What an Ancient Sea Anemone Reveals About the Origins of Animal Complexity
Every cell in an animal’s body carries the same DNA. Yet that single genetic blueprint somehow produces neurons that fire, muscles that contract, and tissues with entirely different jobs. How identical genomes give rise to such variety remains one of biology’s central mysteries.
New research points to gene regulation — not genes alone — as the key to how diverse cell types emerge from a single genome. By analyzing an ancient sea anemone cell by cell, researchers built a detailed map linking DNA control elements to how different cell types form. Reported in Nature Ecology and Evolution, the work suggests that the regulatory framework underlying animal cell diversity was already established early in evolutionary history.
“Expression tells us what cells do, but regulatory DNA tells us where they come from, how they develop, and which germ layer they originate from,” said Dr. Marta Iglesias, co-first author of the study, in a press release.
The Roots of Cellular Diversity
Differences between cell types depend on how genes are controlled rather than on the genes themselves. Yet most of what we understand about this process comes from a small number of well-studied species, leaving its deeper evolutionary origins unclear.
To explore those origins, researchers turned to a starlet sea anemone. Sea anemones, along with jellyfish and corals, belong to the cnidarians — one of the earliest animal groups to evolve, first appearing around half a billion years ago. Despite their ancient lineage, cnidarians possess specialized cell types, making them a valuable system for investigating how cellular diversity first arose.
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Cell Identity Revealed in an Ancient Sea Anemone
To investigate how cell identity is built and maintained, the researchers analyzed roughly 60,000 individual cells from the starlet sea anemone, Nematostella vectensis. The dataset included cells from two life stages — adult animals and early gastrula-stage embryos, when the basic body plan is still being established — allowing the team to capture both developmental origins and mature cell states.
Rather than grouping cells by which genes were active, the researchers focused on the DNA regions that control gene activity. These regulatory elements act as control switches, shaping when and where genes can be used. From this analysis, the team assembled a large catalogue of more than 112,000 regulatory elements across the anemone genome — a surprisingly rich regulatory landscape for an animal of its size.
When cells were organized using these regulatory patterns, a different picture emerged. Instead of clustering only by function, cells grouped according to their developmental origins, revealing which embryonic layers they arose from. This made it possible to distinguish between cell types that perform similar roles but follow different developmental paths.
That distinction was especially clear in muscle cells. Some muscle cells shared similar functions and relied on many of the same genes, even though they originated from different embryonic layers. While their gene activity looked alike, the regulatory instructions controlling those genes were entirely different — showing that similar cell types can be built using distinct regulatory strategies.
Insights Into the Evolution of Animal Cell Types
Cnidarians were among the earliest animals to develop specialized cell types such as neurons and muscle cells. They also evolved a distinctive cell called a cnidocyte, equipped with microscopic, harpoon-like structures used for hunting and defense — the source of the familiar sting of jellyfish and sea anemones.
The findings suggest that these early animals already possessed a flexible way to generate new kinds of cells. By tracing how cell identities are built in an ancient animal, the study offers a new framework for understanding where animal cell types came from — and how today’s biological complexity emerged.
“This study opens a whole new world of possibilities. Going forward, we will investigate animal cellular evolution by comparing genomic sequence information, and for the first time, we can do so systematically and at scale,“ said co-author Arnau Sebe-Pedrós.
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