A morphometric comparison of the cranial shapes of Asian dwarf hamsters (Phodopus, Cricetinae, Rodentia)

Phylogenomic analyses of hamsters (Cricetinae) inferred from GBS data and mitochondrial genomes

Accurate species delimitation and identification is crucial for species conservation, providing a foundation for studies on evolutionary biology, ecology, and essentially all biological disciplines. The subfamily Cricetinae (Cricetidae, Rodentia), known as hamsters, is widely distributed in the Palearctic region. At present, there are nine genera and 18 species of hamsters are recognized worldwide, although the taxonomic status of certain taxa remains unclear. In this study, we collected 146 hamster specimens representing 14 species and generated new mitochondrial genomes and nuclear genome-wide single nucleotide polymorphisms (SNPs) to explore their relationships among these hamsters using multiple species delimitation approaches. Results showed: (1) strong phylogenetic support for the classification of Urocricetus, Nothocricetulus, and Cansumys as separate genera; (2) Urocricetus contained two separate species, U. kamensis and U. lama, with U. alticola and U. tibetanus considered synonyms of U. lama; (3) U. kamensis and U. lama are separated by the Nujiang River, with the matching divergence time suggesting that the formation of the river was the primary evolutionary factor driving the species differentiation, and (4) genetic differentiation occurred within the Tscherskia genus, which included two cryptic species.

Cranial variation in species and subspecies of kangaroo rats (Dipodomys, Dipodomyinae, Rodentia) according to geometric morphometrics

Traditional Dipodomys (sub)species identification uses geography, phenotype, and external/skull measurements. Such measurements are correlated with size and thus redundant. I assessed the value of scaled cranial shape, based on two-dimensional landmarks (analyzed using geometric morphometric methods) in distinguishing Dipodomys taxa, and in summarizing their variation. My dataset includes 601 adult specimens from 20 species (49 operational taxonomic units - OTUs) across 190 localities. Cranial shape was highly useful in classifying Dipodomys taxa without considering geography. The auditory bulla was the most variable region-taxa differed in its hypertrophy, accompanied by different degrees of nearby structure crowding. Cranial shape was weakly allometric, with no significant sexual dimorphism. Weak size dimorphism was detected. (Sub)specific taxonomy is not reflective of shape variation, as the number of subspecies per species is not associated with disparity. Shape had significant phylogenetic signal, but subspecies did not always cluster with conspecifics and species did not always cluster according to phylogenetic relationship/taxonomy. Shape variation was correlated with climate, and species differed in morphological disparity and degree of specialization, which may contribute to divergence in shape variation patterns from phylogeny. D. deserti was the most specialized species, diverging greatly from the genus mean; D. heermanni was the least specialized. This study provides new insights into morphological variation of North American keystone species, several of conservation interest, for example, D. heermanni berkeleyensis, D. h. dixoni, D. nitratoides brevinasus, and D. n. nitratoides.

Cranial variation across spiny pocket mice (Heteromys, Liomys) in new phylogenetic and taxonomic perspectives

Spiny pocket mice are usually divided into two genera, Heteromys and Liomys, and more recently the latter have been subsumed into the former, leaving subfamily Heteromyinae with one genus. However, this arrangement conveys false equivalency among heteromyines, and does not represent the great morphological, molecular, and ecological diversity in this subfamily. To address this, geometric morphometric methods were used to explore interspecific cranial variation in this subfamily, which were then evaluated in the context of recent phylogenetic and taxonomic findings. The dataset consisted of 65 landmarks on the crania of 328 adult voucher specimens (15 species, 114 localities). Allometry and habitat adaptation are potential explanations for some of the variation patterns. Morphometric clustering among some distant relatives suggests convergent adaptation to similar habitats. These results support recent taxonomic proposals for the subfamily based on molecular phylogenies, in which the three to four main lineages are assigned generic status. We summarize the evidence and describe their scaled cranial shape variation. These lineages consist of Heteromys as traditionally defined (i.e., not including Liomys) while the traditionally defined Liomys would be divided into the genera Schaeferia (S. adspersus + S. salvini), Liomys sensu stricto (L. irroratus), and potentially a fourth (new) undescribed/undiagnosed genus for L. pictus + L. spectabilis. The implications of the present study are that scaled cranial shape variation patterns align better with this modified taxonomy than earlier ones. Our results confirm the usefulness of geometric morphometrics in providing taxonomic insights in taxa that appear cryptic using traditional distance-based measurements.

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.

Differential energy expenditure is involved in the difference in activity levels between the Djungarian hamster (Phodopus sungorus) and the Roborovskii hamster (P. roborovskii)

The Djungarian hamster (Phodopus sungorus) shows calm behavior, while the Roborovskii hamster (P. roborovskii) exhibits hyperactivity. Even though they belong to the same genus, Phodopus, these two species are quite different. The current study investigated the relationship between energy expenditure and the markedly different levels of activity shown by these hamsters. Roborovskii hamsters showed significantly higher energy expenditure than Djungarian hamsters under both feeding and fasting conditions during darkness. Roborovskii hamsters showed a repeated increase and decrease in energy expenditure under the feeding condition; however, this changed under the fasting condition, during which the repeated increase and decrease in energy expenditure corresponded to the repeated active and sleeping conditions. Djungarian hamsters had a tendency to keep their energy expenditure constant during the fasting condition, while Roborovskii hamsters moved around a lot to find food. The respiratory quotient (RQ) values in Djungarian hamsters were relatively constant. However, Roborovskii hamsters showed a wide variation in RQ. In particular, the RQ value declined immediately before a dark phase commenced, indicating a switchover from the utilization of glucose to that of lipids as a substrate for energy production. In conclusion, Djungarian hamsters and Roborovskii hamsters showed different behavioral patterns that were related to differences in energy metabolism.

Cranial differences in three-toed jerboas (Dipodinae, Dipodidae, Rodentia) according to recent taxonomic revisions

Recent phylogenetic studies amended the taxonomy of three-toed jerboas (subfamily Dipodinae), including raising subspecies to full species. Here, we use geometric morphometrics to compare scaled-shape differences in dipodine crania while considering their revised taxonomy. We sampled Dipus deasyi, D. sagitta halli, D. s. sowerbyi, Jaculus blanfordi blanfordi, J. hirtipes, J. jaculus, J. loftusi, J. orientalis gerboa, J. o. mauritanicus, and Stylodipus andrewsi. Crania were not sexually dimorphic. Common allometry explained some of the shape variation, for example, reduced braincases in larger specimens. Most operational taxonomic unit pairs differed in both size and shape. Dipus and Stylodipus clustered together based on their cranial shape. Jaculus differed from the aforementioned genera by its larger tympanic bulla, broader braincase, larger infraorbital foramen, along with reduced molars and rostra. Jaculus orientalis differed from other Jaculus by its broader face versus reduced cranial vault. Jaculus blanfordi (subgenus Haltomys) resembles members of the subgenus Jaculus more than its consubgener (J. orientalis). Jaculus loftusi, previously considered a synonym of J. jaculus, clearly differed from the latter by its shorter rostrum, smaller infraorbital foramen, and more caudolaterally expanded tympanic bulla. Jaculus hirtipes, another recent synonym of J. jaculus, resembled J. blanfordi more in scaled cranial shape than it did J. jaculus. Dipus sagitta halli and D. s. sowerbyi were indistinguishable, but they clearly differed from D. deasyi (recently raised to full species) with the latter having a larger molar row, more inflated tympanic bulla, and shorter, slenderer rostrum. Ecological explanations for detected cranial shape differences are considered, including diet and habitat (particularly substrate).

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.

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 populations of the Indian gerbil Tatera indica (Gerbillinae, Rodentia) sampled across its broad geographic range

Populations of broadly distributed species often exhibit geographic structuring, which is sometimes reflected in phenotype. The monotypic Indian gerbil (Tatera indica) is an example of a widely distributed species, with its range encompassing much of Asia. This study aims to determine if T. indica populations exhibit marked variation in skull morphology—this structure is particularly adaptable and thus could be amenable to show such variation. Furthermore, the potential drivers of skull variation are examined, including the role of climate and geography. To achieve these goals, 21 linear measurements were measured on the skulls of 509 specimens, coming from 111 different localities, across this species wide range. The specimens were then assigned into one of four broad geographic groups (≈ populations) based on their geographic proximity, and the overall and the pairwise differences in the 21 skull measurements among these groups were assessed. Specimens from Pakistan significantly differed from those belonging to the West Iran, East Iran, and India populations, which in turn did not significantly differ from each other. Pairwise bioclimatic and geographic distances between the localities explained a significant, yet small amount of variation in the measurements. Thus, while the Pakistani T. indica population was distinct in skull measurements, both climatic and non-climatic spatial factors seem not to account largely for its distinctiveness (from the other populations).

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.

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.