The DOI matches its Crossref record; 43 of the 43 references it cites were found in a registry or an index.
Gene gain and loss across the metazoan tree of life
Open accessAbstract
Although recent research has revealed high genomic complexity in the earliest-splitting animals and their ancestors, the macroevolutionary trends orchestrating gene repertoire evolution throughout the animal phyla remain poorly understood. We used a phylogenomic approach to interrogate genome evolution across all animal phyla. Our analysis uncovered a bimodal distribution of recruitment of orthologous genes, with most genes gained very ‘early’ (that is, at deep nodes) or very ‘late’, representing lineage-specific acquisitions. The emergence of animals was characterized by high values of gene birth and duplications. Deuterostomes, ecdysozoans and Xenacoelomorpha were characterized by no gene gain but rampant differential gene loss. Genes considered as animal hallmarks, such as Notch/Delta, were convergently duplicated in all phyla and at different evolutionary depths. Genes duplicated in all nodes from Metazoa to phylum-specific levels were enriched in functions related to the neural system, suggesting that this system has been continuously and independently reshaped throughout evolution across animals. Our results indicate that animal genomes evolved by unparalleled gene duplication followed by differential gene loss, and provide an atlas of gene repertoire evolution throughout the animal tree of life to navigate how, when and how often each gene in each genome was gained, duplicated or lost. Phylogenomic analysis including representatives of all metazoan phyla shows gene duplication followed by differential gene loss throughout the animal tree of life.
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
“it is not only key innovations but also the evolutionary dynamics of gene gain and loss that shape the vast morphological disparity of animals”
From Current understanding on the Cambrian Explosion: questions and answers (2021) · cites this paper as Fernández and Gabaldón 2020
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
“Under the ctenophore-sister scenario, these are most parsimoniously interpreted as arising on the myriazoan stem after the divergence of ctenophores1,5,59, and include genes associated, in bilaterians and cnidarians, with neuronal function1,5,59, development58 and cell adhesion60.”
From Ancient gene linkages support ctenophores as sister to other animals (2023) · cites this paper as [58]
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
“Comparisons among diverse genomes have identified numerous genes that are present in myriazoans but are absent in ctenophores1,5,58.”
From Ancient gene linkages support ctenophores as sister to other animals (2023) · cites this paper as [58]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“Gene gains, losses and duplications dynamically evolved and have unbalanced distributions across the tree”
From Current understanding on the Cambrian Explosion: questions and answers (2021) · cites this paper as Fernández and Gabaldón 2020
The cited source says what the claim attributes to it.
In the citing paper
“gene duplication ratio was high at deep nodes leading to metazoans and the birth rate decreased progressively as animals diversified into clades”
From Current understanding on the Cambrian Explosion: questions and answers (2021) · cites this paper as Fernández and Gabaldón 2020
The cited source says what the claim attributes to it.
In the citing paper
“deuterostomes, ecdysozoans, and Xenacoelomorpha were characterized by no gene gain but rampant differential gene loss”
From Current understanding on the Cambrian Explosion: questions and answers (2021) · cites this paper as Fernández and Gabaldón 2020
The cited source says what the claim attributes to it.
In the citing paper
“around onethird of genes gained at deep nodes below the Nephrozoa and another one-third comprising linage-specific genes (no homologues in other taxa) acquired very late”
From Current understanding on the Cambrian Explosion: questions and answers (2021) · cites this paper as Fernández and Gabaldón 2020
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Similarly, some genes are present in ctenophores and parahoxozoans but absent in sponges58, and these must be interpreted as gene losses on the sponge lineage.”
From Ancient gene linkages support ctenophores as sister to other animals (2023) · cites this paper as [58]
Experimental — accuracy not yet measured
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
Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010) · Systematic Biology · doi:10.1093/sysbio/syq010 · Cited by 18,376
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Capella-Gutiérrez, S., Silla-Martinez, J., & Gabaldón, T. (2009) · Bioinform. · doi:10.1093/bioinformatics/btp348 · Cited by 12,052
Self-citationInterProScan 5: genome-scale protein function classification
JONES, P. M., Binns, D., Chang, H.-Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., et al. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu031 · Cited by 9,511
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Edgar, R. C. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-113 · Cited by 9,119
OrthoFinder: phylogenetic orthology inference for comparative genomics
Emms, D. M., & Kelly, S. (2019) · Genome Biology · doi:10.1186/s13059-019-1832-y · Cited by 7,676
REVIGO summarizes and visualizes long lists of gene ontology terms
Supek, F., Bošnjak, M., Škunca, N., & Šmuc, T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021800 · Cited by 6,264
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, L., Stoeckert, C. J., & Roos, D. S. (2003) · Genome Research · doi:10.1101/gr.1224503 · Cited by 5,707
Huerta‐Cepas, J., Szklarczyk, D., Heller, D., Hernández-Plaza, A., Forslund, S. K., Cook, H., Mende, D. R., Letunić, I., Rattei, T., Jensen, L. J., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1085 · Cited by 4,934
Kanehisa, M. I., Sato, Y., & Morishima, K. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.11.006 · Cited by 4,106
Emms, D. M., & Kelly, S. (2015) · Genome Biology · doi:10.1186/s13059-015-0721-2 · Cited by 3,408
Cited by
Sorted by citations
Notch signaling pathway: architecture, disease, and therapeutics
Zhou, B., Lin, W., Long, Y., Yang, Y., Zhang, H., Wu, K., & Chu, Q. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-00934-y · Cited by 1,216
Ancient gene linkages support ctenophores as sister to other animals
Schultz, D. T., Haddock, S. H. D., Bredeson, J. V., Green, R. E., Simakov, O., & Rokhsar, D. S. (2023) · Nature · doi:10.1038/s41586-023-05936-6 · Cited by 362
The evolutionary emergence of land plants.
Donoghue, P., Harrison, C. J., Paps, J., & Schneider, H. (2021) · Current Biology · doi:10.1016/j.cub.2021.07.038 · Cited by 153
Diversity and evolution of the animal virome
Harvey, E., & Holmes, E. C. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00665-x · Cited by 178
The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition
Ros-Rocher, N., Pérez-Posada, A., Leger, M. M., & Ruiz‐Trillo, I. (2021) · Open Biology · doi:10.1098/rsob.200359 · Cited by 169
Kenny, N. J., Francis, W. R., Rivera-Vicéns, R. E., Juravel, K., de Mendoza, A., Díez-Vives, C., Lister, R., Bezares-Calderón, L. A., Grombacher, L., Roller, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17397-w · Cited by 129
Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci
Koch, N. M. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab151 · Cited by 126
Origin and Early Evolution of the Eukaryotic Cell
Gabaldón, T. (2021) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090817-062213 · Cited by 121
Self-citationDivergent genomic trajectories predate the origin of animals and fungi
Ocaña-Pallarés, E., Williams, T., López-Escardó, D., Arroyo, A., Pathmanathan, J., Bapteste, É., Tikhonenkov, D., Keeling, P., Szöllősi, G., & Ruiz-Trillo, I. (2022) · Nature · doi:10.1038/s41586-022-05110-4 · Cited by 82
Current understanding on the Cambrian Explosion: questions and answers
Zhang, X., & Shu, D. (2021) · PalZ · doi:10.1007/s12542-021-00568-5 · Cited by 96
Conservative route to genome compaction in a miniature annelid
Martín-Durán, J. M., Vellutini, B. C., Marlétaz, F., Cetrangolo, V., Cvetešić, N., Thiel, D. J., Henriet, S., Grau‐Bové, X., Carrillo‐Baltodano, A. M., Gu, W., et al. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-01327-6 · Cited by 92
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies
Fuentes, D., Molina, M., Chorostecki, U., Capella-Gutiérrez, S., Marcet‐Houben, M., & Gabaldón, T. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab966 · Cited by 74
Self-citationGenome evolution in plants and the origins of innovation
Clark, J. (2023) · New Phytologist · doi:10.1111/nph.19242 · Cited by 69
Sensing the world and its dangers: An evolutionary perspective in neuroimmunology
Kraus, A., Buckley, K. M., & Salinas, I. (2021) · eLife · doi:10.7554/elife.66706 · Cited by 68
Merényi, Z., Krizsán, K., Sahu, N., Liu, X., Bálint, B., Stajich, J., Spatafora, J. W., & Nagy, L. G. (2023) · Nature Ecology & Evolution · doi:10.1038/s41559-023-02095-9 · Cited by 68
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
Evolution of tissue-specific expression of ancestral genes across vertebrates and insects
Mantica, F., Iñiguez, L., Márquez, Y., Permanyer, J., Torres-Méndez, A., Cruz, J., Franch‐Marro, X., Tulenko, F. J., Burguera, D., Bertrand, S., et al. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02398-5 · Cited by 54
Martínez, A., Bonaglia, S., Domênico, M. D., Fonseca, G., Ingels, J., Jörger, K. M., Laumer, C., Leasi, F., Zeppilli, D., Baldrighi, E., et al. (2025) · Communications Biology · doi:10.1038/s42003-025-07888-1 · Cited by 55
Myriapod genomes reveal ancestral horizontal gene transfer and hormonal gene loss in millipedes
So, W. L., Nong, W., Xie, Y., Baril, T., Ma, H.-Y., Qu, Z., Haimovitz, J., Swale, T., Gaitán‐Espitía, J. D., Lau, K., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30690-0 · Cited by 39
Alternative neural systems: What is a neuron? (Ctenophores, sponges and placozoans)
Moroz, L. L., & Romanova, D. Y. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.1071961 · Cited by 39
Systematic errors in orthology inference and their effects on evolutionary analyses
Natsidis, P., Kapli, P., Schiffer, P. H., & Telford, M. J. (2021) · iScience · doi:10.1016/j.isci.2021.102110 · Cited by 41
An episodic burst of massive genomic rearrangements and the origin of non-marine annelids
Vargas-Chávez, C., Benítez-Álvarez, L., Martínez-Redondo, G. I., Álvarez-González, L., Salces-Ortiz, J., Eleftheriadi, K., Escudero, N., Guiglielmoni, N., Flot, J.-F., Novo, M., et al. (2025) · Nature Ecology & Evolution · doi:10.1038/s41559-025-02728-1 · Cited by 35
Self-citationLosing Genes: The Evolutionary Remodeling of Cetacea Skin
Themudo, G. E., Alves, L. Q., Machado, A. M., Lopes‐Marques, M., da Fonseca, R. R., Fonseca, M. M., Ruivo, R., & Castro, L. F. C. (2020) · Frontiers in Marine Science · doi:10.3389/fmars.2020.592375 · Cited by 36
Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms
Crow, M., Suresh, H., Lee, J., & Gillis, J. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac276 · Cited by 34
A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis
Schultz, D. T., Francis, W. R., McBroome, J. D., Christianson, L. M., Haddock, S. H. D., & Green, R. E. (2021) · G3 Genes|Genomes|Genetics · doi:10.1093/g3journal/jkab302 · Cited by 35
Dornburg, A., & Yoder, J. A. (2022) · Immunogenetics · doi:10.1007/s00251-021-01232-7 · Cited by 35
Liu, Y.-L., Qu, M., Jiang, H., Schneider, R., Qin, G., Luo, W., Yu, H., Zhang, B., Wang, X., Zhang, Y.-H., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-35338-7 · Cited by 28
Reticulate evolution: Detection and utility in the phylogenomics era
Bjornson, S., Verbruggen, H., Upham, N. S., & Steenwyk, J. L. (2024) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2024.108197 · Cited by 36
Horta, M. A. C., Steenwyk, J. L., Mead, M. E., dos Santos, L. H. B., Zhao, S., Gibbons, J. G., Marcet‐Houben, M., Gabaldón, T., Rokas, A., & Goldman, G. H. (2022) · mBio · doi:10.1128/mbio.01519-22 · Cited by 28
Self-citationPhylogenomics and the first higher taxonomy of Placozoa, an ancient and enigmatic animal phylum
Tessler, M., Neumann, J. S., Kamm, K., Osigus, H., Eshel, G., Narechania, A., Burns, J. A., DeSalle, R., & Schierwater, B. (2022) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2022.1016357 · Cited by 28
Fish genomics and its impact on fundamental and applied research of vertebrate biology
Ahmad, S. F., Jehangir, M., Srikulnath, K., & Martins, C. (2021) · Reviews in Fish Biology and Fisheries · doi:10.1007/s11160-021-09691-7 · Cited by 29
de Oliveira, A. L., Mitchell, J. H., Girguis, P. R., & Bright, M. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab347 · Cited by 24
Cerón-Romero, M. A., Fonseca, M. M., Martins, L. D. O., Posada, D., & Katz, L. A. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evac119 · Cited by 27
The Curious Case of Multicellularity in the Volvocine Algae
Jiménez‐Marín, B., & Olson, B. J. S. C. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.787665 · Cited by 26
Smelling in the dark: Phylogenomic insights into the chemosensory system of a subterranean beetle
Balart‐García, P., Cieslak, A., Escuer, P., Rozas, J., Ribera, I., & Fernández, R. (2021) · Molecular Ecology · doi:10.1111/mec.15921 · Cited by 25
Self-citationNitric oxide signaling in ctenophores
Moroz, L. L., Mukherjee, K., & Romanova, D. Y. (2023) · Frontiers in Neuroscience · doi:10.3389/fnins.2023.1125433 · Cited by 24
Pascual-Carreras, E., Herrera-Úbeda, C., Rosselló, M., Coronel-Córdoba, P., García‐Fernàndez, J., Saló, E., & Adell, T. (2021) · Scientific Reports · doi:10.1038/s41598-020-80627-0 · Cited by 24
Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes
Deutekom, E. S., Snel, ., & van Dam, T. J. P. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa206 · Cited by 23
Gene Loss may have Shaped the Cnidarian and Bilaterian Hox and ParaHox Complement
Steinworth, B. M., Martindale, M. Q., & Ryan, J. F. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evac172 · Cited by 22
ContScout: sensitive detection and removal of contamination from annotated genomes
Bálint, B., Merényi, Z., Hegedüs, B., Grigoriev, I. V., Hou, Z., Földi, C., & Nagy, L. G. (2024) · Nature Communications · doi:10.1038/s41467-024-45024-5 · Cited by 21
Diversification and Functional Evolution of HOX Proteins
Singh, N. P., & Krumlauf, R. K. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.798812 · Cited by 26
Spiralian genomics and the evolution of animal genome architecture
Liao, I. J.-Y., Lu, T.-M., Chen, M.-E., & Luo, Y. (2023) · Briefings in Functional Genomics · doi:10.1093/bfgp/elad029 · Cited by 21
Lateral Gene Transfer Acts As an Evolutionary Shortcut to Efficient C4 Biochemistry
Phansopa, C., Dunning, L. T., Reid, J. D., & Christin, P. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa143 · Cited by 21
Martí‐Solans, J., Godoy-Marín, H., Diaz-Gracia, M., Onuma, T. A., Nishida, H., Albalat, R., & Cañestro, C. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.700827 · Cited by 21
Human Follicular Mites: Ectoparasites Becoming Symbionts
Smith, G., Manzano-Marı́n, A., Reyes‐Prieto, M., Antunes, C. S. R., Ashworth, V., Goselle, O. N., Jan, A., Moya, A., Latorre, A., Perotti, M. A., et al. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac125 · Cited by 22
The 3D-Evo Space: Evolution of Gene Expression and Alternative Splicing Regulation
Mantica, F., & Irimia, M. (2022) · Annual Review of Genetics · doi:10.1146/annurev-genet-071719-020653 · Cited by 20
Raimondeau, P., Bianconi, M. E., Pereira, L., Parisod, C., Christin, P., & Dunning, L. T. (2023) · New Phytologist · doi:10.1111/nph.19272 · Cited by 20
Rappaport, H. B., & Oliverio, A. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae160 · Cited by 19
Wang, J., Zhang, L., Cavallini, M., Pahlevan, A., Sun, J., Morshedian, A., Fain, G., Sampath, A. P., & Peng, Y. (2024) · Nature Communications · doi:10.1038/s41467-024-55019-x · Cited by 27
Evolution of Protein-Mediated Biomineralization in Scleractinian Corals
Zaquin, T., Malik, A., Drake, J. L., Putnam, H. M., & Mass, T. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.618517 · Cited by 20
Dong, Z., Wang, F., Liu, Y., Li, Y., Yu, H., Peng, S., Sun, T., Qu, M., Sun, K. W., Wang, L., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49848-z · Cited by 18
Phylogenomics provides insights into the evolution of cactophily and host plant shifts in Drosophila
Moreyra, N. N., Almeida, F. C., Allan, C. W., Frankel, N., Matzkin, L. M., & Hasson, E. (2022) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2022.107653 · Cited by 18
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
Martínez‐Redondo, G. I., Vargas-Chávez, C., Eleftheriadi, K., Benítez-Álvarez, L., Vázquez-Valls, M., & Fernández, R. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae235 · Cited by 15
Self-citationComparative genomics reveals a core gene toolbox for lifestyle transitions in Hypocreales fungi
Wu, B., & Cox, M. P. (2021) · Environmental Microbiology · doi:10.1111/1462-2920.15554 · Cited by 17
Evolutionary causes and consequences of gene duplication
Cisneros, A. F., Dibyachintan, S., Bédard, F., Aubé, S., Lemieux, P., & Landry, C. R. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-00935-5 · Cited by 19
Yu, H., Li, Y., Han, W., Bao, L., Liu, F., Ma, Y., Pu, Z., Zeng, Q., Zhang, L., Bao, Z., et al. (2024) · Nature Protocols · doi:10.1038/s41596-024-00966-4 · Cited by 18
Salamanca-Díaz, D. A., Ritschard, E. A., Schmidbaur, H., & Wanninger, A. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.883755 · Cited by 16
Fernández, R., Tonzo, V., Guerrero, C. S., Lozano-Fernández, J., Martínez‐Redondo, G. I., Balart‐García, P., Arístide, L., Eleftheriadi, K., & Vargas-Chávez, C. (2022) · Peer Community Journal · doi:10.24072/pcjournal.177 · Cited by 14
Self-citationImproving 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
Chen, B.-L., Zhang, W., Dong, X.-W., Liu, J., & Bai, Y. (2025) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2025.167879 · Cited by 15
Dornburg, A., Wcisel, D. J., Zapfe, K., Ferraro, E., Roupe-Abrams, L., Thompson, A. W., Braasch, I., Ota, T., & Yoder, J. A. (2021) · Immunogenetics · doi:10.1007/s00251-021-01225-6 · Cited by 16
Ancient fish lineages illuminate toll-like receptor diversification in early vertebrate evolution
Carlson, K. B., Nguyen, C., Wcisel, D. J., Yoder, J. A., & Dornburg, A. (2023) · Immunogenetics · doi:10.1007/s00251-023-01315-7 · Cited by 16
Sheikh, S., Fu, C.-J., Brown, M. W., & Baldauf, S. L. (2024) · Nature Communications · doi:10.1038/s41467-024-54029-z · Cited by 15
Martínez, A., Kohler, S., García‐Cobo, M., Kurtz, M. N., Fontaneto, D., & Macher, J. (2024) · Estuarine Coastal and Shelf Science · doi:10.1016/j.ecss.2024.109092 · Cited by 14
Gene Duplication and Alternative Splicing as Evolutionary Drivers of Proteome Specialization
Mantica, F., & Irimia, M. (2025) · BioEssays · doi:10.1002/bies.202400202 · Cited by 13
Hydrodynamics in early animal evolution
Nielsen, C. (2022) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12909 · Cited by 14
Gene loss during a transition to multicellularity
Jiménez‐Marín, B., Rakijas, J. B., Tyagi, A., Pandey, A., Hanschen, E. R., Anderson, J., Heffel, M. G., Platt, T. G., & Olson, B. J. S. C. (2023) · Scientific Reports · doi:10.1038/s41598-023-29742-2 · Cited by 16
Wu, B., Hao, W., & Cox, M. P. (2022) · BMC Biology · doi:10.1186/s12915-022-01346-8 · Cited by 13
Assembling animals: trees, genomes, cells, and contrast to plants
Paps, J., Rossi, M. E., Bowles, A. M. C., & Álvarez‐Presas, M. (2023) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2023.1185566 · Cited by 13
Redondo, G. I. M., Perez-Canales, F. M., Fernández, J. M., Barrios-Núñez, I., Vázquez-Valls, M., Cases, I., Rojas, A. M., & Fernández, R. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.28.582465 · Cited by 13
Self-citationConvergent genome evolution shaped the emergence of terrestrial animals
Wei, J., Pisani, D., Donoghue, P. C. J., Álvarez‐Presas, M., & Paps, J. (2025) · Nature · doi:10.1038/s41586-025-09722-4 · Cited by 15
Shifting landscapes: the role of 3D genomic organizations in gene regulatory strategies
Hehmeyer, J., Spitz, F., & Marlow, H. Q. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102064 · Cited by 11
Emergence of distinct syntenic density regimes is associated with early metazoan genomic transitions
Robert, N. S. M., Sarigol, F., Zimmermann, B., Meyer, A., Voolstra, C. R., & Simakov, O. (2022) · BMC Genomics · doi:10.1186/s12864-022-08304-2 · Cited by 12
The impact of local genomic properties on the evolutionary fate of genes
Hara, Y., & Kuraku, S. (2023) · eLife · doi:10.7554/elife.82290 · Cited by 11
Sánchez-Serna, G., Badia-Ramentol, J., Bujosa, P., Ferrández-Roldán, A., Torres-Águila, N. P., Fabregá-Torrus, M., Wibisana, J. N., Mansfield, M. J., Plessy, C., Luscombe, N., et al. (2024) · bioRxiv · doi:10.1093/molbev/msae260 · Cited by 11
Gene novelty and gene family expansion in the early evolution of Lepidoptera
Hoile, A. E., Holland, P. W. H., & Mulhair, P. O. (2025) · BMC Genomics · doi:10.1186/s12864-025-11338-x · Cited by 10
Benítez-Álvarez, L., Leria, L., Fernández, R., Mateos, E., Ouanighi, Y. E., Bennas, N., Alami, M. E., Yacoubi-Khebiza, M., Ougougdal, H. A., & Riutort, M. (2022) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2022.107649 · Cited by 10
Self-citationConservative route to genome compaction in a miniature annelidPreprint
Martín-Durán, J. M., Vellutini, B. C., Marlétaz, F., Cetrangolo, V., Cvetešić, N., Thiel, D. J., Henriet, S., Grau‐Bové, X., Carrillo-Baltodano, A. M., Gu, W., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.07.078311 · Cited by 11
Herlyn, H., Hembrom, A. A., Tosar, J. P., Mauer, K., Schmidt, H., Dezfuli, B. S., Hankeln, T., Bachmann, L., Sarkies, P., Peterson, K. J., et al. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf124 · Cited by 10
Adaptive loss of shortwave-sensitive opsins during cartilaginous fish evolution
Zhang, B., Feng, Y., Lv, M., Jia, L., Liao, Y., Xu, X., Meyer, A., Sun, J., Fan, G., Li, Y., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-62544-w · Cited by 9
Evolution of homology: From archetype towards a holistic concept of cell type
Rusin, L. Y. (2023) · Journal of Morphology · doi:10.1002/jmor.21569 · Cited by 8
Intragenomic mutational heterogeneity: structural and functional insights from gene evolution
Hara, Y., & Kuraku, S. (2025) · Trends in Genetics · doi:10.1016/j.tig.2025.03.007 · Cited by 7
Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae
Repetti, S. I., Iha, C., Uthanumallian, K., Jackson, C. J., Chen, Y., Chan, C. X., & Verbruggen, H. (2021) · New Phytologist · doi:10.1111/nph.17926 · Cited by 7
Population Genomics of Premature Termination Codons in Cavefish With Substantial Trait Loss
Roback, E. Y., Ferrufino, E., Moran, R. L., Shennard, D., Mulliniks, C., Gallop, J., Weagley, J. S., Miller, J. T., Fily, Y., Ornelas‐García, C. P., et al. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf012 · Cited by 6
Paradžik, T., Podgorski, I. I., Zeljko, T. V., & Paradžik, M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23105594 · Cited by 6
Wcisel, D. J., Dornburg, A., McConnell, S. C., Hernandez, K. M., Andrade, J., de Jong, J. L. O., Litman, G. W., & Yoder, J. A. (2022) · Immunogenetics · doi:10.1007/s00251-022-01270-9 · Cited by 6
Cheng, Y., Chen, J., Mukhtar, I., & Chen, J. (2021) · Frontiers in Marine Science · doi:10.3389/fmars.2021.653447 · Cited by 6
Kenny, N. J., Francis, W. R., Rivera-Vicéns, R. E., Juravel, K., de Mendoza, A., Díez-Vives, C., Lister, R., Bezares-Calderon, L., Grombacher, L., Roller, M., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.18.954784 · Cited by 6
Bursts of novel composite gene families at major nodes in animal evolutionPreprint
Mulhair, P. O., Moran, R. J., Pathmanathan, J. S., Sussfeld, D., Creevey, C. J., Siu-Ting, K., Whelan, F., Pisani, D., Constantinides, B., Pelletier, É., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.10.548381 · Cited by 6
Chen, X., Zhang, A., Liu, C., Saeed, M., Li, J., Wu, Y., Wu, Y., Gu, H., Yuan, J., Wang, B., et al. (2024) · Plants · doi:10.3390/plants13243507 · Cited by 5
Evolutionary diversification of ancestral genes across vertebrates and insects
Mantica, F., & Irimia, M. (2025) · Genome biology · doi:10.1186/s13059-025-03699-z · Cited by 6
Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms
Gąsiorowski, L. (2025) · Journal of Molecular Evolution · doi:10.1007/s00239-024-10226-4 · Cited by 5
Sabater‐Muñoz, B., & Toft, C. (2020) · Results and problems in cell differentiation · doi:10.1007/978-3-030-51849-3_3 · Cited by 5
Fukunaga, T., & Iwasaki, W. (2021) · Bioinformatics Advances · doi:10.1093/bioadv/vbab014 · Cited by 5
Highly Dynamic Gene Family Evolution Suggests Changing Roles for PON Genes Within Metazoa
Lucas, S. A. M., Graham, A. M., Presnell, J. S., & Clark, N. L. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad011 · Cited by 5
Universal signatures of transposable element compartmentalization across eukaryotic genomesPreprint
Gozashti, L., Hartl, D. L., & Corbett-Detig, R. B. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.17.562820 · Cited by 4
Co-translational assembly promotes functional diversification of paralogous proteinsPreprint
Mallik, S., Cisneros, A. F., Landry, C. R., & Levy, E. D. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.22.634331 · Cited by 5
Evolution of the Metazoan Protein Domain Repertoire Revealed by a Birth-Death-Gain Model
Xiao, Y., Stolzer, M., Wasserman, L., & Durand, D. (2025) · Journal of Molecular Evolution · doi:10.1007/s00239-025-10286-0 · Cited by 4
Maurer‐Alcalá, X. X., Cote‐L’Heureux, A., Pond, S. L. K., & Katz, L. A. (2024) · PLoS ONE · doi:10.1371/journal.pone.0291688 · Cited by 4
Metadata
- Authors
- Fernández, R., & Gabaldón, T.
- Affiliations
- Universitat Pompeu Fabra (ES)
- Institució Catalana de Recerca i Estudis Avançats (ES)
- Corresponding author
- Gabaldón, Toni
- Venue
- Nature Ecology & Evolution
- Published
- 2020-01-28
- Volume
- 4
- Issue
- 4
- Pages
- 524-533
- ISSN
- 2397-334X (ISSN-L)
- PMC
- PMC7124887
- OpenAlex
- W3002804540
- Semantic Scholar
- 78b3b0e78389680640d8434fc1d2eaa9ff186589
- Cited by
- 165
- References
- 42
- Citations by year
- 2026: 9 · 2025: 26 · 2024: 24 · 2023: 31 · 2022: 35 · 2021: 25 · 2020: 14
- FWCI
- 8.52
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Ecology & Evolution (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- gene gain, gene loss, gene duplication, metazoan phylogeny, Xenacoelomorpha, ecdysozoans, deuterostomes, animal origins, macroevolutionary trends
- MeSH terms
- Animals, Phylogeny, Genome, Evolution, Molecular, Gene Duplication, Genomics
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
