scholarly journals Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates

2018 ◽  
Vol 35 (7) ◽  
pp. 1770-1782 ◽  
Author(s):  
Koichiro Tamura ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Theoretical Foundation ◽  
Evolutionary Rates ◽  
Divergence Times ◽  
Variable Evolutionary Rates

scholarly journals Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates

2017 ◽  
Author(s):  
Koichiro Tamura ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Relative Rate ◽  
Molecular Data ◽  
Evolutionary Rates ◽  
Divergence Times ◽  
Computationally Efficient ◽  
Molecular Sequence ◽  
Branch Lengths ◽  
Variable Evolutionary Rates ◽  
Relationship Of ◽  
The Relationship

AbstractRelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It showed excellent performance in estimating divergence times for both simulated and empirical molecular sequence datasets in which evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of datasets. Until now, however, RelTime has not had a formal mathematical foundation. Here, we show that the basis of the RelTime approach is a relative rate framework (RRF) that combines comparisons of evolutionary rates in sister lineages with the principle of minimum rate change between an evolutionary lineage and its descendants. We present analytical solutions for estimating relative lineage rates and divergence times under RRF. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. We conclude that RelTime will be also useful for phylogenies with branch lengths derived not only from molecular data, but also morphological and biochemical traits.

scholarly journals RelTime relaxes the strict molecular clock throughout the phylogeny

2017 ◽  
Author(s):  
Fabia U. Battistuzzi ◽  
Qiqing Tao ◽  
Lance Jones ◽  
Koichiro Tamura ◽  
Sudhir Kumar
Keyword(s):  
Molecular Phylogeny ◽  
Molecular Clock ◽  
Evolutionary Rates ◽  
Molecular Dating ◽  
Divergence Times ◽  
Similar Time ◽  
Time Estimates ◽  
Theoretical Analyses ◽  
Strict Molecular Clock ◽  
Median Rate

AbstractThe RelTime method estimates divergence times when evolutionary rates vary among lineages. Theoretical analyses show that RelTime relaxes the strict molecular clock throughout a molecular phylogeny, and it performs well in the analysis of empirical and computer simulated datasets in which evolutionary rates are variable. Lozano-Fernandez et al. (2017) found that the application of RelTime to one metazoan dataset (Erwin et al. 2011) produced equal rates for several ancient lineages, which led them to speculate that RelTime imposes a strict molecular clock for deep animal divergences. RelTime does not impose a strict molecular clock. The pattern observed by Lozano-Fernandez et al. (2017) was a result of the use of an option to assign the same rate to lineages in RelTime when the rates are not statistically significantly different. The median rate difference was 5% for many deep metazoan lineages for Erwin et al. (2011) dataset, so the rate equality was not rejected. In fact, RelTime analysis with and without the option to test rate differences produced very similar time estimates. We found that the Bayesian time estimates vary widely depending on the root priors assigned, and that the use of less restrictive priors produce Bayesian divergence times that are concordant with those from RelTime for Erwin et al. (2011) dataset. Therefore, it is prudent to discuss Bayesian estimates obtained under a range of priors in any discourse about molecular dating, including method comparisons.

Testing relative evolutionary rates and estimating divergence times among six genera of Rhizophoraceae using cpDNA and nrDNA sequences

2000 ◽  
Vol 45 (11) ◽  
pp. 1011-1015 ◽  
Author(s):  
Yang Zhong ◽  
Suhua Shi ◽  
Xianhua Tang ◽  
Yelin Huang ◽  
Fengxiao Tan ◽  
...  
Keyword(s):  
Evolutionary Rates ◽  
Divergence Times

scholarly journals Evolution of the locomotor skeleton in Anolis lizards reflects the interplay between ecological opportunity and phylogenetic inertia

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nathalie Feiner ◽  
Illiam S. C. Jackson ◽  
Edward L. Stanley ◽  
Tobias Uller
Keyword(s):  
Adaptive Radiation ◽  
Morphological Diversity ◽  
Evolutionary Rates ◽  
Greater Antilles ◽  
Ecological Opportunity ◽  
Morphological Diversification ◽  
Phylogenetic Inertia ◽  
Evolutionary Trajectories ◽  
Repeated Evolution ◽  
Variable Evolutionary Rates

AbstractAnolis lizards originated in continental America but have colonized the Greater Antillean islands and recolonized the mainland, resulting in three major groups (Primary and Secondary Mainland and Greater Antillean). The adaptive radiation in the Greater Antilles has famously resulted in the repeated evolution of ecomorphs. Yet, it remains poorly understood to what extent this island radiation differs from diversification on the mainland. Here, we demonstrate that the evolutionary modularity between girdles and limbs is fundamentally different in the Greater Antillean and Primary Mainland Anolis. This is consistent with ecological opportunities on islands driving the adaptive radiation along distinct evolutionary trajectories. However, Greater Antillean Anolis share evolutionary modularity with the group that recolonized the mainland, demonstrating a persistent phylogenetic inertia. A comparison of these two groups support an increased morphological diversity and faster and more variable evolutionary rates on islands. These macroevolutionary trends of the locomotor skeleton in Anolis illustrate that ecological opportunities on islands can have lasting effects on morphological diversification.

Analysis of nematode-endosymbiont coevolution in the Xiphinema americanum species complex using molecular markers of variable evolutionary rates

Nematology ◽  
2019 ◽  
Vol 21 (5) ◽  
pp. 533-546 ◽  
Author(s):  
Dana K. Howe ◽  
McKinley Smith ◽  
Danielle M. Tom ◽  
Amanda M.V. Brown ◽  
Amy B. Peetz ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Markers ◽  
Species Complex ◽  
Evolutionary Rates ◽  
Biological Processes ◽  
Bacterial Symbionts ◽  
Protein Coding ◽  
Phylogenetic Studies ◽  
Phylogenetic Resolution ◽  
Variable Evolutionary Rates

Summary Bacterial symbioses play important roles in shaping diverse biological processes in nematodes, and serve as targets in nematode biocontrol strategies. Focusing on the Xiphinema americanum species complex, we expanded upon recent research investigating patterns of coevolution between Xiphinema spp. and Xiphinematobacter spp., utilising two symbiont genetic markers of varying evolutionary rates. Phylogenetic analysis of nematode mitochondrial DNA (mtDNA) revealed five strongly supported major clades. Analysis of slow-evolving 16S rDNA in bacterial symbionts resulted in a phylogenetic topology composed of four major clades that grouped taxa highly congruent with the nematode mtDNA topology. A faster evolving protein-coding symbiont gene (nad) provided more phylogenetic resolution with seven well-supported clades, also congruent with the nematode mtDNA tree topology. Our results reinforce recent studies suggesting extensive coevolution between Xiphinema spp. and their vertically transmitted endosymbionts Xiphinematobacter spp. and illustrate the advantages of including genetic markers of varying evolutionary rates in coevolutionary and phylogenetic studies.

The range of sampling times affects Zika virus evolutionary rates and divergence times

2019 ◽  
Vol 164 (12) ◽  
pp. 3027-3034
Author(s):  
Lucia P. Barzilai ◽  
Carlos G. Schrago
Keyword(s):  
Zika Virus ◽  
Evolutionary Rates ◽  
Divergence Times ◽  
Sampling Times

scholarly journals 5S RNA sequence from thePhilosamia silkworm: evidence for variable evolutionary rates in insect 5S RNA

1982 ◽  
Vol 10 (18) ◽  
pp. 5711-5716 ◽  
Author(s):  
Gu Xian-Rong ◽  
Krikor Nicoghosian ◽  
R.J. Cedergren
Keyword(s):  
Evolutionary Rates ◽  
5S Rna ◽  
Rna Sequence ◽  
Variable Evolutionary Rates
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