How did the intricate structures we call digits come into being? This question has perplexed evolutionary biologists for decades, centering on whether digits arose directly from fish fins or represent novel morphological innovations. A groundbreaking study led by the University of Geneva, in collaboration with EPFL, the Collège de France, and esteemed institutions such as Harvard and the University of Chicago, has uncovered compelling evidence that challenges traditional perspectives. Published in the prestigious journal Nature, the research reveals that digits may have evolved through an evolutionary strategy of genomic recycling—repurposing an ancient regulatory landscape once active in the formation of the fish cloaca rather than their fins.
This discovery fundamentally shifts our understanding of how terrestrial vertebrates made the leap from aquatic life some 380 million years ago. During this pivotal period, our distant fish ancestors began colonizing land, developing lungs, limbs, and digit-like extremities essential for terrestrial mobility and survival. The origin of these limbs, especially the digits, long stood as a mystery: were they merely modified fins retooled by evolution, or did they emerge via a previously unrecognized developmental pathway? The study’s insights suggest the answer lies in the latter, highlighting how existing genomic frameworks can be co-opted and repurposed in evolutionary innovation.
The research team turned their attention away from exclusively focusing on the coding regions of the genome—those sequences responsible for building proteins—and instead investigated the vast non-coding regulatory landscapes. These expanses of DNA, often overlooked in the past, arguably hold the master blueprints controlling when and where genes are activated during development. Regulatory landscapes encompass enhancers, silencers, and other DNA elements that function as complex ‘control towers,’ orchestrating gene expression with remarkable precision. Though these regions do not encode proteins themselves, their regulatory influence dictates much of the organism’s developmental fate.
By conducting a comparative genomic analysis between mice and zebrafish, the scientists identified a highly conserved regulatory domain implicated in mouse digit development. This conservation across species spanning hundreds of millions of years indicated crucial functional significance. To probe the role of this regulatory landscape in fish, the team utilized CRISPR/Cas9 genome editing—a revolutionary technology that allows precise deletion or modification of specific DNA sequences. When this regulatory domain was excised from zebrafish, the researchers observed a marked loss of gene expression in the cloacal region but not in the fins, suggesting the regulatory elements originally governed cloacal development.
The cloaca—the multipurpose orifice serving as the exit for intestinal, excretory, and reproductive tracts in many vertebrates—emerged as a surprising focal point for early limb evolution. Although seemingly unrelated to limb formation at first glance, this anatomical terminal shares a conceptual parallel with digits: both represent the distal ends of tubular structures, whether it be the digestive tract or limb appendages. This insight led the team to hypothesize that the genetic regulatory networks orchestrating the cloaca’s formation were co-opted during evolution to mold the emerging digits of terrestrial vertebrates.
Central to this process are the Hox genes, colloquially known as “architect genes.” These genes provide the developmental blueprint for body patterning, determining positional identity along the head-to-tail axis in embryos. Functioning atop a regulatory hierarchy, Hox genes activate cascades of downstream targets that sculpt organs and limbs. Remarkably, the same Hox gene clusters that govern cloacal development appear to have been redeployed through evolutionary tinkering to regulate digit formation. Alterations in these regulatory landscapes would thus produce profound morphological novelties without necessitating entirely new genes, exemplifying evolution’s parsimony.
This mode of evolutionary innovation—where ancestral regulatory elements are retooled to generate new phenotypes—is a compelling example of “evolutionary recycling.” As noted by Denis Duboule, honorary professor at UNIGE and the Collège de France and initiator of the study, rather than inventing new genomic machinery from scratch, nature frequently opts to repurpose existing genetic circuits. This strategy allows complex traits to emerge with efficiency, leveraging deep homologies encoded within the genome’s regulatory architecture.
The implications extend beyond digit evolution, offering a broader framework for understanding how non-coding regions of the genome drive anatomical diversity. While protein-coding genes have remained relatively stable over evolutionary timescales, the regulatory landscapes modifying their expression patterns have undergone dynamic shifts. These shifts, often localized to specific developmental stages or tissues, underpin the morphological innovations that distinguish species. The study illuminates the importance of regulatory architecture evolution—shaping body plans by rewiring genetic control networks rather than altering the toolkit genes themselves.
Moreover, this research underscores the significance of terminal structures in developmental biology. Termini, whether of digestive tubes or limbs, appear especially amenable to genomic repurposing. The shared developmental programs between digit tips and the cloacal region suggest a modular, reusable design in vertebrate ontogeny, facilitating the emergence of novel structures via adaptive reprogramming. This insight opens new avenues for exploring the origins of other terminal anatomical features across taxa.
Looking ahead, the research community faces the exciting challenge of unraveling the precise molecular mechanisms by which these regulatory elements were co-opted and refined during evolution. Investigating the chromatin dynamics, transcription factor bindings, and epigenetic modifications that enabled this transition will deepen our grasp of genomic plasticity. Ultimately, uncovering these processes will bridge gaps between fossil records, developmental biology, and genomics, harmonizing diverse strands of evidence into a coherent evolutionary narrative.
Beyond its fundamental scientific merit, this discovery exemplifies how advanced genome editing methods like CRISPR/Cas9 empower researchers to experimentally test longstanding evolutionary hypotheses with unprecedented precision. By recreating genomic deletions analogous to putative ancestral states, scientists can experimentally mimic evolutionary shifts, transforming theoretical models into empirically validated mechanisms. Such integrative approaches herald a new era where evolutionary developmental biology (evo-devo) moves from descriptive inference to mechanistic elucidation.
In essence, the study reveals that the genesis of digits is not a story of inventing new parts but rather skillfully rewiring existing genomic blueprints initially designed for other functions. This elegant evolutionary strategy, where old regulatory landscapes are refashioned for new purposes, enriches our understanding of vertebrate evolution and the molecular ingenuity underlying complex traits. As we continue to decode the vast regulatory genome, more revelations about life’s evolutionary tapestry undoubtedly await.
Subject of Research: Not applicable
Article Title: ‘Co-option of an ancestral cloacal regulatory landscape during digit evolution’
News Publication Date: 17-Sep-2025
Web References: http://dx.doi.org/10.1038/s41586-025-09548-0
Image Credits: © Brent Hawkins, Harvard
Keywords: digit evolution, cloaca, regulatory landscapes, Hox genes, evolutionary development, genome editing, CRISPR/Cas9, morphological innovation, vertebrate evolution, non-coding genome, gene regulation, evolutionary recycling
