RUI: modularity and plasticity of the HOX FIN/limb toolkit genes is associated with the development of novel morphologies and the evolution of vertebrate diversity

The National Science Foundation Division of Environmental Biology awarded San Francisco State University $1.194 million on September 1, 2026, under the Biological Sciences program (CFDA 47.074) to investigate how modularity and plasticity of Hox fin/limb toolkit genes generate novel morphologies and drive vertebrate diversity.

The research engages undergraduate students in evolutionary developmental biology, using genomic tools to determine how major fish appendages have arisen across species including ghost sharks, sculpins, catfish, and goatfish. The project examines the central hypothesis that Hox limb-building toolkit genes produce more novel structures in vertebrates than previously suspected, building on evidence that fins and limbs are patterned by a shared genetic repertoire arising in the common ancestor of jawed vertebrates.

The award includes development of educational materials for public engagement, including a children's book and curriculum modules for undergraduate biology majors that communicate the genetic underpinnings of fin and limb evolution. The project runs through August 31, 2029, with place of performance in San Francisco, California. San Francisco State University, a Hispanic-Serving Institution within the California State University system, receives the award as a prime grant recipient.

Abstract

We are only beginning to understand the mechanisms responsible for generating biodiversity at the genetic level. Several well-characterized novel morphologies have arisen by trait loss. However, little is known about the genetic underpinnings for the origin of new structures and their adaptive significance. A major challenge for developmental biology is to identify the molecular and developmental basis for such major novel characters that allow the diversification of life. This research will engage undergraduate students in evolutionary developmental biology research using state of the art genomic tools to determine how major fish appendages have arisen. Understanding how the development of novel traits across species will provide valuable insights that may facilitate future biotechnology breakthroughs. The focal species include ghost sharks, sculpins, catfish and goatfish. These animals command intense interest in the public eye. In addition to the training of undergraduates in scientific investigation and biotechnology the project will develop educational materials to engage the general public in understanding the genetic underpinnings of the evolution of FIN and limb evolution. These stories will be shared in a children?s book and in curriculum modules for undergraduate biology majors. The central hypothesis of this proposal is that the HOX limb building tool kit genes produce more novel structures in vertebrates than previously suspected. Fins and limbs are homologous structures that are patterned by a shared genetic repertoire, which has been referred to as the HOX FIN/limb building toolkit. This pattern occurs in paddlefish and catshark paired fins, indicating its role in patterning fins as well as limbs, and that IT arose in the common ancestor of jawed vertebrates. Interestingly, the modularity of the FIN/limb HOX program has not been directly addressed because so few derived morphologies have been evaluated. This problem can only be addressed by investigating a variety of taxa with novel morphologies. The proposed research will examine the role of the 5? Hoxa/d genes in the evolution and development of novel appendages in multiple divergent lineages that exhibit unique body plan features, and for which the ecological or physiological significance is understood. This study will explore the evolution of the gonopodium in marine sculpins, claspers in a group of cartilaginous fish (chimeras) and barbels in RAY-finned fishes. These derived modifications will allow US to evaluate modularity and plasticity of the HOX program in the evolution of vertebrate diversity. The results will expand our understanding of body plan features that are patterned by the HOX repertoire and reveal variation in the HOX code that has gone undetected in derived lineages. The significance of this research is that ancient HOX modules may provide the basis for a shared genetic repertoire that produces a wide array of new features in vertebrates. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the foundation's intellectual merit and broader impacts review criteria.- subawards are not planned for this award.