A hierarchical Bayesian framework accommodates intraspecific and interspecific variation in multivariate traits
- 1University of California, Berkeley
Abstract
Phylogenetic comparative methods are a critical tool in biology, providing the framework to test evolutionary hypotheses of phenotypic diversification. Accommodating intraspecific variation in multivariate analyses is critical for accurate evolutionary inference, but current methods that incorporate intraspecific variation either 1) assume that traits evolve independently or 2) that all taxa share the same intraspecific covariance structure. Violations of these assumptions can produce biased estimates of evolutionary parameters. Here, we introduce a hierarchical Bayesian framework for multivariate traits that jointly estimates taxon-specific intraspecific covariance structures alongside the underlying evolutionary process. This framework propagates uncertainty from sample size discrepancies and missing data, enabling the incorporation of highly variable morphological traits into phylogenetic analyses. Analysis of simulated data confirms that the model and implementation are well calibrated under the assumed generative model, including challenging datasets with more traits than individuals and substantial missing observations. Applied to perikymata spacing across the great ape clade, including modern humans and Neandertals, the framework recovers intraspecific covariance structures that differ among taxa and yields evolutionary rate estimates markedly more uniform across the tooth crown than those obtained when taxon means are fixed. Our method, which is applicable to other multivariate traits, provide a flexible, tractable approach to joint estimation of intraspecific variation and evolutionary process in multivariate traits.
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BibTeX
@misc{raskin2026hierarchical,
title = {{A hierarchical Bayesian framework accommodates intraspecific and interspecific variation in multivariate traits}},
author = {L. Y. Raskin and M. Seselj and J. Huelsenbeck and W. Lim and J. K. Li and D. Guatelli-Steinberg and M. C. O'Hara and B. D. Bitarello},
howpublished = {bioRxiv},
year = {2026},
month = may,
doi = {10.64898/2026.05.28.728593},
url = {https://www.biorxiv.org/content/10.64898/2026.05.28.728593v2},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - A hierarchical Bayesian framework accommodates intraspecific and interspecific variation in multivariate traits
AU - L. Y. Raskin
AU - M. Seselj
AU - J. Huelsenbeck
AU - W. Lim
AU - J. K. Li
AU - D. Guatelli-Steinberg
AU - M. C. O'Hara
AU - B. D. Bitarello
PY - 2026
DA - 2026/05/28
PB - bioRxiv
DO - 10.64898/2026.05.28.728593
UR - https://www.biorxiv.org/content/10.64898/2026.05.28.728593v2
AB - Phylogenetic comparative methods are a critical tool in biology, providing the framework to test evolutionary hypotheses of phenotypic diversification. Accommodating intraspecific variation in multivariate analyses is critical for accurate evolutionary inference, but current methods that incorporate intraspecific variation either 1) assume that traits evolve independently or 2) that all taxa share the same intraspecific covariance structure. Violations of these assumptions can produce biased estimates of evolutionary parameters. Here, we introduce a hierarchical Bayesian framework for multivariate traits that jointly estimates taxon-specific intraspecific covariance structures alongside the underlying evolutionary process. This framework propagates uncertainty from sample size discrepancies and missing data, enabling the incorporation of highly variable morphological traits into phylogenetic analyses. Analysis of simulated data confirms that the model and implementation are well calibrated under the assumed generative model, including challenging datasets with more traits than individuals and substantial missing observations. Applied to perikymata spacing across the great ape clade, including modern humans and Neandertals, the framework recovers intraspecific covariance structures that differ among taxa and yields evolutionary rate estimates markedly more uniform across the tooth crown than those obtained when taxon means are fixed. Our method, which is applicable to other multivariate traits, provide a flexible, tractable approach to joint estimation of intraspecific variation and evolutionary process in multivariate traits.
ER -