title: Analytical methods for detecting paralogy in molecular datasets.
abstract: Paralogy (common ancestry through gene duplication rather than speciation) is widely recognized as an important problem for molecular systematists. This chapter introduces the concepts of paralogy and orthology and explains why paralogy can complicate both systematic work and other studies of molecular evolution. The definition of paralogy is explicitly phylogenetic, and phylogenetic methods are crucial in elucidating the pattern of paralogy. In particular, knowledge of the species phylogeny is key. I introduce the theory behind methods for detecting paralogy and briefly discuss two particular software implementations of phylogenetic methods to detect paralogy from molecular data. I also introduce a statistical method for detecting paralogy and some future directions for work on paralogy detection.
authors.affiliation: Department of Zoology, The Natural History Museum, London SW7 5BD, United Kingdom.
authors.forename: James A
authors.initials: JA
authors.lastname: Cotton
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D030541:Databases, Genetic; D019143:Evolution, Molecular; D020440:Gene Duplication; D022761:Gene Transfer, Horizontal; D006801:Humans; D007770:L-Lactate Dehydrogenase / Q000235:genetics; D008957:Models, Genetic; D015233:Models, Statistical; D005810:Multigene Family; D010802:Phylogeny; D017299:Rod Opsins / Q000235:genetics; D017385:Sequence Homology; D012984:Software; D013045:Species Specificity
chemical_list: D017299:Rod Opsins; D007770:L-Lactate Dehydrogenase