What does this research mean for the field?

The PaNDA software package and its novel polynomial-time algorithm enable efficient maximization of phylogenetic diversity in phylogenetic networks with bounded scanwidth. Novelty: ClaimNovelty.METHODOLOGICAL. Consensus alignment: ConsensusAlignment.NEUTRAL.

What question did this study set out to answer?

To develop efficient algorithms and software for calculating and maximizing phylogenetic diversity in phylogenetic networks that model reticulate evolutionary events such as hybridization and horizontal gene transfer.

September 10, 2026Journal of Computational Biology

PaNDA : Efficient Optimization of Phylogenetic Diversity in Networks

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Authors

NHNiels Holtgrefe LILeo van Iersel RMRuben Meuwese

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Overview

Computational study demonstrates efficient phylogenetic diversity optimization in reticulate networks, highlighting scalable conservation prioritization for complex evolutionary lineages.

Key Points

To develop efficient algorithms and software for calculating and maximizing phylogenetic diversity in phylogenetic networks that model reticulate evolutionary events such as hybridization and horizontal gene transfer.
Developed PaNDA, an open-source software package and graphical user interface implementing a novel polynomial-time algorithm for networks of bounded scanwidth.
Extended phylogenetic diversity formalisms and computational complexity analyses to semi-directed phylogenetic networks.
Evaluated performance on simulated networks (up to level-15 with up to 200 taxa) and validated practical application using an empirical genomic network of Xiphophorus species.
The bounded scanwidth algorithm optimized phylogenetic diversity within seconds on simulated level-15 networks containing up to 200 taxa.
Proved that selecting a diversity-maximizing subset of k taxa is NP-hard on semi-directed networks, while providing a polynomial-time algorithm for semi-directed networks with bounded level.

Cite This Study

Holtgrefe et al. (2026) studied this question.

synapsesocial.com/papers/6aa27b4758559d80afc74618 https://doi.org/10.1177/15578666261481955

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September 10, 2026Journal of Computational Biology

PaNDA : Efficient Optimization of Phylogenetic Diversity in Networks

View Full Paper

Ask AI

Bookmark

Authors

NHNiels Holtgrefe LILeo van Iersel RMRuben Meuwese

Discussion

Member takes

Overview

Computational study demonstrates efficient phylogenetic diversity optimization in reticulate networks, highlighting scalable conservation prioritization for complex evolutionary lineages.

Key Points

To develop efficient algorithms and software for calculating and maximizing phylogenetic diversity in phylogenetic networks that model reticulate evolutionary events such as hybridization and horizontal gene transfer.
Developed PaNDA, an open-source software package and graphical user interface implementing a novel polynomial-time algorithm for networks of bounded scanwidth.
Extended phylogenetic diversity formalisms and computational complexity analyses to semi-directed phylogenetic networks.
Evaluated performance on simulated networks (up to level-15 with up to 200 taxa) and validated practical application using an empirical genomic network of Xiphophorus species.
The bounded scanwidth algorithm optimized phylogenetic diversity within seconds on simulated level-15 networks containing up to 200 taxa.
Proved that selecting a diversity-maximizing subset of k taxa is NP-hard on semi-directed networks, while providing a polynomial-time algorithm for semi-directed networks with bounded level.

Cite This Study

Holtgrefe et al. (2026) studied this question.

synapsesocial.com/papers/6aa27b4758559d80afc74618 https://doi.org/10.1177/15578666261481955

View Full Paper

Ask AI

Bookmark