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
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
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
The origins of genome complexity
Lynch, M., & Conery, J. S. (2003) · Science · doi:10.1126/science.1089370 · Cited by 1,698
Regulatory activities of transposable elements: from conflicts to benefits
Chuong, E. B., Elde, N. C., & Feschotte, C. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2016.139 · Cited by 1,489
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 1,135
Albalat, R., & Cañestro, C. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.39 · Cited by 775
Functional and evolutionary implications of gene orthology
Gabaldón, T., & Koonin, E. V. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3456 · Cited by 643
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
M-Coffee: combining multiple sequence alignment methods with T-Coffee
Wallace, I. M. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl091 · Cited by 589
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
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
Domazet‐Lošo, T., Brajković, J., & Tautz, D. (2007) · Trends in Genetics · doi:10.1016/j.tig.2007.08.014 · Cited by 421
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
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 363
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
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 301
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
Gene family innovation, conservation and loss on the animal stem lineage
(2018) · doi:10.7554/elife.34226 · Cited by 226
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
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
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
Self-citationHuerta-Cepas, J., Dopazo, H., Dopazo, J., & Gabaldón, T. (2007) · Genome Biology · doi:10.1186/gb-2007-8-6-r109 · Cited by 176
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 146
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 141
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 140
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 114
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
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
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
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 63
Toward Reducing Phylostratigraphic Errors and Biases
Moyers, B. A., & Zhang, J. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy161 · Cited by 24
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
Laurent, J. M., Garge, R. K., Teufel, A. I., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/668335 · Cited by 9
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
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
