Phylogeny is the origin and evolution of a set of organisms, usually a set of species and is used to determine the ancestral relationships among known species (both living and extinct). In this page, we explore the phylogenetic history of circadian rhythms across phylogenetic history.
    Many species living in an environment fluctuating with a strong daily rhythm have evolved an internal clock. According to molecular biological studies of circadian clock, many genes and proteins are involved in the biochemical dynamics generating their stable rhythm. Although the identity of genes and proteins may differ between species, the basic mechanism is the same -- there is one or more genes whose products may enter to the nucleus and then suppress the transcription of their own gene(s). This negative feedback with a long time delay can generate the circadian rhythm.

    Circadian rhythms are believed to have originated in the earliest cells to provide protection for replicating DNA, from high ultraviolet radiation during day-time. As a result, replication was relegated to the dark. The fungus Neurospora, which exists today, retains this clock-regulated mechanism.
    The simplest known circadian clock is that of the prokaryotic cyanobacteria. Recent research has demonstrated that the circadian clock of Synechococcus elongatus can be reconstituted in vitro with just the three proteins of their central oscillator. This clock has been shown to sustain a 22 hour rhythm over several days upon the addition of ATP. Previous explanations of the prokaryotic circadian timekeeper were dependent upon a DNA transcription / translation feedback mechanism, and although this has not been shown to be the case, it is still believed to hold true for eukaryotic organisms. Indeed, although the circadian systems of eukaryotes and prokaryotes have the same basic architecture: input - central oscillator - output, they do not share any homology. This implies probable independent origins.
    Even when kept in a dark box, most eukaryotes [and some prokaryotes] still organize their behavior and physiology around a  24-hour day. These endogenous circadian rhythms share a number of remarkable properties across phyla, including high precision(to within minutes per day!), synchronization by light-dark cycles, and temperature compensation (so the period of the rhythm is relatively stable across ambient temperatures). Isolated cells of many organisms are competent circadian oscillators; the essential rhythm-generating mechanism is therefore cell-autonomous and not an emergent property of cellular interactions.
    The phylogenetic conservation of the basic circadian mechanism allows for rapid translation of observations in one species to hypotheses in another, whereas the phylogenetic differences in circadian regulation remind us that chronobiology is still a young field, one that retains great appeal because of all that we don’t know.

Figure 1. Circadian Systems in the Universal Tree of Life shown is an unrooted universal phylogenetic framework reflecting a maximum-likelihood analysis for the relationships among living things. Line segment lengths correspond to evolutionary distance as measured by rates of change in small subunit rRNA (ribosomal RNA) genes. The three major assemblages of organisms, Archaebacteria, Eubacteria, and Eukaryota, diverge from a single ancestor. The portion of the tree representing the “Crown Eukaryotes” that emerged (relatively) rapidly about half a billion years ago is reproduced in greater detail in the upper left. Shown in blue are phylogenetic groups where circadian rhythms have been described and/or that correspond to the well-studied experimental circadian systems, and in red are given the names and placements of those systems where the genetic and molecular analysis of clock mechanism has progressed significantly.
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