Including secondary structure, fossils and molecular dating in the centipede tree of life [X1437] (matrix)

10.7934/x1437 ◽  
2014 ◽  
Author(s):  
M Murienne ◽  
D Edgecombe ◽  
G Giribet
Keyword(s):  
Secondary Structure ◽  
Tree Of Life ◽  
Molecular Dating

Including secondary structure, fossils and molecular dating in the centipede tree of life

2010 ◽  
Vol 57 (1) ◽  
pp. 301-313 ◽  
Author(s):  
Jerome Murienne ◽  
Gregory D. Edgecombe ◽  
Gonzalo Giribet
Keyword(s):  
Secondary Structure ◽  
Tree Of Life ◽  
Molecular Dating

scholarly journals Flying rocks and flying clocks: disparity in fossil and molecular dates for birds

2014 ◽  
Vol 281 (1788) ◽  
pp. 20140677 ◽  
Author(s):  
Daniel T. Ksepka ◽  
Jessica L. Ware ◽  
Kristin S. Lamm
Keyword(s):  
Analytical Methods ◽  
Fossil Record ◽  
Tree Of Life ◽  
Temporal Information ◽  
Molecular Dating ◽  
Critical Nodes ◽  
Molecular Divergence ◽  
Divergence Dates ◽  
Divergence Estimates ◽  
Age Estimates

Major disparities are recognized between molecular divergence dates and fossil ages for critical nodes in the Tree of Life, but broad patterns and underlying drivers remain elusive. We harvested 458 molecular age estimates for the stem and crown divergences of 67 avian clades to explore empirical patterns between these alternate sources of temporal information. These divergence estimates were, on average, over twice the age of the oldest fossil in these clades. Mitochondrial studies yielded older ages than nuclear studies for the vast majority of clades. Unexpectedly, disparity between molecular estimates and the fossil record was higher for divergences within major clades (crown divergences) than divergences between major clades (stem divergences). Comparisons of dates from studies classed by analytical methods revealed few significant differences. Because true divergence ages can never be known with certainty, our study does not answer the question of whether fossil gaps or molecular dating error account for a greater proportion of observed disparity. However, empirical patterns observed here suggest systemic overestimates for shallow nodes in existing molecular divergence dates for birds. We discuss underlying biases that may drive these patterns.

scholarly journals Relative time constraints improve molecular dating

2020 ◽  
Author(s):  
Gergely J. Szöllősi ◽  
Sebastian Höhna ◽  
Tom A. Williams ◽  
Dominik Schrempf ◽  
Vincent Daubin ◽  
...  
Keyword(s):  
Tree Of Life ◽  
Molecular Dating ◽  
Molecular Clocks ◽  
Data Sets ◽  
Relative Age ◽  
Temporal Relationships ◽  
Wide Range ◽  
Other Information ◽  
Life On Earth ◽  
Age Constraints

AbstractDating the tree of life is central to understanding the evolution of life on Earth. Molecular clocks calibrated with fossils represent the state of the art for inferring the ages of major groups. Yet, other information on the timing of species diversification can be used to date the tree of life. This is the case for instance for horizontal gene transfer events and ancient coevolutionary relationships such as (endo)symbioses, which can imply temporal relationships between two nodes in a phylogeny (Davín et al. 2018). This can be particularly helpful when the geological record is sparse, e.g. for microorganisms, which represent the vast majority of extant and extinct biodiversity.Here, we demonstrate that relative age constraints, when combined with fossil calibrations, can significantly improve both the accuracy and resolution of molecular clock estimates. We provide an implementation of relative age constraints in RevBayes (Höhna et al. 2016) that can be combined in a modular manner with the wide range of molecular dating methods available in the software.To validate our method in a realistic data setting we apply it to two data sets of 40 Cyanobacteria and 62 Archaea respectively, and provide cross-validations of fossil calibrations and relative age constraints.

Characterization of Tamm-Horsfall Urinary Glycoprotein

1973 ◽  
Vol 31 ◽  
pp. 420-421
Author(s):  
John P. Robinson ◽  
J. David Puett
Keyword(s):  
Electron Microscopy ◽  
Circular Dichroism ◽  
Secondary Structure ◽  
Quaternary Structure ◽  
Normal Adult ◽  
Morphological Properties ◽  
Adult Males ◽  
Circular Dichroïsm ◽  
Urinary Glycoprotein

Much work has been reported on the chemical, physical and morphological properties of urinary Tamm-Horsfall glycoprotein (THG). Although it was once reported that cystic fibrotic (CF) individuals had a defective THG, more recent data indicate that THG and CF-THG are similar if not identical.No studies on the conformational aspects have been reported on this glycoprotein using circular dichroism (CD). We examined the secondary structure of THG and derivatives under various conditions and have correlated these results with quaternary structure using electron microscopy.THG was prepared from normal adult males and CF-THG from a 16-year old CF female by the method of Tamm and Horsfall. CF female by the method of Tamm and Horsfall.

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