STRIDE: Species Tree Root Inference from Gene Duplication Events
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Abstract
The correct interpretation of any phylogenetic tree is dependent on that tree being correctly rooted. We present STRIDE, a fast, effective, and outgroup-free method for identification of gene duplication events and species tree root inference in large-scale molecular phylogenetic analyses. STRIDE identifies sets of well-supported in-group gene duplication events from a set of unrooted gene trees, and analyses these events to infer a probability distribution over an unrooted species tree for the location of its root. We show that STRIDE correctly identifies the root of the species tree in multiple large-scale molecular phylogenetic data sets spanning a wide range of timescales and taxonomic groups. We demonstrate that the novel probability model implemented in STRIDE can accurately represent the ambiguity in species tree root assignment for data sets where information is limited. Furthermore, application of STRIDE to outgroup-free inference of the origin of the eukaryotic tree resulted in a root probability distribution that provides additional support for leading hypotheses for the origin of the eukaryotes.
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The rooted species tree is required in order to identify the correct out-group in each orthogroup tree, as correct gene tree rooting is critical for the orthology assessment from that tree.
“The rooted species tree is required in order to identify the correct out-group in each orthogroup tree, as correct gene tree rooting is critical for the orthology assessment from that tree [22].”
From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [22]
The Introduction states that the correct species-tree branching order is needed to root an unrooted gene tree and that an incorrect gene-tree root leads to incorrect ortholog identification. It does not say that a rooted species tree is required to identify an outgroup in each orthogroup tree; its discussion of outgroups concerns rooting phylogenies more generally. Page numbers are unavailable in our copy. (LLM, conf=0.84)
Experimental — accuracy not yet measuredSTRIDE was developed to enable rooting of the species tree using only information available in the set of gene trees.
“STRIDE was developed to enable the rooting of the species tree using only information available in the set of gene trees.”
From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [22]
The Introduction says STRIDE uses duplication events from unrooted gene trees to locate the root. But the Results (Application of STRIDE to Real Species Data Sets; page unavailable) say it was run with both gene trees and a published unrooted species tree, so the claim that it uses only information in the gene trees omits a required input. (LLM, conf=0.88)
Experimental — accuracy not yet measuredWhen STRIDE cannot identify the root, ortholog inference should still not be significantly impacted since the rooting of the gene tree only affects ortholog inference in cases where gene duplication events are present.
“In this case, ortholog inference should still not be significantly impacted since the rooting of the gene tree only affects ortholog inference in cases where gene duplication events are present [22].”
From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [22]
The Introduction (page unavailable) illustrates how an incorrect root can change ortholog inference in a gene tree containing a duplication event. It does not say that rooting affects ortholog inference only when duplications are present, or that ortholog inference remains largely unaffected when STRIDE cannot identify the species-tree root. Instead, it describes correct rooting as critically important to orthology inference. (LLM, conf=0.84)
Experimental — accuracy not yet measuredRooted gene trees are required to enable the use of phylogenetic information for ortholog inference, since the correct placement of the root is required for the correct dissection of phylogenetic relationships between genes in the tree.
“Rooted gene trees are required to enable the use of phylogenetic information for ortholog inference, since the correct placement of the root is required for the correct dissection of phylogenetic relationships between genes in the tree [22].”
From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [22]
STRIDE was developed to leverage gene duplication events in the complete set of orthogroup gene trees to efficiently determine the root of the species tree and achieved high accuracy on benchmark data.
“STRIDE was similarly developed to leverage gene duplication events in the complete set of orthogroup gene trees to efficiently determine the root of the species tree and achieved high accuracy on benchmark data [22].”
From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [22]
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 [22]
Automatically rooting gene trees so that they can be correctly interpreted without requiring the user to know the rooted species tree in advance is a technical challenge.
“(2) automatically rooting these gene trees so that they can be correctly interpreted [22] without requiring the user to know the rooted species tree in advance;”
From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [22]
STRIDE has been shown to identify the correct root of the species tree in multiple large-scale molecular phylogenetic data sets spanning a wide range of time scales and taxonomic groups.
“Similarly to STAG, STRIDE has been shown to identify the correct root of the species tree in multiple large-scale molecular phylogenetic data sets spanning a wide range of time scales and taxonomic groups [22].”
From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [22]
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Cites
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209 · see citing works
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571 · see citing works
Resolving difficult phylogenetic questions: Why more sequences are not enough
Philippe, H., Brinkmann, H., Lavrov, D. V., Littlewood, D. T. J., Manuel, M., Wörheide, G., & Baurain, D. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1000602 · Cited by 1,129 · see citing works
Estimating the timing of early eukaryotic diversification with multigene molecular clocks
Parfrey, L. W., Lahr, D. J. G., Knoll, A. H., & Katz, L. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1110633108 · Cited by 899 · cited 1× · see citing works
“Plants (Parfrey et al. 2011).”
New substitution models for rooting phylogenetic trees
Williams, T. A., Heaps, S. E., Cherlin, S., Nye, T. M. W., Boys, R. J., & Embley, T. M. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2014.0336 · Cited by 61 · cited 1× · see citing works
“Although time-irreversible models of sequence evolution exist, they do not provide a method for accurately inferring the direction of time in a tree (Huelsenbeck et al. 2002; Williams et al. 2015).”
Flagged first, then by citations
Research works printed but not linked: 29
- Aslett M, Aurrecoechea C, Berriman M, Brestelli J, Brunk BP, Carrington M, Depledge DP, Fischer S, Gajria B, Gao X. 2010 TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res. 38(suppl_1): D457– D462. 19843604 PMC2808979
- Berger SA, Krompass D, Stamatakis A. 2011 Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood. Syst Biol. 60 3: 291– 302. 21436105 PMC3078422
- Boussau B, Szollosi GJ, Duret L, Gouy M, Tannier E, Daubin V. 2013 Genome-scale coestimation of species and gene trees. Genome Res. 23 2: 323– 330. 23132911 PMC3561873
- Burki F. 2014 The Eukaryotic Tree of Life from a Global Phylogenomic Perspective. Cold Spring Harbor Persp Biol. 6 5: a016147. PMC3996474 24789819
- Chen K, Durand D, Farach-Colton M. 2000 NOTUNG: A program for dating gene duplications and optimizing gene family trees. J Comput Biol. 7(3-4): 429– 447. 11108472
- Donoghue MJ, Mathews S. 1998 Duplicate genes and the root of angiosperms, with an example using phytochrome sequences. Mol Phylogenet. Evol. 9 3: 489– 500. 9667997
- dos Reis M, Donoghue PCJ, Yang ZH. 2014 Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals. Biol Lett. 10 1: 20131003. 24429684 PMC3917342
- Dunne MP, Kelly S. 2017 OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations. bioRxiv. doi: 10.1101/098566. PMC5437544 28521726 · DOI
- Emms DM, Kelly S. 2015 OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 16 1: 157. 26243257 PMC4531804
- Goodstein DM, Shu SQ, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, 2012 Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40(Database issue): D1178– D1186. 22110026 PMC3245001
- Gorecki P, Eulenstein O. 2014 DrML: probabilistic modeling of gene duplications. J Comput Biol. 21 1: 89– 98. 24073895 PMC3880059
- Gorecki P, Eulenstein O, Tiuryn J. 2013 Unrooted Tree Reconciliation: A Unified Approach. IEEE-ACM Trans Comput Biol Bioinformatics 10 2: 522– 536. 23929875
- Gorecki P, Tiuryn J. 2007 Inferring phylogeny from whole genomes. Bioinformatics 23 2: E116– E122. 17237078
- Huelsenbeck JP, Bollback JP, Levine AM. 2002 Inferring the root of a phylogenetic tree. Syst Biol. 51 1: 32– 43. 11943091
- Huerta-Cepas J, Serra F, Bork P. 2016 ETE 3: Reconstruction, analysis, and visualization of phylogenomic data. Mol Biol Evol. 33 6: 1635– 1638. 26921390 PMC4868116
- Huson DH, Scornavacca C. 2012 Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol. 61 6: 1061– 1067. 22780991
- Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, 2014 Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346 6215: 1320– 1331. 25504713 PMC4405904
- Kuck P, Mayer C, Wagele JW, Misof B. 2012 Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model. PLoS One 7(5):e36593. PMC3359070 22662120
- Larsson A. 2014 AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 30 22: 3276– 3278. 25095880 PMC4221126
- Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015 IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32 1: 268– 274. 25371430 PMC4271533
- Rasmussen MD, Kellis M. 2012 Unified modeling of gene duplication, loss, and coalescence using a locus tree. Genome Res. 22 4: 755– 765. 22271778 PMC3317157
- Ruhfel BR, Gitzendanner MA, Soltis PS, Soltis DE, Burleigh JG. 2014 From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evol Biol. 14: 23. 24533922 PMC3933183
- Salichos L, Rokas A. 2013 Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497 7449: 327– 331. 23657258
- Simmons MP, Bailey CD, Nixon KC. 2000 Phylogeny reconstruction using duplicate genes. Mol Biol Evol. 17 4: 469– 473. 10742039
- Szöllősi GJ, Tannier E, Daubin V, Boussau B. 2015 The inference of gene trees with species trees. Syst Biol. 64 1: E42– E62. 25070970 PMC4265139
- Tange O. 2011 GNU Parallel—the command-line power tool.;login: The USENIX Mag. 36: 42– 47.
- Veeckman E, Ruttink T, Vandepoele K. 2016 Are we there yet? Reliably estimating the completeness of plant genome sequences. Plant Cell 28 8: 1759– 1768. 27512012 PMC5006709
- Wu YC, Rasmussen MD, Bansal MS, Kellis M. 2014 Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees. Genome Res. 24 3: 475– 486. 24310000 PMC3941112
- Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, 2016 Ensembl 2016. Nucleic Acids Res. 44(D1): D710– D716. 26687719 PMC4702834
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-citationA rooted phylogeny resolves early bacterial evolution
Coleman, G. A., Davín, A. A., Mahendrarajah, T. A., Szánthó, L. L., Spang, A., Hugenholtz, P., Szöllősi, G. J., & Williams, T. A. (2021) · Science · doi:10.1126/science.abe0511 · Cited by 285 · see citing works
Harris, B. J., Clark, J. W., Schrempf, D., Szöllősi, G. J., Donoghue, P. C. J., Hetherington, A. M., & Williams, T. A. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01885-x · Cited by 187 · see citing works
OrthoFinder: 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, Steven
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-09-26
- Volume
- 34
- Issue
- 12
- Pages
- 3267-3278
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC5850722
- OpenAlex
- W2952556895
- Cited by
- 311
- References
- 5
- Citations by year
- 2026: 46 · 2025: 50 · 2024: 58 · 2023: 42 · 2022: 46 · 2021: 34 · 2020: 20 · 2019: 9 · 2018: 5 · 2014: 1
- FWCI
- 3.70
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- Molecular Biology and Evolution (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Oxford University Research Archive (ORA) (University of Oxford) (submittedVersion, cc-by)
- Funders
- Royal Society
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- probability models, eukaryotic origin, molecular phylogeny, STRIDE
- MeSH terms
- Algorithms, Computer Simulation, Models, Genetic, Phylogeny, Software, Sequence Analysis, DNA, Evolution, Molecular, Gene Duplication
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