Related Experiment Video
Updated: Feb 18, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
16.6K
P3: Phylogenetic Posterior Prediction in RevBayes
Sebastian Höhna1,2, Lyndon M Coghill3, Genevieve G Mount3
1Division of Evolutionary Biology, Ludwig-Maximilians-Universität, München, Germany.
Molecular Biology and Evolution
|November 15, 2017
Summary
We introduce new methods for testing phylogenetic model fit using posterior predictive simulations in RevBayes software. This enables robust phylogenetic inference by ensuring accurate model structures and reliable parameter estimates.
Area of Science:
- Evolutionary biology
- Computational biology
- Statistical modeling
Background:
- Model-based inference relies on accurate model structures to avoid biased parameter estimates.
- Posterior predictive simulations are a powerful tool for assessing absolute model fit in Bayesian inference.
- Implementing these tests in phylogenetics has been hindered by a lack of accessible software.
Purpose of the Study:
- To implement and describe novel tests for absolute model fit in phylogenetic inference.
- To provide a user-friendly and flexible software solution for posterior predictive testing in phylogenetics.
- To enhance the reliability of phylogenetic models and parameter estimation.
Main Methods:
- Developed and integrated posterior predictive testing for model fit within the RevBayes phylogenetics software.
- Utilized both data- and inference-based test statistics for comprehensive model evaluation.
- Leveraged existing Bayesian inference frameworks for seamless implementation.
Main Results:
- Successfully implemented a suite of tests for absolute model fit in RevBayes.
- The new implementation supports a wide range of phylogenetic models.
- The software provides a user-friendly interface for applying these tests.
Conclusions:
- The new RevBayes implementation facilitates rigorous testing of phylogenetic model fit.
- This advancement promotes more accurate and reliable phylogenetic analyses.
- Researchers can now more easily ensure the suitability of their chosen models in phylogenetic studies.
Related Concept Videos
01:03Prediction Intervals
3.5K
The interval estimate of any variable is known as the prediction interval. It helps decide if a point estimate is dependable.
However, the point estimate is most likely not the exact value of the population parameter, but close to it. After calculating point estimates, we construct interval estimates, called confidence intervals or prediction intervals. This prediction interval comprises a range of values unlike the point estimate and is a better predictor of the observed sample value, y.
However, the point estimate is most likely not the exact value of the population parameter, but close to it. After calculating point estimates, we construct interval estimates, called confidence intervals or prediction intervals. This prediction interval comprises a range of values unlike the point estimate and is a better predictor of the observed sample value, y.
3.5K
02:54Evolutionary Relationships through Genome Comparisons
7.1K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
7.1K
01:23Phylogeny
62.7K
Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
62.7K
03:21Phylogenetic Trees
50.2K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
50.2K
02:24Predicting Reaction Outcomes
11.1K
Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...
11.1K
01:07End Point Prediction: Gran Plot
1.3K
A Gran plot is used to predict the equivalence volume or endpoint of a potentiometric or acid-base titration without reaching the endpoint. Typically, titration data is collected as a function of the titrant's volume up to a point less than the equivalence volume and then transformed into a linear format. The straight line is extended to the x-axis, indicating the necessary titrant volume to achieve the equivalence point.
For potentiometric titration, the Gran plot is created by plotting...
For potentiometric titration, the Gran plot is created by plotting...
1.3K