OrthoGLMM: Phylogenetic Association Testing for Gene Content and Trait Evolution
Guhlin, J. G.; Keddell, P.; Dearden, P.
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Motivation: Comparative 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. Results: We 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 Implementation: Source code, documentation, example data, and reproducibility scripts will be available at http://github.com/jguhlin/OrthoGLMM.
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