Evolution: Mammalian Ears Tell the Story

"The 'hairy quadruped furnished with a tail, and pointed ears, probably arboreal in his habits', this good fellow carried hidden in his nature, apparently, something destined to develop into a necessity for humane letters." ~ Matthew Arnold, 1885.

Introduction

Our ears are divided into three major sections. The visible part includes our outer ear, also called the pinna, and the ear canal that leads to the eardrum.  Going deeper, the next section is the middle ear that contains the three small bones called the incus, malleus, and stapes. The last section is the inner ear located in the temporal bone of the skull and contains the organs for balance, the semicircular canals and the organ for hearing, the cochlea. 

Science has revealed how each of these three main auditory sections evolved. A look at our outer ear alone provided important clues to our evolutionary past.

1. Our visible ears - clues to our evolutionary ancestry. 

A. Darwin’s Tubercle - Some people have a small thickened area on their outer ear that scientists and medical researchers have named Darwin’s Tubercle. It matches an ear prominence found in many monkeys. 

Left: For educational purposes only. Fair use attribution. https://jcdr.net/articles/PDF/20343/74434_CE%5BRa1%5D_F(SHU)_QC(SD_IS)_PF1(VD_SHU)_PFA(KM)_PN(IS).pdf Right: For educational purposes only. Fair use attribution. https://commons.wikimedia.org/wiki/File:Darwin-s-tubercle.jpg

B. Vestigial Pinna Muscles - Our pinnae are held onto the skull by at least 6 vestigial muscles. Although some of us can move our ears slightly, our ability to do so pales in comparison to that of other animals. Those vestigial ear muscles, where for example simple connective tissue would have sufficed, attest to human ancestors who could move their ears in many directions. The best and most harmonious explanation is evolution because we evolved from ancestors that could move their ears in many directions.

For educational purposes only. Fair use attribution

https://commons.wikimedia.org/wiki/File:Musculushelicismajor.png

A deer demonstrates how it can move its ears 180 degrees with muscles From: https://x.com/faintsun/status/1275538865512755206

C. Preauricular Sinus Tracts -  Below is a typical sinus tract that can occur in human ears. They are not uncommon and represent congenital abnormalities. How do they point us to human evolution?

In human and vertebrate embryogenesis, tissue arches form next to the developing throat or pharynx. They are called pharyngeal or branchial arches. In fish they are called gill arches because they develop into gills. In tetrapods (four legged animals) the first and second arches develop several tissue thickenings that give rise to the external ear (pinna) after fusion. If they fail to fuse they can form small tunnels or sinus tracts and these are called preauricular (before the auricle, or outer ear) sinus tracts showing us our common ancestry with fish. Further evidence of our connection with fish ancestors can be demonstrated in at least two ways. First, with the rare condition of Otocephaly which occurs due to disruption of the 1st branchial arch. The external ears then form and fuse below the chin. The mandible is missing because it arises also from the 1st branchial cleft. The fetus is stillborn or a miscarriage occurs; the disorder arises from a mutation of the PRRX1 gene on chromosome 1.

For educational purposes only. Fair use attribution. https://en.wikipedia.org/wiki/Otocephaly Second, in 2025 researchers published a study showing a genetic connection between gill development in fish and the tetrapod external ear. The abstract: "... 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."

For educational purposes only. Fair use attribution https://www.nature.com/articles/s41586-024-08577-5 Furthermore, a summary of the above cited regulatory gene confirms confirms the repurposing of a fish gene for vertebrate outer ear formation. "Fish gills and human ears share the same genetic blueprint. Gills and mammalian ears bear little resemblance, yet examination of gene regulation reveals that key supportive cartilage tissue arises from similar embryonic cells guided by an evolutionarily conserved genetic program." https://www.nature.com/articles/d41586-025-00342-6?fbclid=IwY2xjawITEytleHRuA2FlbQIxMQABHbg9vZRZEbCgBWtYQB3KD9968urAaLxRbw1OHOS9QoNE87tAjI9gUXmF3Q_aem_GP_lEoE3E0zis45OJYvLwA

*** See footnote end of this blog article about a similar issue that happened when a nerve (the Recurrent Laryngeal Nerve in all tetrapods) that travels to our larynx or voice box was trapped under a branchial arch in fishes as the neck evolved and how it now must travel a crazy course because of it.

2. Evolution of the middle ear 

The middle ear of mammals contains three bones - the incus, malleus, and stapes (“hammer, anvil, and stirrup”) that connect to the tympanic membrane (ear drum). Scientists have discovered in detail how all these bones evolved. 

When paleontologists classify mammalian fossils, they can’t use common defining characteristics of mammals such as fur and milk production since these don’t normally fossilize. They instead look for the auditory bulla, a bony structure that encases these three bones. 

In reptiles, amphibians, and birds the eardrum is connected to the middle ear by a single bone called the columella. This corresponds to the mammalian stapes. During evolution a bone from the upper jaw (quadrate) migrated to form the incus and a bone from the lower jaw (the articular) migrated to from the malleus. The details of how this happened and when is a triumph of science contributed by many diverse and independent fields of research. The columella became the stapes. 

How do we know this happened? The fossils tell a wonderful story of gradual evolution. But there are several other lines of evidence that also tell the story of this amazing gradual evolution. These are best discussed by Anthwal, et al. in their 2012 article. “Having three ossicles in the middle ear is one of the defining features of mammals. All reptiles and birds have only one middle ear ossicle, the stapes or columella. How these two additional ossicles came to reside and function in the middle ear of mammals has been studied for the last 200 years and represents one of the classic example of how structures can change during evolution to function in new and novel ways. From fossil data, comparative anatomy and developmental biology it is now clear that the two new bones in the mammalian middle ear, the malleus and incus, are homologous to the quadrate and articular, which form the articulation for the upper and lower jaws in non-mammalian jawed vertebrates. The incorporation of the primary jaw joint into the mammalian middle ear was only possible due to the evolution of a new way to articulate the upper and lower jaws, with the formation of the dentary-squamosal joint, or TMJ in humans. The evolution of the three-ossicle ear in mammals is thus intricately connected with the evolution of a novel jaw joint, the two structures evolving together to create the distinctive mammalian skull… Although the fossil record provides clues to the transition it is often incomplete and relies on a few isolated specimens. The ideal solution would be to be able to follow the transition from primary to novel articulation in a living animal. This is indeed possible in marsupials (Maier, 1987). In marsupials the neonate must be able to suckle at an early developmental stage, prior to the formation of the bones that will make up the normal mammalian jaw joint. Marsupials, therefore utilise the joint between the incus and malleus as their primary jaw joint for the first few weeks after birth (Muller, 1968) (Fig. 5). A clear synovial joint between the malleus and incus has been reported at postnatal day (P) 3 in the opossum Monodelphis (Filan, 1991)."In conclusion, the evolution of the mammalian middle ear and jaw joint were pivotal steps in the evolution of mammals. It is also a great example of how classical comparative anatomy, paleontology and developmental biology have come together to piece together how this remarkable transformation of jaw joint to ear ossicles was able to come about. The homologies of the malleus, incus and stapes to the articular, quadrate and columella, and tympanic ring and gonial to the angular and prearticular suggested by comparative anatomy 175 years ago have been recently confirmed by molecular and developmental biology. The recent discovery of new mammaliform fossils has allowed careful documentation of the shift from primary to secondary jaw articulation, creating an opportunity to follow the transformation of the post-dentary skeletal elements. This fossil data has been complemented by the study of marsupial development, providing insight into the changing role of the malleus and incus, and the relationship of the primary and secondary jaw joints.” From: Evolution of the mammalian ear and jaw: adaptations and novel structures https://pmc.ncbi.nlm.nih.gov/articles/PMC3552421/

For educational purposes only. Fair attribution. From: https://www.talkorigins.org/faqs/comdesc/section1.html#morphological_intermediates_ex2

Other references: https://en.wikipedia.org/wiki/Evolution_of_mammalian_auditory_ossicles https://carnegiemnh.org/press/researchers-announce-surprising-clue-in-the-evolution-of-mammalian-middle-ear/

3. Evolution of the cochlea

The cochlea (Latin for "snail or screw") is the coiled structure in the inner ear of mammals that converts vibrations into nerve impulses. These vibrations come from the middle ear bones that are eventually in contact with the eardrum, thus vibrating as air pressure waves. The middle ear bones transfer their vibrations to fluid waves that move hair cells of the Organ of Corti inside the cochlea.

By studying the fossil record especially with micro-CT and present comparative anatomy, scientists have been able to show basically how this organ evolved although the exact evolutionary steps are still under investigation. Lizards and snakes, birds and crocodilians have a basilar papilla for hearing. The Organ of Corti evolved from this probably about 120 million years ago. Manley notes: "Evolution of the cochlea and high-frequency hearing (>20 kHz; ultrasonic to humans) in mammals has been a subject of research for many years. Recent advances in paleontological techniques, especially the use of micro-CT scans, now provide important new insights that are here reviewed. True mammals arose more than 200 million years (Ma) ago. Of these, three lineages survived into recent geological times. These animals uniquely developed three middle ear ossicles, but these ossicles were not initially freely suspended as in modern mammals. The earliest mammalian cochleae were only about 2 mm long and contained a lagena macula. In the multituberculate and monotreme mammalian lineages, the cochlea remained relatively short and did not coil, even in modern representatives. In the lineage leading to modern therians (placental and marsupial mammals), cochlear coiling did develop, but only after a period of at least 60 Ma. Even Late Jurassic mammals show only a 270 ° cochlear coil and a cochlear canal length of merely 3 mm. Comparisons of modern organisms, mammalian ancestors, and the state of the middle ear strongly suggest that high-frequency hearing (>20 kHz) was not realized until the early Cretaceous (~125 Ma). At that time, therian mammals arose and possessed a fully coiled cochlea. The evolution of modern features of the middle ear and cochlea in the many later lineages of therians was, however, a mosaic and different features arose at different times... "Obviously, no old fossil provides remnants of soft tissues except as far as they influence or are shaped by bone. It is, however, possible to use the cladistical outgroup analysis method to investigate comparative structural questions regarding the soft tissues of the hearing organ. If we compare the structure of the cochleae of modern therian mammals with that of modern monotreme mammals and these again to the structures in nonmammals, we come to the conclusion that all modern mammals have similar and unique structural features (synapomorphies) and all their hearing organs deserve to be called “organs of Corti.” No nonmammals have anything similar."

https://pmc.ncbi.nlm.nih.gov/articles/PMC3505590/

A complete examination of the evolution of the inner ear including components of the vestibular system for balance can be referenced in the article by Koppl and Manley: "This review summarizes paleontological data as well as studies on the morphology, function, and molecular evolution of the cochlea of living mammals (monotremes, marsupials, and placentals). The most parsimonious scenario is an early evolution of the characteristic organ of Corti, with inner and outer hair cells and nascent electromotility. Most remaining unique features, such as loss of the lagenar macula, coiling of the cochlea, and bony laminae supporting the basilar membrane, arose later, after the separation of the monotreme lineage, but before marsupial and placental mammals diverged. The question of when hearing sensitivity first extended into the ultrasonic range (defined here as >20 kHz) remains speculative, not least because of the late appearance of the definitive mammalian middle ear. The last significant change was optimizing the operating voltage range of prestin, and thus the efficiency of the outer hair cells’ amplifying action, in the placental lineage only." https://pmc.ncbi.nlm.nih.gov/articles/PMC6546037/#s3

Conclusion

The evolution of the mammalian ear is evident in all three basic ear sections. These are the outer ear or pinna, the three middle ear bones, and the inner ear, containing the auditory structures and vestibular apparatus.

The evolution of the mammalian outer ear and its connections to fish anatomy was discussed along with how a genetic abnormality can help support these connections. The middle ear bones are perhaps one of the best documented evolutionary examples of gradual evolution. The history of ear evolution with scientists detailing their gradual formation from jaw bones through the fossil record is introduced. Lastly, the evolution of the inner ear structures involved in auditory nerve processing have been discussed in the literature and several references were provided for readers wanting to know further details.

What would seem to be a near impossible task for science to reveal how a complex organ such as the mammalian ear could have evolved through natural processes and gradually has indeed yielded to careful study, driving curiosity, and new technologies.

[Note: just as our outer ear can be traced to the gill arches in fish, so also the long course of the recurrent laryngeal nerve can be explained by evolution and our ancestry with fish. In some dinosaurs it would have been ridiculously long. Instead of branching off the vagus nerve at the level of the larynx as the superior nerves do, the RLN is forced to travel all the way to the heart before coming back up to where it was originally at the level of the voicebox to finally innervate the lower side of the larynx. It became trapped by the 6th gill arch in fish as the neck evolved. For a discussion of this bizarre adaptation route and why evolution explains it, see the first section of Why Not Intelligent Design. ]

"Nothing in Biology Makes Sense Except in the Light of Evolution" ~ Theodosius Dobzhansky, 1973. Evolutionary Biologist, Christian