Evolution molecular clocks

Douzery, E.J.P., Snell, E.A., Bapteste, E., Delsuc, F. and Philippe, H. (2004) The timing of eukaryotic evolution does a relaxed molecular clock reconcile proteins and fossils Proceedings of the National Academy of Sciences USA 1 01, 1 5386-1 5391. 

There are also strong hints that protein structures fulfil relations very similar to those reported for the RNA structures. In a recent paper [25] it was shown that the first regularity, the existence of a few common and many rare structures, is indeed observed with lattice protein models as well. Extensive neutrality seems to be present with proteins, as the data on the molecular clock of evolution derived lfom sequence comparisons show [1]. 

Fig. 4 Calculation of a molecular clock, (a) The ml tree shown in Edvardsen et al. (2000) has been linearized (Kooistra and Medlin 1996) so that all rates of evolution are the same. Fossil dates from coccolithophore taxa are placed on nodes where these taxa have their first appearance in the fossil record (open circles on tree), (b) A regression of branch lengths against fossil dates has been performed...

Even 30 years ago paleontology was virtually the only source of information about the periods when common ancestors lived. Indeed, the mammalian fossil record was not particularly good. Early writers on comparative biochemistry, such as Baldwin and Florkin, were limited in their sources. Perhaps the first person to perceive the unique value of the molecular evolution of proteins and nucleic acids was Anfinsen (1959), who wrote of this subject in his important book. However, it appears to have been Zuckerkandl and Pauling who, in 1960—1965, introduced the concept of the molecular clock (for a historical review which is part of a group of important critical papers in an issue of the Journal of Molecular Evolution, see Zuckerkandl, 1987). 

In addition to comparison of amino acid and nucleotide sequences of a-lactalbumin, and their rates of change as molecular clocks, a considerable amount of comparative information has accumulated on the three-dimensional structure of these proteins their physical properties in soludon effects of amino acid subsdtudons, in both genetic and cloned variants and their funcdons and immunological properties. In assessing this informadon it is important not to lose sight of the known paleontological informadon on the origin and evolution of mammals. 

Pesole, G., Bozzetti, M. P., Lanave, C., Preparata, G., and Saccone, C. (1991). Glutamine synthetase gene evolution—A good molecular clock. Proc. Natnl. Acad. Sci. USA. 88, 522—526. 

Molecular clocks make use of the genetic differences between present-day species to predict the time since their divergence from a common ancestor. When an ancestral species splits off new species, these new species and their descendants all gradually accumulate different genetic changes — mutations in the DNA — over time, that eventually make them very different from each other. As different, for example, as humans are now from fruit flies. The basic assumption is that species drift away from one other, in terms of their shared genetic inheritance, at a steady rate. At face value, this assumption is of course nonsense — we have crossed a lot more evolutionary space over the last 600 million years than have worms, for example. The difficulty is to specify a distance across evolutionary space on the basis of averaging the rate of evolution in dif-... 

Pawlowski, J., Berney, C. (2003). Episodic evolution of nuclear small subunit ribosomal RNA gene in the stem-lineage of Foraminlfera. In Donoghue, P.C.J., Smith, M.P. (eds.), Telling the Evolutionary Time Molecular Clocks and The Fossil Record, pp. 107-118. Systematics Association special volume 66. London Taylor and Francis. 

Taylor CE, Powell JR (1978) Habitat choice in natural populations of Drosophila, Oecologia 37 69-75 Thorpe JP ( 1982) The molecular clock hypothesis biochemical evolution, genetic differentiation and systematics..Ann Rev Ecol Syst 13 139-168... 

Sanderson, M. J. (2003) r8s Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics, 19 301-302. 

Takezaki, N., Rzhetsky, A. and Nei, M. (1995) Phylogenetic test of the molecular clock and linearized tree . Molecular Biology and Evolution, 12, 823-33. 

Hasegawa, M., Kishino, H. and Yano, T. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA , Journal of Molecular Evolution, ll, 160-74. 

Rosbash You could back off the specifics of PAS domains in BMAL and White Collar. The more general question is whether we are in a position to say with confidence that these things did evolve multiple times, or are there very strong molecular connectors between systems Ravi Allada and I have recently published a paper on CK2, a kinase and a new clock mutant (Lin et al 2002). CK2 is implicated in plant clocks, Neurosopora clocks and now in animal clocks. My feeling is that the jury is still out as to whether we have hit on the key common proteins or whether it is independent evolution. 

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