ArticleSystematic biology2018
Phylogenetic Factor Analysis.
Article in Systematic biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed.
- An Evolving View of Character Macroevolution.Systematic biology · 2026Review
- Diel activity correlates with colour pattern morphology of heterobranch sea slugs.The Journal of animal ecology · 2025Article
- Leveraging graphical model techniques to study evolution on phylogenetic networks.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Body size and life history shape the historical biogeography of tetrapods.Nature ecology & evolution · 2023Article
- Accelerating Bayesian inference of dependency between mixed-type biological traits.PLoS computational biology · 2023Article
- Data integration in Bayesian phylogenetics.Annual review of statistics and its application · 2023Article
- Principled, practical, flexible, fast: a new approach to phylogenetic factor analysis.Methods in ecology and evolution · 2022Article
- Ancestral protein sequence reconstruction using a tree-structured Ornstein-Uhlenbeck variational autoencoder.... International Conference on Learning Representations · 2022Article
- Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements.Journal of the American Statistical Association · 2022Article
- Marginal Likelihoods in Phylogenetics: A Review of Methods and Applications.Systematic biology · 2019Review
- Quantifying climate sensitivity and climate-driven change in North American amphibian communities.Nature communications · 2018Article
- Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10.Virus evolution · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that generates model residuals or the traits themselves. For high-dimensional traits, inferring all pair-wise correlations within the multivariate diffusion is limiting. To circumvent this problem, we propose phylogenetic factor analysis (PFA) that assumes a small unknown number of independent evolutionary factors arise along the phylogeny and these factors generate clusters of dependent traits. Set in a Bayesian framework, PFA provides measures of uncertainty on the factor number and groupings, combines both continuous and discrete traits, integrates over missing measurements and incorporates phylogenetic uncertainty with the help of molecular sequences. We develop Gibbs samplers based on dynamic programming to estimate the PFA posterior distribution, over 3-fold faster than for multivariate diffusion and a further order-of-magnitude more efficiently in the presence of latent traits. We further propose a novel marginal likelihood estimator for previously impractical models with discrete data and find that PFA also provides a better fit than multivariate diffusion in evolutionary questions in columbine flower development, placental reproduction transitions and triggerfish fin morphometry.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.