Ruminant inner ear shape records 35 million years of neutral evolution

An almost complete cranium of Asoriculus gibberodon (Petényi, 1864) (Mammalia, Soricidae) from the early Pliocene of the Jradzor site, Armenia

We describe an almost complete fossil cranium of a shrew, identified as Asoriculus gibberodon (Petényi, 1864) from the early Pliocene of Jradzor site, Armenia. The sedimentary unit, which yielded the specimen, is an 11-m-thick package composed of white thinly-parallel-laminated diatomite laying at the base of the Jradzor section. It was dated at 4.29 ± 0.09 Ma based on the magnetostratigraphy and 40Ar/39Ar radioisotopic dating of a tephra layer located at the top of the diatomite package. The skull from Jradzor shows several synapomorphies that allow its assignment to the Soricinae subfamily and Neomyini tribe. Among Neomyini, as far as the cranium anatomy is known, the specimen from Jradzor is most similar to that of Soriculus and Episoriculus. Both petrosal bones are preserved and are studied thanks to a 3D modelling of their morphology based on a CT-scan. Compared with other eulipotyphlans, the bony labyrinth of A. gibberodon from Jradzor shows a morphology typical of soricids. Its anatomy also indicates a high-frequency auditory capability similar to that of modern shrews but cannot confirm an echolocation system neither does it shows any feature that can be related to a specific locomotory adaption or ecological characteristic. The discovery of this cranium inside diatomites, corresponding to a distal lacustrine environment, raises the question of the possible semi-aquatic adaptation of this species (this adaptation being known for other extant species of the family). However, Soriculus and Episoriculus, the two genera closest to Asoriculus based on cranial anatomy are not semi-aquatic and are clearly distinguished from semi-aquatic Neomys shrews. The inner ear morphology is more similar to that of terrestrial shrews despite the general similarities among soricids and suggests an echolocation-based orientation using high frequencies to navigate through low vegetation, which is often essential in high metabolic rate organisms to reduce energy expenditure. We therefore propose a terrestrial locomotion for A. gibberodon, consistent with its previously proposed paleoecological model, depicting it was a terrestrial species inhabiting wet or humid environments in close proximity to permanent bodies of water.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13358-025-00357-6.

The differentiated impacts and constraints of allometry, phylogeny, and environment on the ruminants' ankle bone

The astragalus is a hinged bony organ common to many tetrapods. Several factors, including allometry, phylogeny, and environment, constrain its morphology. Due to the underlying risk of these factors being confounding, previous works have frequently highlighted the difficulty in discerning the specific influence of each factor. Here, we conducted allometric and size-adjusted clade and ecomorphological analyses to assess the contribution of each of these three parameters to the morphological variation of the astragalus in ruminant artiodactyls. 3D geometric morphometric analyses confirm the astragalus' highly integrated structure and multifactorial morphological responses. Sturdier astragali are correlated with heavier bodies. Bovids tend to display larger proximal trochlear ridges, and moschids show a prominent posterior process. The degree of development of areas where joints and ligaments intersect reflects the degree of freedom of the ankle and the locomotion type. This study provides new perspectives on the evolution of ruminants and their interactions with their environment.

Semicircular canals shed light on bottleneck events in the evolution of the Neanderthal clade

Revealing the evolutionary processes which resulted in the derived morphologies that characterize the Neanderthal clade has been an important task for paleoanthropologists. One critical method to quantify evolutionary changes in the morphology of hominin populations is through evaluating morphological phenotypic diversity (i.e., disparity) in phylogenetically informative bones as a close proxy to neutral evolutionary processes. The goal of this study is to quantify the degree of disparity in the Neanderthal clade. We hypothesize that a reduction in bony labyrinth disparity is indicative of the underlying genetic variation resulting from bottleneck events. We apply a deformation-based geometric morphometric approach to investigate semicircular canal and vestibule shape of a chronologically broad sample of individuals belonging to the Neanderthal lineage. Our results identify a significant reduction in disparity after the start of Marine Isotope Stage 5 supporting our hypothesis of a late bottleneck, possibly leading to the derived morphology of Late Pleistocene Neanderthals.

Divergent otolithic systems in the inner ear of Paranthropus robustus and Australopithecus africanus

The bony labyrinth of the inner ear houses the sensory end-organs responsible for balance (otolithic system in the utricle and saccule, and semicircular canal system) and hearing (cochlea). Study of the bony labyrinth has revealed considerable morphological diversity in the hominin lineage (semicircular canals and cochleae) and aided in reconstructing essential aspects of primate evolution, including positional behavior, audition, and phylogenic affinities. However, evidence of evolutionary change in the hominin otolithic system remains elusive. Such morphological variation in these gravitoinertial sensory end-organs may suggest functional differences as their geometry is linked with positional behavior. We approach the question of evolutionary morphological change in the hominin otolithic system by examining bony vestibule morphology in two South African hominin taxa Paranthropus robustus (n = 9) and Australopithecus africanus (n = 6), compared to extant hominids (Pongo pygmaeus, Gorilla gorilla, Pan troglodytes, and Homo sapiens). We use landmark-based shape analyses of 78 extant hominid inner ears by means of virtual three-dimensional models derived from micro-CT scans. Thirty bony landmarks were chosen to approximate otolithic organ morphology and relative configuration. Results show a distinctive morphology in P. robustus compared to A. africanus and extant hominids. Specifically, P. robustus exhibits anterolateral-posteromedial compression in bony otolithic organ structure, reducing the size of the saccule and vestibular aqueduct. In contrast, A. africanus exhibits a modern-human-like otolithic system. This newfound morphological diversity identifies unique bony features of the P. robustus inner ear which 1) offers potential evidence for differential positional behavior between P. robustus and A. africanus and 2) presents osteological markers to be used in taxonomic identification of P. robustus remains and in future assessments of Paranthropus classification.

Data-driven guidelines for phylogenomic analyses using SNP data

Premise

There is a general lack of consensus on the best practices for filtering of single-nucleotide polymorphisms (SNPs) and whether it is better to use SNPs or include flanking regions (full "locus") in phylogenomic analyses and subsequent comparative methods.

Methods

Using genotyping-by-sequencing data from 22 Glycine species, we assessed the effects of SNP vs. locus usage and SNP retention stringency. We compared branch length, node support, and divergence time estimation across 16 datasets with varying amounts of missing data and total size.

Results

Our results revealed five aspects of phylogenomic data usage that may be generally applicable: (1) tree topology is largely congruent across analyses; (2) filtering strictly for SNP retention (e.g., 90-100%) reduces support and can alter some inferred relationships; (3) absolute branch lengths vary by two orders of magnitude between SNP and locus datasets; (4) data type and branch length variation have little effect on divergence time estimation; and (5) phylograms alter the estimation of ancestral states and rates of morphological evolution.

Discussion

Using SNP or locus datasets does not alter phylogenetic inference significantly, unless researchers want or need to use absolute branch lengths. We recommend against using excessive filtering thresholds for SNP retention to reduce the risk of producing inconsistent topologies and generating low support.

Convergent evolution in Afrotheria and non-afrotherians demonstrates high evolvability of the mammalian inner ear

Evolutionary convergence in distantly related species is among the most convincing evidence of adaptive evolution. The mammalian ear, responsible for balance and hearing, is not only characterised by its spectacular evolutionary incorporation of several bones of the jaw, it also varies considerably in shape across modern mammals. Using a multivariate approach, we show that in Afrotheria, a monophyletic clade with morphologically and ecologically highly disparate species, inner ear shape has evolved similar adaptations as in non-afrotherian mammals. We identify four eco-morphological trait combinations that underlie this convergence. The high evolvability of the mammalian ear is surprising: Nowhere else in the skeleton are different functional units so close together; it includes the smallest bones of the skeleton, encapsulated within the densest bone. We suggest that this evolvability is a direct consequence of the increased genetic and developmental complexity of the mammalian ear compared to other vertebrates.

Inner ear morphology in wild versus laboratory house mice

The semicircular canals of the inner ear are involved in balance and velocity control. Being crucial to ensure efficient mobility, their morphology exhibits an evolutionary conservatism attributed to stabilizing selection. Release of selection in slow-moving animals has been argued to lead to morphological divergence and increased inter-individual variation. In its natural habitat, the house mouse Mus musculus moves in a tridimensional space where efficient balance is required. In contrast, laboratory mice in standard cages are severely restricted in their ability to move, which possibly reduces selection on the inner ear morphology. This effect was tested by comparing four groups of mice: several populations of wild mice trapped in commensal habitats in France; their second-generation laboratory offspring, to assess plastic effects related to breeding conditions; a standard laboratory strain (Swiss) that evolved for many generations in a regime of mobility reduction; and hybrids between wild offspring and Swiss mice. The morphology of the semicircular canals was quantified using a set of 3D landmarks and semi-landmarks analyzed using geometric morphometric protocols. Levels of inter-population, inter-individual (disparity) and intra-individual (asymmetry) variation were compared. All wild mice shared a similar inner ear morphology, in contrast to the important divergence of the Swiss strain. The release of selection in the laboratory strain obviously allowed for an important and rapid drift in the otherwise conserved structure. Shared traits between the inner ear of the lab strain and domestic pigs suggested a common response to mobility reduction in captivity. The lab-bred offspring of wild mice also differed from their wild relatives, suggesting plastic response related to maternal locomotory behavior, since inner ear morphology matures before birth in mammals. The signature observed in lab-bred wild mice and the lab strain was however not congruent, suggesting that plasticity did not participate to the divergence of the laboratory strain. However, contrary to the expectation, wild mice displayed slightly higher levels of inter-individual variation than laboratory mice, possibly due to the higher levels of genetic variance within and among wild populations compared to the lab strain. Differences in fluctuating asymmetry levels were detected, with the laboratory strain occasionally displaying higher asymmetry scores than its wild relatives. This suggests that there may indeed be a release of selection and/or a decrease in developmental stability in the laboratory strain.

The comparative anatomy of the petrosal bone and bony labyrinth of four small-sized deer

Here we provide complete 3D reconstructions of the petrosal bone and bony labyrinth of four kinds of small-sized deer (Elaphodus cephalophus, Muntiacus reevesi, Muntiacus muntjak, Hydropotes inermis) based on high-resolution CT scanning, and select one musk deer (Moschus moschiferus) as a comparative object. The petrosal bone and bony labyrinth of E. cephalophus are illustrated for the first time, as well as the petrosal bones of M. reevesi and H. inermis. Some morphological characters of petrosal bone and bony labyrinth can be used to distinguish the above-mentioned species. For example, M. moschiferus shows a prominent transpromontorial sulcus and a ventral basicapsular groove on the petrosal bone; there is a bifurcate cochlear aqueduct on the bony labyrinth of E. cephalophus; there is a distinct fusion between the lateral and posterior semicircular canals on the bony labyrinth of H. inermis. Meanwhile, there are some intraspecific variations on the subarcuate fossa, the tegmen tympani, the cochlear aqueduct, as well as the endolymphatic sac. Our results further confirm that the petrosal bone and bony labyrinth have enormous potential for taxonomy. This work will provide new anatomical data for the phylogenetic study of ruminants in the future, and it will be very practical to identify the isolated ruminants' petrosal bones that are frequently unearthed from paleontological or archeological sites.

Response to comment on "Sexual selection promotes giraffoid head-neck evolution and ecological adaptation"

Hou et al. challenged the giraffoid affinity of Discokeryx and its ecology and behavior. In our response we reiterate that Discokeryx is a giraffoid that, along with Giraffa, shows extreme evolution of head-neck morphologies that were presumably shaped by selective pressure from sexual competition and marginal environments.