Adaptation has been defined and recognized by two different criteria: historical genesis (fea- tures built by natural selection for their present role) and current utility (features now enhancing fitness no matter how they arose). Biologists have often failed to recognize the potential confusion between these different definitions because we have tended to view natural selection as so dominant among evolutionary mechanisms that historical process and current product become one. Yet if many features of organisms are non-adapted, but available for useful cooptation in descendants, then an important concept has no name in our lexicon (and unnamed ideas generally remain unconsidered): features that now enhance fitness but were not built by natural selection for their current role. We propose that such features be called exaptations and that adaptation be restricted, as Darwin suggested, to features built by selection for their current role. We present several examples of exaptation, indicating where a failure to concep- tualize such an idea limited the range of hypotheses previously available. We explore several consequences of exaptation and propose a terminological solution to the problem of preadaptation.

Exaptation; a missing term in the science of form

It is concluded from a review of the literature that plant cell culture itself generates genetic variability (somaclonal variation). Extensive examples are discussed of such variation in culture subclones and in regenerated plants (somaclones). A number of possible mechanisms for the origin of this phenomenon are considered. It is argued that this variation already is proving to be of significance for plant improvement. In particular the phenomenon may be employed to enhance the exchange required in sexual hybrids for the introgression of desirable alien genes into a crop species. It may also be used to generate variants of a commercial cultivar in high frequency without hybridizing to other genotypes.

Somaclonal variation — a novel source of variability from cell cultures for plant improvement

Simple repetitive DNA sequences are a widespread and abundant feature of genomic DNA. The following several features characterize such sequences: (1) they typically consist of a variety of repeated motifs of 1-10 bases--but may include much larger repeats as well; (2) larger repeat units often include shorter ones within them; (3) long polypyrimidine and poly-CA tracts are often found; and (4) tandem arrangements of closely related motifs are often found. We propose that slipped-strand mispairing events, in concert with unequal crossing-over, can readily account for all of these features. The frequent occurrence of long tandem repeats of particular motifs (polypyrimidine and poly-CA tracts) appears to result from nonrandom patterns of nucleotide substitution. We argue that the intrahelical process of slipped-strand mispairing is much more likely to be the major factor in the initial expansion of short repeated motifs and that, after initial expansion, simple tandem repeats may be predisposed to further expansion by unequal crossing-over or other interhelical events because of their propensity to mispair. Evidence is presented that single-base repeats (the shortest possible motifs) are represented by longer runs in mammalian introns than would be expected on a random basis, supporting the idea that SSM may be a ubiquitous force in the evolution of the eukaryotic genome. Simple repetitive sequences may therefore represent a natural ground state of DNA unselected for coding functions.

Slipped-strand mispairing: a major mechanism for DNA sequence evolution.

Few genetic markers, if any, have found such widespread use as microsatellites, or simple/short tandem repeats. Features such as hypervariability and ubiquitous occurrence explain their usefulness, but these features also pose several questions. For example, why are microsatellites so abundant, why are they so polymorphic and by what mechanism do they mutate? Most importantly, what governs the intricate balance between the frequent genesis and expansion of simple repetitive arrays, and the fact that microsatellite repeats rarely reach appreciable lengths? In other words, how do microsatellites evolve?

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Microsatellites: simple sequences with complex evolution

Cytosine methylation and the ecology of intragenomic parasites

Natural selection operating within genomes will inevitably result in the appearance of DNAs with no phenotypic expression whose only ‘function’ is survival within genomes. Prokaryotic transposable elements and eukaryotic middle-repetitive sequences can be seen as such DNAs, and thus no phenotypic or evolutionary function need be assigned to them.

Selfish genes, the phenotype paradigm and genome evolution.

The genomes of the extremely halophilic bacteria, Halobacterium halobium and Halobacterium volcanii, contain many repeated sequences. These sequences comprise many families, seem to be highly mobile and are arranged in both clustered and dispersed fashions within these genomes. At least some repeated sequences are more strongly conserved between the two species than are unique sequence DNAs.

Unusual physical organization of the Halobacterium genome

Halobacterium halobium is an obligately halophilic archaebacterium1 of interest to molecular biologists for many reasons2–5, one of which is the unexplained high frequency (10−4–10−2 mutants per cell plated) at which it yields readily identifiable and unstable mutants4. We showed previously5 that the genome of H. halobium contains many (>50) families of repeated sequences whose members are dispersed on both chromosome and plasmid. Here we report that most if not all of the members of most of these repeat sequence families effect or are affected by spontaneous genomic rearrangements. Quantitative analyses show that such repeat sequence-associated rearrangements (which may be of several kinds) occur at high frequencies (>4 × 10−3 events per family per cell generation), while unique-sequence DNAs are physically stable. The presence of so many families of elements of such great instability in the halobacterial genome gives it an unusual degree of structural and perhaps functional plasticity.

Carmen Sapienza

Papers

Selfish genes, the phenotype paradigm and genome evolution.

Unusual physical organization of the Halobacterium genome

High-frequency genomic rearrangements involving archaebacterial repeat sequence elements

"Selfish DNA" [Editorial letter]

Repeated Sequences in the Genomes of Halobacteria