Cargando…

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

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 othe...

Descripción completa

Detalles Bibliográficos
Autores principales: Garcia, Eric, Wright, Daniel, Gatins, Remy, Roberts, May B., Pinheiro, Hudson T., Salas, Eva, Chen, Jei-Ying, Winnikoff, Jacob R., Bernardi, Giacomo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8244886/
https://www.ncbi.nlm.nih.gov/pubmed/34191803
http://dx.doi.org/10.1371/journal.pone.0251878
_version_ 1783716014400208896
author Garcia, Eric
Wright, Daniel
Gatins, Remy
Roberts, May B.
Pinheiro, Hudson T.
Salas, Eva
Chen, Jei-Ying
Winnikoff, Jacob R.
Bernardi, Giacomo
author_facet Garcia, Eric
Wright, Daniel
Gatins, Remy
Roberts, May B.
Pinheiro, Hudson T.
Salas, Eva
Chen, Jei-Ying
Winnikoff, Jacob R.
Bernardi, Giacomo
author_sort Garcia, Eric
collection PubMed
description 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.
format Online
Article
Text
id pubmed-8244886
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-82448862021-07-12 Haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks Garcia, Eric Wright, Daniel Gatins, Remy Roberts, May B. Pinheiro, Hudson T. Salas, Eva Chen, Jei-Ying Winnikoff, Jacob R. Bernardi, Giacomo PLoS One Research Article 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. Public Library of Science 2021-06-30 /pmc/articles/PMC8244886/ /pubmed/34191803 http://dx.doi.org/10.1371/journal.pone.0251878 Text en © 2021 Garcia et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Garcia, Eric
Wright, Daniel
Gatins, Remy
Roberts, May B.
Pinheiro, Hudson T.
Salas, Eva
Chen, Jei-Ying
Winnikoff, Jacob R.
Bernardi, Giacomo
Haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks
title Haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks
title_full Haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks
title_fullStr Haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks
title_full_unstemmed Haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks
title_short Haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks
title_sort haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8244886/
https://www.ncbi.nlm.nih.gov/pubmed/34191803
http://dx.doi.org/10.1371/journal.pone.0251878
work_keys_str_mv AT garciaeric haplotypenetworkbranchdiversityanewmetriccombininggeneticandtopologicaldiversitytocomparethecomplexityofhaplotypenetworks
AT wrightdaniel haplotypenetworkbranchdiversityanewmetriccombininggeneticandtopologicaldiversitytocomparethecomplexityofhaplotypenetworks
AT gatinsremy haplotypenetworkbranchdiversityanewmetriccombininggeneticandtopologicaldiversitytocomparethecomplexityofhaplotypenetworks
AT robertsmayb haplotypenetworkbranchdiversityanewmetriccombininggeneticandtopologicaldiversitytocomparethecomplexityofhaplotypenetworks
AT pinheirohudsont haplotypenetworkbranchdiversityanewmetriccombininggeneticandtopologicaldiversitytocomparethecomplexityofhaplotypenetworks
AT salaseva haplotypenetworkbranchdiversityanewmetriccombininggeneticandtopologicaldiversitytocomparethecomplexityofhaplotypenetworks
AT chenjeiying haplotypenetworkbranchdiversityanewmetriccombininggeneticandtopologicaldiversitytocomparethecomplexityofhaplotypenetworks
AT winnikoffjacobr haplotypenetworkbranchdiversityanewmetriccombininggeneticandtopologicaldiversitytocomparethecomplexityofhaplotypenetworks
AT bernardigiacomo haplotypenetworkbranchdiversityanewmetriccombininggeneticandtopologicaldiversitytocomparethecomplexityofhaplotypenetworks