Jumping Genes Divide the Animal Kingdom into Sea and Land Clades

Transposable elements are often described as genomic parasites, DNA sequences that copy and paste themselves around the genome of their host. Yet these mobile fragments are far more than molecular clutter. They reshape genome architecture, drive the birth of new genes, and leave an evolutionary record that scientists can read across hundreds of millions of years. A new study published in Heredity by Laure Lamothe, Khouloud Klai, Sarah Farhat, Eric Bonnivard and colleagues turns the spotlight on one particular family of these mobile elements, the Copia superfamily of LTR-retrotransposons, and asks a deceptively simple question: which members of this family live where in the animal tree of life?

The Copia superfamily belongs to the long terminal repeat, or LTR, retrotransposons. These elements replicate through an RNA intermediate, in a manner reminiscent of retroviruses, using a reverse transcriptase enzyme to copy their RNA back into DNA that is then inserted at a new genomic location. Genome-based surveys had previously identified roughly 25 distinct Copia clades, which are deep evolutionary lineages within the superfamily, each defined by characteristic sequences in the reverse transcriptase and RNase H domains of the pol region. Importantly, the earlier work revealed a striking pattern: Copia clades appeared to be strongly partitioned between marine and terrestrial animals, as though a boundary drawn at the water’s edge also ran through the repetitive DNA content of animal genomes.

That earlier picture, however, came with a caveat. It was built largely from whole-genome sequences, and genomes are expensive to produce. As a result, the taxonomic sampling was uneven, dominated by a handful of well-studied model organisms and major phyla while many minor lineages of the animal kingdom remained unexamined. Whether the marine-terrestrial dichotomy held across the full breadth of metazoan diversity, or whether entirely new clades were hiding in unexplored genomes, could not be answered with confidence from genome data alone.

The French team, based at the Station Biologique de Roscoff, Nantes University and the Muséum national d’Histoire naturelle, took a different route. Rather than relying on genomes, they mined transcriptomes, the sets of expressed RNA sequences, across 315 species, supplementing these with additional database searches. Transcriptomes are far more numerous than genomes, because RNA sequencing has been applied broadly across biodiversity sampling efforts, even for organisms whose genomes will never be assembled. The strategy pushed taxonomic coverage into 12 phyla that had previously gone unsampled, including many of the so-called minor taxa, small-bodied and evolutionarily pivotal groups such as springtails, two-pronged bristletails, velvet worms and tardigrades.

From this expanded dataset the researchers recovered 1,285 Copia elements, most of which could be confidently assigned to known clades through analysis of the reverse transcriptase and RNase H protein domains, the standard markers used to classify LTR-retrotransposons. Two major conclusions emerged. First, the diversity of Copia clades in animals appears to be close to exhaustive: despite broadening the search into a dozen new phyla, the team detected no previously unknown clades. This saturation is itself informative, suggesting that the catalog of animal Copia lineages assembled over the past two decades is nearly complete and that future discoveries, if any, will be rare.

Second, the marine-terrestrial dichotomy survived the broader test intact. Copia clades consistently fell into two environmental groups, one dominated by marine species and the other by terrestrial ones. The conservation of this pattern across such a wide range of animals implies that it is not a statistical artifact of sparse sampling but a genuine biological signal. What could explain it? The authors point to a combination of ecology and phylogeny. The water-to-land transition in animal history was a major evolutionary event, and the major lineages that made that transition carried with them a specific set of retrotransposon lineages. Environment and ancestry are therefore intertwined: the clades animals carry today reflect both where they live and who their ancestors were.

The study also refined the ranges of clades that appear restricted to particular animal groups. Most taxon-specific clades remain confined to their known hosts, although improved sampling tightened the estimates of their distribution. The most striking case concerns the CoCol clade, which had previously been found only in Collembola, the springtails, tiny hexapods that abound in soils worldwide. The new transcriptome survey confirmed the strong specificity of CoCol for springtails and, crucially, extended it to the Diplura, the two-pronged bristletails, another group of entognathous hexapods. This shared presence suggests that CoCol colonized the common ancestor of these early-diverging hexapod lineages, a single ancient invasion whose descendants persist in both groups today.

That finding becomes even more interesting when set against the broader arthropod context. Other terrestrial euarthropods, including the insects proper, crustaceans on land, arachnids and myriapods, display high Copia diversity, carrying representatives of many clades rather than a single host-specific lineage. The velvet worms, or Onychophora, close relatives of arthropods that live in moist terrestrial habitats, likewise show a rich complement of Copia elements. In other words, being terrestrial did not impose a uniform retrotransposon profile on all land animals. Springtails and bristletails stand out as exceptions, likely reflecting a distinctive early evolutionary history among the hexapods, whereas their terrestrial arthropod relatives accumulated a more diverse and dynamic Copia community.

Methodologically, the work demonstrates that transcriptomes, despite capturing only expressed sequences and typically only fragments of full-length retrotransposons, are a powerful resource for cataloguing transposable element diversity at the clade level. The reverse transcriptase and RNase H domains are conserved enough to be detected even in short expressed fragments, which is precisely what clade-level classification requires. The cost of this approach is that transcriptomes underestimate element copy number and may miss inactive, non-expressed families, so they complement rather than replace genome-based analyses. Used together, the two data types offer a far more comprehensive census of mobile element evolution than either alone.

The broader significance of the study lies in what it says about genome evolution across the animal kingdom. Transposable elements are key drivers of genome change, influencing genome size, recombination, gene regulation and adaptation. Understanding which element lineages are present in which animals provides a baseline for interpreting these processes. The confirmation that Copia clade diversity is nearly saturated, the robustness of the marine-terrestrial partition, and the phylogenetic resolution of the CoCol clade within early hexapods together sketch a coherent picture: the mobile element complement of an animal is a mosaic of deep ancestry and ecological circumstance. Minor taxa, often overlooked in genomic surveys, proved essential to seeing that picture clearly. As transcriptomic data continue to accumulate for understudied phyla, similar surveys promise to sharpen our understanding not only of Copia but of the full repertoire of mobile DNA that has accompanied animal evolution from the oceans onto land.

Subject of Research: Distribution and evolution of Copia LTR-retrotransposon clades across metazoans

Article Title: The analysis of minor taxa highlights the role of the environment and phylogeny in the distribution of the LTR-retrotransposon Copia clades

Article References: Lamothe, L., Klai, K., Farhat, S., & Bonnivard, E. (2026). The analysis of minor taxa highlights the role of the environment and phylogeny in the distribution of the LTR-retrotransposon Copia clades. Heredity. https://doi.org/10.1038/s41437-026-00888-9

Image Credits: AI Generated

DOI: 10.1038/s41437-026-00888-9

Keywords: Copia retrotransposons, LTR-retrotransposons, transposable elements, metazoans, transcriptomics, marine-terrestrial dichotomy, Collembola, Diplura, Hexapoda, genome evolution, phylogeny, Heredity