The DOI matches its Crossref record; 55 of the 55 references it cites were found in a registry or an index.
Phylotranscriptomic consolidation of the jawed vertebrate timetree
Open accessAbstract
Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on "standards" for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes and some relationships remain controversial. We tested a novel bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and find this phylotranscriptomic approach successful and highly cost-effective. Increased sequencing effort up to ca. 10Gbp allows recovering more genes, but shallower sequencing (1.5Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large curated nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.
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?
In the citing paper
“The remaining 662 were screened for contaminations with Forty-Two [12, 13] using 78 ribosomal protein markers, and 89 samples were further discarded because they were too contaminated (Data file 1, Data set 1), leaving 573 samples.”
From Decontamination, pooling and dereplication of the 678 samples of the Marine Microbial Eukaryote Transcriptome Sequencing Project (2021) · cites this paper as [13]
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
The global diversity of birds in space and time
Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K., & Mooers, A. O. (2012) · Nature · doi:10.1038/nature11631 · Cited by 3,934 · cited 1×
“5, 8, 9).”
Cellular Scaling Rules for the Brains of Marsupials: Not as “Primitive” as Expected
Santos, S. E. D., Porfírio, J., Cunha, F., Manger, P. R., Tavares, W. C., Pessôa, L. M., Raghanti, M. A., Sherwood, C. C., & Herculano‐Houzel, S. (2017) · Brain Behavior and Evolution · doi:10.1159/000452856 · Cited by 2,652
The delayed rise of present-day mammals
Bininda-Emonds, O. R. P., Cardillo, M., Jones, K. E., MacPhee, R. D. E., Beck, R. M. D., Grenyer, R., Price, S. A., Vos, R. A., Gittleman, J. L., & Purvis, A. (2007) · Nature · doi:10.1038/nature05634 · Cited by 2,082
Whole-genome analyses resolve early branches in the tree of life of modern birds
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., et al. (2014) · Science · doi:10.1126/science.1253451 · Cited by 1,901 · cited 2×
“…hypothesis, the main diversification bursts of these hyperdiverse radiations have been proposed to coincide with the Cretaceous-Paleogene boundary5,15, but due to uncertainties in timetree reconstruction and methodological disputes on molecular dating, this hypothesis remains contentious,…”
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes
Pyron, R. A., Burbrink, F. T., & Wiens, J. J. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-93 · Cited by 1,673 · cited 2×
“The results of these correlation analyses were confirmed by a Bayesian joint modelling of the above traits with parameters of the evolutionary process at the sequence level (see Supplementary Table 7).”
Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification
Meredith, R. W., Janečka, J. E., Gatesy, J., Ryder, O. A., Fisher, C. A., Teeling, E. C., Goodbla, A., Eizirik, E., Simão, T. L. L., Stadler, T., et al. (2011) · Science · doi:10.1126/science.1211028 · Cited by 1,464 · cited 2×
“We used a conservative approach to setting calibrations, starting from multiple well-established calibrations with solid paleontological evidence and used conservative intervals to account for dating and phylogenetic uncertainty43 (Supplementary Table 8).”
Pyron, R. A., & Wiens, J. J. (2011) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2011.06.012 · Cited by 1,417 · cited 1×
“(iv) The earliest offshoot within salamanders was Andrias (Cryptobranchidae) plus Hynobius (Hynobiidae)34 and the alternative position of Siren (Sirenidae) as the earliest-branching salamander clade37 was statistically rejected.”
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
Self-citationLartillot, N., Rodrigue, N., Stubbs, D., & Richer, J. (2013) · Systematic Biology · doi:10.1093/sysbio/syt022 · Cited by 871
Research works printed but not linked: 1
- Zhu, M. & Schultze, H.-P. in Major Events in Early Vertebrate Evolution: Paleontology, Phylogeny and Development (ed. Ahlberg, P. E.) 289–314 (Taylor & Francis, 2001).
Cited by
Sorted by citations
Items 201–300 of 300
Iijima, M., Mayerl, C. J., Munteanu, V. D., & Blob, R. W. (2024) · Journal of Anatomy · doi:10.1111/joa.14011 · Cited by 4
“The phyloge - netic relationships of four taxa, particularly the placement of tur - tles, followed molecular evaluations (Chiari et al., 2012 ; Crawford et al., 2012 ; Kumazawa & Nishida, 1999 ; Zardoya & Meyer, 1998 ), and their divergence times followed Irisarri et al. (2017).”
BackgroundGiustini, C., Bo, D. D., Storti, M., Vlierberghe, M. V., Baurain, D., Cardol, P., Zhang, Y., Fernie, A. R., Fitzpatrick, D., Aro, E., et al. (2025) · Physiologia Plantarum · doi:10.1111/ppl.70640 · Cited by 6
“The broadly sampled orthogroup OG0001460 (including P. tricornutum MCFc) obtained in Van Vlierberghe, Philippe, and Baurain (2021) was aligned with MAFFT (Katoh and Standley 2013) and its largest photosynthetic subtree (=clan OG0001460-8) was enriched using Forty-Two (Irisarri et al. 2017; Simion et al. 2017) with seq…”
Self-citationWolf, M., Janke, A., & Smith, K. T. (2026) · BMC Biology · doi:10.1186/s12915-026-02552-4 · Cited by 3
“…genes representing all major squamate lineages except Scincoidea is one of the largest of its kind and confirms the broad structure of squamate phylogeny [12, 16, 17, 44], as supported also by transcriptomes [19], noncoding ultraconserved elements [14, 15], and anchored hybrid enrichment loci [20].”
Falconieri, A., Boarolo, G., Boschelle, C., Spagnolli, G., Marchioretti, C., Zuccaro, E., Palazzolo, I., Tosatto, L., Hegazy, A. K. O., Rosati, J. D., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf688 · Cited by 3
Phylogenetic Paradigm Shifts in Early Amniote Evolution
Jenkins, K. M., Meyer, D. L., & Bhullar, B.-A. S. (2025) · Systematic Biology · doi:10.1093/sysbio/syaf087 · Cited by 3
Unbiasing Genome-Based Analyses of Selection: An Example Using Iconic Shark Species
Yamaguchi, K., & Kuraku, S. (2021) · Frontiers in Marine Science · doi:10.3389/fmars.2021.573853 · Cited by 3
“It was previously cautioned that imprecise alignments containing erroneous ORFs likely induce ω value inflation in the detection of positively selected genes (Jordan and Goldman, 2012). Our reanalysis illustrates the use of mis-predicted ORF sequences and excessively distant sequences by Marra et al. (2019). The satur…”
BackgroundMethodInfluentialdos Santos, R. O., Laurin, M., & Zaher, H. (2020) · Preprints.org · doi:10.20944/preprints202006.0264.v1 · Cited by 3
“…some variants, gymnophionans are more closely related to amniotes than to batrachians (e.g. Anderson et al., 2008), whereas this is contradicted by nearly all molecular (e.g. Irisarri et al., 2017), total evidence (Pyron, 2011) and some paleontological (Marjanović & Laurin, 2009, 2019) phylogenies.”
BackgroundRedmond, A. K., Gundappa, M. K., Macqueen, D. J., & McLysaght, A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.16.492067 · Cited by 3
Giustini, C., Bo, D. D., Storti, M., Vlierberghe, M. V., Baurain, D., Cardol, P., Zhang, Y., Fernie, A. R., Fitzpatrick, D., Aro, E., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.14.638225 · Cited by 3
Self-citationPhylogenomics and the origins of sharksPreprint
Brownstein, C. D., & Near, T. J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.13.705779 · Cited by 3
Jeanne, F., Pilet, S., Combarnous, Y., Bernay, B., Dufour, S., Favrel, P., & Sourdaine, P. (2025) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2025.112553 · Cited by 2
“Indeed, the chon-drichthyes are the sister group to osteichthyes (bony vertebrates), whose divergence occurred around 450 million years ago (Irisarri et al., 2017), and include the holocephalans (chimaeras) and elasmobranchs (sharks and rays).”
Evolutionary insights into Interleukin-12 family targets across 405 species
Wang, W., Li, D., Luo, K., Chen, B., Li, X., Hao, T., Guo, D., Dong, Y., & Yu, N. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1584460 · Cited by 2
“Chondrichthyes separated from a common ancestor with other vertebrates roughly 450 Mya (71, 72).”
Nishihara, H., & Komiya, A. (2026) · Genome biology · doi:10.1186/s13059-026-04050-w · Cited by 2
“Phylogenetic relationships were based on previous reports [78, 79], taking into account the polytomy of the last common ancestor of eutherians [80, 81].”
The Greenland shark genome: Insights into lifespan extremes and population dynamics
Yang, K., Nishiwaki, K., Mizobata, H., Liang, J., Asakawa, S., Yoshitake, K., Watanabe, Y. Y., Hussey, N. E., Kovacs, K. M., Lydersen, C., et al. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2601272123 · Cited by 7
Expression of 20 SCPP genes during tooth and bone mineralization in Senegal bichir
Delgado, S., Fernández-Trujillo, Houée, G., Silvent, J., Liu, X., Corre, E., & Sire, J. (2023) · Development Genes and Evolution · doi:10.1007/s00427-023-00706-w · Cited by 2
“Sequencing resulted in 183,350,013 × 2 paired reads from the P. senegalus jaw transcriptome (Irisarri et al. 2017).”
Self-citationKuraku, S. (2024) · Developmental Dynamics · doi:10.1002/dvdy.710 · Cited by 3
“45 One remarkable observation is in the branch lengths — the branch for the early chondrichthyan lineage is much longer than expected from divergence times for the split between chimaeras and sharks/rays which is about 400 million years ago 46 (Figure 5).”
Rapid radiations underlie most of the known diversity of life
Wiens, J. J., & Moen, D. S. (2025) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2025.1596591 · Cited by 3
Jenkins, K., Behlke, A. D., & Sues, H. (2025) · Palaeontology · doi:10.1111/pala.70038 · Cited by 2
“(2022), which hypothesize a root age for the origin of amniotes to be 315 – 330 Ma which is consistent with the known fossil record (Carroll & Baird 1972; Tuinen & Hadley 2004) and estimates from genomic datasets (Irisarri et al .”
Neoceratodus forsteri (Australian lungfish)
Schartl, M., & Meyer, A. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.02.005 · Cited by 2
Self-citationShen, J., Zhou, S., Chen, Y., & Qi, J. (2023) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.14179 · Cited by 2
“…to the costly whole genome sequencing, transcriptomes are more affordable and widely applied in phyloge - nomic studies, providing more efficiently inferred coding gene sets (Fernandez et al., 2018; Siu-Ting et al., 2019) across various research fields (Cheon et al., 2020 ; Irisarri et al., 2017 ).”
Cornet, L., Cleenwerck, I., Praet, J., Léonard, R. R., Vereecken, N. J., Michez, D., Smagghe, G. J., Baurain, D., & Vandamme, P. A. R. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.10.472130 · Cited by 2
Self-citationIrisarri, I. (2020) · Wiley eBooks · doi:10.1002/9780470015902.a0029211 · Cited by 2
Self-citationAlignment-free Phylogenetic Placement and its Applications
Blanke, M. (2023) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-9762 · Cited by 3
Phylociraptor – A unified computational framework for reproducible phylogenomic inferencePreprint
Resl, P., & Hahn, C. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.22.558970 · Cited by 4
Recent Advances in Understanding the Immune System of Reptiles
Sandmeier, F. C. (2024) · Elsevier eBooks · doi:10.1016/b978-0-128-24465-4.00038-7 · Cited by 2
A novel data filtering method resolves the controversy in the phylogeny of the ChondrichthyesPreprint
Huang, J., Hofreiter, M., Noble, L. R., Straube, N., Naylor, G. J. P., & Li, C. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.19.671162 · Cited by 2
“We analyzed 4,593 amino acid alignments from Irisarri et al. (2017), reducing the dataset to 24 representative taxa for computational efficiency.”
Phylogenomics and comparative genomics in ant-eating mammals
Allio, R. (2021) · theses.fr (ABES) · doi:10.70675/0b3fded9z0768z4976z9f7cz8b7e4a9f1114 · Cited by 2
Identification and characterization of archaeal pseudomurein biosynthesis genes through pangenomics
Lupo, V., Roomans, C., Royen, E., Ongena, L., Jacquemin, O., Mullender, C., Kerff, F., & Baurain, D. (2025) · mSystems · doi:10.1128/msystems.01401-24 · Cited by 5
Self-citationShi, T., & He, J. G. (2025) · Frontiers in Plant Science · doi:10.3389/fpls.2025.1511582 · Cited by 1
Jeanne, F., Pilet, S., Bernay, B., Lagadu, S., Delépée, R., Dufour, S., & Sourdaine, P. (2025) · General and Comparative Endocrinology · doi:10.1016/j.ygcen.2025.114734 · Cited by 1
Evolution of chondrichthyan jaw morphology, from ecological generalists to specialists
Griffin, B. W., Keating, J. N., Carmona, P. S. M., Johanson, Z., Dearden, R. P., Donoghue, P. C. J., & Rayfield, E. J. (2025) · Paleobiology · doi:10.1017/pab.2025.10077 · Cited by 1
“…as the earliest branching chondrichthyan as per Greif et al. (2022) and the minimum age equal to the earliest currently known chondrichth-yan, Fanjingshania renovata (Andreev et al. 2022), while key internal nodes were dated using mean posterior age estimates from Irisarri et al. (2017).”
A dynamic programming algorithm for the maximum s -club problem on trees
Fernández‐Zepeda, J. A., Flores-Lamas, A., Hague, M., & Trejo-Sánchez, J. A. (2025) · European Journal of Operational Research · doi:10.1016/j.ejor.2025.08.031 · Cited by 1
Fleming, J. F., & Struck, T. H. (2026) · Systematic Biology · doi:10.1093/sysbio/syag009 · Cited by 1
“…21 previously published multi-protein phylogenetic data sets from 21 previously published papers ( Misof et al. 2014 ; Fernández et al. 2016 , 2017 ; Irisarri et al. 2017 ; Kocot et al. 2017 ; Peters et al. 2017 ; Johnson et al. 2018 ; Sharma et al. 2018 ; Shen, Jin, et al. 2018 ; Shen, Opulente,…”
Hou, Z.-S., Wu, Q., Ramezani, J., Li, P., Chen, Y., Zhu, M., & Shen, S. (2026) · Geological Society of America Bulletin · doi:10.1130/b38662.1 · Cited by 1
Kim, M. (2026) · Mycological Progress · doi:10.1007/s11557-026-02151-1 · Cited by 1
“The phylogenetic relationships were based on previously published phylogenetic frameworks for plants and animals derived from large-scale transcriptomic and phylogenomic analyses (Irisarri et al. 2017; Puttick et al. 2018).”
WANG, Y.-H., Tihelka, E., Kočárek, P., Engel, M. S., Lozano-Fernández, J., Yin, Z., Rota‐Stabelli, O., Huang, D., Pisani, D., Donoghue, P. C. J., et al. (2026) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2025.3174 · Cited by 1
Singtuen, V., Charoentitirat, T., Preedeesanith, P., & Sukplum, W. (2025) · Scientific Reports · doi:10.1038/s41598-025-90012-4 · Cited by 1
fastTIGER: A rapid method for estimating evolutionary rates of sites from large datasets
Le, T. K., & Le, V. S. (2021) · International Conference on Knowledge and Systems Engineering/Proceedings · doi:10.1109/kse53942.2021.9648748 · Cited by 1
“Irisarri [16] Jawed vertebrates 100 40 15698”
Emerling, C. A. (2022) · Cambridge University Press eBooks · doi:10.1017/9781108938891.015 · Cited by 1
Jansen, M., & Marjanović, D. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.27.460658 · Cited by 1
Castillo, H., Godoy, F., Gilbert, C., Aguilera, F., Spicuglia, S., & Marcellini, S. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.30.555543 · Cited by 1
The origin of Amniota in phylogenetic contextPreprint
Marjanović, D. (2024) · doi:10.31233/osf.io/tja8b · Cited by 1
(2023) · doi:10.1016/j.isci.2023.108740 · Cited by 1
“…(Revell, 2012) 181 was used to generate a 20-species vertebrate tree and phenogram, 14-species tetrapod tree and 10-species mammalian tree, based on divergence times drawn from A´lvarez-Carretero et al. (2022) 78 for mammals, and Irisarri et al. (2017) 79 for earlier-branching vertebrates.”
MethodInfluentialVerstrepen, K. J., & Voordeckers, K. (2018) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.734380463.793553343
Janbon, G. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.734380463.793554773
Editorial: Timetrees: Incorporating fossils and molecules
Laurin, M., Didier, G., & Warnock, R. C. M. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.937763
“These problems are illustrated through a detailed analysis of the 30 calibrations used to produce the largest available vertebrate timetree (Irisarri et al., 2017).”
BackgroundAccessing the relative performance of fast molecular dating methods for phylogenomic dataPreprint
Costa, F. P., Schrago, C. G., & Mello, B. (2022) · Research Square · doi:10.21203/rs.3.rs-1805291/v1
Gower, D. J., & Zaher, H. (2022) · Cambridge University Press eBooks · doi:10.1017/9781108938891.013
Scoutknife: A naïve, whole genome informed phylogenetic robusticity metric
Fleming, J. F., Eriksen, P. M., & Struck, T. H. (2023) · F1000Research · doi:10.12688/f1000research.139356.1
Loss of noggin1, a Classic Embryonic Inducer Gene, in ElasmobranchsPreprint
Bayramov, A. V., Алексеевна, Е. Г., Meyntser, I. V., & Zaraisky, A. G. (2023) · Research Square · doi:10.21203/rs.3.rs-3370621/v1
Cornet, L., Zaidi, S. S., Li, J., Ngapout, Y., Shakir, S., Loic, M., Callot, C., Marande, W., Hanikenne, M., Rombauts, S., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.19.563145
Marcellini, S., Castillo, H., Hanna, P., Sachs, L. M., Buisine, N., Godoy, F., Gilbert, C., Aguilera, F., Muñoz, D., Boisvert, C. A., et al. (2024) · SSRN Electronic Journal · doi:10.2139/ssrn.4755772
A coevolução dos animais e do oxigênio no Neoproterozóico
Belato, F. A. (2024) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.41.2024.tde-13062024-144828
Academician E.M. Kreps – founder оf the science of evolutionary biochemistry of brain lipids
Parnova, R. G., & Firsov, M. L. (2024) · Успехи физиологических наук · doi:10.31857/s0301179824020045
Vertebrate TNF Superfamily: Evolution and Functional Insights
Marı́n, I. (2025) · Biology · doi:10.3390/biology14010054
Bayramov, A. V., Ermakova, G. V., Kucheryavyy, A. V., Eroshkin, F. M., & Zaraisky, A. G. (2024) · Paleontological Journal · doi:10.1134/s0031030124601208
“…groups occurred about 450 million years ago, and a comparison of the structural features and formation of the cartilaginous representatives that have survived to this day can be an important component in reconstructing the evolutionary history of gna-thostomes (Irisarri et al., 2017; Kuraku, 2021).”
Cornet, L., Zaidi, S. S., Li, J., Ngapout, Y., Shakir, S., Meunier, L., Callot, C., Marande, W., Hanikenne, M., Rombauts, S., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03620-8 · Cited by 1
“1416 (65, 66).”
A public collection of phylogenetics experiences in audio and video form
Chesters, D. (2025) · Journal of Systematics and Evolution · doi:10.1111/jse.13195
Knee tissue diversity and evolution in different reptile taxa
Sánchez, R. S., Manzano, A. S., Lazarte, M. D. L. Á., & Abdala, V. S. L. (2025) · Journal of Anatomy · doi:10.1111/joa.70039
“Selected morphological characters were optimized based on phylogenetic hypotheses from Blankers et al. (2013), Irisarri et al. (2016), Montero & Autino (2018), and Streicher and Wiens (2017).”
Perez, T., Bell, R. C., Lavoie, C., Fujita, M. K., Gower, D. J., Streicher, J. W., Thomas, K. N., & Schott, R. K. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.31.685797
Amphibious Transitions Drive Lineage-Specific Diversification of Olfactory Receptors in VertebratesPreprint
Panda, B., Nath, R., Dey, A., & Krishnan, A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.03.686341
“This likely reflects their dual respiratory capabilities and their basal phylogenetic position as the closest extant relatives of tetrapods ( 110, 111 ).”
Spillane, J. L., LaPolice, T. M., MacManes, M. D., & Plachetzki, D. C. (2021) · Figshare · doi:10.6084/m9.figshare.14228492
Spillane, J. L., LaPolice, T. M., MacManes, M. D., & Plachetzki, D. C. (2021) · Figshare · doi:10.6084/m9.figshare.14228489
Meiri, S., Murali, G., Zimin, A., Shak, L., Itescu, Y., Caetano, G., & Roll, U. (2021) · Figshare · doi:10.6084/m9.figshare.13787893
Vlierberghe, M. V., Philippe, H., & Baurain, D. (2021) · Figshare · doi:10.6084/m9.figshare.14446480
Self-citationLeberstein, N., Remenick, T., Becker, M., & Mark, S.-I. (2026) · PLoS Biology · doi:10.2139/ssrn.6169717
On the Origin and Evolution of Sweet Taste Mediated by Tas1r2–Tas1r3 in Vertebrates
Feng, H., Li, Y., Shen, T., & Zhao, H. (2026) · Integrative Zoology · doi:10.1111/1749-4877.70073
Ribeiro, A. C., Mayrinck, D., Bockmann, F. A., & de Pinna, M. (2026) · Papers in Palaeontology · doi:10.1002/spp2.70072
“2013; Irisarri et al .”
The Road so Far: Tracing the Molecular Evolution of Hexokinase Family in Metazoa
Messeder, D. J., de Souza-Vieira, Y., Oliveira, G. A. P., Margis, R., Mello, B., & Sachetto‐Martins, G. (2026) · Genome Biology and Evolution · doi:10.1093/gbe/evag062
Torres‐Sánchez, M. (2026) · Journal of Evolutionary Biology · doi:10.1093/jeb/voag017
Franco, A. D. (2019) · theses.fr (ABES) · doi:10.70675/9c8d2b6cz53cfz4351za1cbz83d9c20217f1
“Creation of phylogenomic datasets For each compartment, we assembled the datasets following a semi-automatic protocol similar to the one described in our previous phylogenomic studies (Simion et al. 2017, Irisarri et al. 2017).”
MethodRamos, E. K. S., Hilgers, L., Carrasco-Valenzuela, T., Panis, D. N. D., Picorelli, A., Sullivan, J. K., Uliano‐Silva, M., Bentley, B. P., Scott, P. A., Hiller, M., et al. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag114
Conservation of Human IgSF Proteins Throughout Eukaryotic Evolution
Grudman, S., & Fiser, A. (2026) · Genome Biology and Evolution · doi:10.1093/gbe/evag133
The oldest shark face—anatomy of the Devonian elasmobranch Phoebodus
Klug, C. (2026) · Acta Palaeontologica Polonica · doi:10.4202/app.01290.2025
Convergent genomic trajectories shape adaptation to life on land across animal lineages
Martínez‐Redondo, G. I., Eleftheriadi, K., Salces-Ortiz, J., Escudero, N., Fernández‐Álvarez, F. Á., Carbonetto, B., Vargas-Chávez, C., García‐Vernet, R., Palma‐Guerrero, J., Renteria, L., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-75551-2 · Cited by 1
Casey, D., Niezabitowski, L., Gundappa, M. K., Matz, H. C., Venugopalan, A., Hanson, L. A., Dooley, H. M., Macqueen, D. J., Redmond, A. K., & McLysaght, A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.13.744671
Two Paralogues as They Like It: Conserved and Divergent Evolution of Vertebrate Gcm Genes
Shono, T., Tatsumi, N., Miyake, T., Kuraku, S., & Okabe, M. (2026) · Evolution & Development · doi:10.1111/ede.70057
Kim, M. (2026) · Research Square · doi:10.21203/rs.3.rs-10940516/v1
Metadata
- Authors
- Irisarri, I., Baurain, D., Brinkmann, H., Delsuc, F., Sire, J.-Y., Kupfer, A., Petersen, J., Jarek, M., Meyer, A., Vences, M., & Philippe, H.
- Affiliations
- Uppsala University (SE)
- University of Liège (BE)
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures (DE)
- Centre National de la Recherche Scientifique (FR)
- Sorbonne Université (FR)
- Staatliches Museum für Naturkunde Stuttgart (DE)
- Helmholtz Centre for Infection Research (DE)
- University of Konstanz (DE)
- Corresponding author
- Irisarri, Iker
- Philippe, Hervé
- ORCID
- Venue
- Nature Ecology & Evolution
- Published
- 2017-07-24
- Volume
- 1
- Issue
- 9
- Pages
- 1370-1378
- ISSN
- 2397-334X (ISSN-L)
- PMC
- PMC5584656
- OpenAlex
- W2739198517
- Cited by
- 299
- References
- 55
- Citations by year
- 2026: 22 · 2025: 26 · 2024: 23 · 2023: 35 · 2022: 31 · 2021: 52 · 2020: 32 · 2019: 48 · 2018: 27 · 2017: 3
- FWCI
- 12.29
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Ecology & Evolution (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- KOPS (University of Konstanz) (submittedVersion)
- HZI (Helmholtz Centre for Infection Research) (submittedVersion, cc-by-nc-sa)
- HAL (submittedVersion, other-oa)
- ORBi (University of Liège) (submittedVersion)
- Funders
- Alexander von Humboldt-Stiftung (1150725)
- European Commission (273900)
- Deutsche Forschungsgemeinschaft (1117545)
- Agence Nationale de la Recherche (ANR-10-LABX-0041, 2017-, ANR-12-BSV7-0020, ANR-10-LABX- 41, 12-BSV7-020, ANR-12, ANR-10, 10-LABX-41)
- Fonds De La Recherche Scientifique - FNRS (# 2.5020.11, 1117545, 2.5020)
- Fédération Wallonie-Bruxelles (1117545, 2.5020.11)
- Universität Konstanz
- Instituto de Física de Cantabria
- 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 › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Keywords
- jawed vertebrates, Gnathostomata, timetree, phylotranscriptomics, phylogenomics, divergence time estimation, mitochondrial genome, transcriptome assembly, phylogenetic diversity, macroevolution
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
