence for the primacy of selection in molding genome sizes via impacts on cell size and division rates. Moreover, processes inducing quantum or doubling series variation in gametic or somatic genome sizes are common. These abrupt shifts have broad effects on phenotypic attributes at both cellular and organismal levels and may play an important role in explaining episodes of rapid—or even saltational—character state evolution.

Nuclear DNA amounts in angiosperms

Nuclear DNA amounts have been estimated for more than 200 angiosperm species since the last collected list of such values for about 750 species was published by Bennett & Smith in 1976 ( Phil. Trans. R. Soc. Lond. B 274, 227- 274). These new estimates are either scattered in a wide range of scientific journals or, in many cases, unpublished; so they are not readily accessible. A publication, collecting these data in a single list is required. This paper contains a supplementary list of absolute DNA values, including estimates for 240 angiosperm species not listed by Bennett & Smith in 1976, as well as additional estimates for 41 species already listed by them. These data are assembled primarily for reference purposes. Consequently, the species are listed in alphabetical order, as this was felt to be more helpful to cyto- and biochemists, who it is anticipated will be among the major users.

HETEROMORPHISM FOR A HIGHLY REPEATED SEQUENCE IN THE NEW ZEALAND FROG LEIOPELMA HOCHSTETTERI

A satellite DNA sequence, Lhl, was cloned from the New Zealand endemic frog Leiopelma hochstetteri. Large tandem arrays of Lh1 were localized by in situ hybridization to the long arm of a small telocentric autosome in some individuals, but these arrays were absent from other individuals. Lh1 is also present in varying amounts on some supernumerary chromosomes in some individuals. Heteromorphism for the presence of Lh1 exists in two populations that have been separated by a sea channel since the end of the Pleistocene, indicating that the heteromorphism either has arisen repeatedly or has persisted for at least 10,000 years. Individuals lacking Lh1 thus appear to be at no significant selective disadvantage. The variation in Lh1 copy number probably results from its interstitial chromosomal location, which exposes it to more frequent unequal crossovers than the pericentromeric or telocentric locations of most satellite DNA. Lh1 may be parasitic or simply inert junk, but in either case it may be deleted or dispersed throughout the rest of the genome through unequal crossing over.

Evolutionary dynamics of transposable elements in prokaryotes and eukaryotes

This paper summarizes some recent theories about the evolution of transposable genetic elements in outbreeding, sexual eukaryotic organisms. The evolutionary possibilities available to self-replicating transposable elements are shown to vary depending on the reproductive biology of the host genome. This effect can be used to explain, in part, the differences in abundance of transposable elements between prokaryotes and eukaryotes. It is argued that the pattern of sexual outbreeding seen in mammals and plants is especially favorable to the spread of transposons. Moreover, because transposon spread is facilitated by zygote formation, the evolutionary origin of sexual conjugation may have been due to selection on transposon-encoded genes. Finally, evidence is also presented that introns could have originated as transposable genetic elements.

A branching-process model for the evolution of transposable elements incorporating selection

We have formulated a very general mathematical model to analyze the evolution of transposable genetic elements in prokaryotic populations. Transposable genetic elements are DNA sequences able to replicate and insert copies of themselves at new locations in the genome. This work characterizes the equilibrium distribution of copy number under the influence of copy number-dependent selection, transposition and deletion. Our principal results concern the equilibrium distribution of copy number in response to various selective regimes. For particular transposition patterns (e.g., unregulated transposition or copy number-dependent transposition), equilibrium distributions are calculated numerically for a variety of specific selection patterns. Selection is quantified through specification of the expected number of offspring for individuals of each type, which is generally a non-increasing function of copy number, in accord with the usual evolutionary speculations.

Gene regulation and DNA C-value paradox: a model based on diffusion of regulatory molecules

The general idea of the model is that regulatory molecules can move stochastically from site to site along DNA and that according to their chromosomal position, genes should have a more or less high probability to be activated (or repressed) during differentiation. In this model the role of non coding DNA is to maintain genes in a relative position that determines what is usually called the "differentiation programme".

Genome evolution in mosquitoes: intraspecific and interspecific variation in repetitive DNA amounts and organization

DNA reassociation kinetics were used to determine the amounts and organization of repetitive and unique DNA in four mosquito species:Anopheles quadrimaculatus(Say),Culex pipiens(L.),Aedes albopictus(Skuse) andAe. triseriatus(Say). Intraspecific variation in repetitive DNA amounts was examined in two geographic strains ofAe. albopictusfom Calcutta, India and the island of Mauritius. Repetitive and unique sequences inAn. quadrimaculatuswere distributed in a pattern of long period interspersion. Repetitive DNA in all other mosquito species exhibited a pattern of short period interspersion. The amounts of fold-back, middle repetitive, and highly repetitive sequences increased with genome size. The amount of foldback DNA increased at a much slower rate than the middle and highly repetitive sequences. Intraspecific variation in genome size inAe. albopictuswas due primarily to the amounts of highly repetitive DNA. S1 nuclease digestion of repetitive DNA in all species revealed a positive correlation between genome size and the proportion of the repetitive DNA consisting of short repeats. The amounts of long and short repeats increased with genome size but short repeats increased at a higher rate. The repetitive DNA of the Mauritius strain contained approximately 15% more short repeats than the Calcutta strain. These findings suggest that genome evolution in mosquitoes has resulted from changes in both the amounts and organization of repetitive elements.

Proteins, exons and molecular evolution

The discovery of the eukaryotic gene structure has prompted research into the potential relationship between protein structure and function and the corresponding exon/intron patterns. The exon shuffling hypothesis put forward by Gilbert and Blake suggests the encodement of structural and functional protein elements by exons which can recombine to create novel proteins. This provides an explanation for the relatively rapid evolution of proteins from a few primordial molecules. As the number of gene and protein structures increases, evidence of exon shuffling is becoming more apparent and examples are presented both from modern multi-domain proteins and ancient proteins. Recent work into the chemical properties and catalytic functions of RNA have led to hypotheses based upon the early existence of RNA. These theories suggest that the split gene structure originated in the primordial soup as a result of random RNA synthesis. Stable regions of RNA, or exons, were utilised as primitive enzymes. In response to selective pressures for information storage, the activity was directly transferred from the RNA enzymes or ribozymes, to proteins. These short polypeptides fused together to create larger proteins with a wide range of functions. Recent research into RNA processing and exon size, discussed in this review, provides a clearer insight into the evolutionary development of the gene and protein structure.

The triosephosphate isomerase gene from maize: introns antedate the plant-animal divergence

We have cloned and characterized a cDNA and genomic DNA for the triosephosphate isomerase expressed in maize roots. The gene is interrupted by eight introns. If we compare this gene with that for the protein in chicken, which has six introns, we see that five of the introns are at identical places, one has shifted by three codons, and two are totally new. This great matching leads us to conclude that the introns were in place before the plant-animal divergence, and that the parental gene had at least eight introns, two of which were lost in the line that leads to animals.

The Croonian Lecture, 1981. Lampbrush chromosomes

Lampbrush chromosomes were first observed nearly 100 years ago, and this lecture attempts a historical survey of what has been learnt from their study, particularly that over the past 30 years. There have been many controversies concerning the structure and functional significance of lampbrush chromosomes, and although their general structural layout has now, after several misconceptions, been firmly established their functional significance remains controversial. Research on lampbrush chromosomes played a significant part in establishing that chromatids in the germ lines of eukaryotic organisms are unineme in regard to DNA, and thereby exposed the C-value paradox. It also helped to establish that a DNA duplex is continuous throughout the length of a chromatid, but that the DNA/histone complex is at intervals reflected back on itself to form lateral loops. This organization, at one time thought to be a special feature of lampbrush chromosomes, now appears to be widespread in chromosomes undergoing compaction. However, despite attempts to determine the sequence organization of those portions of the DNA that are transcribed by lampbrush chromosomes, the function of these transcripts remains an open question, and the C-value paradox is still unresolved.

Nucleotide sequences of highly repeated DNAs; compilation and comments

The nucleotide sequence data from highly repeated DNAs of inverte-brates and mammals are summarized and briefly discussed. Very similar conclusions can be drawn from the two data bases. Sequence complexities can vary from 2 bp to at least 359 bp in invertebrates and from 3 bp to at least 2350 bp in mammals. The larger sequences may or may not exhibit a substructure. Significant sequence variation occurs for any given repeated array within a species, but the sources of this heterogeneity have not been systematically partitioned. The types of alterations in a basic repeating unit can involve base changes as well as deletions or additions which can vary from 1 bp to at least 98 bp in length. These changes indicate that sequenceper seis unlikely to be under significant biological constraints and may sensibly be examined by analogy to Kimura's neutral theory for allelic variation. It is not possible with the present evidence to discriminate between the roles ofneutralandselectivemechanisms in the evolution of highly repeated DNA.

Tandemly repeated arrays are constantly subjected to cycles of amplification and deletion by mechanisms for which the available data stem largely from ribosomal genes. It is a matter of conjecture whether the solutions to the mechanistic puzzles involved in amplification or rapid redeployment of satellite sequences throughout a genome will necessarily give any insight into biological functions.

The lack of significant somatic effects when the satellite DNA content of a genome is significantly perturbed indicates that the hunt for specific functions at thecellularlevel is unlikely to prove profitable.

The presence or in some cases theamountof satellite DNA on a chromosome, however, can have significant effects in the germ line. There the data show that localized condensed chromatin, rich in satellite DNA, can have the effect of rendering adjacent euchromatic regionsrec−, or of altering levels of recombination on different chromosomes. No data stemming from natural populations however are yet available to tell us if these effects are of adaptive or evolutionary significance.