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Phylogenetic Trees

Phylogenetic Trees

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.

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Phylogeny

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What is Biodiversity?

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Biodiversity describes the variety of living things at multiple organizational levels: genetic, species and ecosystem diversity. Species diversity includes all branches of the evolutionary tree from single-celled prokaryotic organisms, bacteria, and archaea, to the eukaryotic kingdoms: plants; animals; fungi; and protists. To date, there have been about 1.75 million species identified, and new species are discovered every week.

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Related Experiment Video

Updated: May 27, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Neutral phylogenetic models and their role in tree-based biodiversity measures.

¹Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand.

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences

|February 20, 2025

Summary

Stochastic models yield similar phylogenetic tree shapes but vary in edge lengths. This impacts biodiversity measures like phylogenetic diversity (PD) and feature diversity under extinction.

Keywords:

birth–death process feature diversity phylogenetic diversity phylogenetic tree

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Last Updated: May 27, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

Evolutionary biology
Biodiversity science
Mathematical modeling

Background:

Stochastic models of cladogenesis (speciation and extinction) often result in identical phylogenetic tree shapes when edge lengths are disregarded.
The distribution of edge lengths in phylogenetic trees is highly sensitive to the specific model used.

Purpose of the Study:

To review how model choices influence phylogenetic tree shape and edge length distributions.
To assess the impact of these distributions on phylogenetic diversity (PD) as a biodiversity measure and its loss during extinction events.
To compare PD with stochastic feature diversity models and analyze their mathematical relationships and predictions regarding biodiversity loss.

Main Methods:

Review of existing literature on stochastic models of cladogenesis.
Analysis of the mathematical properties of phylogenetic tree shape and edge length distributions.
Comparison of phylogenetic diversity (PD) with stochastic feature diversity models.
Investigation of mathematical inequalities between diversity measures.

Main Results:

Phylogenetic tree shape distribution is invariant across many cladogenesis models when edge lengths are ignored.
Edge length distributions are model-dependent, significantly affecting biodiversity assessments.
PD and feature diversity models exhibit distinct predictions for biodiversity loss under extinction.

Conclusions:

Model choice critically influences the interpretation of phylogenetic diversity and biodiversity loss.
Understanding the interplay between tree structure, edge lengths, and diversity metrics is crucial for accurate biodiversity assessments.
Mathematical comparisons reveal insights into the behavior of different biodiversity measures under extinction scenarios.