Assessing phenotypic correlation through the multivariate phylogenetic latent liability model
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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 in Salmonella and epitope evolution in influenza.
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Cites work
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- Statistical challenges in tracking the evolution of SARS-CoV-2
- Large-scale inference of correlation among mixed-type biological traits with phylogenetic multivariate probit models
- Efficient Bayesian inference of general Gaussian models on large phylogenetic trees
- Testing for correlation between traits under directional evolution
- Modeling complex phenotypes: generalized linear models using spectrogram predictors of animal communication signals
- scientific article; zbMATH DE number 1159376 (Why is no real title available?)
- Assessing the relationship of evolutionary rates and functional variables by mixture estimating equations
- Massive Parallelization Boosts Big Bayesian Multidimensional Scaling
- Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements
- On the covariance of phylogenetic quantitative trait evolution models and their matrix condition
- Assessing phenotypic correlation through the multivariate phylogenetic latent liability model
- Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts
- A phylogenetic comparative method for studying multivariate adaptation
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