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Related Experiment Video

Updated: Oct 14, 2025

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

Discrete coalescent trees.

Lena Collienne¹, Kieran Elmes¹, Mareike Fischer²

¹Department of Computer Science, University of Otago, Dunedin, New Zealand.

Journal of Mathematical Biology

|November 5, 2021

Summary

This summary is machine-generated.

We introduce a novel discrete coalescent tree space, offering a unique geometry for phylogenetic inference. This work provides new algorithms and insights into evolutionary history modeling for applications like cancer and virus evolution.

Keywords:

Algorithms Coalescent trees Metric geometry Phylogenetics Ranked tree Time trees Tree distance Tree space

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Area of Science:

Phylogenetics and Evolutionary Biology
Computational Biology
Statistical Modeling

Background:

Time trees are crucial for understanding evolutionary dynamics in fields like cancer and virus evolution.
Coalescent theory is widely used for modeling clock-like trees, where all sampled leaves share the same time depth.
The geometric properties of tree spaces significantly influence phylogenetic inference algorithms.

Purpose of the Study:

To introduce and analyze a new mathematical space for discrete coalescent trees.
To explore the geometric properties of this discrete tree space and its implications for phylogenetic analysis.
To generalize existing results on ranked trees and provide new computational tools.

Main Methods:

Development of a discrete coalescent tree space based on tree-rearrangement operations.
Generalization of algorithms for computing distances within ranked tree spaces.
Analysis of the geometric properties of the proposed discrete coalescent tree space.

Main Results:

Established several key geometrical properties of the discrete coalescent tree space.
Provided a polynomial-time algorithm for distance computation within this space.
Demonstrated how these geometric properties impact phylogenetic inference algorithms.

Conclusions:

The discrete coalescent tree space offers a valuable framework for phylogenetic inference, particularly for computational applications.
The derived geometric properties and algorithms can approximate solutions to existing problems in continuous time tree spaces (t-space).
This research advances the computational and statistical understanding of evolutionary history reconstruction.