title: Molecular evolution and population genetics of circadian clock genes.
abstract: This article discusses a number of common methodologies used in the field of population genetics and evolution and reviews their application within circadian rhythm research. We examine the basic principles behind phylogenetic analysis and how these can be used to illuminate clock gene evolution. We then discuss genetic variation between and within species and show how neutrality tests can reveal the signatures of selection or drift on clock genes. These tests are particularly important for moving beyond "just so" stories when discussing the evolution of clock phenotypes, and we provide relevant circadian examples. We also focus on methods that can be used to study genetic variation, such as quantitative trait loci analysis. We discuss the various bootstrapping or resampling techniques that can be applied to generate confidence intervals in the various methodologies and then examine the use of interspecific transformation studies, which can, and have, provide some useful insights, not only into clock gene evolution in particular, but "behavioral" gene evolution in general. Finally, we assess gene/protein alignments and protein structure predictions and their implicit evolutionary bases.
authors.forename: Eran
authors.initials: E
authors.lastname: Tauber
authors.forename: Charalambos P
authors.initials: CP
authors.lastname: Kyriacou
mesh_terms: D000818:Animals; D001483:Base Sequence; D001683:Biological Clocks / Q000235:genetics*; D056926:CLOCK Proteins; D002940:Circadian Rhythm / Q000235:genetics*; D004330:Drosophila / Q000235:genetics; D029721:Drosophila Proteins; D004331:Drosophila melanogaster / Q000235:genetics; D019143:Evolution, Molecular; D017344:Genes, Insect; D005821:Genetic Techniques; D005828:Genetics, Population; D006801:Humans; D009492:Neurospora crassa / Q000235:genetics; D009687:Nuclear Proteins / Q000235:genetics; D056950:Period Circadian Proteins; D010802:Phylogeny; D011110:Polymorphism, Genetic; D040641:Quantitative Trait Loci; D012641:Selection, Genetic; D015534:Trans-Activators / Q000235:genetics*
chemical_list: D029721:Drosophila Proteins; D009687:Nuclear Proteins; C539040:PER protein, Drosophila; D056950:Period Circadian Proteins; D015534:Trans-Activators; D056926:CLOCK Proteins; C538943:CLOCK protein, human