scholarly journals Response to Comment on “The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals”

Science ◽  
2013 ◽  
Vol 341 (6146) ◽  
pp. 613.3-613 ◽  
Author(s):  
Maureen A. O’Leary ◽  
Jonathan I. Bloch ◽  
John J. Flynn ◽  
Timothy J. Gaudin ◽  
Andres Giallombardo ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Explanatory Power ◽  
Placental Mammal ◽  
Substitution Rates ◽  
Power Application ◽  
Tree Building ◽  
Diverse Data ◽  
Clock Models

Tree-building with diverse data maximizes explanatory power. Application of molecular clock models to ancient speciation events risks a bias against detection of fast radiations subsequent to the Cretaceous-Paleogene (K-Pg) event. Contrary to Springer et al., post–K-Pg placental diversification does not require “virus-like” substitution rates. Even constraining clade ages to their model, the explosive model best explains placental evolution.

scholarly journals Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations

2015 ◽  
Vol 32 (11) ◽  
pp. 2986-2995 ◽  
Author(s):  
David A. Duchêne ◽  
Sebastian Duchêne ◽  
Edward C. Holmes ◽  
Simon Y.W. Ho
Keyword(s):  
Molecular Clock ◽  
Clock Models ◽  
Predictive Simulations

scholarly journals Time as the ink that music is written with: A review of internal clock models and their explanatory power in audiovisual perception

2020 ◽  
Vol 29 ◽  
Author(s):  
Xinyue Wang ◽  
Clemens Wöllner
Keyword(s):  
Empirical Studies ◽  
Explanatory Power ◽  
Real Life ◽  
Internal Clock ◽  
Auditory Signal ◽  
Subjective Time ◽  
Clock Model ◽  
Audiovisual Perception ◽  
Neuropsychological Evidence ◽  
Clock Models

The current review addresses two internal clock models that have dominated discussions in timing research for the last decades. More specifically, it discusses whether the central or the intrinsic clock model better describes the fluctuations in subjective time. Identifying the timing mechanism is critical to explain and predict timing behaviours in various audiovisual contexts. Music stands out for its prominence in real life scenarios along with its great potential to alter subjective time. An emphasis on how music as a complex dynamic auditory signal affects timing accuracy led us to examine the behavioural and neuropsychological evidence that supports either clock model. In addition to the timing mechanisms, an overview of internal and external variables, such as attention and emotions as well as the classic experimental paradigms is provided, in order to examine how the mechanisms function in response to changes occurring particularly during music experiences. Neither model can explain the effects of music on subjective timing entirely: The intrinsic model applies primarily to subsecond timing, whereas the central model applies to the suprasecond range. In order to explain time experiences in music, one has to consider the target intervals as well as the contextual factors mentioned above. Further research is needed to reconcile the gap between theories, and suggestions for future empirical studies are outlined.

scholarly journals Synonymous Rates at the RpII215 Gene of Drosophila: Variation Among Species and Across the Coding Region

Genetics ◽  
1999 ◽  
Vol 152 (1) ◽  
pp. 269-280 ◽  
Author(s):  
Ana Llopart ◽  
Montserrat Aguadé
Keyword(s):  
Rna Polymerase Ii ◽  
Molecular Clock ◽  
Constitutive Expression ◽  
Synonymous Substitution ◽  
Coding Region ◽  
Substitution Rates ◽  
Synonymous Mutations ◽  
Molecular Clock Hypothesis ◽  
Synonymous Substitution Rates ◽  
Clock Hypothesis

Abstract The region encompassing the RpII215 gene that encodes the largest component of the RNA polymerase II complex (1889 amino acids) has been sequenced in Drosophila subobscura, D. madeirensis, D. guanche, and D. pseudoobscura. Nonsynonymous divergence estimates (Ka) indicate that this gene has a very low rate of amino acid replacements. Given its low Ka and constitutive expression, synonymous substitution rates are, however, unexpectedly high. Sequence comparisons have allowed the molecular clock hypothesis to be tested. D. guanche is an insular species and it is therefore expected to have a reduced effective size relative to D. subobscura. The significantly higher rate of synonymous substitutions detected in the D. guanche lineage could be explained if synonymous mutations behave as nearly neutral. Significant departure from the molecular clock hypothesis for synonymous and nonsynonymous substitutions was detected when comparing the D. subobscura, D. pseudoobscura, and D. melanogaster lineages. Codon bias and synonymous divergence between D. subobscura and D. melanogaster were negatively correlated across the RpII215 coding region, which indicates that selection coefficients for synonymous mutations vary across the gene. The C-terminal domain (CTD) of the RpII215 protein is structurally and functionally differentiated from the rest of the protein. Synonymous substitution rates were significantly different in both regions, which strongly indicates that synonymous mutations in the CTD and in the non-CTD regions are under detectably different selection coefficients.

scholarly journals Biogeographic calibrations for the molecular clock

2015 ◽  
Vol 11 (9) ◽  
pp. 20150194 ◽  
Author(s):  
Simon Y. W. Ho ◽  
K. Jun Tong ◽  
Charles S. P. Foster ◽  
Andrew M. Ritchie ◽  
Nathan Lo ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Temporal Information ◽  
Rate Variation ◽  
Molecular Clocks ◽  
Climatic Data ◽  
Absolute Time ◽  
Biological Studies ◽  
Clock Models

Molecular estimates of evolutionary timescales have an important role in a range of biological studies. Such estimates can be made using methods based on molecular clocks, including models that are able to account for rate variation across lineages. All clock models share a dependence on calibrations, which enable estimates to be given in absolute time units. There are many available methods for incorporating fossil calibrations, but geological and climatic data can also provide useful calibrations for molecular clocks. However, a number of strong assumptions need to be made when using these biogeographic calibrations, leading to wide variation in their reliability and precision. In this review, we describe the nature of biogeographic calibrations and the assumptions that they involve. We present an overview of the different geological and climatic events that can provide informative calibrations, and explain how such temporal information can be incorporated into dating analyses.

scholarly journals Variation in the molecular clock of primates

2016 ◽  
Author(s):  
Priya Moorjani ◽  
Carlos Eduardo G. Amorim ◽  
Peter F. Arndt ◽  
Molly Przeworski
Keyword(s):  
Gene Conversion ◽  
Molecular Clock ◽  
Primate Evolution ◽  
Primate Species ◽  
Recent Common Ancestor ◽  
New World Monkeys ◽  
Substitution Rates ◽  
Cpg Sites ◽  
Most Recent Common Ancestor ◽  
Biased Gene Conversion

Events in primate evolution are often dated by assuming a "molecular clock", i.e., a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from differences in life-history traits, suggesting that it should also be found among primates. Motivated by these considerations, we analyze whole genomes from ten primate species, including Old World Monkeys (OWMs), New World Monkeys (NWMs) and apes, focusing on putatively neutral autosomal sites and controlling for possible effects of biased gene conversion and methylation at CpG sites. We find that substitution rates are ~65% higher in lineages leading from the hominoid-NWM ancestor to NWMs than to apes. Within apes, rates are ~2% higher in chimpanzees and ~7% higher in the gorilla than in humans. Substitution types subject to biased gene conversion show no more variation among species than those not subject to it. Not all mutation types behave similarly, however: in particular, transitions at CpG sites exhibit a more clock-like behavior than do other types, presumably due to their non-replicative origin. Thus, not only the total rate, but also the mutational spectrum varies among primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions. Taking this approach, we estimate that the average time to the most recent common ancestor of human and chimpanzee is 12.1 million years and their split time 7.9 million years.

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