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Protocols for the Molecular Evolutionary Analysis of Membrane Protein Gene Duplicates

  • Laurel R. Yohe
  • Liang Liu
  • Liliana M. Dávalos
  • David A. Liberles
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1851)

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.

Key words

Gene duplication Gene tree Birth-death models Molecular evolution dN/dS 

Notes

Acknowledgements

This research was supported in part by DEB-1442142 to L.M.D., DEB-1701414 to L.M.D., D.A.L., and L.R.Y., and DBI-1222940 to D.A.L. and L.L.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Geology & GeophysicsYale UniversityNew HavenUSA
  2. 2.Department of Ecology and EvolutionStony Brook UniversityStony BrookUSA
  3. 3.Department of Statistics and Institute of BioinformaticsUniversity of GeorgiaAthensUSA
  4. 4.Department of Biology and Center for Computational Genetics and GenomicsTemple UniversityPhiladelphiaUSA

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