Summary
Bootstrap and posterior probabilities measure confidence in the branches of evolutionary trees.
In depth
Bootstrap support above 70 to 95 percent is considered good; Bayesian posterior probabilities tend to be higher. Model selection by AIC or BIC. Topology tests compare alternative trees.
Bootstrap values are not probabilities that clades are true. Long-branch attraction can mislead. Use multiple methods.
Key idea: support values summarise confidence.
Phylogenetic trees are estimates, so their reliability must be assessed. The bootstrap resamples the alignment columns many times with replacement, builds a tree each time, and reports for each branch the percentage of trees that contain it; values above about 70 to 95 percent are considered well supported.
In Bayesian analysis, posterior probabilities show support directly, and maximum likelihood tests different models of evolution (using AIC or BIC). Other methods include likelihood ratio tests and approximate versions (aLRT, UFBoot). Support does not guarantee truth if the model is wrong or data are biased, for example long-branch attraction.
Example: a node with 100 percent bootstrap support is consistently recovered.
Remember: support values refer to branches, not to the whole tree.
Frequently asked questions
What is Phylogenetic Statistics?
Bootstrap and posterior probabilities measure confidence in the branches of evolutionary trees.
Which area of biology covers Phylogenetic Statistics, and how advanced is it?
Phylogenetic Statistics is one of the 51 topics in Lab Methods & Biostatistics. It is rated Advanced, so it suits learners who want specialist depth. Related topics in this area include Bayesian Statistics, ANOVA, Reproducibility in Science.
Can you give an example of Phylogenetic Statistics?
SH test compares tree likelihoods.
What should I learn before Phylogenetic Statistics?
Work through the Beginner topics in Lab Methods & Biostatistics first, such as Scientific Method, Hypothesis, Variables, then return to Phylogenetic Statistics. Advanced topics assume the Intermediate vocabulary.
What topics are related to Phylogenetic Statistics?
The closest topics to Phylogenetic Statistics are Bayesian Statistics, ANOVA, Reproducibility in Science, P-Values and Multiple Testing. Comparing them side by side is a good way to see how the ideas connect.
How can I check that I understand Phylogenetic Statistics?
Read the summary and the in-depth section, then use the quick check on the interactive lesson for Phylogenetic Statistics. To practise the whole of Lab Methods & Biostatistics, use the Lab Methods & Biostatistics quiz.
How is Phylogenetic Statistics different from Bayesian Statistics?
Phylogenetic Statistics: Bootstrap and posterior probabilities measure confidence in the branches of evolutionary trees. Bayesian Statistics: Updates probabilities for hypotheses using prior knowledge and observed data. Read both side by side and note what each one explains.
How should I study Phylogenetic Statistics step by step?
First, read the summary and write the definition in your own words. Second, read the in-depth section and note any example. Third, compare it with Bayesian Statistics and explain the difference aloud. Finally, take the Lab Methods & Biostatistics quiz and come back to this page for any question you miss.