Contentious relationships in phylogenomic studies can be driven by a handful of genes
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Phylogenomic studies have resolved countless branches of the tree of life, but remain strongly contradictory on certain, contentious relationships. Here, we use a maximum likelihood framework to quantify the distribution of phylogenetic signal among genes and sites for 17 contentious branches and 6 well-established control branches in plant, animal and fungal phylogenomic data matrices. We find that resolution in some of these 17 branches rests on a single gene or a few sites, and that removal of a single gene in concatenation analyses or a single site from every gene in coalescence-based analyses diminishes support and can alter the inferred topology. These results suggest that tiny subsets of very large data matrices drive the resolution of specific internodes, providing a dissection of the distribution of support and observed incongruence in phylogenomic analyses. We submit that quantifying the distribution of phylogenetic signal in phylogenomic data is essential for evaluating whether branches, especially contentious ones, are truly resolved. Finally, we offer one detailed example of such an evaluation for the controversy regarding the earliest-branching metazoan phylum, for which examination of the distributions of gene-wise and site-wise phylogenetic signal across eight data matrices consistently supports ctenophores as the sister group to all other metazoans.
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The study assessed robustness of age estimates by running analyses under autocorrelated and uncorrelated relaxed molecular-clock models, three fossil calibration sets, three root age priors (800, 1000, 1360 Ma), and three alternative placements of Ctenophora.
“In order to assess the robustness of our age estimates to a number of prior assumptions, we ran analyses under (1) an autocorrelated and an uncorrelated relaxed molecular-clock model – the former assuming that the rate of molecular evolution of a lineage is correlated with the rate of its mother lineage, the latter allowing completely independent rates from lineage to lineage; (2) three different”
From Dating early animal evolution using phylogenomic data (2017) · cites this paper as [26]
The Methods section, “The root of the Metazoan phylogeny” (page unavailable), examines three hypotheses about the earliest-branching metazoan lineage, including alternative relationships involving Ctenophora. But it tests phylogenetic support, not the robustness of age estimates; the searched passages do not report relaxed-clock models, fossil calibration sets, or root-age priors of 800, 1000, and 1360 Ma. (LLM, conf=0.82)
Experimental — accuracy not yet measuredUse of other site-heterogeneous models that may not suffer from problems associated with CAT-F81 resulted in Ctenophora sister to all other animals.
“Use of other siteheterogeneous models that may not suffer from problems associated with CAT-F81 (see 24 and Supplementary Discussion) resulted in Ctenophora sister to all other animals 21 , consistent with our findings (Fig. 2, Supplementary Fig. S1-S14) and those of two recent papers that employed novel methods 25,26 .”
From Ctenophore relationships and their placement as the sister group to all other animals (2017) · cites this paper as [26]
The Results section (‘What is the earliest branch of the metazoan phylogeny?’; page unavailable) reports robust support for Ctenophora as sister to the other animals. The Methods section (‘The root of the Metazoan phylogeny’; page unavailable) describes constraint maximum-likelihood analyses, not the use of other site-heterogeneous models. The cited paper therefore supports the placement but not the claim about which models produced it or their relationship to CAT-F81. (LLM, conf=0.88)
Experimental — accuracy not yet measuredAnalysis methods to assess underlying support in phylogenomic datasets at the level of individual sites and genes have revealed underlying support favouring Ctenophora sister, but so far only under standard site-homogeneous models.
“This approach has, conversely, revealed underlying support favouring Ctenophora sister4,40, but so far has only been performed under standard site-homogeneous models.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [40]
The primary remaining lines of evidence supporting Ctenophora sister, partitioned phylogenomics and measures of underlying support (such as ΔPSlnl values), do not do so when better-fitting site-heterogeneous models are incorporated into the analysis.
“Here, we have consolidated these findings by directly showing that the primary remaining lines of evidence supporting Ctenophora sister, partitioned phylogenomics4,7 and measures of underlying support (such as ΔPSlnl values)4,40, do not do so when better-fitting site-heterogeneous models are incorporated into the analysis.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [40]
The ΔPSlnl strategy has previously shown support for Ctenophora sister, in the form of a greater proportion of sites and gene partitions favouring comb jellies over sponges as the sister group to other animals.
“This strategy has previously shown support for Ctenophora sister, in the form of a greater proportion of sites and gene partitions favouring comb jellies over sponges as the sister group to other animals4,40.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [40]
Our results reject previous studies taking the ΔPSlnl approach that have found support for the Ctenophora-sister hypothesis.
“Quantifying and comparing support for alternative hypotheses for a given gene/site allows for dissection of the signal favouring one hypothesis or another in a dataset, and our results reject previous studies taking this approach that have found support for the Ctenophora-sister hypothesis4,40.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [40]
These irreversible FWM events provided powerful phylogenomic markers, offering strong evidence for resolving the long-debated relationships between ctenophores, sponges, and the rest of Metazoa.
“These irreversible FWM events provided powerful phylogenomic markers (97), offering strong evidence for resolving the long-debated relationships (104, 105) between ctenophores, sponges, and the rest of Metazoa.”
From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [105]
Some differences between the results of RAxML/ExaML and IQ-TREE correspond to contentious relationships in phylogenomic studies.
“Importantly, some of the differences between the results of RAxML/ExaML and IQ-TREE correspond to contentious relationships in phylogenomic studies (e.g., in data set ChenA4: The relative positions of pigeon, falcon, and other Neoaves; and in data set WickD3a: The relationships between Chloranthales, Eudicots, and Magnoliids) (Shen et al. 2017).”
From Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets (2018) · cites this paper as Shen et al. 2017
Shen et al. [11] generated datasets that excluded the few genes they identified as outliers.
“Shen et al. [11] generated datasets that excluded the few genes that they identified as ''outliers,''”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [11]
Shen et al. [11] analyzed their outlier-excluded datasets under LG+G and found support for Ctenophora-sister.
“analyzed these datasets under LG+G, and found support for Ctenophora-sister”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [11]
The conclusion of Shen et al. [11] that signal for Porifera-sister is limited to 'outlier genes' is rejected, and their approach is model dependent.
“This result rejects the conclusions of [11] that signal for Porifera-sister is limited to ''outlier genes'' and indicates that their approach is model dependent: arguments about model adequacy should be considered when implementing it.”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [11]
LG+G was used by [11].
“LG+G was used by [11]”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [11]
CAT-GTR+G analyses of a dataset from Whelan et al. [10] from which Shen et al. [11] removed 'outlier genes' still finds support for Porifera-sister (PP = 0.98 and PP = 0.99, respectively).
“Indeed, CAT-GTR+G analyses (with and without Dayhoff-6 recoding) of a dataset of [10] from which [11] removed ''outlier genes'' still finds support for Porifera-sister (PP = 0.98 and PP = 0.99, respectively; Figures S3I and S3J).”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [11]
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- Authors
- Shen, X.-X., Hittinger, C. T., & Rokas, A.
- Affiliations
- Vanderbilt University (US)
- University of Wisconsin–Madison (US)
- Corresponding author
- Rokas, Antonis
- Venue
- Nature Ecology & Evolution
- Published
- 2017-04-10
- Volume
- 1
- Issue
- 5
- Pages
- 126-126
- ISSN
- 2397-334X (ISSN-L)
- PMC
- PMC5560076
- OpenAlex
- W2607411230
- Semantic Scholar
- 1a74377821782786bf6787cb988e289469f977ac
- Cited by
- 520
- References
- 62
- Citations by year
- 2026: 25 · 2025: 39 · 2024: 41 · 2023: 49 · 2022: 36 · 2021: 67 · 2020: 70 · 2019: 78 · 2018: 74 · 2017: 41
- FWCI
- 29.45
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Ecology & Evolution (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- National Science Foundation (1442148, BER DE-FC02-07ER64494, 1003258, 1442113)
- U.S. Department of Energy (FC02-07ER64494, 07ER64494, DEFC0207ER64494, BER DE‐FC02‐07ER64494)
- U.S. Department of Agriculture (DE-FC02-07ER64494)
- Vanderbilt University
- National Institutes of Health
- National Institute of Food and Agriculture (1003258, DE-FC02-07ER64494)
- Office of Science (BER DE-FC02-07ER64494, FC02-07ER64494, DEFC0207ER64494)
- Great Lakes Bioenergy Research Center (BER-DE-FC02-07ER64494, DE‐FC02‐07ER64494)
- National Institute of Allergy and Infectious Diseases (AI105619, R21AI105619)
- 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
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Keywords
- phylogenetic incongruence, ctenophores, phylogenomics, phylogenetic support
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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