Australian Rodents Reveal Conserved Cranial Evolutionary Allometry across 10 Million Years of Murid Evolution

Facing the facts: adaptive trade-offs along body size ranges determine mammalian craniofacial scaling

The mammalian cranium (skull without lower jaw) is representative of mammalian diversity and is thus of particular interest to mammalian biologists across disciplines. One widely retrieved pattern accompanying mammalian cranial diversification is referred to as 'craniofacial evolutionary allometry' (CREA). This posits that adults of larger species, in a group of closely related mammals, tend to have relatively longer faces and smaller braincases. However, no process has been officially suggested to explain this pattern, there are many apparent exceptions, and its predictions potentially conflict with well-established biomechanical principles. Understanding the mechanisms behind CREA and causes for deviations from the pattern therefore has tremendous potential to explain allometry and diversification of the mammalian cranium. Here, we propose an amended framework to characterise the CREA pattern more clearly, in that 'longer faces' can arise through several kinds of evolutionary change, including elongation of the rostrum, retraction of the jaw muscles, or a more narrow or shallow skull, which all result in a generalised gracilisation of the facial skeleton with increased size. We define a standardised workflow to test for the presence of the pattern, using allometric shape predictions derived from geometric morphometrics analysis, and apply this to 22 mammalian families including marsupials, rabbits, rodents, bats, carnivores, antelopes, and whales. Our results show that increasing facial gracility with size is common, but not necessarily as ubiquitous as previously suggested. To address the mechanistic basis for this variation, we then review cranial adaptations for harder biting. These dictate that a more gracile cranium in larger species must represent a structural sacrifice in the ability to produce or withstand harder bites, relative to size. This leads us to propose that facial gracilisation in larger species is often a product of bite force allometry and phylogenetic niche conservatism, where more closely related species tend to exhibit more similar feeding ecology and biting behaviours and, therefore, absolute (size-independent) bite force requirements. Since larger species can produce the same absolute bite forces as smaller species with less effort, we propose that relaxed bite force demands can permit facial gracility in response to bone optimisation and alternative selection pressures. Thus, mammalian facial scaling represents an adaptive by-product of the shifting importance of selective pressures occurring with increased size. A reverse pattern of facial 'shortening' can accordingly also be found, and is retrieved in several cases here, where larger species incorporate novel feeding behaviours involving greater bite forces. We discuss multiple exceptions to a bite force-mediated influence on facial proportions across mammals which lead us to argue that ecomorphological specialisation of the cranium is likely to be the primary driver of facial scaling patterns, with some developmental constraints as possible secondary factors. A potential for larger species to have a wider range of cranial functions when less constrained by bite force demands might also explain why selection for larger sizes seems to be prevalent in some mammalian clades. The interplay between adaptation and constraint across size ranges thus presents an interesting consideration for a mechanistically grounded investigation of mammalian cranial allometry.

Dynamic evolutionary interplay between ontogenetic skull patterning and whole-head integration

The arrangement and morphology of the vertebrate skull reflect functional and ecological demands, making it a highly adaptable structure. However, the fundamental developmental and macroevolutionary mechanisms leading to different vertebrate skull phenotypes remain unclear. Here we exploit the morphological diversity of squamate reptiles to assess the developmental and evolutionary patterns of skull variation and covariation in the whole head. Our geometric morphometric analysis of a complex squamate ontogenetic dataset (209 specimens, 169 embryos, 44 species), covering stages from craniofacial primordia to fully ossified bones, reveals that morphological differences between snake and lizard skulls arose gradually through changes in spatial relationships (heterotopy) followed by alterations in developmental timing or rate (heterochrony). Along with dynamic spatiotemporal changes in the integration pattern of skull bone shape and topology with surrounding brain tissues and sensory organs, we identify a relatively higher phenotypic integration of the developing snake head compared with lizards. The eye, nasal cavity and Jacobson's organ are pivotal in skull morphogenesis, highlighting the importance of sensory rearrangements in snake evolution. Furthermore, our findings demonstrate the importance of early embryonic, ontogenetic and tissue interactions in shaping craniofacial evolution and ecological diversification in squamates, with implications for the nature of cranio-cerebral relations across vertebrates.

Functionally mediated cranial allometry evidenced in a genus of rock-wallabies

In assessments of skeletal variation, allometry (disproportionate change of shape with size) is often corrected to examine size-independent variation for hypotheses relating to function. However, size-related trade-offs in functional demands may themselves be an underestimated driver of mammalian cranial diversity. Here, we use geometric morphometrics alongside dental measurements to assess craniodental allometry in the rock-wallaby genus Petrogale (all 17 species, 370 individuals). We identified functional aspects of evolutionary allometry that can be both extensions of, and correlated negatively with, static or ontogenetic allometric patterns. Regarding constraints, larger species tended to have relatively smaller braincases and more posterior orbits, the former of which might represent a constraint on jaw muscle anatomy. However, they also tended to have more anterior dentition and smaller posterior zygomatic arches, both of which support the hypothesis of relaxed bite force demands and accommodation of different selective pressures that favour facial elongation. By contrast, two dwarf species had stouter crania with divergent dental adaptations that together suggest increased relative bite force capacity. This likely allows them to feed on forage that is mechanically similar to that consumed by larger relatives. Our results highlight a need for nuanced considerations of allometric patterns in future research of mammalian cranial diversity.

Multivariate analyses of skull morphology inform the taxonomy and evolution of geomyoid rodents

Morphological analyses are critical to quantify phenotypic variation, identify taxa, inform phylogenetic relationships, and shed light on evolutionary patterns. This work is particularly important in groups that display great morphological disparity. Such is the case in geomyoid rodents, a group that includes 2 of the most species-rich families of rodents in North America: the Geomyidae (pocket gophers) and the Heteromyidae (kangaroo rats, pocket mice, and their relatives). We assessed variation in skull morphology (including both shape and size) among geomyoids to test the hypothesis that there are statistically significant differences in skull measurements at the family, genus, and species levels. Our sample includes 886 specimens representing all geomyoid genera and 39 species. We used the geometric mean to compare size across taxa. We used 14 measurements of the cranium and lower jaw normalized for size to compare shape among and within taxa. Our results show that skull measurements enable the distinction of geomyoids at the family, genus, and species levels. There is a larger amount of size variation within Geomyidae than within Heteromyidae. Our phylomorphospace analysis shows that the skull shape of the common ancestor of all geomyoids was more similar to the common ancestor of heteromyids than that of geomyids. Geomyid skulls display negative allometry whereas heteromyid skulls display positive allometry. Within heteromyids, dipodomyines, and non-dipodomyines show significantly different allometric patterns. Future analyses including fossils will be necessary to test our evolutionary hypotheses.

Multiple modes of inference reveal less phylogenetic signal in marsupial basicranial shape compared with the rest of the cranium

Incorporating morphological data into modern phylogenies allows integration of fossil evidence, facilitating divergence dating and macroevolutionary inferences. Improvements in the phylogenetic utility of morphological data have been sought via Procrustes-based geometric morphometrics (GMM), but with mixed success and little clarity over what anatomical areas are most suitable. Here, we assess GMM-based phylogenetic reconstructions in a heavily sampled source of discrete characters for mammalian phylogenetics-the basicranium-in 57 species of marsupial mammals, compared with the remainder of the cranium. We show less phylogenetic signal in the basicranium compared with a 'Rest of Cranium' partition, using diverse metrics of phylogenetic signal (K_mult, phylogenetically aligned principal components analysis, comparisons of UPGMA/neighbour-joining/parsimony trees and cophenetic distances to a reference phylogeny) for scaled, Procrustes-aligned landmarks and allometry-corrected residuals. Surprisingly, a similar pattern emerged from parsimony-based analyses of discrete cranial characters. The consistent results across methods suggest that easily computed metrics such as K_mult can provide good guidance on phylogenetic information in a landmarking configuration. In addition, GMM data may be less informative for intricate but conservative anatomical regions such as the basicranium, while better-but not necessarily novel-phylogenetic information can be expected for broadly characterized shapes such as entire bones. This article is part of the theme issue 'The mammalian skull: development, structure and function'.

Diversification of the ruminant skull along an evolutionary line of least resistance

Clarifying how microevolutionary processes scale to macroevolutionary patterns is a fundamental goal in evolutionary biology, but these analyses, requiring comparative datasets of population-level variation, are limited. By analyzing a previously published dataset of 2859 ruminant crania, we find that variation within and between ruminant species is biased by a highly conserved mammalian-wide allometric pattern, CREA (craniofacial evolutionary allometry), where larger species have proportionally longer faces. Species with higher morphological integration and species more biased toward CREA have diverged farther from their ancestors, and Ruminantia as a clade diversified farther than expected in the direction of CREA. Our analyses indicate that CREA acts as an evolutionary "line of least resistance" and facilitates morphological diversification due to its alignment with the browser-grazer continuum. Together, our results demonstrate that constraints at the population level can produce highly directional patterns of phenotypic evolution at the macroevolutionary scale. Further research is needed to explore how CREA has been exploited in other mammalian clades.

The relative performance of geometric morphometrics and linear‐based methods in the taxonomic resolution of a mammalian species complex

Morphology-based taxonomic research frequently applies linear morphometrics (LMM) in skulls to quantify species distinctions. The choice of which measurements to collect generally relies on the expertise of the investigators or a set of standard measurements, but this practice may ignore less obvious or common discriminatory characteristics. In addition, taxonomic analyses often ignore the potential for subgroups of an otherwise cohesive population to differ in shape purely due to size differences (or allometry). Geometric morphometrics (GMM) is more complicated as an acquisition technique but can offer a more holistic characterization of shape and provides a rigorous toolkit for accounting for allometry. In this study, we used linear discriminant analysis (LDA) to assess the discriminatory performance of four published LMM protocols and a 3D GMM dataset for three clades of antechinus known to differ subtly in shape. We assessed discrimination of raw data (which are frequently used by taxonomists); data with isometry (i.e., overall size) removed; and data after allometric correction (i.e., with nonuniform effects of size removed). When we visualized the principal component analysis (PCA) plots, we found that group discrimination among raw data was high for LMM. However, LMM datasets may inflate PC variance accounted in the first two PCs, relative to GMM. GMM discriminated groups better after isometry and allometry were removed in both PCA and LDA. Although LMM can be a powerful tool to discriminate taxonomic groups, we show that there is substantial risk that this discrimination comes from variation in size, rather than shape. This suggests that taxonomic measurement protocols might benefit from GMM-based pilot studies, because this offers the option of differentiating allometric and nonallometric shape differences between species, which can then inform on the development of the easier-to-apply LMM protocols.

Skull variation in Afro-Eurasian monkeys results from both adaptive and non-adaptive evolutionary processes

Afro-Eurasian monkeys originated in the Miocene and are the most species-rich modern primate family. Molecular and fossil data have provided considerable insight into their evolutionary divergence, but we know considerably less about the evolutionary processes that underlie these differences. Here, we apply tests developed from quantitative genetics theory to a large (n > 3000) cranio-mandibular morphometric dataset, investigating the relative importance of adaptation (natural selection) and neutral processes (genetic drift) in shaping diversity at different taxonomic levels, an approach applied previously to monkeys of the Americas, apes, hominins, and other vertebrate taxa. Results indicate that natural selection, particularly for differences in size, plays a significant role in diversifying Afro-Eurasian monkeys as a whole. However, drift appears to better explain skull divergence within the subfamily Colobinae, and in particular the African colobine clade, likely due to habitat fragmentation. Small and declining population sizes make it likely that drift will continue in this taxon, with potentially dire implications for genetic diversity and future resilience in the face of environmental change. For the other taxa, many of whom also have decreasing populations and are threatened, understanding adaptive pressures similarly helps identify relative vulnerability and may assist with prioritising scarce conservation resources.

The morphological allometry of four closely related and coexisting insect species reveals adaptation to the mean and variability of the resource size

The size of organisms may result from various, sometimes antagonistic forces operating on distinct traits, within an evolutionary framework that may also be constraining. Morphological allometry, referring to the way trait size scales with body size, has been shown to reflect ecological adaptation to the mean size of the resource exploited. We examined the allometric relationships between rostrum and body size among four insect (Curculio spp.) specialists of oak acorns. In all four species, weevil females drill a hole with their rostrum prior depositing one or a few eggs inside the seed. The four weevil species, that coexist on the same individual trees, displayed partitioned egg-laying periods in the year, thereby encountering acorns of different size and maturation stage. We found marked differences in the allometric slope among females: species laying eggs late in the season had a steeper slope, leading to increasingly longer rostrum relative to body length, along with the mean size of the growing acorns. Females of the smallest species had the longest oviposition period and also had the steepest slope, which provided them with the most variable rostrum length, thereby matching the variable size of the resource through time. Our work highlights the need to consider not only the average size but also the degree of variability in resource size to understand the adaptive value of allometric relationships.

A new genus and species of shrew-like mouse (Rodentia: Muridae) from a new center of endemism in eastern Mindanao, Philippines

The Philippine archipelago hosts an exceptional diversity of murid rodents that have diversified following several independent colonization events. Here, we report the discovery of a new species of rodent from Mt. Kampalili on eastern Mindanao Island. Molecular and craniodental analyses reveal this species as a member of a Philippine "New Endemic" clade consisting of Tarsomys, Limnomys, and Rattus everetti (tribe Rattini). This new species of "shrew-mouse" is easily distinguished from its relatives in both craniodental and external characteristics including a long, narrow snout; small eyes and ears; short, dark, dense fur dorsally and ventrally; stout body with a tapering, visibly haired tail shorter than head and body length; stout forepaws; bulbous and nearly smooth braincase; narrow, tapering rostrum; short incisive foramina; slender mandible; and narrow, slightly opisthodont incisors. This new genus and species of murid rodent illustrates that murids of the tribe Rattini have exhibited greater species and morphological diversification within the Philippines than previously known and provides evidence that Mt. Kampalili represents a previously unrecognized center of mammalian endemism on Mindanao Island that is deserving of conservation action.

A geometric morphometric analysis of geographic variation in the Cape Short-eared gerbil, Desmodillus auricularis (Rodentia: Gerbillinae)

The genus Desmodillus is monospecific, consisting of only the Cape short-eared gerbil (Desmodillus auricularis). Despite being widely distributed across southern Africa, previous studies did not find evidence of intraspecific phenotypic geographic differentiation. The objectives of this study is to use geometric morphometrics to investigate if and how the skull of D. auricularis varies spatially. It examines the covariation of skull morphology with broad spatial (latitude and longitude) and climatic variables, based on a sample of 580 specimens from southern Africa (Botswana, Namibia, and South Africa). The results did not support the differentiation of D. auricularis populations into distinct geographically isolated phenotypic groups. However, there is strong evidence for clinal variation in skull morphology; the most prominent pattern being a decrease in size from the west (closest to the South Atlantic coast) to the east (towards the continent’s interior). Shape variation was not localized in any skull region and seem to be driven mostly by size (allometry), although it also covaried significantly with latitude and longitude. Statistically significant skull shape sexual dimorphism was also detected, with males having larger crania than females. Spatial clinal variation in skull morphology was mostly associated with differences in the aridity of the habitats relative to their distance from the coast as evidenced by precipitation-related bioclimatic variables—annual precipitation (BIO12), precipitation of driest month (BIO14), and precipitation of driest quarter (BIO17)—covarying the most with skull morphology. This could be driven by either the climate influencing local resources available to populations or by the climate directly instigating phenotypic climatic adaptations.

Evolution of the bovid cranium: morphological diversification under allometric constraint

The role of environmental selection in generating novel morphology is often taken for granted, and morphology is generally assumed to be adaptive. Bovids (antelopes and relatives) are widely differentiated in their dietary and climatic preferences, and presumably their cranial morphologies are the result of adaptation to different environmental pressures. In order to test these ideas, we performed 3D geometric morphometric analyses on 141 crania representing 96 bovid species in order to assess the influence of both extrinsic (e.g. diet, habitat) and intrinsic (size, modularity) factors on cranial shape. Surprisingly, we find that bovid crania are highly clumped in morphospace, with a large number of ecologically disparate species occupying a very similar range of morphology clustered around the mean shape. Differences in shape among dietary, habitat, and net primary productivity categories are largely non-significant, but we found a strong interaction between size and diet in explaining shape. We furthermore found no evidence for modularity having played a role in the generation of cranial differences across the bovid tree. Rather, the distribution of bovid cranial morphospace appears to be mainly the result of constraints imposed by a deeply conserved size-shape allometry, and dietary diversification the result of adaptation of existing allometric pathways.

The influence of divergent reproductive strategies in shaping modularity and morphological evolution in mammalian jaws

Marsupial neonates are born at an earlier developmental stage than placental mammals, but the rapid development of their forelimbs and cranial skeleton allows them to climb to the pouch, begin suckling and complete their development ex utero. The mechanical environment in which marsupial neonates develop is vastly different from that of placental neonates, which exhibit a more protracted development of oral muscles and bones. This difference in reproductive strategy has been theorized to constrain morphological evolution in the oral region of marsupials. Here, we use 3D morphometrics to characterize one of these oral bones, the lower jaw (dentary), and assess modularity (pattern of covariation among traits), morphological disparity and rates of morphological evolution in two clades of carnivorous mammals: the marsupial Dasyuromorphia and placental fissiped Carnivora. We find that dasyuromorph dentaries have fewer modules than carnivorans and exhibit tight covariation between the angular and coronoid processes, the primary attachment sites for jaw-closing muscles. This pattern of modularity may result from the uniform action of muscles on the developing mandible during suckling. Carnivorans are free from this constraint and exhibit a pattern of modularity that more strongly reflects genetic and developmental signals of trait covariation. Alongside differences in modularity, carnivorans exhibit greater disparity and faster rates of morphological evolution compared with dasyuromorphs. Taken together, this suggests dasyuromorphs have retained a signal of trait covariation that reflects the outsized influence of muscular force during early development, a feature that may have impacted the ability of marsupial carnivores to explore specialized regions of morphospace.

Desmodilliscus braueri crania compared to Pachyuromys duprasi (Desmodilliscini, Gerbillinae, Rodentia)

Molecular phylogenies support the monophyly of Desmodilliscus braueri and Pachyuromys duprasi as a clade basally split from all other gerbillines. While this monophyly supports their placement in a single tribe (Desmodilliscini), no morphological synapomorphies exist among desmodilliscines. This study compares the scale-independent cranial shapes of these two species using geometric morphometrics to determine how they differ and/or converge. Tribal synapomorphies, should they exist, may appear as interspecifically invariable cranial regions. No such invariable cranial regions were detected. The two species significantly differed in cranial size and shape. A small part of shape variation was allometric, with a weak unique allometric effect. No sexual size nor shape dimorphism was found. The sister taxa greatly differed in almost all cranial features, with Pachyuromys (when compared to Desmodilliscus) having a larger-sized cranium, with a larger bulla and suprameatal triangle, a more posteriorly placed palatine foramina, and more anteriorly shifted (and reduced) rostral cranial structures, due to being crowded by the hypertrophied bulla. Cranial variation patterns are consistent with the literature. The extreme morphological divergence among these species is explained by the distant divergence time and ecological differences. Absence of cranial shape synapomorphies does not preclude synapomorphies in other craniodental morphological features (e.g., detailed morphology of the dentition and cranial foramina) or in other morphological structures, such as the postcranial skeleton.

Global elongation and high shape flexibility as an evolutionary hypothesis of accommodating mammalian brains into skulls

Little is known about how the large brains of mammals are accommodated into the dazzling diversity of their skulls. It has been suggested that brain shape is influenced by relative brain size, that it evolves or develops according to extrinsic or intrinsic mechanical constraints, and that its shape can provide insights into its proportions and function. Here, we characterize the shape variation among 84 marsupial cranial endocasts of 57 species including fossils, using three-dimensional geometric morphometrics and virtual dissections. Statistical shape analysis revealed four main patterns: over half of endocast shape variation ranges from elongate and straight to globular and inclined; little allometric variation with respect to centroid size, and none for relative volume; no association between locomotion and endocast shape; limited association between endocast shape and previously published histological cortex volumes. Fossil species tend to have smaller cerebral hemispheres. We find divergent endocast shapes in closely related species and within species, and diverse morphologies superimposed over the main variation. An evolutionarily and individually malleable brain with a fundamental tendency to arrange into a spectrum of elongate-to-globular shapes-possibly mostly independent of brain function-may explain the accommodation of brains within the enormous diversity of mammalian skull form.