Employing phylogenetic tree shape statistics to resolve the underlying host population structure.

ABSTRACT:

Background

Host population structure is a key determinant of pathogen and infectious disease transmission patterns. Pathogen phylogenetic trees are useful tools to reveal the population structure underlying an epidemic. Determining whether a population is structured or not is useful in informing the type of phylogenetic methods to be used in a given study. We employ tree statistics derived from phylogenetic trees and machine learning classification techniques to reveal an underlying population structure.

Results

In this paper, we simulate phylogenetic trees from both structured and non-structured host populations. We compute eight statistics for the simulated trees, which are: the number of cherries; Sackin, Colless and total cophenetic indices; ladder length; maximum depth;

SUBMITTER: Kayondo HW 

PROVIDER: S-EPMC8579572 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature