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

Methanogens: reevaluation of a unique biological group.

Ribosomal DNA (rDNA) sequences have been aligned and compared in a number of living organisms, and this approach has provided a wealth of information about phylogenetic relationships. Studies of rDNA sequences have been used to infer phylogenetic history across a very broad spectrum, from studies among the basal lineages of life to relationships among closely related species and populations. The reasons for the systematic versatility of rDNA include the numerous rates of evolution among different regions of rDNA (both among and within genes), the presence of many copies of most rDNA sequences per genome, and the pattern of concerted evolution that occurs among repeated copies. These features facilitate the analysis of rDNA by direct RNA sequencing, DNA sequencing (either by cloning or amplification), and restriction enzyme methodologies. Constraints imposed by secondary structure of rRNA and concerted evolution need to be considered in phylogenetic analyses, but these constraints do not appear to impede seriously the usefulness of rDNA. An analysis of aligned sequences of the four nuclear and two mitochondrial rRNA genes identified regions of these genes that are likely to be useful to address phylogenetic problems over a wide range of levels of divergence. In general, the small subunit nuclear sequences appear to be best for elucidating Precambrian divergences, the large subunit nuclear sequences for Paleozoic and Mesozoic divergences, and the organellar sequences of both subunits for Cenozoic divergences. Primer sequences were designed for use in amplifying the entire nuclear rDNA array in 15 sections by use of the polymerase chain reaction; these "universal" primers complement previously described primers for the mitochondrial rRNA genes. Pairs of primers can be selected in conjunction with the analysis of divergence of the rRNA genes to address systematic problems throughout the hierarchy of life.

Ribosomal DNA: molecular evolution and phylogenetic inference.

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.

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.

Partial sequence analyses of 16S ribosomal RNAs of blue-green algae and chloroplasts reveal that blue-green algae are typically prokaryotic and related to the bacilli, that red algal chloroplasts are probably of blue-green algal origin, and that euglenoid and red algal chloroplasts may have arisen independently.

Partial sequences of 16S rRNA and the phylogeny of blue-green algae and chloroplasts

Selfish DNAs with self-restraint

THE blue-green algae are a major group of prokaryotes in many ways resembling, and perhaps phylogenetically related to, the chloroplasts of photosynthetic eukaryotes. Metabolic control mechanisms in this group are of interest because of its unique evolutionary position and because many of its members are obligate photoautotrophs and as such may show patterns of control different from those known in heterotrophic bacteria. Indeed, Carr and his collaborators1–3 have proposed that blue-greens do not in general regulate metabolism at the level of gene expression, as heterotrophs commonly do. An exogenous metabolite may be assimilated, but its presence in the cell does not induce (or repress) the synthesis of enzymes responsible for its own catabolism (or biosynthesis). Thus, these workers argue, exogenous substrates do not usually support significant dark growth, or even stimulate growth in the light, because blue-greens simply cannot adjust the levels of the enzymes of intermediary metabolism to accommodate any source of carbon other than CO2 or any source of energy other than light1.

W. F. Doolittle

Papers

Selfish genes, the phenotype paradigm and genome evolution.

Partial sequences of 16S rRNA and the phylogeny of blue-green algae and chloroplasts

Selfish DNAs with self-restraint

Control of gene expression in blue-green algae.