# A Practical Guide for Harnessing Phylogenomics in Biocontrol: Accounting for Topological Uncertainty and Phylogenetic Distance in the Centrifugal Phylogenetic Method and Beyond

## TL;DR

This paper provides practical guidance on using phylogenomics in biological control, focusing on phylogenetic distance and topological uncertainty to improve decision-making.

## Contribution

The paper introduces practical recommendations for interpreting phylogenetic trees and accounting for topological uncertainty in biocontrol applications.

## Key findings

- Phylogenetic distance measures vary across different tree types and can impact biocontrol decisions.
- Topological uncertainty affects inferences drawn from phylogenetic distance in host specificity testing.
- Case studies demonstrate the application of phylogenomics in real-world biocontrol scenarios.

## Abstract

In the genomic era, phylogenomics is playing an increasingly important role in biological control research for prioritising species in host specificity testing, species delimitation, and elucidating the origins of introduced species. This paper outlines key concepts in phylogenomics relevant to biocontrol practitioners and provides practical guidance on the construction and interpretation of phylogenetic trees. We examine the patterns and distributions of degrees of separation and phylogenetic distance (also known as patristic distance) across different types of phylogenetic trees, including cladograms, phylograms, and chronograms, and offer recommendations for their application. Further, we consider the impact of topological uncertainty on these distance measures and the inferences they inform for decision‐making in biological control. These concepts are illustrated through two case study datasets representing distinct evolutionary contexts. The first explores a recently published phylogeny of Asteraceae tribe Senecioneae derived from traditionally used nuclear and chloroplast Sanger molecular markers, using common groundsel (
Senecio vulgaris
) as the hypothetical target weed. The second case study dataset focuses on the biocontrol of stinking passionflower (
Passiflora foetida
) in Australia, presenting a novel target capture (Angiosperms353) phylogeny for this group. Equipping biocontrol practitioners with a deeper understanding of phylogenomics will facilitate more efficient and data‐driven decision‐making in biological control.