Comprehensive Phylogenomic Inference of Eucalypts Reveals Taxonomic Limits through Gene Tree Concordance
- 1The Australian National University
Abstract
Speciation can be a slow process for long-lived organisms with large populations due to persistent incomplete lineage sorting, while hybridisation can further obscure species boundaries through admixture. In eucalypts, there is tremendous morphological and environmental variation with almost a thousand described species, subspecies, and hybrid taxa falling into multiple subgenera and intermediate sections. Multilocus molecular studies have generated concatenated species trees supporting deeper divergence between the Corymbia + Blakella + Angophora clade with the rest of eucalypts. However, the proportion of gene trees that recover the concatenated tree topology, including the taxonomic relationships among individual subgenera and sections, remains underappreciated. In this study, we assessed the predictive power of current eucalypt taxonomy - represented as a concatenated tree - in explaining topological variation across gene trees. To do this, we first extracted 1,187 BUSCO loci from short-read data of 701 samples representing roughly 500 described species using CAPTUS. We then inferred individual gene trees and a concatenated species tree using IQ-TREE2. Finally, we calculated the concordance factors for every described subgenus and section on the concatenated tree, and developed a taxonomic consistency test that tracks the taxonomic placement of each sample across gene trees. We show that, even though most taxonomic groups are monophyletic on the concatenated tree with 100% bootstrap support, several groups exhibit very low concordance, indicating that most gene trees do not recover their relationships as represented by the concatenated tree. These results highlight important considerations for current eucalypt taxonomic classification and provide a phylogenomic inference pipeline that can be applied not only to future eucalypt studies, but also to other evolutionarily complex groups of taxa.
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BibTeX
@misc{ivan2026comprehensive,
title = {{Comprehensive Phylogenomic Inference of Eucalypts Reveals Taxonomic Limits through Gene Tree Concordance}},
author = {J. Ivan and B. S. Martin and K. Murray and A.-C. Colin and C. Kuelheim and R. L. Andrew and D. Nicolle and Z. A. Myburg and J. Leebens-Mack and A. Jones and R. Lanfear and J. O. Borevitz},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.25.753384},
url = {https://www.biorxiv.org/content/10.64898/2026.09.25.753384v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Comprehensive Phylogenomic Inference of Eucalypts Reveals Taxonomic Limits through Gene Tree Concordance
AU - J. Ivan
AU - B. S. Martin
AU - K. Murray
AU - A.-C. Colin
AU - C. Kuelheim
AU - R. L. Andrew
AU - D. Nicolle
AU - Z. A. Myburg
AU - J. Leebens-Mack
AU - A. Jones
AU - R. Lanfear
AU - J. O. Borevitz
PY - 2026
DA - 2026/09/25
PB - bioRxiv
DO - 10.64898/2026.09.25.753384
UR - https://www.biorxiv.org/content/10.64898/2026.09.25.753384v1
AB - Speciation can be a slow process for long-lived organisms with large populations due to persistent incomplete lineage sorting, while hybridisation can further obscure species boundaries through admixture. In eucalypts, there is tremendous morphological and environmental variation with almost a thousand described species, subspecies, and hybrid taxa falling into multiple subgenera and intermediate sections. Multilocus molecular studies have generated concatenated species trees supporting deeper divergence between the Corymbia + Blakella + Angophora clade with the rest of eucalypts. However, the proportion of gene trees that recover the concatenated tree topology, including the taxonomic relationships among individual subgenera and sections, remains underappreciated. In this study, we assessed the predictive power of current eucalypt taxonomy - represented as a concatenated tree - in explaining topological variation across gene trees. To do this, we first extracted 1,187 BUSCO loci from short-read data of 701 samples representing roughly 500 described species using CAPTUS. We then inferred individual gene trees and a concatenated species tree using IQ-TREE2. Finally, we calculated the concordance factors for every described subgenus and section on the concatenated tree, and developed a taxonomic consistency test that tracks the taxonomic placement of each sample across gene trees. We show that, even though most taxonomic groups are monophyletic on the concatenated tree with 100% bootstrap support, several groups exhibit very low concordance, indicating that most gene trees do not recover their relationships as represented by the concatenated tree. These results highlight important considerations for current eucalypt taxonomic classification and provide a phylogenomic inference pipeline that can be applied not only to future eucalypt studies, but also to other evolutionarily complex groups of taxa.
ER -