Section: Mathematical & Computational Biology
Topic: Evolution, Genetics/genomics, Microbiology

A systematic assessment of phylogenomic approaches for microbial species tree reconstruction

Weiner, Samson1; Feng, Yutian2; Gogarten, J. Peter2, 3 ; Bansal, Mukul S.1, 3  
1 School of Computing, University of Connecticut, Storrs, Connecticut, USA
2 Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
3 The Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA

Corresponding author(s): Bansal, Mukul S. (mukul.bansal@uconn.edu)

10.24072/pcjournal.579 - Peer Community Journal, Volume 5 (2025), article no. e72.

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A key challenge in microbial phylogenomics is that microbial gene families are often affected by extensive horizontal gene transfer (HGT). As a result, most existing methods for microbial phylogenomics can only make use of a small subset of the gene families present in the microbial genomes under consideration, potentially biasing their results and affecting their accuracy. To address this challenge, several methods have recently been developed for inferring microbial species trees from genome-scale datasets of gene families affected by evolutionary events such as HGT, gene duplication, and gene loss. In this work, we use extensive simulated and real biological datasets to systematically assess the accuracies of four recently developed methods for microbial phylogenomics, SpeciesRax, ASTRAL-Pro 2, PhyloGTP, and AleRax, under a range of different conditions.  Our analysis reveals important insights into the relative performance of these methods on datasets with different characteristics, identifies shared weaknesses when analyzing complex biological datasets, and demonstrates the importance of accounting for gene tree inference error/uncertainty for improved species tree reconstruction. Among other results, we find that (i) AleRax, the only method that explicitly accounts for gene tree inference error/uncertainty, shows the best species tree reconstruction accuracy among all tested methods, (ii) PhyloGTP (developed previously by the authors of this paper) shows the best overall accuracy among methods that do not account for gene tree error and uncertainty, (iii)  ASTRAL-Pro 2 is less accurate than the other methods across nearly all tested conditions, and (iv) explicitly accounting for gene tree inference error/uncertainty can lead to substantial improvements in species tree reconstruction accuracy. Importantly, we also find that all methods, including AleRax and PhyloGTP, are susceptible to biases present in complex real biological datasets and can sometimes yield misleading phylogenies.

Published online:
DOI: 10.24072/pcjournal.579
Type: Research article
Keywords: Phylogenomics, microbial evolution, horizontal gene transfer

Weiner, Samson 1; Feng, Yutian 2; Gogarten, J. Peter 2, 3; Bansal, Mukul S. 1, 3

1 School of Computing, University of Connecticut, Storrs, Connecticut, USA
2 Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
3 The Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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Weiner, S.; Feng, Y.; Gogarten, J. P.; Bansal, M. S. A systematic assessment of phylogenomic approaches for microbial species tree reconstruction. Peer Community Journal, Volume 5 (2025), article  no. e72. https://doi.org/10.24072/pcjournal.579

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.mcb.100408

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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