The DOI matches its Crossref record; 62 of the 62 references it cites were found in a registry or an index.
Contentious relationships in phylogenomic studies can be driven by a handful of genes
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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 cited source says what the claim attributes to it.
In the citing paper
“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 cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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]
In the citing paper
“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
In the citing paper
“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]
In the citing paper
“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]
In the citing paper
“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]
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu300 · Cited by 26,046
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Gentleman R: R: A language for data analysis and graphics
Ihaka, R., & Gentleman, R. (1996) · Journal of Computational and Graphical Statistics · doi:10.1080/10618600.1996.10474713 · Cited by 11,747
A Rapid Bootstrap Algorithm for the RAxML Web Servers
Stamatakis, A., Hoover, P., & Rougemont, J. (2008) · Systematic Biology · doi:10.1080/10635150802429642 · Cited by 7,028
An approximately unbiased test of phylogenetic tree selection
Shimodaira, H. (2002) · Systematic Biology · doi:10.1080/10635150290069913 · Cited by 2,791
Phylogenomics resolves the timing and pattern of insect evolution
Misof, B., Liu, S., Meusemann, K., Peters, R. S., Donath, A., Mayer, C., Frandsen, P. B., Ware, J., Flouri, T., Beutel, R. G., et al. (2014) · Science · doi:10.1126/science.1257570 · Cited by 2,694
CONSEL: for assessing the confidence of phylogenetic tree selection
Shimodaira, H., & Hasegawa, M. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.12.1246 · Cited by 2,049
Gene tree discordance, phylogenetic inference and the multispecies coalescent
Degnan, J. H., & Rosenberg, N. A. (2009) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2009.01.009 · Cited by 1,978
Broad phylogenomic sampling improves resolution of the animal tree of life
Dunn, C. W., Hejnol, A., Matus, D. Q., Pang, K., Browne, W. E., Smith, S. A., Seaver, E., Rouse, G. W., Obst, M., Edgecombe, G. D., et al. (2008) · Nature · doi:10.1038/nature06614 · Cited by 1,921
Research works printed but not linked: 1
- Borowiec, M. L., Lee, E. K., Chiu, J. C. & Plachetzki, D. C. Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa. BMC Genomics 16, 987 (2015). · DOI · Paper page
Cited by
Sorted by citations
Items 201–300 of 524
Gruenstaeudl, M. (2019) · Plant Systematics and Evolution · doi:10.1007/s00606-019-01610-5 · Cited by 27
Assessing support for Blaberoidea phylogeny suggests optimal locus quality
Evangelista, D. A., Simon, S., Wilson, M., Kawahara, A. Y., Kohli, M. K., Ware, J. L., Wipfler, B., Béthoux, O., Grandcolas, P., & Legendre, F. (2020) · Systematic Entomology · doi:10.1111/syen.12454 · Cited by 27
Orr, M. C., Branstetter, M. G., Straka, J., Yuan, F., Leijs, R., Zhang, D., Zhou, Q., & Zhu, C. (2022) · Insect Systematics and Diversity · doi:10.1093/isd/ixac022 · Cited by 27
Myers, E. A., Rautsaw, R. M., Borja, M., Jones, J. M., Grünwald, C. I., Holding, M. L., Grazziotin, F. G., & Parkinson, C. L. (2024) · Systematic Biology · doi:10.1093/sysbio/syae018 · Cited by 25
Chafin, T. K., Douglas, M. R., Bangs, M. R., Martin, B. T., Mussmann, S. M., & Douglas, M. E. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab200 · Cited by 26
He, B., Zhao, Y., Su, C., Lin, G., Wang, Y., Li, L., Ma, J., Yang, Q., & Hao, J. (2023) · Systematic Entomology · doi:10.1111/syen.12592 · Cited by 28
Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae
Thureborn, O., Wikström, N., Razafimandimbison, S. G., & Rydin, C. (2024) · PLoS ONE · doi:10.1371/journal.pone.0302365 · Cited by 25
Gene-tree misrooting drives conflicts in phylogenomic coalescent analyses of palaeognath birds
Simmons, M. P., Springer, M. S., & Gatesy, J. (2021) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2021.107344 · Cited by 24
Jewari, C. A., & Baldauf, S. L. (2022) · Systematic Biology · doi:10.1093/sysbio/syac029 · Cited by 25
Presnell, J. S., Bubel, M. M., Knowles, T., Patry, W. L., & Browne, W. E. (2022) · Nature Protocols · doi:10.1038/s41596-022-00702-w · Cited by 25
Variation across Species and Levels: Implications for Model Species Research
Striedter, G. F. (2019) · Brain Behavior and Evolution · doi:10.1159/000499664 · Cited by 28
Releasing uncurated datasets is essential for reproducible phylogenomics
Salomaki, E. D., Eme, L., Brown, M. W., & Kolísko, M. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-01296-w · Cited by 24
Hawlitschek, O., Ortiz, E. M., Noori, S., Webster, K. C., Husemann, M., & Pereira, R. J. (2022) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2022.107439 · Cited by 24
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush
Fedosov, A. E., Zaharias, P., Lemarcis, T., Modica, M. V., Holford, M., Oliverio, M., Kantor, Y., & Puillandre, N. (2024) · Systematic Biology · doi:10.1093/sysbio/syae010 · Cited by 24
Detecting introgression despite phylogenetic uncertainty: The case of the South American siskins
Beckman, E. J., Benham, P. M., Cheviron, Z. A., & Witt, C. C. (2018) · Molecular Ecology · doi:10.1111/mec.14795 · Cited by 25
Zhang, J., Heraty, J. M., Darling, C., Kresslein, R. L., Baker, A. J., Torréns, J., Rasplus, J., Lemmon, A. R., & Lemmon, E. M. (2022) · Systematic Entomology · doi:10.1111/syen.12533 · Cited by 23
Černý, D., & Simonoff, A. L. (2023) · Scientific Reports · doi:10.1038/s41598-023-35784-3 · Cited by 23
Appelhans, M. S., Paetzold, C., Wood, K. R., & Wagner, W. L. (2020) · Journal of Systematics and Evolution · doi:10.1111/jse.12668 · Cited by 23
de Guinea, M., Estrada, A., Janmaat, K. R. L., Nekaris, K. A. I., & Belle, S. V. (2021) · Animal Behaviour · doi:10.1016/j.anbehav.2020.12.017 · Cited by 34
Codon use and aversion is largely phylogenetically conserved across the tree of life
Miller, J. B., Harmon, L. M., Whiting, M. F., & Ridge, P. G. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.106697 · Cited by 22
Organelle Phylogenomics and Extensive Conflicting Phylogenetic Signals in the Monocot Order Poales
Wu, H., Yang, J., Liu, J., Li, D.-Z., & Ma, P. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2021.824672 · Cited by 22
Drábková, M., Kocot, K. M., Halanych, K. M., Oakley, T. H., Moroz, L. L., Cannon, J. T., Kuris, A. M., Garcia‐Vedrenne, A. E., Pankey, M. S., Ellis, E. A., et al. (2022) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2022.0683 · Cited by 26
la Hoz, C. J. P., Magain, N., Piatkowski, B. T., Cornet, L., Forno, M. D., Carbone, I., Miądlikowska, J., & Lutzoni, F. M. (2023) · Systematic Biology · doi:10.1093/sysbio/syad008 · Cited by 25
Rapid Laurasian diversification of a pantropical bird family during the Oligocene–Miocene transition
Oliveros, C. H., Andersen, M. J., Hosner, P. A., Mauck, W. M., Sheldon, F. H., Cracraft, J. L., & Moyle, R. G. (2019) · Ibis · doi:10.1111/ibi.12707 · Cited by 24
Moreland, R. T., Nguyen, A., Ryan, J. F., & Baxevanis, A. D. (2020) · Database · doi:10.1093/database/baaa029 · Cited by 20
The Emergence of Shell Valuable Exchange in the New Guinea Highlands
Gaffney, D., Summerhayes, G. R., Szabó, K., & Koppel, B. (2018) · American Anthropologist · doi:10.1111/aman.13154 · Cited by 21
Evolutionary sparse learning for phylogenomics
Kumar, S., & Sharma, S. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab227 · Cited by 22
Presnell, J. S., & Browne, W. E. (2021) · Development · doi:10.1242/dev.199771 · Cited by 21
Murillo‐A, J., Valencia-D, J., Orozco, C. I., Parra‐O., C., & Neubig, K. M. (2022) · American Journal of Botany · doi:10.1002/ajb2.16025 · Cited by 21
Pastrana, C. C., DeBiasse, M. B., & Ryan, J. F. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz052 · Cited by 20
The genus Cortinarius should not (yet) be split
Gallone, B., Kuyper, T. W., & Nuytinck, J. (2024) · IMA Fungus · doi:10.1186/s43008-024-00159-4 · Cited by 20
Records of ctenophores from South Africa
Gibbons, M. J., Haddock, S. H. D., Matsumoto, G. I., & Foster, C. (2021) · PeerJ · doi:10.7717/peerj.10697 · Cited by 20
Phylogenetic Resolution and Conflict in the Species-Rich Flowering Plant Family Leguminosae
Zhang, R., Stull, G. W., Jin, J., Wang, Y., Guo, Y., Yang, Z., Li, H., An, K.-L., Charboneau, J. L. M., Folk, R. A., et al. (2025) · Systematic Biology · doi:10.1093/sysbio/syaf057 · Cited by 19
Environment‐Organism Feedbacks Drive Changes in Ecological Interactions
Meacock, O. J., & Mitri, S. (2024) · Ecology Letters · doi:10.1111/ele.70027 · Cited by 19
Zhong, B., & Betancur‐R, R. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx233 · Cited by 19
Aharon, S., Ballesteros, J. A., Crawford, A. R., Friske, K., Gainett, G., Langford, B., Santibáñez‐López, C. E., Ya‘aran, S., Gavish‐Regev, E., & Sharma, P. P. (2019) · Invertebrate Systematics · doi:10.1071/is19002 · Cited by 19
Differences in Performance among Test Statistics for Assessing Phylogenomic Model Adequacy
Duchêne, D. A., Duchêne, S., & Ho, S. Y. W. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy094 · Cited by 19
Yuan, C., Sha, X.-F., Xiong, M., Zhong, W., Wei, Y., Li, M., Tao, S., Mou, F., Peng, F., & Zhang, C. (2021) · Scientific Reports · doi:10.1038/s41598-020-80225-0 · Cited by 18
Brain size evolution in whales and dolphins: new data from fossil mysticetes
McCurry, M. R., Marx, F. G., Evans, A. R., Park, T., Pyenson, N. D., Kohno, N., Castiglione, S., & Fitzgerald, E. M. G. (2021) · Biological Journal of the Linnean Society · doi:10.1093/biolinnean/blab054 · Cited by 18
Liu, T.-J., Zhang, S., Wei, L., Lin, W., Yan, H., Hao, G., & Ge, X. (2023) · BMC Plant Biology · doi:10.1186/s12870-023-04363-z · Cited by 18
Yu, H. Y., Chu, K. H., Tsang, L. M., & Ma, K. Y. (2024) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2024.1243221 · Cited by 23
Müller, W. E. G., Schröder, H. C., & Wang, X. (2017) · Marine Drugs · doi:10.3390/md15060172 · Cited by 19
Whole genome phylogeny of Gallus: introgression and data-type effects
Tiley, G. P., Pandey, A., Kimball, R. T., Braun, E. L., & Burleigh, J. G. (2020) · Avian Research · doi:10.1186/s40657-020-00194-w · Cited by 18
Britz, R., Dahanukar, N., Anoop, V. K., Philip, S., Clark, B. L., Raghavan, R., & Rüber, L. (2020) · Scientific Reports · doi:10.1038/s41598-020-73129-6 · Cited by 21
Molloy, E. K., Gatesy, J., & Springer, M. S. (2021) · Systematic Biology · doi:10.1093/sysbio/syab086 · Cited by 18
Is Phenotypic Evolution Affected by Spiders’ Construction Behaviors?
Shao, L., Zhao, Z., & Li, S. (2022) · Systematic Biology · doi:10.1093/sysbio/syac063 · Cited by 17
Placing human gene families into their evolutionary context
Dornburg, A., Mallik, R., Wang, Z., Bernal, M. A., Thompson, B., Bruford, E. A., Nebert, D. W., Vasiliou, V., Yohe, L. R., Yoder, J. A., et al. (2022) · Human Genomics · doi:10.1186/s40246-022-00429-5 · Cited by 21
Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny
McCarthy, C. G. P., Mulhair, P. O., Siu-Ting, K., Creevey, C. J., & O’Connell, M. J. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac276 · Cited by 19
Structural Variation of the Turtle Mitochondrial Control Region
Bernacki, L. E., & Kilpatrick, C. W. (2020) · Journal of Molecular Evolution · doi:10.1007/s00239-020-09962-0 · Cited by 17
Unraveling the history of the genus Gallus through whole genome sequencing
Mariadassou, M., Suez, M., Sathyakumar, S., Alain Vignal, A., Arca, M., Nicolas, P., Faraut, T., Esquerré, D., Nishibori, M., Vieaud, A., et al. (2020) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2020.107044 · Cited by 17
Population Genomics of Early-Splitting Lineages of Metazoans
Pérez‐Portela, R., & Riesgo, A. (2018) · Population genomics · doi:10.1007/13836_2018_13 · Cited by 17
Koch, N. M., Ekin, T., Miller, A. K., Stiller, J., & Rouse, G. W. (2023) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2023.0988 · Cited by 16
Dating Ammonia-Oxidizing Bacteria with Abundant Eukaryotic Fossils
Liao, T., Wang, S., Zhang, H., Stüeken, E. E., & Luo, H. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae096 · Cited by 17
The link between ancient whole‐genome duplications and cold adaptations in the Caryophyllaceae
Feng, K., Walker, J. F., Marx, H. E., Yang, Y. J., Brockington, S. F., Moore, M. J., Rabeler, R. K., & Smith, S. A. (2024) · American Journal of Botany · doi:10.1002/ajb2.16350 · Cited by 16
Du, Y., Wu, S., Edwards, S. V., & Liu, L. (2019) · BMC Evolutionary Biology · doi:10.1186/s12862-019-1534-9 · Cited by 16
Inferring Ancient Relationships with Genomic Data: A Commentary on Current Practices
Laumer, C. (2018) · Integrative and Comparative Biology · doi:10.1093/icb/icy075 · Cited by 15
Phang, A., Pezzini, F. F., Burslem, D. F. R. P., Khew, G. S.-W., Middleton, D. J., Ruhsam, M., & Wilkie, P. (2023) · Botanical Journal of the Linnean Society · doi:10.1093/botlinnean/boad022 · Cited by 15
Distinct hybridization modes in wide- and narrow-ranged lineages of Causonis (Vitaceae)
Yu, J., Zhao, H. C., Niu, Y., You, Y., Barrett, R. L., Ranaivoson, R. M., Rabarijaona, R. N., Parmar, G., Yuan, L., Jin, X., et al. (2023) · BMC Biology · doi:10.1186/s12915-023-01718-8 · Cited by 14
Winn, J. C., Maduna, S. N., & der Merwe, A. E. B. (2023) · Genomics · doi:10.1016/j.ygeno.2023.110771 · Cited by 15
Pinniped Diphyly and Bat Triphyly: More Homology Errors Drive Conflicts in the Mammalian Tree
Springer, M. S., & Gatesy, J. (2017) · Journal of Heredity · doi:10.1093/jhered/esx089 · Cited by 15
Saavedra, L. M., Saldías, G. S., Broitman, B. R., & Vargas, C. A. (2020) · ICES Journal of Marine Science · doi:10.1093/icesjms/fsaa127 · Cited by 15
Are fleas highly modified Mecoptera? Phylogenomic resolution of Antliophora (Insecta: Holometabola)Preprint
Meusemann, K., Trautwein, M., Friedrich, F., BEUTEL, R. G., Wiegmann, B. M., Donath, A., Podsiadłowski, L., Petersen, M., Niehuis, O., Mayer, C., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.19.390666 · Cited by 15
Yan, H., Liu, T.-J., Yuan, X., Xu, Y., Zhang, S., Hao, G., & Ge, X. (2025) · Journal of Systematics and Evolution · doi:10.1111/jse.13154 · Cited by 14
A phylogenomic tree of wood-warblers (Aves: Parulidae): Dealing with good, bad, and ugly samples
Zhao, M., Oswald, J. A., Allen, J. M., Owens, H. L., Hosner, P. A., Guralnick, R., Braun, E. L., & Kimball, R. T. (2024) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2024.108235 · Cited by 12
Genome-Scale Profiling Reveals Noncoding Loci Carry Higher Proportions of Concordant Data
Literman, R., & Schwartz, R. S. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab026 · Cited by 14
Walker, J. F., Smith, S. A., Hodel, R. G. J., & Moyroud, E. (2021) · Systematic Biology · doi:10.1093/sysbio/syab052 · Cited by 14
Phylogenomic analyses of ochrophytes (stramenopiles) with an emphasis on neglected lineages
Cho, A., Lax, G., & Keeling, P. J. (2024) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2024.108120 · Cited by 11
Ruiz, D. C., Vallès, J., Bayer, R. J., Palazzesi, L., Pellicer, J., Pérez-Lorenzo, I., Maurin, O., Françoso, E., Roy, S. R., Leitch, I. J., et al. (2024) · Journal of Systematics and Evolution · doi:10.1111/jse.13118 · Cited by 13
Höhna, S., Lower, S. E., Duchen, P., & Catalán, A. (2024) · Systematic Biology · doi:10.1093/sysbio/syae065 · Cited by 13
Zhang, M., Xiang, Q., & Zhang, X.-C. (2022) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2022.107507 · Cited by 13
The ctenophore Mnemiopsis leidyi regulates egg production via conspecific communication
Sasson, D. A., Jacquez, A. A., & Ryan, J. F. (2018) · BMC Ecology · doi:10.1186/s12898-018-0169-9 · Cited by 13
The synergistic effect of concatenation in phylogenomics: the case in Pantoea
Palmer, M., Venter, S. N., McTaggart, A. R., Coetzee, M. P. A., van Wyk, S., Avontuur, J. R., Beukes, C. W., Fourie, G., Santana, Q. C., van der Nest, M. A., et al. (2019) · PeerJ · doi:10.7717/peerj.6698 · Cited by 14
Miller, J. B., Harmon, L. M., Whiting, M. F., Kauwe, J. S. K., & Ridge, P. G. (2020) · PLoS ONE · doi:10.1371/journal.pone.0232260 · Cited by 15
Dong, S., Li, H., Goffinet, B., & Liu, Y. (2020) · Journal of Systematics and Evolution · doi:10.1111/jse.12706 · Cited by 13
Owen, C. L., Marshall, D. C., Wade, E. J., Meister, R. C., Goemans, G., Kunte, K. K., Moulds, M. S., Hill, K. B. R., Villet, M. H., Pham, T.-H., et al. (2022) · Systematic Biology · doi:10.1093/sysbio/syac043 · Cited by 12
Siozios, S., Pilgrim, J., Darby, A. C., Baylis, M., & Hurst, G. D. D. (2019) · PeerJ · doi:10.7717/peerj.6448 · Cited by 13
Zhao, N., Park, S., Zhang, Y., Nie, Z., Ge, X., Kim, S., & Yan, H. (2022) · Annals of Botany · doi:10.1093/aob/mcac057 · Cited by 12
Mito-nuclear coevolution and phylogenetic artifacts: the case of bivalve mollusks
Formaggioni, A., Plazzi, F., & Passamonti, M. (2022) · Scientific Reports · doi:10.1038/s41598-022-15076-y · Cited by 12
Knyshov, A., Gordon, E. R. L., Masonick, P., Castillo, S., Forero, D., Hoey‐Chamberlain, R., Hwang, W. S., Johnson, K. P., Lemmon, A. R., Lemmon, E. M., et al. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad168 · Cited by 12
Lovegrove, J., Upchurch, P., & Barrett, P. M. (2024) · Journal of Systematic Palaeontology · doi:10.1080/14772019.2024.2345333 · Cited by 12
Liang, Y., Xue, T., Gadagkar, S. R., Qin, F., Janssens, S., & Yu, S. (2025) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2025.108325 · Cited by 12
RETRACTED: Integrative phylogenomics positions sponges at the root of the animal tree
Steenwyk, J. L., & King, N. (2025) · Science · doi:10.1126/science.adw9456 · Cited by 16
RetractedWhat is an archaeon and are the Archaea really unique?
Harish, A. (2018) · PeerJ · doi:10.7717/peerj.5770 · Cited by 12
Naser-Khdour, S., Minh, B. Q., & Lanfear, R. (2020) · ANU Open Research (Australian National University) · doi:10.5061/dryad.fj6q573rx · Cited by 12
Interpreting phylogenetic conflict: Hybridization in the most speciose genus of lichen-forming fungi
Keuler, R., Jensen, J., Bárcenas-Peña, A., Grewe, F., Lumbsch, H. T., Huang, J., & Leavitt, S. D. (2022) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2022.107543 · Cited by 12
A HYBRID CAPTURE BAIT SET FOR BEGONIA
Michel, T., Tseng, Y., Wilson, H. P., Chung, K., & Kidner, C. A. (2022) · Edinburgh Journal of Botany · doi:10.24823/ejb.2022.409 · Cited by 12
More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae)
Köhler, M., Reginato, M., Jin, J., & Majure, L. C. (2023) · Annals of Botany · doi:10.1093/aob/mcad098 · Cited by 12
The taxonomy of the model filamentous fungus Podospora anserina
Ament‐Velásquez, S. L., Johannesson, H., Giraud, T., Debuchy, R., Saupe, S. J., Debets, A. J. M., Bastiaans, E., Malagnac, F., Grognet, P., Peraza‐Reyes, L., et al. (2020) · MycoKeys · doi:10.3897/mycokeys.75.55968 · Cited by 12
Orthology: definitions, inference, and impact on species phylogeny inferencePreprint
Fernández, R., Gabaldón, T., & Dessimoz, C. (2019) · arXiv (Cornell University) · doi:10.48550/arxiv.1903.04530 · Cited by 15
Stukel, M., Porczak, A. E., Gordon, E. R. L., Vailionis, J. L., Haji, D., Buckley, T. R., Lemmon, A. R., Lemmon, E. M., & Simon, C. (2023) · Systematic Entomology · doi:10.1111/syen.12613 · Cited by 10
Tolman, E., Beatty, C. D., Kohli, M. K., Abbott, J. C., Bybee, S., Frandsen, P. B., Gosnell, J. S., Guralnick, R., Kalkman, V. J., Newton, L. G., et al. (2024) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2024.108185 · Cited by 11
A Tale of Too Many Trees: A Conundrum for Phylogenetic Regression
Adams, R. H. J., Lozano, J. R., Duncan, M., Green, J. E., Assis, R., & DeGiorgio, M. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf032 · Cited by 11
Comparing Likelihood Ratios to Understand Genome-Wide Variation in Phylogenetic Support
Mount, G. G., & Brown, J. M. (2022) · Systematic Biology · doi:10.1093/sysbio/syac014 · Cited by 12
Campbell, M. A., Alfaro, M. E., Belasco, M., & Lopez, J. A. (2017) · PeerJ · doi:10.7717/peerj.3548 · Cited by 12
Phylogenomic analysis of Fundulidae (Teleostei: Cyprinodotiformes) using RNA-sequencing data
Rodgers, R., Roach, J. L., Reid, N. M., Whitehead, A., & Duvernell, D. D. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.12.030 · Cited by 11
Parker, E., Dornburg, A., Domínguez‐Domínguez, O., & Piller, K. R. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.01.025 · Cited by 11
Rivas-Sánchez, D. F., Morris, J., Salazar, C. A., Pardo‐Díaz, C., Merrill, R. M., & Montgomery, S. H. (2025) · Evolution Letters · doi:10.1093/evlett/qraf017 · Cited by 10
Botting, J. P., & Muir, L. A. (2018) · Palaeoworld · doi:10.1016/j.palwor.2018.03.002 · Cited by 10
Brain size growth in wild and captive chimpanzees (Pan troglodytes)
Cofran, Z. (2018) · American Journal of Primatology · doi:10.1002/ajp.22876 · Cited by 10
Intragenic Conflict in Phylogenomic Data Sets
Smith, S. A., Walker‐Hale, N., & Walker, J. F. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa170 · Cited by 10
Metadata
- 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 › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › 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 ›
Are you an author, or do you see a problem with this page? Request a review
