The findings support a stepwise model for how the genetic program that builds vertebrate paired fins and limbs may have evolved. An ancestral Hox9–10 program may first have helped establish posterior appendages, later expanded into a broader Hox patterning system, and eventually been redeployed in anterior paired appendages.
Image after H. Nakazawa et al., (2026) CC BY-NC-ND.
Creationists who insist that fish and terrestrial vertebrates are separately created “kinds” have another piece of evidence to explain away. Beneath the obvious differences between a fish’s pelvic fins and an amphibian’s hindlimbs lies a shared developmental inheritance: related genes performing an essential early role in establishing the cells from which those structures develop. Evolutionary relationships are recorded not only in fossils and adult anatomy, but also in the processes that build living bodies.
This is illustrated by research led by scientists at Saitama University, Japan, published in Proceedings of the National Academy of Sciences (PNAS). The researchers investigated Hox genes, regulatory genes involved in organising the developing body. Their experiments reveal a shared requirement for members of the Hox9–10 groups at the beginning of pelvic-fin and hindlimb development.
In zebrafish, disrupting five of these genes together eliminated the detectable populations of pelvic-fin progenitor cells—the cells that would normally give rise to the developing fins—and the pelvic fins failed to form. In Iberian ribbed newts, disrupting seven related genes likewise impaired the establishment of hindlimb progenitors. These results support the inference that this developmental function was already present in the common ancestor of ray-finned and lobe-finned vertebrates, before the evolutionary separation of the lineages represented by zebrafish and newts.
The significance extends beyond the discovery that different animals use related genes. The findings help connect the genetic programme that organises the rear of the body with the programme that initiates its paired hind appendages. They are consistent with an evolutionary model in which an ancestral programme was recruited, expanded and redeployed as the developmental machinery of paired fins and limbs evolved. The experiments do not directly reconstruct that entire historical sequence, but they provide functional evidence with which to assess it.
For intelligent design creationism, the familiar difficulty is that evolutionary innovation need not involve inventing every component afresh. Existing genes and developmental relationships can acquire additional roles as evolution modifies inherited systems. Calling those systems “designed” supplies no comparable account of when, where or how the changes occurred, nor does it improve the experimental explanation.
Meanwhile, the scientists are doing precisely the opposite of what creationist claims of a collapsing theory of evolution would lead us to expect: using common ancestry to frame productive questions, testing them experimentally and refining our understanding of how vertebrate bodies evolved. The question driving this research is how the evolutionary changes happened. The shared developmental machinery offers another revealing part of the answer.
What are Hox genes, and what do they do? Hox genes help establish the regional organisation of an animal’s body during development. They contribute to determining which structures develop at different positions along the head-to-tail axis, and some also have important roles in building appendages such as fins and limbs.The paper in PNAS is accompanied by a Saitama University news release through EurekAlert!:
Genes that regulate other genes
Hox genes encode transcription factors: proteins that bind to DNA and help regulate the activity of other genes. Their effects depend on the other proteins present, the regulatory DNA available and the developmental state of the cell. They therefore work within interacting networks, rather than acting as independent instructions for complete body parts.
All Hox genes belong to the larger homeobox family, but not all homeobox genes are Hox genes. A homeobox is a DNA sequence that encodes a DNA-binding region of a protein, called a homeodomain.
A positional identity system
A useful analogy is a system of positional labels. Different combinations of active Hox genes help cells acquire the appropriate regional identity. In vertebrates, for example, this contributes to the differences between regions of the backbone. The genes do not give cells conscious knowledge of their location: their proteins influence which developmental processes occur there.
Many Hox genes occur in clusters on chromosomes. In vertebrates, their order within a cluster broadly corresponds to the order of their activity along the developing body, and often to the sequence in which they become active. This relationship is called collinearity. It is a general organisational pattern, with exceptions and additional layers of regulation.
Why disrupt several genes at once?
Gene duplication has produced related Hox genes with partly overlapping functions. One gene can sometimes compensate for the loss of another, so disrupting a single gene may reveal only part of their collective role. Experiments that disrupt several related genes can expose a requirement that would otherwise remain hidden.
Related genes produced by duplication are called paralogs. The designation Hox9–10 refers to two groups of related genes; it does not mean that there are only two individual genes involved.
From body patterning to fins and limbs
In the study discussed here, researchers found that combinations of Hox9–10 genes are needed at a very early stage of pelvic-fin development in zebrafish and hindlimb development in Iberian ribbed newts. Their role begins with establishing the progenitor cells from which these appendages develop, before a recognisable fin or limb bud appears.
The shared requirement supports an ancient evolutionary origin for this function. It also helps explain how changes in the deployment of existing regulatory genes could contribute to new structures. Evolution can modify when, where and in what combinations genes act, as well as changing the proteins they encode.
An important distinction: showing that a gene is essential for a structure in a living animal does not establish that it always had that role, or that the entire system had to originate at once. Present-day dependence and evolutionary origin are different questions.
Ancient Hox code reveals the developmental roots of vertebrate hind fins and limbs
Paired appendages — the pectoral and pelvic fins of fishes and the forelimbs and hindlimbs of tetrapods — were a major innovation in vertebrate evolution. Their emergence greatly expanded the ways vertebrates could move through their environments and ultimately provided the developmental foundation for the evolution of limbs. Yet how the genetic system responsible for building paired appendages was assembled during evolution remains an unresolved question.
Hox genes are central regulators of vertebrate body patterning. In particular, HoxA and HoxD paralog groups 9–13 are known to control the later patterning of both fish fins and tetrapod limbs. This deeply conserved role has suggested a connection between the Hox code that specifies positions along the main body axis and the developmental program that patterns paired appendages. However, direct functional evidence showing that posterior Hox genes are required at the very earliest stages of hind appendage formation has been limited.
A research group led by Associate Professor Akinori Kawamura of the Graduate School of Science and Engineering, Saitama University, working with researchers from Tottori University, the National Institute of Genetics, the National Institute for Basic Biology, and the Exploratory Research Center on Life and Living Systems, aimed to determine whether posterior Hox genes are required for the initial establishment of hind appendage progenitor cells and whether this function is conserved across distantly related vertebrates. Using zebrafish carrying combinations of Hox gene mutations, fluorescent reporter lines that visualize developing pelvic fin progenitors, skeletal imaging, and CRISPR-Cas9-mediated disruption of Hox genes in the Iberian ribbed newt, the team revealed an evolutionarily conserved requirement for Hox9–10 genes during the earliest stages of hind appendage formation. The study was published online on October 16, 2026, in the Proceedings of the National Academy of Sciences (PNAS).
In zebrafish, the researchers found that simultaneously disrupting five HoxA/D paralog group 9–10 genes — hoxa9a, hoxa9b, hoxa10b, hoxd9a, and hoxd10a — resulted in the complete loss of pelvic fins. Fluorescent reporter analyses using markers associated with pelvic fin progenitor cells further showed that the characteristic bilateral progenitor populations could no longer be detected in these mutants, indicating that HoxA/D PG9–10 genes act before morphologically recognizable pelvic fin buds form. A hoxa10b reporter also marked cells in the presumptive pelvic fin field before fin bud formation, further supporting an early role for these genes.
The researchers then asked whether this function extends beyond ray-finned fishes. In the Iberian ribbed newt, a lobe-finned vertebrate lineage, they simultaneously disrupted all seven Hox9–10 paralogs using CRISPR-Cas9. Animals showing hindlimb loss also displayed corresponding loss or marked reduction of Prdm16 expression in prospective hindlimb-forming regions. Together, the zebrafish and newt experiments indicate that the requirement for Hox9–10 genes in establishing hind appendage progenitors predates the evolutionary divergence of these distantly related vertebrate lineages.
Our results show that Hox9–10 genes are involved not only in the later patterning of paired appendages, but also at a much earlier step, when the progenitor cells that will form the pelvic fin or hindlimb are first established. This provides a developmental connection between the posterior Hox code of the body axis and the Hox system used to build paired appendages, and gives functional support to the idea that an ancestral posterior Hox program contributed to the evolutionary assembly of this system.
Hidemichi Nakazawa, co-first author
Division of Life Science
Graduate School of Science and Engineering
Saitama University
Saitama, Japan.
The findings are consistent with a stepwise evolutionary model in which an ancestral Hox9–10 program involved in early hind appendage development was subsequently expanded to include additional posterior Hox genes and later redeployed in anterior paired appendages. The study does not directly reconstruct this evolutionary sequence, but provides developmental evidence linking an ancient posterior Hox program to the origin of the broader vertebrate paired appendage-patterning system.
This is fundamental research into how the vertebrate body plan was assembled through evolution, rather than research aimed at an immediate clinical or industrial application. Over the next five to ten years, however, understanding how Hox genes establish appendage progenitor cells should help us uncover more general principles governing vertebrate development. Combined with advances in genome editing and comparative developmental biology, this knowledge could also provide an important conceptual foundation for future research into limb development, developmental disorders, and regenerative biology.
Associate Professor Akinori Kawamura.
Integrated Medical Sciences
Graduate School of Medical Sciences
Tottori University
Yonago, Japan.
Publication:
Once again, evolutionary biology has connected apparently different structures through their shared developmental inheritance. A zebrafish’s pelvic fins and a newt’s hindlimbs differ in form and function, yet their development depends on related genes acting at a comparable early stage. This is precisely the sort of underlying continuity that descent with modification leads us to expect: inherited developmental machinery retained and modified as lineages diverge.
The findings also illustrate why the present-day necessity of a component is not evidence that an entire system must have appeared fully formed. Disrupting these genes prevents normal appendage development, but that tells us how the existing system works, not that its evolutionary predecessors required exactly the same arrangement. The creationist argument from “irreducible complexity” confuses dependence in a modern organism with an inability to evolve through earlier, different configurations.
There is an important distinction between demonstrating this shared genetic requirement and reconstructing every step by which the system evolved. The researchers provide evidence for the former and support for a model of the latter. That distinction is a strength of the science: conclusions remain proportionate to the evidence, and unresolved details become questions for further investigation. They do not become invitations to insert a supernatural designer.
Nor is there any sign here of biologists abandoning evolution because it cannot explain their findings. Common ancestry supplies the framework that makes the comparison meaningful, while experiments reveal how inherited developmental systems operate. An assertion of “common design” can accommodate the results after the event, but supplies no independently testable account of the supposed designer’s methods or intentions. Evolution, meanwhile, continues to generate questions that can be answered—and answers that deepen our understanding of the natural world.
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