STAG: Species Tree Inference from All Genes
Open accessAbstract
Species tree inference is fundamental to our understanding of the evolution of life on earth. However, species tree inference from molecular sequence data is complicated by gene duplication events that limit the availably of suitable data for phylogenetic reconstruction. Here we propose a novel method for species tree inference called STAG that is specifically designed to leverage data from multi-copy gene families. By application to 12 real species datasets sampled from across the eukaryotic domain we demonstrate that species trees inferred from multi-copy gene families are comparable in accuracy to species trees inferred from single-copy orthologues. We further show that the ability to utilise data from multi-copy gene families increases the amount of data available for species tree inference by an average of 8 fold. We reveal that on real species datasets STAG has higher accuracy than other leading methods for species tree inference; including concatenated alignments of protein sequences, ASTRAL & NJst. Finally we show that STAG is fast, memory efficient and scalable and thus suitable for analysis of large multispecies datasets.
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STAG was developed to leverage the vast amount of phylogenetic information already available in the complete set of orthogroup gene trees inferred by OrthoFinder and to be robust to high levels of gene duplication and loss that can hamper methods that rely on sets of single-copy orthologs.
“STAG was developed to leverage the vast amount of phylogenetic information already available in the complete set of orthogroup gene trees inferred by OrthoFinder. It was also developed to be robust to high levels of gene duplication and loss that can hamper methods that rely on sets of single-copy orthologs [33].”
From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [33]
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Experimental — accuracy not yet measuredSTAG outperformed popular species tree inference methods on benchmark data and scaled well to large datasets.
“It outperformed popular species tree inference methods on benchmark data and scaled well to large datasets [33].”
From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [33]
STAG was developed to allow species tree inference even for species sets with few or no complete sets of one-to-one orthologs present in all species.
“A new algorithm, Species Tree from All Genes (STAG), was developed to allow species tree inference even for species sets with few or no complete sets of one-to-one orthologs present in all species [33].”
From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [33]
The accuracy of key component algorithms of OrthoFinder has been independently assessed in this work and in dedicated publications.
“The accuracy of key component algorithms of OrthoFinder has been independently assessed in this work and in dedicated publications [5, 10, 22, 24, 33].”
From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [33]
Sets of one-to-one orthologs present in all species are often used for species tree inference, but in real-world large-scale analyses they can be rare.
“Sets of one-to-one orthologs that are present in all species are often used for species tree inference; however, in real-world large-scale analyses, these can be rare [33].”
From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [33]
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Cited by
Sorted by citations
OrthoFinder: phylogenetic orthology inference for comparative genomics
Emms, D. M., & Kelly, S. (2019) · Genome Biology · doi:10.1186/s13059-019-1832-y · Cited by 7,676 · see citing works
Self-citationOrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability
Emms, D. M., Liu, Y., Belcher, L., Holmes, J., & Kelly, S. (2026) · Nature Methods · doi:10.1038/s41592-026-03126-6 · Cited by 25 · see citing works
Self-citation
- Authors
- Emms, D. M., & Kelly, S.
- Affiliations
- University of Oxford (GB)
- Corresponding author
- Kelly, S.
- ORCID
- Venue
- bioRxiv (Cold Spring Harbor Laboratory)
- Publisher
- openRxiv
- Published
- 2018-02-19
- OpenAlex
- W2793316497
- Cited by
- 332
- References
- 3
- Citations by year
- 2026: 43 · 2025: 62 · 2024: 49 · 2023: 50 · 2022: 56 · 2021: 39 · 2020: 26 · 2019: 5 · 2018: 2
- Type
- posted content
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by
- Locations
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Funders
- University of Oxford
- European Commission (637765, HORIZON2020)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
- Keywords
- species tree inference, gene duplication, stags, eukaryotic phylogeny, orthologs, concatenated alignment, ASTRAL, phylogenomics
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