Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications.

ABSTRACT: Genomic data have provided evidence of previously unknown ancient whole genome duplications (WGDs) and highlighted the role of WGDs in the evolution of many eukaryotic lineages. Ancient WGDs often are detected by examining distributions of synonymous substitutions per site (Ks) within a genome, or "Ks plots." For example, WGDs can be detected from Ks plots by using univariate mixture models to identify peaks in Ks distributions. We performed gene family simulation experiments to evaluate the effects of different Ks estimation methods and mixture models on our ability to detect ancient WGDs from Ks plots. The simulation experiments, which accounted for variation in substitution rates and gene duplication and loss rates across gene families, tested the effects of WGD age and gene retention r

SUBMITTER: Tiley GP 

PROVIDER: S-EPMC6225891 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature