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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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“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
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“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]
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“Comparisons among diverse genomes have identified numerous genes that are present in myriazoans but are absent in ctenophores1,5,58.”
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“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
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“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
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“deuterostomes, ecdysozoans, and Xenacoelomorpha were characterized by no gene gain but rampant differential gene loss”
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“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”
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“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.”
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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
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