Since the early nineteenth century, scientists have observed that many animals, from the very simple to the complex, shared similar embryonic morphology and development. Surprisingly, a human embryo and a frog embryo, at a certain stage of embryonic development, look remarkably alike! For a long time, scientists did not understand why so many animal species looked similar during embryonic development but were very different as adults. They wondered what dictated the developmental direction that a fly, mouse, frog, or human embryo would take. Near the end of the twentieth century, a particular class of genes was discovered that had this very job. These genes that determine animal structure are called “homeotic genes,” and they contain DNA sequences called homeoboxes. Genes with homeoboxes encode protein transcription factors. One group of animal genes containing homeobox sequences is specifically referred to as Hox genes. This cluster of genes is responsible for determining the general body plan, such as the number of body segments of an animal, the number and placement of appendages, and animal head-tail directionality. The first Hox genes to be sequenced were those from the fruit fly (Drosophila melanogaster). A single Hox mutation in the fruit fly can result in an extra pair of wings or even legs growing from the head in place of antennae (this is because antennae and legs are embryologic homologous structures and their appearance as antennae or legs is dictated by their origination within specific body segments of the head and thorax during development). Now, Hox genes are known from virtually all other animals as well.

Figure 1. Shown here is the homology between Hox genes in mice and humans. Note how Hox gene expression, as indicated with orange, pink, blue, and green shading, occurs in the same body segments in both the mouse and the human. While at least one copy of each Hox gene is present in humans and other vertebrates, some Hox genes are missing in some chromosomal sets.

While there are a great many genes that play roles in the morphological development of an animal, including other homeobox-containing genes, what makes Hox genes so powerful is that they serve as “master control genes” that can turn on or off large numbers of other genes. Hox genes do this by encoding transcription factors that control the expression of numerous other genes. Hox genes are homologous across the animal kingdom, that is, the genetic sequences of Hox genes and their positions on chromosomes are remarkably similar across most animals because of their presence in a common ancestor, from worms to flies, mice, and humans (Figure 1).

Hox genes are highly conserved genes encoding transcription factors that determine the course of embryonic development in animals. In vertebrates, the genes have been duplicated into four clusters: Hox-A, Hox-B, Hox-C, and Hox-D. Genes within these clusters are expressed in certain body segments at certain stages of development.

In addition, the order of the genes reflects the anterior-posterior axis of the animal’s body. One of the contributions to increased animal body complexity is that Hox genes have undergone at least two and perhaps as many as four duplication events during animal evolution, with the additional genes allowing for more complex body types to evolve. All vertebrates have four (or more) sets of Hox genes, while invertebrates have only one set.

Two of the five clades within the animal kingdom do not have Hox genes: the Ctenophora and the Porifera. In spite of the superficial similarities between the Cnidaria and the Ctenophora, the Cnidaria have a number of Hox genes, but the Ctenophora have none. The absence of Hox genes from the ctenophores has led to the suggestion that they might be “basal” animals, in spite of their tissue differentiation. Ironically, the Placozoa, which have only a few cell types, do have at least one Hox gene. The presence of a Hox gene in the Placozoa, in addition to similarities in the genomic organization of the Placozoa, Cnidaria and Bilateria, has led to the inclusion of the three groups in a “Parahoxozoa” clade. However, we should note that at this time the reclassification of the Animal Kingdom is still tentative and requires much more study.