Slow Time: The Suspension of a Tension

2021 ◽  
pp. 66-93
Keyword(s):  
Genetics ◽  
2000 ◽  
Vol 154 (3) ◽  
pp. 1403-1417 ◽  
Author(s):  
David J Cutler

Abstract Rates of molecular evolution at some protein-encoding loci are more irregular than expected under a simple neutral model of molecular evolution. This pattern of excessive irregularity in protein substitutions is often called the “overdispersed molecular clock” and is characterized by an index of dispersion, R(T) > 1. Assuming infinite sites, no recombination model of the gene R(T) is given for a general stationary model of molecular evolution. R(T) is shown to be affected by only three things: fluctuations that occur on a very slow time scale, advantageous or deleterious mutations, and interactions between mutations. In the absence of interactions, advantageous mutations are shown to lower R(T); deleterious mutations are shown to raise it. Previously described models for the overdispersed molecular clock are analyzed in terms of this work as are a few very simple new models. A model of deleterious mutations is shown to be sufficient to explain the observed values of R(T). Our current best estimates of R(T) suggest that either most mutations are deleterious or some key population parameter changes on a very slow time scale. No other interpretations seem plausible. Finally, a comment is made on how R(T) might be used to distinguish selective sweeps from background selection.


1985 ◽  
Vol 84 (3) ◽  
pp. 663-673 ◽  
Author(s):  
Hiroyuki Akagi ◽  
Shiro Konishi ◽  
Masanori Otsuka ◽  
Mitsuhiko Yanagisawa

2016 ◽  
Vol 9 (6) ◽  
pp. 2689-2707 ◽  
Author(s):  
Alan D. Griffiths ◽  
Scott D. Chambers ◽  
Alastair G. Williams ◽  
Sylvester Werczynski

Abstract. Dual-flow-loop two-filter radon detectors have a slow time response, which can affect the interpretation of their output when making continuous observations of near-surface atmospheric radon concentrations. While concentrations are routinely reported hourly, a calibrated model of detector performance shows that ∼ 40 % of the signal arrives more than an hour after a radon pulse is delivered. After investigating several possible ways to correct for the detector's slow time response, we show that a Bayesian approach using a Markov chain Monte Carlo sampler is an effective method. After deconvolution, the detector's output is redistributed into the appropriate counting interval and a 10 min temporal resolution can be achieved under test conditions when the radon concentration is controlled. In the case of existing archived observations, collected under less ideal conditions, the data can be retrospectively reprocessed at 30 min resolution. In one case study, we demonstrate that a deconvolved radon time series was consistent with the following: measurements from a fast-response carbon dioxide monitor; grab samples from an aircraft; and a simple mixing height model. In another case study, during a period of stable nights and days with well-developed convective boundary layers, a bias of 18 % in the mean daily minimum radon concentration was eliminated by correcting for the instrument response.


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