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.
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Of the remaining 662 samples, 89 were discarded as too contaminated after screening with Forty-Two using 78 ribosomal protein markers, leaving 573 samples.
“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]
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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 · see citing works
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 · see citing works
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 2,651 · see citing works
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 · see citing works
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 · see citing works
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 1,642 · see citing works
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 · see citing works
Pyron, R. A., & Wiens, J. J. (2011) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2011.06.012 · Cited by 1,397 · 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
Self-citationLartillot, N., Rodrigue, N., Stubbs, D., & Richer, J. (2013) · Systematic Biology · doi:10.1093/sysbio/syt022 · Cited by 871 · see citing works
Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates
Alfaro, M. E., Santini, F., Brock, C. D., Alamillo, H., Dornburg, A., Rabosky, D. L., Carnevale, G., & Harmon, L. J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0811087106 · Cited by 821 · see citing works
Phylogenomics: The beginning of incongruence?
JEFFROY, O., BRINKMANN, H., DELSUC, F., & PHILIPPE, H. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.02.003 · Cited by 698 · see citing works
Self-citationZheng, Y., & Wiens, J. J. (2015) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2015.10.009 · Cited by 644 · see citing works
Assembling the Squamate Tree of Life: Perspectives from the Phenotype and the Fossil Record
Gauthier, J. A., Kearney, M., Maisano, J. A., Rieppel, O. C., & Behlke, A. D. (2012) · Bulletin of the Peabody Museum of Natural History · doi:10.3374/014.053.0101 · Cited by 552 · see citing works
A general comparison of relaxed molecular clock models
Lepage, T., Bryant, D., Philippe, H., & Lartillot, N. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm193 · Cited by 546 · see citing works
Self-citationdos Reis, M., Inoue, J., Hasegawa, M., Asher, R. J., Donoghue, P. C. J., & Yang, Z. (2012) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2012.0683 · Cited by 526 · see citing works
Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes
Near, T. J., Dornburg, A., Eytan, R. I., Keck, B. P., Smith, W. L., Kuhn, K. L., Moore, J. A., Price, S. A., Burbrink, F. T., Friedman, M., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1304661110 · Cited by 497 · see citing works
Song, S., Liu, L., Edwards, S. V., & Wu, S. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1211733109 · Cited by 461 · see citing works
Townsend, T. M., Larson, A., Louis, E. E., & Macey, J. R. (2004) · Systematic Biology · doi:10.1080/10635150490522340 · Cited by 459 · see citing works
Crawford, N. G., Faircloth, B. C., McCormack, J. E., Brumfield, R. T., Winker, K., & Glenn, T. C. (2012) · Biology Letters · doi:10.1098/rsbl.2012.0331 · Cited by 355 · see citing works
Chiari, Y., Cahais, V., Galtier, N., & Delsuc, F. (2012) · BMC Biology · doi:10.1186/1741-7007-10-65 · Cited by 340 · see citing works
Self-citationNear, T. J., Meylan, P. A., & Shaffer, H. B. (2005) · The American Naturalist · doi:10.1086/427734 · Cited by 270 · see citing works
Initial Diversification of Living Amphibians Predated the Breakup of Pangaea
Mauro, D. S., Miguel Vences, B., Alcobendas, M., Zardoya, R., & Meyer, A. (2005) · The American Naturalist · doi:10.1086/429523 · Cited by 246 · see citing works
Self-citationInoue, J. G., Miya, M. U., Lam, K., Tay, B.-H., Danks, J. A., Bell, J. D., Walker, T. I., & Venkatesh, B. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq147 · Cited by 236 · see citing works
Additional molecular support for the new chordate phylogeny
Delsuc, F., Tsagkogeorga, G., Lartillot, N., & Philippe, H. (2008) · genesis · doi:10.1002/dvg.20450 · Cited by 231 · see citing works
Self-citationHsiang, A. Y., Field, D. J., Webster, T. H., Behlke, A. D., Davis, M. B., Racicot, R. A., & Gauthier, J. A. (2015) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0358-5 · Cited by 226 · see citing works
Jones, M. E. H., Anderson, C. L., Hipsley, C. A., Müller, J., Evans, S. E., & Schoch, R. R. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-208 · Cited by 220 · see citing works
Warnock, R. C. M., Parham, J. F., Joyce, W. G., Lyson, T. R., & Donoghue, P. C. J. (2014) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2014.1013 · Cited by 204 · see citing works
The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference
Tarver, J. E., dos Reis, M., Mirarab, S., Moran, R. J., Parker, S., O’Reilly, J., King, B. L., O’Connell, M. J., Asher, R. J., Warnow, T. J., et al. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evv261 · Cited by 198 · see citing works
SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics
Roure, B., Rodríguez‐Ezpeleta, N., & Philippe, H. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-s1-s2 · Cited by 190 · see citing works
Self-citationInsertion–deletion biases and the evolution of genome size
Gregory, T. R. (2003) · Gene · doi:10.1016/j.gene.2003.09.030 · Cited by 181 · see citing works
Zhang, P., & Wake, D. B. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.07.010 · Cited by 179 · see citing works
A Middle Triassic stem-turtle and the evolution of the turtle body plan
Schoch, R. R., & Sues, H. (2015) · Nature · doi:10.1038/nature14472 · Cited by 170 · see citing works
Romiguier, J., Ranwez, V., Delsuc, F., Galtier, N., & Douzery, E. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst116 · Cited by 170 · see citing works
Self-citationBrown, J. M., & Thomson, R. C. (2016) · Systematic Biology · doi:10.1093/sysbio/syw101 · Cited by 155 · see citing works
The oldest record of ornithuromorpha from the early cretaceous of China
Wang, M., Zheng, X., O'Connor, J. K., Lloyd, G. T., Wang, X., Wang, Y., Zhang, X., & Zhou, Z. (2015) · Nature Communications · doi:10.1038/ncomms7987 · Cited by 139 · see citing works
King, B., Qiao, T., Lee, M. S. Y., Zhu, M., & Long, J. A. (2016) · Systematic Biology · doi:10.1093/sysbio/syw107 · Cited by 125 · see citing works
Heterogeneous Models Place the Root of the Placental Mammal Phylogeny
Morgan, C. C., Foster, P. G., Webb, A. E., Pisani, D., McInerney, J. O., & O’Connell, M. J. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst117 · Cited by 123 · see citing works
The evolutionary position of turtles revised
Zardoya, R., & Meyer, A. (2001) · Die Naturwissenschaften · doi:10.1007/s001140100228 · Cited by 121 · see citing works
Self-citationChen, M., Liang, D., & Zhang, P. (2015) · Systematic Biology · doi:10.1093/sysbio/syv059 · Cited by 120 · see citing works
Janke, A., Erpenbeck, D., Nilsson, M., & Árnason, Ú. (2001) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2000.1402 · Cited by 119 · see citing works
Tang, Y., Yukawa, T., Bateman, R. M., Jiang, H., & Peng, H. (2015) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0376-3 · Cited by 114 · see citing works
MicroRNAs support a turtle + lizard clade
Lyson, T. R., Sperling, E. A., Heimberg, A. M., Gauthier, J. A., King, B. L., & Peterson, K. J. (2011) · Biology Letters · doi:10.1098/rsbl.2011.0477 · Cited by 111 · see citing works
Evaluating molecular clock calibrations using Bayesian analyses with soft and hard bounds
Sanders, K. L., & Lee, M. S. Y. (2007) · Biology Letters · doi:10.1098/rsbl.2007.0063 · Cited by 97 · see citing works
Hara, Y., Tatsumi, K., Yoshida, M., Kajikawa, E., Kiyonari, H., & Kuraku, S. (2015) · BMC Genomics · doi:10.1186/s12864-015-2007-1 · Cited by 92 · see citing works
Phylogenetic informativeness reconciles ray-finned fish molecular divergence times
Dornburg, A., Townsend, J. P., Friedman, M., & Near, T. J. (2014) · BMC Evolutionary Biology · doi:10.1186/s12862-014-0169-0 · Cited by 86 · see citing works
Dating cryptodiran nodes: Origin and diversification of the turtle superfamily Testudinoidea
Lourenço, J. M., Claude, J., Galtier, N., & Chiari, Y. (2011) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2011.10.022 · Cited by 74 · see citing works
Irisarri, I., Mauro, D. S., Abascal, F., Ohler, A., Miguel Vences, B., & Zardoya, R. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-626 · Cited by 73 · see citing works
Self-citationA symmoriiform chondrichthyan braincase and the origin of chimaeroid fishes
Coates, M. I., Gess, R. W., Finarelli, J. A., Criswell, K. E., & Tietjen, K. (2017) · Nature · doi:10.1038/nature20806 · Cited by 72 · see citing works
Fong, J. J., Brown, J. M., Fujita, M. K., & Boussau, B. (2012) · PLoS ONE · doi:10.1371/journal.pone.0048990 · Cited by 71 · see citing works
Geomolecular Dating and the Origin of Placental Mammals
Phillips, M. J. (2015) · Systematic Biology · doi:10.1093/sysbio/syv115 · Cited by 68 · see citing works
Irisarri, I., & Meyer, A. (2016) · Systematic Biology · doi:10.1093/sysbio/syw057 · Cited by 56 · see citing works
Self-citationBewick, A. J., Chain, F. J. J., Heled, J., & Evans, B. J. (2012) · Systematic Biology · doi:10.1093/sysbio/sys039 · Cited by 54 · see citing works
Irisarri, I., Miguel Vences, B., Mauro, D. S., Glaw, F., & Zardoya, R. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-114 · Cited by 53 · see citing works
Self-citationSpringer, M. S., Emerling, C. A., Meredith, R. W., Janečka, J. E., Eizirik, E., & Murphy, W. J. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.09.017 · Cited by 44 · see citing works
Flagged first, then by citations
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
Feiner, N., Motone, F., Meyer, A., & Kuraku, S. (2019) · Scientific Reports · doi:10.1038/s41598-019-40055-1 · Cited by 1,988 · see citing works
Self-citationTempo and Mode of Genome Evolution in the Budding Yeast Subphylum
Shen, X.-X., Opulente, D. A., Kominek, J., Zhou, X., Steenwyk, J. L., Buh, K. V., Haase, M. A. B., Wisecaver, J. H., Wang, M., Doering, D. T., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.023 · Cited by 619 · see citing works
Deeply conserved synteny resolves early events in vertebrate evolution
Simakov, O., Marlétaz, F., Yue, J.-X., O’Connell, B., Jenkins, J., Brandt, A., Calef, R., Tung, C.-H., Huang, T.-K., Schmutz, J., et al. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-1156-z · Cited by 363 · see citing works
The evolution of a tropical biodiversity hotspot
Harvey, M. G., Bravo, G. A., Claramunt, S., Cuervo, A. M., Derryberry, G. E., Battilana, J., Seeholzer, G. F., McKay, J., O’Meara, B. C., Faircloth, B. C., et al. (2020) · Science · doi:10.1126/science.aaz6970 · Cited by 391 · see citing works
The origin of squamates revealed by a Middle Triassic lizard from the Italian Alps
Simões, T. R., Caldwell, M. W., Tałanda, M., Bernardi, M., Palci, A., Vernygora, O. V., Bernardini, F., Mancini, L., & Nydam, R. L. (2018) · Nature · doi:10.1038/s41586-018-0093-3 · Cited by 256 · see citing works
Cyanobacteria evolution: Insight from the fossil record
Demoulin, C., Lara, Y. J., Cornet, L., François, C., Baurain, D., Wilmotte, A., & Javaux, E. (2019) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2019.05.007 · Cited by 239 · see citing works
Self-citationIrisarri, I., Singh, P., Koblmüller, S., Torres‐Dowdall, J., Henning, F., Franchini, P., Fischer, C., Lemmon, A. R., Lemmon, E. M., Thallinger, G., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05479-9 · Cited by 221 · see citing works
Self-citationPhylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
Hime, P. M., Lemmon, A. R., Lemmon, E. C. M., Prendini, E., Brown, J. M., Thomson, R. C., Kratovil, J. D., Noonan, B. P., Pyron, R. A., Peloso, P. L. V., et al. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa034 · Cited by 213 · see citing works
A phylogenomic framework and timescale for comparative studies of tunicates
Delsuc, F., Philippe, H., Tsagkogeorga, G., Simion, P., Tilak, M., Turón, X., López‐Legentil, S., Piette, J., Lemaire, P., & Douzery, E. (2018) · BMC Biology · doi:10.1186/s12915-018-0499-2 · Cited by 219 · see citing works
Self-citationGiant lungfish genome elucidates the conquest of land by vertebrates
Meyer, A., Schloissnig, S., Franchini, P., Du, K., Woltering, J. M., Irisarri, I., Wong, W. Y., Nowoshilow, S., Kneitz, S., Kawaguchi, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03198-8 · Cited by 211 · see citing works
Self-citationCombining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae
Bossert, S., Murray, E. A., Almeida, E. A. B., Brady, S. G., Blaimer, B. B., & Danforth, B. N. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.10.012 · Cited by 196 · see citing works
Franco, A. D., Poujol, R., Baurain, D., & Philippe, H. (2019) · BMC Evolutionary Biology · doi:10.1186/s12862-019-1350-2 · Cited by 155 · see citing works
Self-citationGarcia‐Porta, J., Irisarri, I., Kirchner, M., Rodríguez, A., Kirchhof, S., Brown, J. L., MacLeod, A., Turner, A. P., Ahmadzadeh, F., Albaladejo‐Robles, G., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11943-x · Cited by 151 · see citing works
Self-citationEmbracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
Bravo, G. A., Antonelli, A., Bacon, C. D., Bartoszek, K., Blom, M. P. K., Huynh, S., Jones, G., Knowles, L. L., Lamichhaney, S., Marcussen, T., et al. (2019) · PeerJ · doi:10.7717/peerj.6399 · Cited by 143 · see citing works
Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci
Koch, N. M. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab151 · Cited by 121 · see citing works
The hagfish genome and the evolution of vertebrates
Marlétaz, F., Timoshevskaya, N. Y., Timoshevskiy, V. A., Parey, E., Simakov, O., Gavriouchkina, D., Suzuki, M., Kubokawa, K., Brenner, S., Smith, J. J., et al. (2024) · Nature · doi:10.1038/s41586-024-07070-3 · Cited by 126 · see citing works
Marjanović, D., & Laurin, M. (2019) · PeerJ · doi:10.7717/peerj.5565 · Cited by 135 · see citing works
The macroevolutionary singularity of snakes
Title, P. O., Singhal, S., Gründler, M. C., Costa, G. C., Pyron, R. A., Colston, T. J., Grundler, M. R., Prates, I., Stepanova, N., Jones, M. E. H., et al. (2024) · Science · doi:10.1126/science.adh2449 · Cited by 121 · see citing works
Successive climate crises in the deep past drove the early evolution and radiation of reptiles
Simões, T. R., Kammerer, C. F., Caldwell, M. W., & Pierce, S. E. (2022) · Science Advances · doi:10.1126/sciadv.abq1898 · Cited by 100 · see citing works
The Emerging Phylogenetic Perspective on the Evolution of Actinopterygian Fishes
Dornburg, A., & Near, T. J. (2021) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-122120-122554 · Cited by 94 · see citing works
A large-scale systematic framework of Chinese snakes based on a unified multilocus marker system
Li, J., Liang, D., Wang, Y.-Y., Guo, P., Huang, S., & Zhang, P. (2020) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2020.106807 · Cited by 91 · see citing works
Simões, T. R., Caldwell, M. W., & Pierce, S. E. (2020) · BMC Biology · doi:10.1186/s12915-020-00901-5 · Cited by 90 · see citing works
Is Phylotranscriptomics as Reliable as Phylogenomics?
Cheon, S., Zhang, J., & Park, C. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa181 · Cited by 88 · see citing works
Contamination detection in genomic data: more is not enough
Cornet, L., & Baurain, D. (2022) · Genome biology · doi:10.1186/s13059-022-02619-9 · Cited by 80 · see citing works
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Zhu, Y.-A., Li, Q., Lü, J., Chen, Y., Wang, J., Gai, Z., Zhao, W., Wei, G., Yu, Y., Ahlberg, P., et al. (2022) · Nature · doi:10.1038/s41586-022-05136-8 · Cited by 78 · see citing works
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Redmond, A. K., Casey, D., Gundappa, M. K., Macqueen, D. J., & McLysaght, A. (2023) · Nature Communications · doi:10.1038/s41467-023-38714-z · Cited by 71 · see citing works
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Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics
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Foley, S., Lüddecke, T., Cheng, D.-Q., Krehenwinkel, H., Künzel, S., Longhorn, S. J., Wendt, I., von Wirth, V., Tänzler, R., Miguel Vences, B., et al. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.106573 · Cited by 64 · see citing works
Stöck, M., Kratochvíl, L., Kuhl, H., Rovatsos, M., Evans, B. J., Suh, A., Valenzuela, N., Veyrunes, F., Zhou, Q., Gamble, T., et al. (2021) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2020.0426 · Cited by 64 · see citing works
Singhal, S., Colston, T. J., Grundler, M. R., Smith, S. A., Costa, G. C., Colli, G. R., Moritz, C. C., Pyron, R. A., & Rabosky, D. L. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa054 · Cited by 64 · see citing works
Capobianco, A., & Friedman, M. (2018) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12473 · Cited by 63 · see citing works
Dissecting Incongruence between Concatenation- and Quartet-Based Approaches in Phylogenomic Data
Shen, X., Steenwyk, J. L., & Rokas, A. (2021) · Systematic Biology · doi:10.1093/sysbio/syab011 · Cited by 64 · see citing works
Simões, T. R., & Pyron, R. A. (2021) · Bulletin of the Museum of Comparative Zoology · doi:10.3099/0027-4100-163.2.47 · Cited by 63 · see citing works
The genomes of all lungfish inform on genome expansion and tetrapod evolution
Schartl, M., Woltering, J. M., Irisarri, I., Du, K., Kneitz, S., Pippel, M., Brown, T., Franchini, P., Li, J., Li, M., et al. (2024) · Nature · doi:10.1038/s41586-024-07830-1 · Cited by 64 · see citing works
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Irisarri, I., Uribe, J. E., Eernisse, D. J., & Zardoya, R. (2020) · BMC Evolutionary Biology · doi:10.1186/s12862-019-1573-2 · Cited by 62 · see citing works
Self-citationPhylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders
Rancilhac, L., Irisarri, I., Angelini, C., Arntzen, J. W., Babik, W., Bossuyt, F., Künzel, S., Lüddecke, T., Pasmans, F., Sanchez, E., et al. (2020) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2020.106967 · Cited by 58 · see citing works
Self-citationPhylogenomic insights into the first multicellular streptophyte
Bierenbroodspot, M. J., Darienko, T., de Vries, S., Fürst‐Jansen, J. M. R., Buschmann, H., Pröschold, T., Irisarri, I., & de Vries, J. (2024) · Current Biology · doi:10.1016/j.cub.2023.12.070 · Cited by 57 · see citing works
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Portik, D. M., & Wiens, J. J. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa064 · Cited by 54 · see citing works
Macroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages
Domazet-Lošo, M., Široki, T., Šimičević, K., & Domazet‐Lošo, T. (2024) · Nature Communications · doi:10.1038/s41467-024-47017-w · Cited by 53 · see citing works
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Rodríguez, A., Burgon, J. D., Lyra, M. L., Irisarri, I., Baurain, D., Blaustein, L., Göçmen, B., Künzel, S., Mable, B. K., Nolte, A. W., et al. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.07.009 · Cited by 53 · see citing works
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Recknagel, H., Carruthers, M., Yurchenko, A. A., Nokhbatolfoghahai, M., Kamenos, N. A., Bain, M., & Elmer, K. R. (2021) · Nature Ecology & Evolution · doi:10.1038/s41559-021-01555-4 · Cited by 51 · see citing works
Matsunami, M., Suzuki, M., Haramoto, Y., Fukui, A., Inoue, T., Yamaguchi, K., Uchiyama, I., Mori, K., Tashiro, K., Ito, Y., et al. (2019) · DNA Research · doi:10.1093/dnares/dsz003 · Cited by 51 · see citing works
Sobral, G., Simões, T. R., & Schoch, R. R. (2020) · Scientific Reports · doi:10.1038/s41598-020-58883-x · Cited by 51 · see citing works
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Tosches, M. A. (2021) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-120319-112654 · Cited by 44 · see citing works
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Peijnenburg, K. T. C. A., JANSSEN, A. W., Wall-Palmer, D., Goetze, E., Maas, A. E., Todd, J. A., & Marlétaz, F. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1920918117 · Cited by 47 · see citing works
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Scherz, M. D., Masonick, P., Meyer, A., & Hulsey, C. D. (2022) · Systematic Biology · doi:10.1093/sysbio/syac006 · Cited by 46 · see citing works
Self-citationMatz, H. C., Taylor, R. S., Redmond, A. K., Hill, T. M., Daniels, R. R., Beltrán, M., Henderson, N. C., Macqueen, D. J., & Dooley, H. M. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112664 · Cited by 43 · see citing works
Cornet, L., Bertrand, A. R., Hanikenne, M., Javaux, E., Wilmotte, A., & Baurain, D. (2018) · Microbial Genomics · doi:10.1099/mgen.0.000212 · Cited by 44 · see citing works
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Drillon, G., Champeimont, R., Oteri, F., Fischer, G., & Carbone, A. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa114 · Cited by 40 · see citing works
Burgon, J. D., Miguel Vences, B., Steinfartz, S., Bogaerts, S., Bonato, L., Donaire‐Barroso, D., Martínez-Solano, Í., Velo‐Antón, G., Vieites, D. R., Mable, B. K., et al. (2020) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2020.107063 · Cited by 42 · see citing works
Shark and ray genomics for disentangling their morphological diversity and vertebrate evolution
Kuraku, S. (2021) · Developmental Biology · doi:10.1016/j.ydbio.2021.06.001 · Cited by 42 · see citing works
Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses
Simmons, M. P., Sloan, D. B., Springer, M. S., & Gatesy, J. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.10.001 · Cited by 40 · see citing works
Debiais‐Thibaud, M., Simion, P., Ventéo, S., Muñoz, D., Marcellini, S., Mazan, S., & Haitina, T. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz145 · Cited by 40 · see citing works
Cell culture-based karyotyping of orectolobiform sharks for chromosome-scale genome analysis
Uno, Y., Nozu, R., Kiyatake, I., Higashiguchi, N., Sodeyama, S., Murakumo, K., Sato, K., & Kuraku, S. (2020) · Communications Biology · doi:10.1038/s42003-020-01373-7 · Cited by 40 · see citing works
Alda, F., Ludt, W. B., Elías, D. J., McMahan, C. D., & Chakrabarty, P. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab161 · Cited by 39 · see citing works
Cornet, L., Cleenwerck, I., Praet, J., Léonard, R. R., Vereecken, N. J., Michez, D., Smagghe, G. J., Baurain, D., & Vandamme, P. A. R. (2022) · mSystems · doi:10.1128/msystems.01500-21 · Cited by 40 · see citing works
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Jones, M. E. H., Benson, R., Skutschas, P. P., Hill, L., Panciroli, E., Schmitt, A. D., Walsh, S. A., & Evans, S. E. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2114100119 · Cited by 40 · see citing works
Qian, Y., Meng, M., Zhou, C., Liu, H., Jiang, H., Xu, Y., Chen, W., Ding, Z., Liu, Y., Gong, X., et al. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad129 · Cited by 37 · see citing works
Self-citationKoch, N. M., & Gauthier, J. A. (2018) · PLoS ONE · doi:10.1371/journal.pone.0202729 · Cited by 37 · see citing works
Funk, W. C., Zamudio, K. R., & Crawford, A. J. (2018) · Population genomics · doi:10.1007/13836_2018_61 · Cited by 37 · see citing works
Skeletons of the Eye: An Evolutionary and Developmental Perspective
Franz‐Odendaal, T. A. (2018) · The Anatomical Record · doi:10.1002/ar.24043 · Cited by 37 · see citing works
Evaluating the role of fish as surrogates for amphibians in pesticide ecological risk assessment
Glaberman, S. R., Kiwiet, J., & Aubee, C. B. (2019) · Chemosphere · doi:10.1016/j.chemosphere.2019.06.166 · Cited by 37 · see citing works
Large-scale evolution of body temperatures in land vertebrates
Moreira, M. O., Qu, Y., & Wiens, J. J. (2021) · Evolution Letters · doi:10.1002/evl3.249 · Cited by 37 · see citing works
Evaluating Genome Assemblies and Gene Models Using gVolante
Nishimura, O., Hara, Y., & Kuraku, S. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9173-0_15 · Cited by 36 · see citing works
Liu, L., Zhang, J., Rheindt, F. E., Lei, F., Qu, Y., Wang, Y., Zhang, Y., Sullivan, C., Nie, W., Wang, J., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1715371114 · Cited by 36 · see citing works
Li, X., Hou, Z., Xu, C., Shi, X., Yang, L., Lewis, L. A., & Zhong, B. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab101 · Cited by 34 · see citing works
Different Genes are Recruited During Convergent Evolution of Pregnancy and the Placenta
Foster, C. S. P., Dyke, J. U. V., Thompson, M. B., Smith, N. M. A., Simpfendorfer, C. A., Murphy, C. R., & Whittington, C. M. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac077 · Cited by 33 · see citing works
Reconstructing evolution at the community level: A case study on Mediterranean amphibians
Ehl, S., Miguel Vences, B., & Veith, M. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.02.013 · Cited by 32 · see citing works
Lamichhaney, S., Catullo, R., Keogh, J. S., Clulow, S., Edwards, S. V., & Ezaz, T. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2011649118 · Cited by 31 · see citing works
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Matz, H. C., & Dooley, H. M. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1245704 · Cited by 31 · see citing works
Surmounting the Large-Genome “Problem” for Genomic Data Generation in Salamanders
Weisrock, D. W., Hime, P. M., Nunziata, S. O., Jones, K. S., Murphy, M. O., Hotaling, S., & Kratovil, J. D. (2018) · Population genomics · doi:10.1007/13836_2018_36 · Cited by 31 · see citing works
Torres‐Sánchez, M., Creevey, C. J., Kornobis, É., Gower, D. J., Wilkinson, M., & Mauro, D. S. (2018) · DNA Research · doi:10.1093/dnares/dsy034 · Cited by 30 · see citing works
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Abalde, S., Jimenez-Tenorio, M., Uribe, J. E., & Zardoya, R. (2019) · Zoologica Scripta · doi:10.1111/zsc.12329 · Cited by 30 · see citing works
Maugars, G., Nourizadeh-Lillabadi, R., & Weltzien, F. (2020) · Frontiers in Endocrinology · doi:10.3389/fendo.2020.538196 · Cited by 30 · see citing works
Meiri, S., Murali, G., Zimin, A., Shak, L., Itescu, Y., Caetano, G. H. D. O., & Roll, U. (2021) · Journal of Biological Research - Thessaloniki · doi:10.1186/s40709-021-00134-9 · Cited by 30 · see citing works
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Portik, D. M., Streicher, J. W., Blackburn, D. C., Moen, D. S., Hutter, C. R., & Wiens, J. J. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad109 · Cited by 30 · see citing works
Transcriptomic data support a nocturnal bottleneck in the ancestor of gecko lizards
Pinto, B. J., Nielsen, S. V., & Gamble, T. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.106639 · Cited by 29 · see citing works
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Yurchenko, A. A., Recknagel, H., & Elmer, K. R. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa161 · Cited by 29 · see citing works
Whiteley, S. L., Wagner, S., Holleley, C. E., Deveson, I. W., Graves, J. A. M., & Georges, A. (2022) · Science Advances · doi:10.1126/sciadv.abk0275 · Cited by 29 · see citing works
Van Vlierberghe, M., Di Franco, A., Philippe, H., & Baurain, D. (2021) · BMC Research Notes · doi:10.1186/s13104-021-05717-2 · Cited by 27 · see citing works
Self-citationEnault, S., Muñoz, D., Simion, P., Ventéo, S., Sire, J., Marcellini, S., & Debiais‐Thibaud, M. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1241-y · Cited by 28 · see citing works
Self-citationRedmond, A. K., Macqueen, D. J., & Dooley, H. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1290-2 · Cited by 26 · see citing works
Esteve‐Altava, B., Molnar, J. L., Johnston, P., Hutchinson, J. R., & Diogo, R. (2018) · Evolution · doi:10.1111/evo.13430 · Cited by 26 · see citing works
Parsimony analysis of phylogenomic datasets (II): evaluation of PAUP*, MEGA and MPBoot
Goloboff, P. A., Catalano, S. A., & Torres, A. (2021) · Cladistics · doi:10.1111/cla.12476 · Cited by 26 · see citing works
IgNAR antibody: Structural features, diversity and applications
Khalid, Z., Chen, Y., Du, Y., Abbas, M., Ma, H., Naz, Z., Mengist, H. M., Cao, M., & Jin, T. (2022) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2022.01.027 · Cited by 27 · see citing works
Simões, T. R., Kinney-Broderick, G., & Pierce, S. E. (2022) · Communications Biology · doi:10.1038/s42003-022-03144-y · Cited by 25 · see citing works
Roscito, J. G., Sameith, K., Pippel, M., Françoijs, K., Winkler, S., Dahl, A., Papoutsoglou, G., Myers, E. W., & Hiller, M. (2018) · GigaScience · doi:10.1093/gigascience/giy141 · Cited by 23 · see citing works
Quek, Z. B. R., & Huang, D. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.01.012 · Cited by 25 · see citing works
Moreno, N., López, J. M., Morona, R., Lozano, D. D., Jiménez, S., & González, A. (2018) · Frontiers in Neuroanatomy · doi:10.3389/fnana.2018.00042 · Cited by 24 · see citing works
Phylogenomics recovers monophyly and early Tertiary diversification of Dipteronia (Sapindaceae)
Feng, Y., Comes, H. P., Zhou, X.-P., & Qiu, Y. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.09.012 · Cited by 24 · see citing works
Assessing the relative performance of fast molecular dating methods for phylogenomic data
Costa, F. P. D. F., Schrago, C. G., & Mello, B. (2022) · BMC Genomics · doi:10.1186/s12864-022-09030-5 · Cited by 23 · see citing works
Engel, K. M., Sampels, S., Dzyuba, B., Podhorec, P., Policar, T., Dannenberger, D., & Schiller, J. (2019) · Chemistry and Physics of Lipids · doi:10.1016/j.chemphyslip.2019.03.014 · Cited by 23 · see citing works
Reinstating reptiles: from clueless creatures to esteemed models of cognitive biology
Meester, G. D., & Baeckens, S. (2021) · Behaviour · doi:10.1163/1568539x-00003718 · Cited by 22 · see citing works
Zeb, U., Wang, X., Azizullah, A., Fiaz, S., Khan, H., Ullah, S., Ali, H., & Shahzad, K. (2021) · Saudi Journal of Biological Sciences · doi:10.1016/j.sjbs.2021.10.070 · Cited by 22 · see citing works
Diversity, biogeography, and reproductive evolution in the genus Pipa (Amphibia: Anura: Pipidae)
Antoine Fouquet, A., Cornuault, J., Rodrigues, M. T., Werneck, F. P., Hrbek, T., Acosta‐Galvis, A. R., Massemin, D., Kok, P. J. R., & Ernst, R. (2022) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2022.107442 · Cited by 22 · see citing works
- 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 › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- jawed vertebrates, Gnathostomata, timetree, phylotranscriptomics, phylogenomics, divergence time estimation, mitochondrial genome, transcriptome assembly, phylogenetic diversity, macroevolution
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