Rosa Rubicondior: Common Origins - How The Mammalian Outer Ear Evolved

An earful of gill: USC Stem Cell study points to the evolutionary origin of the mammalian outer ear | USC Stem Cell

I'm sorry if this spoils a creationists new year, but a bunch of scientists from the Stem Cell Lab of the University of Southern California have just published a paper showing an ancient ancestor of mammals, including of course us humans, was a fish.

It comes in the form of evidence that our outer ear develops from the same tissues in the embryo as the gills of fish. These tissues have been exapted by evolution for many new structures, one of which is the outer ear of mammals.

What is known about the evolutionary origins of the outer ear of mammals and its origins as the gills of fish? The evolutionary origins of the mammalian outer ear (the pinna) are fascinating. It is part of a complex evolutionary transition involving the modification of fish jaw and gill structures into ear components in tetrapods. Here’s how this transition is understood:

Fish Jaw and Gill Arches

Early jawless fish had a series of gill arches supporting their gills.
In jawed fish (gnathostomes), the first pharyngeal arch evolved into the upper and lower jaws.
The second pharyngeal arch (hyoid arch) supported the jaws and gill slits, and later contributed to structures in the ear.

Transition to Tetrapods

As vertebrates transitioned to land, some gill arch elements evolved into parts of the middle ear to adapt to hearing in air.
The spiracle (a small opening behind the eye in fish used for breathing) is thought to be the precursor of the middle ear cavity.
The hyomandibula (from the second arch) in fish became the stapes (or columella in non-mammalian tetrapods), the first middle ear bone.

Evolution of the Mammalian Ear

In early amniotes, the stapes transmitted sound vibrations to the inner ear.
In mammals, two more jaw bones (the articular and quadrate) from the first arch evolved into the malleus and incus of the middle ear, enhancing hearing sensitivity.
This left the jaw independent and more specialized for feeding.

Development of the Outer Ear (Pinna)

The pinna is unique to mammals and evolved later as a structure to collect and funnel sound waves into the ear canal.
It likely evolved from soft tissues around the first and second pharyngeal arches, but it has no direct connection to gill structures.
Its role is entirely in sound direction and amplification, adapting mammals to diverse hearing environments.

Key Transitional Fossils

Fossils like Tiktaalik show transitional features between fish and tetrapods, including modifications in the skull that prefigure middle ear adaptations.
Early synapsids (mammal ancestors) like Morganucodon illustrate the gradual detachment of jaw bones transitioning to the ear.

Conclusion
The outer ear (pinna) did not evolve directly from gills but arose from soft tissue modifications, while parts of the middle ear bones trace their origins to fish jaw and gill arch elements. This evolutionary story highlights how structures adapt and change function over millions of years.

The team, led by Professor J. Gage Crump have recently published their finding in the journal, Nature. They explain it in a UCS Keck School of Medicine press release.

An earful of gill: USC Stem Cell study points to the evolutionary origin of the mammalian outer ear
The outer ear is unique to mammals, but its evolutionary origin has remained a mystery. According to a new study published in Nature from the USC Stem Cell lab of Gage Crump, this intricate coil of cartilage has a surprisingly ancient origin in the gills of fishes and marine invertebrates.

When we started the project, the evolutionary origin of the outer ear was a complete black box. We had been studying the development and regeneration of the jawbones of fishes, and an inspiration for us was Stephen Jay Gould’s famous essay ‘An earful of jaw,’ which laid out how fish jawbones transformed into the middle ear bones of mammals. This made us wonder whether the cartilaginous outer ear may also have arisen from some ancestral fish structure.

Professor J Cage Crump, corresponding author
Department of Stem Cell Biology and Regenerative Medicine University of Southern California Keck School of Medicine, Los Angeles, CA, USA.

The first clue toward cracking this mystery was the team’s discovery that gills and outer ears are both composed of a relatively rare tissue type: elastic cartilage.

When we started the study, there was very little out there about whether elastic cartilage existed outside of mammals, so it wasn’t really known if fish had elastic cartilage or not. It turns out that they do.

Professor J Cage Crump.

Gills and outer ears look and function quite differently from one another. They also do not mineralize, which means they are rarely recovered in the fossil record. Therefore, a new type of approach was needed to determine if they were evolutionarily related. The study’s first author Mathi Thiruppathy, a PhD student in the Crump lab, focused on gene control elements called enhancers. While the genes that these enhancers control are often involved in the development of many unrelated tissues and organs, enhancers tend to be much more tissue specific.

The scientists were able to incorporate enhancers that help form the elastic cartilage of the human outer ear into the genomes of zebrafish . Remarkably, the human outer ear enhancers were active specifically in the gills of these transgenic zebrafish. The scientists also succeeded in doing the experiment in reverse, creating transgenic mice with genomes incorporating zebrafish enhancers typically involved in the formation of the gills, and found them active in the outer ears of the mice. These enhancers were key in connecting structures that at first glance do not appear to be very similar.

With collaborators, the researchers then investigated whether the human outer ear and fish gill enhancers could be used to follow the evolution of gills into outer ears across intermediate species, such as amphibians and reptiles. They found that when either human ear or fish gill enhancers were incorporated into the genomes of tadpoles, the enhancers showed activity in their gills. However, when reptiles came on the scene, the elastic cartilage of gills moved to the ear canal, which the scientists demonstrated in a series of experiments with green anole lizards. This cartilage eventually became further elaborated to form the prominent outer ears of early mammals.

An additional surprise was that the elastic cartilage of gills may have arisen much earlier than previously thought. Older reports had characterized cartilage-like tissue in the gills and tentacles of several marine invertebrates, including horseshoe crabs, which have changed very little since emerging close to 400 million years ago. The researchers performed DNA sequencing on individual cells of the horseshoe crab gills and discovered a crab enhancer that, when placed in the genome of zebrafish, had gill activity. This suggests that the very first elastic cartilage, similar to what is in our outer ears, may have first arisen in ancient marine invertebrates.

This work provides a new chapter to the evolution of the mammalian ear. While the middle ear arose from fish jawbones, the outer ear arose from cartilaginous gills. By comparing how the same gene control elements can drive development of gills and outer ears, the scientists introduce a new method of revealing how structures can dramatically change during evolution to perform new and unexpected functions.

Professor J Cage Crump.

About the study
Additional authors are Lauren Teubner, Ryan R. Roberts, Seth Ruffins, Arijita Sarkar, Jade Tassey, Denis Evseenko, and Thomas P. Lozito from USC; Micaela Lasser and Helen Rankin Willsey from the University of California, San Francisco; Alessandra Moscatello and Ya-Wen Chen from the Icahn School of Medicine at Mount Sinai; Christian Hochstim from Children’s Hospital Los Angeles and USC; and J. Andrew Gillis from the Marine Biological Laboratory at Woods Hole.

Abstract
How novel structures emerge during evolution has long fascinated biologists. A dramatic example is how the diminutive bones of the mammalian middle ear arose from ancestral fish jawbones1. In contrast, the evolutionary origin of the outer ear, another mammalian innovation, remains a mystery, in part because it is supported by non-mineralized elastic cartilage rarely recovered in fossils. Whether the outer ear arose de novo or through reuse of ancestral developmental programs is unknown. Here we show that the outer ear shares gene regulatory programs with the gills of fishes and amphibians for both its initial outgrowth and later development of elastic cartilage. Comparative single-nuclei multiomics of the human outer ear and zebrafish gills reveals conserved gene expression and putative enhancers enriched for common transcription factor binding motifs. This is reflected by transgenic activity of human outer ear enhancers in gills, and fish gill enhancers in the outer ear. Further, single-cell multiomics of the cartilaginous book gills of horseshoe crabs reveal a shared DLX-mediated gill program with vertebrates, with a book gill distalless enhancer driving expression in zebrafish gills. We propose that elements of an invertebrate gill program were reutilized in vertebrates to generate first gills and then the outer ear.

Thiruppathy, M., Teubner, L., Roberts, R.R. et al. Repurposing of a gill gene regulatory program for outer ear evolution. Nature (2025). https://doi.org/10.1038/s41586-024-08577-5

© 2025 Springer Nature Ltd.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

This work provides an example of something that creationists prefer to pretend doesn't happen. Instead of de novo genes being needed to produce a unique structure such as the mammalian outer ear, redundant genes can be repurposed by natural selection, resulting in new structures. All creationists need to do now is to explain why this isn't 'macro-evolution' but just another example of evolution within a 'kind'. Which flexible definition of 'kind' includes mammals and fish?

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