Old Genes Create a New Organ: How Sea Robin Pectoral Fins Turned into Legs

Graphical abstract（Image source：Herbert AL et al. (2024)， CC BY 4.0 

In evolutionary biology, many studies have focused on the loss of traits—for example, snakes losing their limbs or cavefish losing pigmentation. In contrast, the evolutionary origins of entirely new traits have been investigated less frequently. A recent study on the Triglidae (sea robins) provides insight into how ancient developmental genes can be redeployed to generate new anatomical structures and behaviors.

Sea robins belong to the suborder Scorpaenoidei and typically inhabit shallow marine seafloors. In these fishes, the three ventralmost rays of the pectoral fin have evolved into freely movable appendages often described as "legs," known as free rays. These structures originate from the pectoral fin during development and can support the body as the fish walks across the substrate or digs through sand in search of food. Each of these leg-like appendages is associated with a corresponding lobe in the central nervous system, forming a one-to-one neural connection that coordinates both movement and sensory input. The emergence of these "legs" does not rely on newly evolved genes; instead, it reflects the redeployment of ancient developmental regulatory genes activated in new spatial and temporal contexts.

Northern sea robin（Courtesy of Anik Grearson ）

To investigate the genetic basis of this evolutionary innovation, researchers used the northern sea robin Prionotus carolinus as a model species. They compared gene expression patterns in the free rays, other regions of the pectoral fin, and the pelvic fin at different developmental stages. Transcriptomic analyses revealed that the gene expression profile of the free rays differed markedly from that of the other pectoral fin rays. Interestingly, their expression patterns resembled those of the pelvic fin more closely than those of the pectoral fin from which they originate. This suggests that the developmental identity of the free rays has been substantially reprogrammed at the genetic level.

Fin structures. Upper: pectoral fin; lower: pelvic fin (pel)（Image source：Herbert AL et al. (2024)， CC BY 4.0 ）

Among the genes showing particularly strong differential expression, the transcription factor gene tbx3a emerged as a central regulatory component. This gene belongs to the ancient and highly conserved T-box family of transcription factors. Transcription factors are proteins that regulate the activity of other genes, and the tbx3a gene produces the Tbx3a protein, which influences the expression of genes involved in the development of multiple embryonic structures in fishes, including the heart, fins, otic vesicles, and visual system. In tetrapods, Tbx3 also plays an important role in limb development.

The expression level of Tbx3a in the free ray region of sea robins is much higher than in other fin tissues, suggesting that it may function as a key regulator driving the development of these leg-like appendages. When researchers experimentally disrupted tbx3a using CRISPR-Cas9 genome editing, the fish exhibited a range of morphological abnormalities. The free rays became shorter, displayed abnormal angles, or changed in number. In some individuals, the appendages reverted toward a condition resembling ordinary pectoral fin rays. These altered structures lacked the segmentation and robust skeletal support normally associated with the "legs," leading to reduced coordination during walking and digging behaviors. At the same time, the neural structures responsible for controlling these appendages were noticeably reduced in size. These results demonstrate that Tbx3a plays a crucial role not only in shaping the morphology of the free rays but also in establishing the sensory and behavioral systems associated with them.

(Left) Pectoral fin of a normal Prionotus carolinus; (right) pectoral fin of a tbx3a mutant（Image source：Herbert AL et al. (2024)， CC BY 4.0 ）

(G) Diagram showing the connection between free rays and the central nervous system; (H) comparison of brain lobes in normal Prionotus carolinus and tbx3a mutants（Image source：Herbert AL et al. (2024)， CC BY 4.0 ）

The study also compared Prionotus carolinus with a closely related species, Prionotus evolans. In P. carolinus, the free rays are thicker and covered with dense sensory papillae, enabling the fish to probe the seafloor and detect buried prey during digging. By contrast, P. evolans possesses thinner free rays without sensory papillae, and these appendages function mainly in locomotion rather than sensory detection. This difference illustrates how morphological divergence between closely related species can arise through modifications in gene regulation.

Morphological comparison between Prionotus carolinus and Prionotus evolans（Image source：Herbert AL et al. (2024)， CC BY 4.0 ）

Gene expression comparisons showed that tbx3a is expressed at significantly higher levels in P. carolinus than in P. evolans, which may explain why the former develops more robust and functionally specialized appendages. Hybrid experiments further revealed that this difference in expression is primarily driven by variation in the upstream transcriptional environment—that is, changes in trans-regulatory factors rather than alterations directly within the tbx3a gene itself. This indicates that the evolution of the free rays involves multiple layers of regulatory modification within the gene network controlling appendage development.

In addition, genes regulated by Tbx3a may have been incorporated into new developmental pathways through the acquisition of novel binding sites for this transcription factor. Such cis-regulatory gains could recruit previously unrelated genes into the genetic program responsible for constructing the new appendages. Through this process, an existing regulatory framework can be extended and modified to produce entirely new morphological features.

Together, these findings illustrate a fundamental principle of evolutionary innovation: the emergence of new anatomical structures does not necessarily require the origin of new genes. Instead, evolution can repurpose ancient developmental regulators, redeploying them in new contexts to generate novel structures, neural circuits, and behaviors. In sea robins, this redeployment has transformed part of the pectoral fin into functional "legs," allowing these fishes to walk across the ocean floor and probe the sediment for hidden prey.

Author: Shui-Ye You

Reference:

Herbert AL et al. (2024). Ancient developmental genes underlie evolutionary novelties in walking fish. Current Biology.