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.
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The evolutionary dynamics of gene gain and loss, not only key innovations, shape the vast morphological disparity of animals.
“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
The Conclusions link gene gain, duplication and loss to animal evolution and say their dynamics may have provided an arena for increased cell-type and tissue complexity. But the claim states more definitively that gene gain and loss shape animals’ morphological disparity; the paper says increased morphological complexity must involve other phenomena, including co-option following duplication. (LLM, conf=0.84)
Experimental — accuracy not yet measuredUnder the ctenophore-sister scenario, these genes are most parsimoniously interpreted as arising on the myriazoan stem after the divergence of ctenophores, and include genes associated with neuronal function, development and cell adhesion.
“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]
The Results and Discussion section on orthology-informed functions reports that genes gained at nodes from Metazoa to Nephrozoa were enriched for functions related to synapses and nervous-system development. The Methods say the reported analyses use a ctenophore-sister topology. The paper does not specifically place these genes on the myriazoan stem after ctenophores diverged; the citing sentence assigns development and cell adhesion to other references, not this one. (LLM, conf=0.84)
Experimental — accuracy not yet measuredComparisons among diverse genomes have identified numerous genes that are present in myriazoans but are absent in ctenophores.
“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]
The Results and Discussion section on rampant gene loss reports high pairwise gene-loss values across animal taxa, supporting the general point that genome comparisons find genes present in one lineage but absent in another. It does not specifically identify numerous genes present in myriazoans but absent in ctenophores; the Methods mention Ctenophora only in discussing tree topology. No page numbers are available in our copy. (LLM, conf=0.76)
Experimental — accuracy not yet measuredGene gains, losses and duplications dynamically evolved and have unbalanced distributions across the metazoan tree.
“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
Gene duplication ratio was high at deep nodes leading to metazoans and the birth rate decreased progressively as animals diversified into clades.
“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
Deuterostomes, ecdysozoans, and Xenacoelomorpha were characterized by no gene gain but rampant differential gene loss.
“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
Around one-third of genes gained at deep nodes below the Nephrozoa and another one-third comprising lineage-specific genes were acquired very late.
“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
Some genes are present in ctenophores and parahoxozoans but absent in sponges, and these must be interpreted as gene losses on the sponge lineage.
“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]
The citation is attached to the claim that some genes are present in ctenophores and parahoxozoans but absent in sponges. The Results and Discussion passages describe gene loss across animal lineages, but do not identify that specific distribution. Searches for the ctenophore–sponge comparison and sponge-lineage loss found no passage establishing it. (LLM, conf=0.72)
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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 · see citing works
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 · see citing works
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 9,181 · see citing works
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Edgar, R. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-113 · Cited by 8,948 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 4,943 · see citing works
Kanehisa, M., Sato, Y., & Morishima, K. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.11.006 · Cited by 3,810 · see citing works
Emms, D. M., & Kelly, S. (2015) · Genome Biology · doi:10.1186/s13059-015-0721-2 · Cited by 3,408 · see citing works
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
Huerta-Cepas, J., Forslund, K., Coelho, L. P., Szklarczyk, D., Jensen, L. J., von Mering, C., & Bork, P. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx148 · Cited by 2,709 · see citing works
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
Gascuel, O. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025808 · Cited by 1,850 · see citing works
The origins of genome complexity
Lynch, M., & Conery, J. S. (2003) · Science · doi:10.1126/science.1089370 · Cited by 1,698 · see citing works
Regulatory activities of transposable elements: from conflicts to benefits
Chuong, E. B., Elde, N. C., & Feschotte, C. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.139 · Cited by 1,343 · see citing works
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes
Al‐Shahrour, F., Díaz‐Uriarte, R., & Dopazo, J. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg455 · Cited by 1,118 · see citing works
Albalat, R., & Cañestro, C. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.39 · Cited by 775 · see citing works
Functional and evolutionary implications of gene orthology
Gabaldón, T., & Koonin, E. V. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3456 · Cited by 643 · 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
M-Coffee: combining multiple sequence alignment methods with T-Coffee
Wallace, I. M. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl091 · Cited by 585 · see citing works
MAFFT: Iterative Refinement and Additional Methods
Katoh, K., & Standley, D. M. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-646-7_8 · Cited by 520 · see citing works
Contentious relationships in phylogenomic studies can be driven by a handful of genes
Shen, X.-X., Hittinger, C. T., & Rokas, A. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0126 · Cited by 520 · see citing works
Domazet‐Lošo, T., Brajković, J., & Tautz, D. (2007) · Trends in Genetics · doi:10.1016/j.tig.2007.08.014 · Cited by 409 · see citing works
Xenacoelomorpha is the sister group to Nephrozoa
Cannon, J. T., Vellutini, B. C., Smith, J., Ronquist, F., Jondelius, U., & Hejnol, A. (2016) · Nature · doi:10.1038/nature16520 · Cited by 364 · see citing works
ETE: a python Environment for Tree Exploration
Huerta‐Cepas, J., Dopazo, J., & Gabaldón, T. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-24 · Cited by 361 · see citing works
Self-citationRevisiting metazoan phylogeny with genomic sampling of all phyla
Laumer, C. E., Fernández, R., Lemer, S., Combosch, D., Kocot, K. M., Riesgo, A., Andrade, S. C. S., Sterrer, W., Sørensen, M. V., & Giribet, G. (2019) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2019.0831 · Cited by 360 · see citing works
Self-citationEarly metazoan cell type diversity and the evolution of multicellular gene regulation
Sebé-Pedrós, A., Chomsky, E., Pang, K., Lara‐Astiaso, D., Gaiti, F., Mukamel, Z., Amit, I., Hejnol, A., Degnan, B. M., & Tanay, A. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0575-6 · Cited by 292 · see citing works
A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans
Marlétaz, F., Peijnenburg, K. T. C. A., Goto, T., Satoh, N., & Rokhsar, D. S. (2019) · Current Biology · doi:10.1016/j.cub.2018.11.042 · Cited by 268 · see citing works
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome
Huerta-Cepas, J., Capella-Gutiérrez, S., Pryszcz, L. P., Marcet-Houben, M., & Gabaldón, T. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1177 · Cited by 217 · see citing works
Self-citationStandardized benchmarking in the quest for orthologs
Quest for Orthologs consortium, Altenhoff, A. M., Boeckmann, B., Capella-Gutierrez, S., Dalquen, D. A., DeLuca, T., Forslund, K., Huerta-Cepas, J., Linard, B., Pereira, C., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3830 · Cited by 214 · see citing works
Self-citationLarge-scale assignment of orthology: back to phylogenetics?
Gabaldón, T. (2008) · Genome biology · doi:10.1186/gb-2008-9-10-235 · Cited by 199 · see citing works
Self-citationHuerta-Cepas, J., Dopazo, H., Dopazo, J., & Gabaldón, T. (2007) · Genome Biology · doi:10.1186/gb-2007-8-6-r109 · Cited by 176 · see citing works
Self-citationNemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads
Luo, Y., Kanda, M., Koyanagi, R., Hisata, K., Akiyama, T., Sakamoto, H., Sakamoto, T., & Satoh, N. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0389-y · Cited by 144 · see citing works
Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty
Paps, J., & Holland, P. W. H. (2018) · Nature Communications · doi:10.1038/s41467-018-04136-5 · Cited by 135 · see citing works
Enzyme Annotation and Metabolic Reconstruction Using KEGG
Kanehisa, M. I. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7015-5_11 · Cited by 133 · see citing works
Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias
Laumer, C. E., Gruber-Vodicka, H., Hadfield, M. G., Pearse, V. B., Riesgo, A., Marioni, J. C., & Giribet, G. (2018) · eLife · doi:10.7554/elife.36278 · Cited by 112 · see citing works
Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution
Moyers, B. A., & Zhang, J. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu286 · Cited by 111 · see citing works
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment
Lassmann, T., & Sonnhammer, E. L. L. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl191 · Cited by 99 · see citing works
DendroBLAST: Approximate Phylogenetic Trees in the Absence of Multiple Sequence Alignments
Kelly, S., & Maini, P. K. (2013) · PLoS ONE · doi:10.1371/journal.pone.0058537 · Cited by 73 · see citing works
Laurent, J. M., Garge, R. K., Teufel, A. I., Wilke, C. O., Kachroo, A. H., & Marcotte, E. M. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3000627 · Cited by 56 · see citing works
Toward Reducing Phylostratigraphic Errors and Biases
Moyers, B. A., & Zhang, J. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy161 · Cited by 24 · see citing works
Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution
Moyers, B. A., & Zhang, J. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw202 · Cited by 15 · see citing works
Laurent, J. M., Garge, R. K., Teufel, A. I., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/668335 · Cited by 9 · see citing works
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- [17]Emms DM Kelly S OrthoFinder2: fast and accurate phylogenomic orthology analysis from gene sequences 2018 10.1101/466201 · DOI
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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 1,145 · see citing works
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 · see citing works
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 · see citing works
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 165 · see citing works
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 160 · see citing works
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 · 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
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 · see citing works
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 · see citing works
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 · see citing works
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 91 · see citing works
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 · see citing works
Self-citationGenome evolution in plants and the origins of innovation
Clark, J. (2023) · New Phytologist · doi:10.1111/nph.19242 · Cited by 69 · see citing works
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 63 · see citing works
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 60 · 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
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 50 · see citing works
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 54 · see citing works
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 43 · see citing works
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 · see citing works
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 · see citing works
An episodic burst of massive genomic rearrangements and the origin of non-marine annelids
Vargas-Chávez, C., Benítez-Álvarez, L., Redondo, G. I. M., Álvarez-González, L., Salces-Ortiz, J., Eleftheriadi, K., Escudero, N., Guiglielmoni, N., Flot, J., Novo, M., et al. (2025) · Nature Ecology & Evolution · doi:10.1038/s41559-025-02728-1 · Cited by 36 · see citing works
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 · see citing works
Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms
Crow, M., Suresh, H., Lee, J., & Gillis, J. A. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac276 · Cited by 36 · see citing works
A chromosome-scale genome assembly and karyotype of the ctenophore <i>Hormiphora californensis</i>
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 · see citing works
Dornburg, A., & Yoder, J. A. (2022) · Immunogenetics · doi:10.1007/s00251-021-01232-7 · Cited by 35 · see citing works
Liu, Y., Qu, M., Jiang, H., Schneider, R., Qin, G., Luo, W., Yu, H., Zhang, B., Wang, X., Zhang, Y., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-35338-7 · Cited by 33 · see citing works
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 34 · see citing works
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 30 · see citing works
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 · see citing works
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 27 · see citing works
de Oliveira, A. L., Mitchell, J. H., Girguis, P. R., & Bright, M. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab347 · Cited by 27 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 25 · see citing works
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 23 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 21 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 20 · see citing works
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 19 · see citing works
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 · see citing works
Rappaport, H. B., & Oliverio, A. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae160 · Cited by 19 · see citing works
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 · see citing works
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 19 · see citing works
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 · see citing works
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 · see citing works
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 17 · see citing works
Redondo, G. I. M., 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 · see citing works
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 · see citing works
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 16 · see citing works
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 17 · see citing works
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 · see citing works
Fernández, R., Tonzo, V., Guerrero, C. S., Lozano-Fernández, J., Redondo, G. I. M., Balart‐García, P., Arístide, L., Eleftheriadi, K., & Vargas-Chávez, C. (2022) · Peer Community Journal · doi:10.24072/pcjournal.177 · Cited by 16 · see citing works
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 16 · see citing works
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 · see citing works
Dornburg, A., Wcisel, D. J., Zapfe, K. L., 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 15 · see citing works
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 14 · see citing works
Sheikh, S., Fu, C.-J., Brown, M. W., & Baldauf, S. L. (2024) · Nature Communications · doi:10.1038/s41467-024-54029-z · Cited by 14 · see citing works
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 · see citing works
Gene Duplication and Alternative Splicing as Evolutionary Drivers of Proteome Specialization
Mantica, F., & Irimia, M. (2025) · BioEssays · doi:10.1002/bies.202400202 · Cited by 14 · see citing works
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 · see citing works
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 13 · see citing works
Wu, B., Hao, W., & Cox, M. P. (2022) · BMC Biology · doi:10.1186/s12915-022-01346-8 · Cited by 13 · see citing works
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 · see citing works
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 · see citing works
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 12 · see citing works
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 12 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 8 · see citing works
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 8 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
Paradžik, T., Podgorski, I. I., Zeljko, T. V., & Paradžik, M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23105594 · Cited by 6 · see citing works
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 · see citing works
Cheng, Y., Chen, J., Mukhtar, I., & Chen, J. (2021) · Frontiers in Marine Science · doi:10.3389/fmars.2021.653447 · Cited by 6 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 5 · see citing works
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 · see citing works
Sabater‐Muñoz, B., & Toft, C. (2020) · Results and problems in cell differentiation · doi:10.1007/978-3-030-51849-3_3 · Cited by 5 · see citing works
Fukunaga, T., & Iwasaki, W. (2021) · Bioinformatics Advances · doi:10.1093/bioadv/vbab014 · Cited by 5 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
- 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 › Agricultural and Biological Sciences › Plant Science › 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
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