Haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks.

Eric Garcia,Jacob R Winnikoff,Eva Salas,Daniel Wright,Remy Gatins,May B Roberts,Jei-Ying Chen,Hudson T Pinheiro,Giacomo Bernardi,Jeffrey A Eble

doi:10.1371/journal.pone.0251878

Abstract

A common way of illustrating phylogeographic results is through the use of haplotype networks. While these networks help to visualize relationships between individuals, populations, and species, evolutionary studies often only quantitatively analyze genetic diversity among haplotypes and ignore other network properties. Here, we present a new metric, haplotype network branch diversity (HBd), as an easy way to quantifiably compare haplotype network complexity. Our metric builds off the logic of combining genetic and topological diversity to estimate complexity previously used by the published metric haplotype network diversity (HNd). However, unlike HNd which uses a combination of network features to produce complexity values that cannot be defined in probabilistic terms, thereby obscuring the values’ implication for a sampled population, HBd uses frequencies of haplotype classes to incorporate topological information of networks, keeping the focus on the population and providing easy-to-interpret probabilistic values for randomly sampled individuals. The goal of this study is to introduce this more intuitive metric and provide an R script that allows researchers to calculate diversity and complexity indices from haplotype networks. A group of datasets, generated manually (model dataset) and based on published data (empirical dataset), were used to illustrate the behavior of HBd and both of its terms, haplotype diversity, and a new index called branch diversity. Results followed a predicted trend in both model and empirical datasets, from low metric values in simple networks to high values in complex networks. In short, the new combined metric joins genetic and topological diversity of haplotype networks, into a single complexity value. Based on our analysis, we recommend the use of HBd, as it makes direct comparisons of network complexity straightforward and provides probabilistic values that can readily discriminate situations that are difficult to resolve with available metrics.

Highlights

In the past decades, the use of molecular data has allowed evolutionary, ecological, and conservation questions to be applied to non-model organisms in natural settings [1]
A variety of network features explained by graph theory such as node degrees, clustering coefficient, centralities, link prediction, and network density, among others, can be exploited to study the evolutionary inter-relationships between individuals illustrated in haplotype networks [8]
We introduce branch diversity (Bd), a new index that mirrors the logic used by haplotype diversity (Hd) to estimate topological diversity of networks

Summary

Introduction

The use of molecular data has allowed evolutionary, ecological, and conservation questions to be applied to non-model organisms in natural settings [1]. One way of illustrating molecular data for phylogeographic or intraspecific studies is the use of haplotype networks. These networks help to visualize relationships between individuals, populations, and species intuitively, revealing insights about migration, population structure, and speciation [2,3,4]. Values of HNd (which incorporate haplotype and topological diversity of networks) were used to explore the correlation of endemism and genetic signatures of Galapagos fishes and test predictions of population structure in endemic, insular, and widely-distributed species [3]. The premise for the introduction of the HNd metric was a need for a single value to describe the complexity of haplotype networks in terms of their genetic and topological diversity, that would be simple and intuitive [3]. Since most scientists that use haplotype networks are usually familiar with the concept and values of haplotype diversity (Hd), the intent was to produce a value similar in concept to Hd that would, in addition, capture the topological diversity of the haplotype network

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Results