Paper List
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Exactly Solvable Population Model with Square-Root Growth Noise and Cell-Size Regulation
This paper addresses the fundamental gap in understanding how microscopic growth fluctuations, specifically those with size-dependent (square-root) no...
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Assessment of Simulation-based Inference Methods for Stochastic Compartmental Models
This paper addresses the core challenge of performing accurate Bayesian parameter inference for stochastic epidemic models when the likelihood functio...
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Realistic Transition Paths for Large Biomolecular Systems: A Langevin Bridge Approach
This paper addresses the core challenge of generating physically realistic and computationally efficient transition paths between distinct protein con...
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MoRSAIK: Sequence Motif Reactor Simulation, Analysis and Inference Kit in Python
This work addresses the computational bottleneck in simulating prebiotic RNA reactor dynamics by developing a Python package that tracks sequence moti...
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The BEAT-CF Causal Model: A model for guiding the design of trials and observational analyses of cystic fibrosis exacerbations
This paper addresses the critical gap in cystic fibrosis exacerbation management by providing a formal causal framework that integrates expert knowled...
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A Theoretical Framework for the Formation of Large Animal Groups: Topological Coordination, Subgroup Merging, and Velocity Inheritance
This paper addresses the core problem of how large, coordinated animal groups form in nature, challenging the classical view of gradual aggregation by...
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ANNE Apnea Paper
This paper addresses the core challenge of achieving accurate, event-level sleep apnea detection and characterization using a non-intrusive, multimoda...
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DeeDeeExperiment: Building an infrastructure for integrating and managing omics data analysis results in R/Bioconductor
This paper addresses the critical bottleneck of managing and organizing the growing volume of differential expression and functional enrichment analys...
Fast and Accurate Node-Age Estimation Under Fossil Calibration Uncertainty Using the Adjusted Pairwise Likelihood
Department of Statistics, University of Georgia, Athens, 30601, USA
The 30-Second View
IN SHORT: This paper addresses the dual challenge of computational inefficiency and sensitivity to fossil calibration errors in Bayesian divergence time estimation for large phylogenomic datasets.
Innovation (TL;DR)
- Methodology Introduces two Adjusted Pairwise Likelihood (APW) formulations (APW1 and APW2) that use asymptotic moment-matching weights to correct composite likelihoods within a Bayesian MCMC framework.
- Methodology Demonstrates that APW methods reduce computational cost by more than an order of magnitude compared to full-likelihood methods while maintaining comparable accuracy in node-age estimation.
- Methodology Shows that APW methods exhibit greater robustness to fossil misplacement and prior misspecification due to the reduced sensitivity of composite likelihoods to local calibration errors.
Key conclusions
- APW methods produce node-age estimates statistically comparable to full-likelihood methods across diverse simulation scenarios, with reduced sensitivity to local calibration errors.
- Applied to a genome-scale avian dataset, APW recovered divergence time patterns consistent with recent studies while achieving a >10x reduction in computational cost.
- The robustness of APW to fossil misplacement stems from the composite likelihood's inherent property of being less sensitive to errors in individual calibration points, as demonstrated in simulations modeling various prior misspecifications.
Abstract: Estimating divergence times from molecular sequence data is central to reconstructing the evolutionary history of lineages. Although Bayesian relaxed-clock methods provide a principled framework for incorporating fossil information, their dependence on repeated evaluations of the full phylogenetic likelihood makes them computationally demanding for large genomic datasets. Furthermore, because disagreements in divergence-time estimates often arise from uncertainty or error in fossil placement and prior specification, there is a need for methods that are both computationally efficient and robust to fossil-calibration uncertainty. In this study, we introduce fast and accurate alternatives based on the phylogenetic pairwise composite likelihood, presenting two adjusted pairwise likelihood (APW) formulations that employ asymptotic moment-matching weights to better approximate the behavior of the full likelihood within a Bayesian MCMC framework. Extensive simulations across diverse fossil-calibration scenarios show that APW methods produce node-age estimates comparable to those obtained from the full likelihood while offering greater robustness to fossil misplacement and prior misspecification, due to the reduced sensitivity of composite likelihoods to local calibration errors. Applied to a genome-scale dataset of modern birds, APW methods recover divergence time patterns consistent with recent studies, while reducing computational cost by more than an order of magnitude. Overall, our results demonstrate that adjusted pairwise likelihoods provide a calibration-robust and computationally efficient framework for Bayesian node dating, especially suited for large phylogenomic datasets and analyses in which fossil priors may be uncertain or imperfectly placed.