OrthoGLMM: Phylogenetic Association Testing for Gene Content and Trait Evolution

1MotivationComparative genome projects can now assemble and annotate hundreds of species, creating an opportunity to test whether species-level traits are associated with repeated changes in gene content. These tests must account for shared ancestry, sparse orthogroups, rare trait origins, and thousands of simultaneous associations. ResultsWe present OrthoGLMM, a phylogenetically informed framework for the association of traits and orthogroup presence/absence or copy number across species. OrthoGLMM combines deterministic GLMM scans with solver-rerun empirical calibration and calibrated FDR estimation. In three benchmark datasets, OrthoGLMM recovered expected signals for bacterial diazotrophy, plant nodulation, and marine mammals. Availability and ImplementationSource code, documentation, example data, and reproducibility scripts will be available at http://github.com/jguhlin/OrthoGLMM. Contactjoseph.guhlin@gmail.com