scholarly journals A General Comparison of Relaxed Molecular Clock Models

2007 ◽  
Vol 24 (12) ◽  
pp. 2669-2680 ◽  
Author(s):  
T. Lepage ◽  
D. Bryant ◽  
H. Philippe ◽  
N. Lartillot
Keyword(s):  
Molecular Clock ◽  
Clock Models ◽  
Relaxed Molecular Clock

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 Characterization of four mitochondrial genomes of family Neritidae (Gastropoda: Neritimorpha) and insight into its phylogenetic relationships

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jian-tong Feng ◽  
Li-ping Xia ◽  
Cheng-rui Yan ◽  
Jing Miao ◽  
Ying-ying Ye ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Gene Order ◽  
Phylogenetic Relationships ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Phylogenetic Resolution ◽  
Relaxed Molecular Clock ◽  
Insight Into ◽  
Complete Mitochondrial Genomes

AbstractNeritidae is one of the most diverse families of Neritimorpha and possesses euryhaline properties. Members of this family usually live on tropical and subtropical coasts and are mainly gregarious. The phylogenetic relationships between several subclasses of Gastropoda have been controversial for many years. With an increase in the number of described species of Neritidae, the knowledge of the evolutionary relationships in this family has improved. In the present study, we sequenced four complete mitochondrial genomes from two genera (Clithon and Nerita) and compared them with available complete mitochondrial genomes of Neritidae. Gene order exhibited a highly conserved pattern among three genera in the Neritidae family. Our results improved the phylogenetic resolution within Neritidae, and more comprehensive taxonomic sampling of subclass Neritimorpha was proposed. Furthermore, we reconstructed the divergence among the main lineages of 19 Neritimorpha taxa under an uncorrelated relaxed molecular clock.

scholarly journals Nucleotide substitutions during speciation may explain substitution rate variation

2020 ◽  
Author(s):  
Thijs Janzen ◽  
Folmer Bokma ◽  
Rampal S. Etienne
Keyword(s):  
Molecular Clock ◽  
Molecular Mechanisms ◽  
Phylogenetic Reconstruction ◽  
Mutation Rates ◽  
Rate Variation ◽  
Nucleotide Substitutions ◽  
Strict Molecular Clock ◽  
Substitution Rate Variation ◽  
Relaxed Molecular Clock ◽  
Evolutionary Lineages

ABSTRACTAlthough molecular mechanisms associated with the generation of mutations are highly conserved across taxa, there is widespread variation in mutation rates between evolutionary lineages. When phylogenies are reconstructed based on nucleotide sequences, such variation is typically accounted for by the assumption of a relaxed molecular clock, which, however, is just a statistical distribution of mutation rates without any underlying biological mechanism. Here, we propose that variation in accumulated mutations may be partly explained by an elevated mutation rate during speciation. Using simulations, we show how shifting mutations from branches to speciation events impacts inference of branching times in phylogenetic reconstruction. Furthermore, the resulting nucleotide alignments are better described by a relaxed than by a strict molecular clock. Thus, elevated mutation rates during speciation potentially explain part of the variation in substitution rates that is observed across the tree of life.

scholarly journals An examination of phylogenetic models of substitution rate variation among lineages

2009 ◽  
Vol 5 (3) ◽  
pp. 421-424 ◽  
Author(s):  
Simon Y.W. Ho
Keyword(s):  
Significant Variation ◽  
Divergence Times ◽  
Rate Variation ◽  
Rate Heterogeneity ◽  
Phylogenetic Methods ◽  
Molecular Evolutionary Rates ◽  
Clock Models ◽  
Substitution Rate Variation ◽  
Relaxed Molecular Clock ◽  
Phylogenetic Models

Molecular evolutionary rates can show significant variation among lineages, complicating the task of estimating substitution rates and divergence times using phylogenetic methods. Accordingly, relaxed molecular clock models have been developed to accommodate such rate heterogeneity, but these often make the assumption of rate autocorrelation among lineages. In this paper, I examine the validity of this assumption.

Divergence time estimation in Cichorieae (Asteraceae) using a fossil-calibrated relaxed molecular clock

2012 ◽  
Vol 13 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Karin Tremetsberger ◽  
Birgit Gemeinholzer ◽  
Holger Zetzsche ◽  
Stephen Blackmore ◽  
Norbert Kilian ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Divergence Time ◽  
Time Estimation ◽  
Divergence Time Estimation ◽  
Relaxed Molecular Clock
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