EvolQG - An R package for evolutionary quantitative genetics

F1000Res. 2015 Sep 30:4:925. doi: 10.12688/f1000research.7082.3. eCollection 2015.

Abstract

We present an open source package for performing evolutionary quantitative genetics analyses in the R environment for statistical computing. Evolutionary theory shows that evolution depends critically on the available variation in a given population. When dealing with many quantitative traits this variation is expressed in the form of a covariance matrix, particularly the additive genetic covariance matrix or sometimes the phenotypic matrix, when the genetic matrix is unavailable and there is evidence the phenotypic matrix is sufficiently similar to the genetic matrix. Given this mathematical representation of available variation, the \textbf{EvolQG} package provides functions for calculation of relevant evolutionary statistics; estimation of sampling error; corrections for this error; matrix comparison via correlations, distances and matrix decomposition; analysis of modularity patterns; and functions for testing evolutionary hypotheses on taxa diversification.

Keywords: G-matrix; P-matrix; covariance matrix; directional selection; drift; matrix comparison; morphological evolution; multivariate evolution.

Grants and funding

This work was supported by funding from FAPESP. D.M. was funded by grants 2012/20180-0 and 2014/01694-9; G.G. was funded by grant 2011/52469-4; A.H. was funded by grant 2012/24937-9; A.P.A was funded by grants 2008/56886-6 and 2010/52369-0; G.M. was funded by grant 2011/14295-7.