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Fast and Accurate Species Trees from Weighted Internode Distances

Authors Baqiao Liu , Tandy Warnow

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Author Details

Baqiao Liu
  • Department of Computer Science, University of Illinois Urbana-Champaign, IL, USA
Tandy Warnow
  • Department of Computer Science, University of Illinois Urbana-Champaign, IL, USA

Funding

  • Liu, Baqiao: This work was supported in part by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under the Secure Biosystems Design Initiative and by the Laboratory Directed Research and Development (LDRD) program of Sandia National Laboratories, which is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc, for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
  • Warnow, Tandy: NSF grant 2006069

Acknowledgements

The authors thank the members of the Warnow lab for insightful comments.

Cite AsGet BibTex

Baqiao Liu and Tandy Warnow. Fast and Accurate Species Trees from Weighted Internode Distances. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 8:1-8:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
https://doi.org/10.4230/LIPIcs.WABI.2022.8

Abstract

Species tree estimation is a basic step in many biological research projects, but is complicated by the fact that gene trees can differ from the species tree due to processes such as incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT), which can cause different regions within the genome to have different evolutionary histories (i.e., "gene tree heterogeneity"). One approach to estimating species trees in the presence of gene tree heterogeneity resulting from ILS operates by computing trees on each genomic region (i.e., computing "gene trees") and then using these gene trees to define a matrix of average internode distances, where the internode distance in a tree T between two species x and y is the number of nodes in T between the leaves corresponding to x and y. Given such a matrix, a tree can then be computed using methods such as neighbor joining. Methods such as ASTRID and NJst (which use this basic approach) are provably statistically consistent, very fast (low degree polynomial time) and have had high accuracy under many conditions that makes them competitive with other popular species tree estimation methods. In this study, inspired by the very recent work of weighted ASTRAL, we present weighted ASTRID, a variant of ASTRID that takes the branch uncertainty on the gene trees into account in the internode distance. Our experimental study evaluating weighted ASTRID shows improvements in accuracy compared to the original (unweighted) ASTRID while remaining fast. Moreover, weighted ASTRID shows competitive accuracy against weighted ASTRAL, the state of the art. Thus, this study provides a new and very fast method for species tree estimation that improves upon ASTRID and has comparable accuracy with the state of the art while remaining much faster. Weighted ASTRID is available at https://github.com/RuneBlaze/internode.

Subject Classification

ACM Subject Classification
  • Applied computing → Molecular evolution
Keywords
  • Species tree estimation
  • ASTRID
  • ASTRAL
  • multi-species coalescent
  • incomplete lineage sorting

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