On the shoulder of giants: Mitogenome recovery from non‐targeted genome projects for phylogenetic inference and molecular evolution studies

2020 ◽  
Vol 59 (1) ◽  
pp. 5-30
Author(s):  
Silvia Adrián‐Serrano ◽  
Jesus Lozano‐Fernandez ◽  
Joan Pons ◽  
Julio Rozas ◽  
Miquel A. Arnedo
Keyword(s):  
Molecular Evolution ◽  
Phylogenetic Inference ◽  
Genome Projects

Ribosomal DNA: Molecular Evolution and Phylogenetic Inference

1991 ◽  
Vol 66 (4) ◽  
pp. 411-453 ◽  
Author(s):  
David M. Hillis ◽  
Michael T. Dixon
Keyword(s):  
Molecular Evolution ◽  
Ribosomal Dna ◽  
Phylogenetic Inference

scholarly journals MOLECULAR EVOLUTION OF GPCRS: Ghrelin/ghrelin receptors

2013 ◽  
Vol 52 (3) ◽  
pp. T87-T100 ◽  
Author(s):  
Hiroyuki Kaiya ◽  
Kenji Kangawa ◽  
Mikiya Miyazato
Keyword(s):  
Molecular Evolution ◽  
Plate Tectonics ◽  
Current Knowledge ◽  
Laboratory Animals ◽  
Peptide Ligand ◽  
Ghrelin Receptor ◽  
Receptor Isoforms ◽  
Ghrelin Receptors ◽  
G Protein Coupled ◽  
Genome Projects

After the discovery in 1996 of the GH secretagogue-receptor type-1a (GHS-R1a) as an orphan G-protein coupled receptor, many research groups attempted to identify the endogenous ligand. Finally, Kojima and colleagues successfully isolated the peptide ligand from rat stomach extracts, determined its structure, and named it ghrelin. The GHS-R1a is now accepted to be the ghrelin receptor. The existence of the ghrelin system has been demonstrated in many animal classes through biochemical and molecular biological strategies as well as through genome projects. Our work, focused on identifying the ghrelin receptor and its ligand ghrelin in laboratory animals, particularly nonmammalian vertebrates, has provided new insights into the molecular evolution of the ghrelin receptor. In mammals, it is assumed that the ghrelin receptor evolution is in line with the plate tectonics theory. In contrast, the evolution of the ghrelin receptor in nonmammalian vertebrates differs from that of mammals: multiplicity of the ghrelin receptor isoforms is observed in nonmammalian vertebrates only. This multiplicity is due to genome duplication and polyploidization events that particularly occurred in Teleostei. Furthermore, it is likely that the evolution of the ghrelin receptor is distinct from that of its ligand, ghrelin, because only one ghrelin isoform has been detected in all species examined so far. In this review, we summarize current knowledge related to the molecular evolution of the ghrelin receptor in mammalian and nonmammalian vertebrates.

scholarly journals An ancient adaptive episode of convergent molecular evolution confounds phylogenetic inference

2008 ◽  
Author(s):  
Todd Castoe* ◽  
A.P. Jason de Koning* ◽  
Hyun-Min Kim ◽  
Wanjun Gu ◽  
Brice Noonan ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Phylogenetic Inference

scholarly journals The Interaction between Base Compositional Heterogeneity and Among-Site Rate Variation in Models of Molecular Evolution

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Nathan C. Sheffield
Keyword(s):  
Bayesian Inference ◽  
Molecular Evolution ◽  
Phylogenetic Inference ◽  
Heterogeneous Data ◽  
Rate Variation ◽  
Compositional Heterogeneity ◽  
Heterogeneous Datasets ◽  
Compositional Homogeneity

Many commonly used models of molecular evolution assume homogeneous nucleotide frequencies. A deviation from this assumption has been shown to cause problems for phylogenetic inference. However, some claim that only extreme heterogeneity affects phylogenetic accuracy and suggest that violations of other model assumptions, such as variable rates among sites, are more problematic. In order to explore the interaction between compositional heterogeneity and variable rates among sites, I reanalyzed 3 real heterogeneous datasets using several models. My Bayesian inference recovers accurate topologies under variable rates-among-sites models, but fails under some models that account for compositional heterogeneity. I also ran simulations and found that accounting for rates among sites improves topology accuracy in compositionally heterogeneous data. This indicates that in some cases, models accounting for among-site rate variation can improve outcomes for data that violates the assumption of compositional homogeneity.

Molecular evolution of a cytochrome P450 for the synthesis of potential antidepressant (2R,6R)-hydroxynorketamine

2021 ◽  
Author(s):  
Ansgar Bokel ◽  
Michael C. Hutter ◽  
Vlada B. Urlacher
Keyword(s):  
Cytochrome P450 ◽  
Molecular Evolution ◽  
Cytochrome P450 Monooxygenase ◽  
P450 Monooxygenase ◽  
Effective Synthesis

Engineered cytochrome P450 monooxygenase CYP154E1 enables the effective synthesis of the potential antidepressant (2R,6R)-hydroxynorketamine via N-demethylation and regio- and stereoselective hydroxylation of (R)-ketamine.

Sign in / Sign up

Export Citation Format

Share Document