treestructure: an R package to detect population structure in phylogenetic trees

Area of Science:

• Population genetics
• Phylogenetics
• Computational biology

Background:

• Understanding how population structure influences genetic diversity is a key challenge in population genetics.
• Geographic data aids in determining population structure, but its absence or ambiguity complicates analysis.
• Detecting unobserved population structure is crucial for accurate evolutionary inference.

Purpose of the Study:

• To present an updated version of the treestructure R package.
• To provide a statistical method for detecting unobserved population structure in phylogenetic trees.
• To enhance the analysis of genetic diversity without explicit geographic metadata.

Main Methods:

• Utilizes coalescent theory for statistical inference.
• Implements a test within the treestructure R package.
• Analyzes time-scaled phylogenetic trees to identify population structure.

Main Results:

• The updated treestructure package offers improved capabilities for detecting hidden population structure.
• The method effectively identifies population structure even when geographic metadata is unavailable.
• Provides a robust statistical framework for population genetic analyses.

Conclusions:

• The treestructure package is a valuable tool for inferring population structure from phylogenetic data.
• Facilitates the study of genetic diversity and evolutionary processes in the absence of location information.
• Contributes to advancing methods in computational phylogenetics and population genetics.