title: ASSESSING PHENOTYPIC CORRELATION THROUGH THE MULTIVARIATE PHYLOGENETIC LATENT LIABILITY MODEL.
abstract: Understanding which phenotypic traits are consistently correlated throughout evolution is a highly pertinent problem in modern evolutionary biology. Here, we propose a multivariate phylogenetic latent liability model for assessing the correlation between multiple types of data, while simultaneously controlling for their unknown shared evolutionary history informed through molecular sequences. The latent formulation enables us to consider in a single model combinations of continuous traits, discrete binary traits, and discrete traits with multiple ordered and unordered states. Previous approaches have entertained a single data type generally along a fixed history, precluding estimation of correlation between traits and ignoring uncertainty in the history. We implement our model in a Bayesian phylogenetic framework, and discuss inference techniques for hypothesis testing. Finally, we showcase the method through applications to columbine flower morphology, antibiotic resistance inSalmonella, and epitope evolution in influenza.
authors.affiliation: Federal University of Rio Grande do Sul.
authors.forename: Gabriela B
authors.initials: GB
authors.lastname: Cybis
authors.affiliation: University of California, Los Angeles.
authors.forename: Janet S
authors.initials: JS
authors.lastname: Sinsheimer
authors.affiliation: Fred Hutchinson Cancer Research Center.
authors.forename: Trevor
authors.initials: T
authors.lastname: Bedford
authors.affiliation: Wellcome Trust Sanger Institute.
authors.forename: Alison E
authors.initials: AE
authors.lastname: Mather
authors.affiliation: KU Leuven.
authors.forename: Philippe
authors.initials: P
authors.lastname: Lemey
authors.affiliation: University of California, Los Angeles.
authors.forename: Marc A
authors.initials: MA
authors.lastname: Suchard
keywords: Bayesian phylogenetics; Evolution; Genotype-phenotype correlation; Threshold model