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Codon equilibrium II: Its use in estimating silent-substitution rates.

We study the equilibrium in the use of synonymous codons by eukaryotic organisms and find five equations involving substitution rates that we believe embody the important implications of equilibrium for the process of silent substitution. We then combine these five equations with additional criteria to determine sets of substitution rates applicable to eukaryotic organisms. One method employs the equilibrium equations and a principle of maximum entropy to find the most uniform set of rates consistent with equilibrium. In a second method we combine the equilibrium equations with data on the man-mouse divergence to determine that set of rates that is most neutral yet consistent with both types of data (i.e., equilibrium and divergence data). Simulations show this second method to be quite reliable in spite of significant saturation in the substitution process. We find that when divergence data are included in the calculation of rates, even though these rates are chosen to be as neutral as possible, the strength of selection inferred from the nonuniformity of the rates is approximately doubled. Both sets of rates are applied to estimate the human-mouse divergence time based on several independent subsets of the divergence data consisting of the quartet, C- or T-ending duet, and A- or G-ending duet codon sets. Both rate sets produce patterns of divergence times that are shortest for the quartet data, intermediate for the CT-ending duets, and longest for the AG-ending duets. This indicates that rates of transitions in the duet-codon sets are significantly higher than those in the quartet-codon sets; this effect is especially marked for A----G, the rate of which in duets must be about double that in quartets.

Animals↗
PubMed1987

On the molecular evolutionary clock.

The conceptual framework surrounding the origin of the molecular evolutionary clock and circumstances of this origin are described. In regard to the quest for the best available molecular clocks, a return to protein clocks is conditionally recommended. On the basis of recent data and certain considerations, it is pointed out that the realm of neutrality in evolution is probably less extensive than is now commonly thought, in the three distinct senses of the term neutrality--neutrality as nonfunctionality of mutations, neutrality as equifunctionality of mutations, and neutrality as a mode of fixation of mutations. The possibility is raised that complex sets of interacting components forming a system that is bounded with respect to its environment may quite generally display an intrinsic trend to a quasi-clockwise evolutionary behavior.

Biological Evolution↗
PubMed2006

The question of questions: what is a gene? Comments on Rolston and Griffiths & Stotz.

If the question "What is a gene?'' proves to be worth asking it must be able to elicit an answer which both recognizes and address the reasons why the concept of the gene ever seemed to be something worth getting excited about in the first place as well analyzing and evaluating the latest develops in the molecular biology of DNA. Each of the preceding papers fails to do one of these and suffers the consequences. Where Rolston responds to the apparent failure of molecular biology to make good on the desideratum of the classical gene by veering off into fanciful talk about "cybernetic genes,'' Griffiths and Stotz lose themselves in the molecular fine print and forget to ask themselves why "genes'' should be of any special interest anyway.

Animals↗
PubMed1994

DNA sequences encoding enolase are remarkably conserved from yeast to mammals.

Enolase (2-phospho-D-glycerate hydrolase, EC 4.2.1.11), particularly isoform neuron-specific enolase (NSE), is primarily localized in neurons and neuroendocrine cells and is a cancer diagnostic marker for brain tumors. Homology of enolase-coding DNA sequences from human, dog, cow, rat, mouse, rabbit, chicken, and yeast cells was investigated using hybridization techniques, percent sequence divergence, and amino acid analysis. Because enolase is a significant enzyme of the glycolytic pathway, enolase-coding DNA sequences have been found in all organisms tested so far. The human enzyme was found to be more like those of monkey and dog in structure than to those of chicken and yeast. The implications of the existence of the genetic conservation of enolase-coding DNA sequences in understanding concerted evolution as well as post-transcriptional regulation during differentiation are discussed. This is the first report is which sequence divergence in the coding region for enolase has been determined in a variety of organisms.

Amino Acid Sequence↗
PubMed1983

Evidence that natural selection acts on silent mutation.

Analysis of nucleic acid sequence data of mammalian hemoglobin, yeast cytochrome c, and human interferon reveals strong biases in favor of specific codons. These biases do not appear to dissipate over time, suggesting that an indirect form of selection acts on silent mutations. The data are compatible with the "bootstrapping" hypothesis that silent mutations which alter the rate of evolution can hitchhike with traits whose appearance they facilitate. Selection involving modulating effects of codon usage on gene expression may also be involved, but the data appear to exclude simple maximization of gene expression.

Animals↗