The hybrid number of a ploidy profile

TL;DR

This paper introduces the concept of a ploidy profile and provides a formula to compute the hybrid number, representing the minimal polyploidization events needed to explain evolutionary history, demonstrated on a Viola dataset.

Contribution

It formalizes ploidy profiles within phylogenetic networks and derives a closed formula for hybrid number calculation, enhancing understanding of polyploidization events.

Findings

Closed formula for hybrid number of ploidy profiles

Applicable to datasets with small ploidy numbers

Validated on a Viola dataset

Abstract

Polyploidization, whereby an organism inherits multiple copies of the genome of their parents, is an important evolutionary event that has been observed in plants and animals. One way to study such events is in terms of the ploidy number of the species that make up a dataset of interest. It is therefore natural to ask: How much information about the evolutionary past of the set of species that form a dataset can be gleaned from the ploidy numbers of the species? To help answer this question, we introduce and study the novel concept of a ploidy profile which allows us to formalize it in terms of a multiplicity vector indexed by the species the dataset is comprised of. Using the framework of a phylogenetic network, we present a closed formula for computing the hybrid number (i.e. the minimal number of polyploidization events required to explain a ploidy profile) of a large class of ploidy profiles. This formula relies on the construction of a certain phylogenetic network from the simplification sequence of a ploidy profile and the hybrid number of the ploidy profile with which this construction is initialized. Both of them can be computed easily in case the ploidy numbers that make up the ploidy profile are not too large. To help illustrate the applicability of our approach, we apply it to a simplified version of a publicly available Viola dataset.