New Evo-SETI Results About Civilizations and Molecular Clock

Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1, acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7–2.4-fold more transmissible, and that previous (non-P.1) infection provides 54–79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

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Clustered Mutations Have No Effect on the Overdispersed Molecular Clock: A Response to Huai and Woodruff

Genetics ◽

10.1093/genetics/149.1.463 ◽

1998 ◽

Vol 149 (1) ◽

pp. 463-464

Author(s):

David J Cutler

Keyword(s):

Molecular Clock

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Natural Zeitgebers Under Temperate Conditions Cannot Compensate for the Loss of a Functional Circadian Clock in Timing of a Vital Behavior in Drosophila

Journal of Biological Rhythms ◽

10.1177/0748730421998112 ◽

2021 ◽

pp. 074873042199811

Author(s):

Franziska Ruf ◽

Oliver Mitesser ◽

Simon Tii Mungwa ◽

Melanie Horn ◽

Dirk Rieger ◽

...

Keyword(s):

Molecular Clock ◽

Time Window ◽

Fruit Fly ◽

Diel Activity ◽

Wild Type ◽

Statistical Measures ◽

Clock Mutant ◽

Full Complement ◽

The Right

The adaptive significance of adjusting behavioral activities to the right time of the day seems obvious. Laboratory studies implicated an important role of circadian clocks in behavioral timing and rhythmicity. Yet, recent studies on clock-mutant animals questioned this importance under more naturalistic settings, as various clock mutants showed nearly normal diel activity rhythms under seminatural zeitgeber conditions. We here report evidence that proper timing of eclosion, a vital behavior of the fruit fly Drosophila melanogaster, requires a functional molecular clock under quasi-natural conditions. In contrast to wild-type flies, period01 mutants with a defective molecular clock showed impaired rhythmicity and gating in a temperate environment even in the presence of a full complement of abiotic zeitgebers. Although period01 mutants still eclosed during a certain time window during the day, this time window was much broader and loosely defined, and rhythmicity was lower or lost as classified by various statistical measures. Moreover, peak eclosion time became more susceptible to variable day-to-day changes of light. In contrast, flies with impaired peptidergic interclock signaling ( Pdf01 and han5304 PDF receptor mutants) eclosed mostly rhythmically with normal gate sizes, similar to wild-type controls. Our results suggest that the presence of natural zeitgebers is not sufficient, and a functional molecular clock is required to induce stable temporal eclosion patterns in flies under temperate conditions with considerable day-to-day variation in light intensity and temperature. Temperate zeitgebers are, however, sufficient to functionally rescue a loss of PDF-mediated clock-internal and -output signaling

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Understanding the Overdispersed Molecular Clock

Genetics ◽

10.1093/genetics/154.3.1403 ◽

2000 ◽

Vol 154 (3) ◽

pp. 1403-1417 ◽

Cited By ~ 1

Author(s):

David J Cutler

Keyword(s):

Molecular Evolution ◽

Molecular Clock ◽

Time Scale ◽

Population Parameter ◽

Deleterious Mutations ◽

Slow Time ◽

Slow Time Scale ◽

Key Population ◽

Protein Encoding ◽

Rates Of Molecular Evolution

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.

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Clusters of Identical New Mutations Can Account for the “Overdispersed” Molecular Clock

Genetics ◽

10.1093/genetics/147.1.339 ◽

1997 ◽

Vol 147 (1) ◽

pp. 339-348 ◽

Cited By ~ 3

Author(s):

Haiying Huai ◽

R C Woodruff

Keyword(s):

Population Dynamics ◽

Cell Differentiation ◽

Germ Cell ◽

Molecular Clock ◽

Germ Cell Differentiation ◽

Multiple Copies ◽

Premeiotic Clusters ◽

T Values ◽

Independent Mutant ◽

New Mutations

Abstract Germ-cell mutations may occur during meiosis, giving rise to independent mutant gametes in a Poisson process, or before meiosis, giving rise to multiple copies of identical mutant gametes at a much higher probability than the Poisson expectation. We report that the occurrence of these early premeiotic clusters of new identical mutant alleles increases the variance-to-mean ratio of mutation rate (R(u) > 1). This leads to an expected variance-to-mean ratio (R(t)) of the molecular clock that is always greater than one and may cover the observed range of R(t) values. Hence, the molecular clock may not be overdispersed based on this new mutational model that includes clusters. To get a better estimation of R(u) and R(t), one needs measurements of the intrageneration variation of reproductive success (Ni/Ne(i)), population dynamics (k‒i), and the proportion of new mutations that occur in clusters (rc), especially those formed before germ-cell differentiation.

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The fossil record of Phasmida (Insecta: Neoptera)

Insect Systematics & Evolution ◽

10.1163/187631200x00507 ◽

2000 ◽

Vol 31 (4) ◽

pp. 473-480 ◽

Cited By ~ 21

Author(s):

Erich Tilgner

Keyword(s):

Dominican Republic ◽

Molecular Clock ◽

Fossil Record ◽

Sister Group ◽

Baltic Amber ◽

Molecular Clock Dating

AbstractA review of the Phasmida fossil record is provided. No fossils of Timema Scudder are known. Euphasmida fossils include: Agathemera reclusa Scudder, Electrobaculum gracilis Sharov, Eophasma oregonense Sellick, Eophasma minor Sellick, Eophasmina manchesteri Sellick, Pseudoperla gracilipes Pictet, Pseudoperla lineata Pictet and various unclassified species from Grube Messel, Baltic amber, and Dominican Republic amber. The oldest documented Euphasmida fossils are 44-49 million years old; molecular clock dating underestimates the origin of the sister group Timema by at least 24 million years.

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