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• W2898037249 abstract "Gene duplication is an important process in the evolution of gene content in eukaryotic genomes. Understanding when gene duplicates contribute new molecular functions to genomes through molecular adaptation is one important goal in comparative genomics. In large gene families, however, characterizing adaptation and neofunctionalization across species is challenging, as models have traditionally quantified the timing of duplications without considering underlying gene trees. This protocol combines multiple approaches to detect adaptation in protein duplicates at a phylogenetic scale. We include a description of models for gene tree-species tree reconciliation that enable different types of inference, as well as a practical guide to their use. Although simulation-based approaches successfully detect shifts in the rate of duplication/retention, the conflation between the duplication and retention processes, the distinct trajectories of duplicates under non-, sub-, and neofunctionalization, as well as dosage effects offer hitherto unexplored analytical avenues. We introduce mathematical descriptions of these probabilities and offer a road map to computational implementation whose starting point is parsimony reconciliation. Sequence evolution information based on the ratio of nonsynonymous to synonymous nucleotide substitution rates (dN/dS) can be combined with duplicate survival probabilities to better predict the emergence of new molecular functions in retained duplicates. Together, these methods enable characterization of potentially adaptive candidate duplicates whose neofunctionalization may contribute to phenotypic divergence across species." @default.
• W2898037249 created "2018-10-26" @default.
• W2898037249 creator A5003554962 @default.
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• W2898037249 date "2018-09-27" @default.
• W2898037249 modified "2023-09-27" @default.
• W2898037249 title "Protocols for the Molecular Evolutionary Analysis of Membrane Protein Gene Duplicates" @default.
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• W2898037249 doi "https://doi.org/10.1007/978-1-4939-8736-8_3" @default.
• W2898037249 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/30298391" @default.
• W2898037249 hasPublicationYear "2018" @default.
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