Molecular phylogeny and divergence times of the genus Hedysarum (Fabaceae) with special reference to section Multicaulia in Southwest Asia

2019 ◽  
Vol 305 (10) ◽  
pp. 1001-1017 ◽  
Author(s):  
Haniyeh Nafisi ◽  
Shahrokh Kazempour-Osaloo ◽  
Valiollah Mozaffarian ◽  
Gerald M. Schneeweiss
Keyword(s):  
Molecular Phylogeny ◽  
Special Reference ◽  
Divergence Times ◽  
Southwest Asia

Phylogenetics and divergence times of Papilioninae (Lepidoptera) with special reference to the enigmatic genera Teinopalpus and Meandrusa

Cladistics ◽  
2011 ◽  
Vol 27 (2) ◽  
pp. 113-137 ◽  
Author(s):  
Thomas J. Simonsen ◽  
Evgeny V. Zakharov ◽  
Marie Djernaes ◽  
Adam M. Cotton ◽  
R.I. Vane-Wright ◽  
...  
Keyword(s):  
Special Reference ◽  
Divergence Times

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.

scholarly journals Transcriptome phylogenies support ancient evolutionary transitions in bioluminescence traits of cypridinid ostracods

2021 ◽  
Author(s):  
Emily A. Ellis ◽  
Jessica A. Goodheart ◽  
Nicholai M. Hensley ◽  
Vanessa L. González ◽  
Nicholas J. Reda ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Molecular Phylogeny ◽  
Divergence Times ◽  
Evolutionary Transitions ◽  
Single Origin ◽  
Molecular Phylogenetic ◽  
The Caribbean ◽  
Character Mapping ◽  
Molecular Phylogenetic Data ◽  
Relaxed Clock

AbstractBioluminescence evolved many times independently, leading to dramatic effects on ecosystems by influencing communication both within and between species. One origin of bioluminescence is within cypridinid ostracods. Bioluminescent cypridinids probably all use light as an anti-predator display, while a subset that diversified in the Caribbean also use light for courtship signaling. Despite their importance for understanding the evolution of bioluminescence, very little molecular phylogenetic data are available for cypridinids and the timing of evolutionary transitions of luminous traits is poorly understood. Here, we estimate the first transcriptome-based molecular phylogeny and divergence times of Cypridinidae. Our results strongly support previous hypotheses of a single origin of bioluminescent courtship signaling, nested within a single origin of bioluminescence, and the secondary loss of courtship signaling in Vargula tsujii. We propose the name Luminini for the Tribe of bioluminescent cypridinids and Luxorina for the Sub-tribe of cypridinids with courtship signaling. Our relaxed-clock estimates of divergence times coupled with stochastic character mapping show luminous courtship evolved at least 151 Million Years Ago (MYA) and cypridinid bioluminescence originated at least 197 MYA, making it one of the oldest documented origins of bioluminescence. The molecular phylogeny of cypridinids will serve as a foundation for integrative and comparative studies on the biochemistry, molecular evolution, courtship, diversification, and ecology of cypridinid bioluminescence.

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