Regulation of physiological functions with approximate daily periodicity, or circadian rhythms, is a characteristic feature of eukaryotes. Until recently, cyanobacteria were the only prokaryotes reported to possess circadian rhythmicity. It is controlled by a cluster of three genes: kaiA, kaiB, and kaiC. Using sequence data of Ϸ70 complete prokaryotic genomes from the various public depositories, we show here that the kai genes and their homologs have quite a different evolutionary history and occur in Archaea and Proteobacteria as well. Among the three genes, kaiC is evolutionarily the oldest, and kaiA is the youngest and likely evolved only in cyanobacteria. Our data suggest that the prokaryotic circadian pacemakers have evolved in parallel with the geological history of the earth, and that natural selection, multiple lateral transfers, and gene duplications and losses have been the major factors shaping their evolution.

Cyanobacteria are the only prokaryotes known thus far possessing regulation of physiological functions with approximate daily periodicity, or circadian rhythms, that are controlled by a cluster of three genes, kaiA, kaiB, and kaiC. Here we demonstrate considerably higher genetic polymorphism and extremely rapid evolution of the kaiABC gene family in a filamentous cyanobacterium, Nostoc linckia, permanently exposed to the acute natural environmental stress in the two microsite evolutionary models known as ''Evolution Canyons,'' I (Mount Carmel) and II (Upper Galilee) in Israel. The family consists of five distinct subfamilies (kaiI-kaiV) comprising at least 20 functional genes and pseudogenes. The obtained data suggest that the duplications of kai genes have adaptive significance, and some of them are evolutionarily quite recent (Ϸ80,000 years ago). The observed patterns of within-and between-subfamily polymorphisms indicate that positive diversifying, balancing, and purifying selections are the principal driving forces of the kai gene family's evolution.T he problem of the relative importance of various driving forces in genome evolution requires a comprehensive critical testable approach. The challenging question is that of how selective or nonselective factors influence the evolution of organisms living under contrasting ecological conditions. Lower Nahal Oren, Mount Carmel, and Lower Nahal Keziv, western Upper Galilee, Israel, known as ''Evolution Canyons'' (ECs) I and II, respectively (1-3), represent microsites with highly contrasting environmental conditions on opposite slopes separated by only 300-400 m at the top and 50-100 m at the bottom. They were eroded in the Plio-Pleistocene period. The ''African'' southfacing slopes (SFSs) receive up to 600% more solar radiation and are warmer, drier, and spatiotemporally more heterogeneous and fluctuating than ''European'' north-facing slopes (NFSs). Such ecological contrasts on a microscale provide an excellent opportunity to test various hypotheses regarding the influence of natural environmental stress on patterns of genome evolution and shaping genetic variability of populations (1), adaptive radiation, and incipient speciation across life (2, 3).Cyanobacteria (blue-green algae, Cyanoprokaryota, Cyanophyta) can occupy various ecotopes and have high ecological adaptability (4) and thus are suitable model organisms for testing various predictions about probable evolutionary forces affecting patterns of genetic polymorphism under contrasting ecological conditions. Thus far, extensive studies have been done to ascertain molecular and genetic mechanisms of cyanobacterial responses to various stresses (see refs. 5-9).However, despite the extensive studies of cyanobacteria, data about the effect of long-time natural environmental stress on the level and patterns of nucleotide polymorphism in these prokaryotes are lacking. Such data can highlight the evolutionary forces contributing to adaptive genetic radiation and speciation. This issue is of particular interest, b...

Species diversity of epilithic cyanobacteria was studied in a 90 m deep prehistoric elWad cave eroded in Cenomanian limestones of Mount Carmel, Israel. The degree of illumination is the most variable index throughout the cave, whereas humidity and temperature vary moderately. In a number of sites inside the cave dripping water occurs due to filtration of rain water. In el-Wad cave 42 species from 20 genera of blue-green algae were found. The share of coccoid forms decreased and filamentous (especially oscillatorial) ones increased from the entrance to the end of the cave. Intensity oflight was the governing factor for distribution of cyanobacteria in el-Wad cave; the availability of dripping affected it to a lesser extent due to the constantly high humidity of the air. Diversity of species composition and taxonomic spectrum of cyanophytes was reduced from the entrance to the end of the cave, covarying positively with darkness stress.