Cochlea development shapes bat sensory system evolution.

Sensory organs must develop alongside the skull within which they are largely encased, and this relationship can manifest as the skull constraining the organs, organs constraining the skull, or organs constraining one another in relative size. How this interplay between sensory organs and the developing skull plays out during the evolution of sensory diversity; however, remains unknown. Here, we examine the developmental sequence of the cochlea, the organ responsible for hearing and echolocation, in species with distinct diet and echolocation types within the ecologically diverse bat super-family Noctilionoidea. We found the size and shape of the cochlea largely correlates with skull size, with exceptions of Pteronotus parnellii, whose high duty cycle echolocation (nearly constant emission of sound pulses during their echolocation process allowing for detailed information gathering, also called constant frequency echolocation) corresponds to a larger cochlear and basal turn, and Monophyllus redmani, a small-bodied nectarivorous bat, for which interactions with other sensory organs restrict cochlea size. Our findings support the existence of developmental constraints, suggesting that both developmental and anatomical factors may act synergistically during the development of sensory systems in noctilionoid bats.

Neuronal scaling in the olfactory system of bats.

Comparative studies are a common way to address large-scale questions in sensory biology. For studies that investigate olfactory abilities, the most commonly used metric is olfactory bulb size. However, recent work has called into question the broad-scale use of olfactory bulb size. In this paper, we use three neuroanatomical measures with a more mechanistic link to olfactory function (number of olfactory sensory neurons (OSNs), number of mitral cells (MCs), and number of glomeruli) to ask how species with different diets may differ with respect to olfactory ability. We use phyllostomid bats as our study system because behavioral and physiological work has shown that fruit- and nectar-feeding phyllostomids rely on odors for detecting, localizing, and assessing potential foods, while insect-eating species do not. Therefore, we predicted that fruit- and nectar-feeding bats would have larger numbers of these three neuroanatomical measures than insect-eating species. In general, our results supported the predictions. We found that fruit-eaters had greater numbers of OSNs and glomeruli than insect-eaters, but we found no difference between groups in number of MCs. We also examined the allometric relationship between the three neuroanatomical variables and olfactory bulb volume, and we found isometry in all cases. These findings lend support to the notion that neuroanatomical measures can offer valuable insights into comparative olfactory abilities, and suggest that the size of the olfactory bulb may be an informative parameter to use at the whole-organism level.

Disentangling Mechanical and Sensory Modules in the Radiation of Noctilionoid Bats.

AbstractWith diverse mechanical and sensory functions, the vertebrate cranium is a complex anatomical structure whose shifts between modularity and integration, especially in mechanical function, have been implicated in adaptive diversification. Yet how mechanical and sensory systems and their functions coevolve, as well as how their interrelationship contributes to phenotypic disparity, remain largely unexplored. To examine the modularity, integration, and evolutionary rates of sensory and mechanical structures within the head, we analyzed hard and soft tissue scans from ecologically diverse bats in the superfamily Noctilionoidea, a clade that ranges from insectivores and carnivores to frugivores and nectarivores. We identified eight regions that evolved in a coordinated fashion, thus recognizable as evolutionary modules: five associated with bite force and three linked to olfactory, visual, and auditory systems. Interrelationships among these modules differ between Neotropical leaf-nosed bats (family Phyllostomidae) and other noctilionoids. Consistent with the hypothesis that dietary transitions begin with changes in the capacity to detect novel food items followed by adaptations to process them, peak rates of sensory module evolution predate those of some mechanical modules. We propose that the coevolution of structures influencing bite force, olfaction, vision, and hearing constituted a structural opportunity that allowed the phyllostomid ancestor to take advantage of existing ecological opportunities and contributed to the clade's remarkable radiation.

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.

Find the food first: An omnivorous sensory morphotype predates biomechanical specialization for plant based diets in phyllostomid bats.

The role of mechanical morphologies in the exploitation of novel niche space is well characterized; however, the role of sensory structures in unlocking new niches is less clear. Here, we investigate the relationship between the evolution of sensory structures and diet during the radiation of noctilionoid bats. With a broad range of foraging ecologies and a well-supported phylogeny, noctilionoids constitute an ideal group for studying this relationship. We used diffusible iodine-based contrast enhanced computed tomography scans of 44 noctilionoid species to analyze relationships between the relative volumes of three sensory structures (olfactory bulbs, orbits, and cochleae) and diet. We found a positive relationship between frugivory and both olfactory and orbit size. However, we also found a negative relationship between nectarivory and cochlea size. Ancestral state estimates suggest that larger orbits and olfactory bulbs were present in the common ancestor of family Phyllostomidae, but not in other noctilionoid. This constellation of traits indicates a shift toward omnivory at the base of Phyllostomidae, predating their radiation into an exceptionally broad range of dietary niches. This is consistent with a scenario in which changes in sensory systems associated with foraging and feeding set the stage for subsequent morphological modification and diversification.

Foraging shifts and visual preadaptation in ecologically diverse bats.

Changes in behaviour may initiate shifts to new adaptive zones, with physical adaptations for novel environments evolving later. While new mutations are commonly considered engines of adaptive change, sensory evolution enabling access to new resources might also arise from standing genetic diversity, and even gene loss. We examine the relative contribution of molecular adaptations, measured by positive and relaxed selection, acting on eye-expressed genes associated with shifts to new adaptive zones in ecologically diverse bats from the superfamily Noctilionoidea. Collectively, noctilionoids display remarkable ecological breadth, from highly divergent echolocation to flight strategies linked to specialized insectivory, the parallel evolution of diverse plant-based diets (e.g., nectar, pollen and fruit) from ancestral insectivory, and-unusually for echolocating bats-often have large, well-developed eyes. We report contrasting levels of positive selection in genes associated with the development, maintenance and scope of visual function, tracing back to the origins of noctilionoids and Phyllostomidae (the bat family with most dietary diversity), instead of during shifts to novel diets. Generalized plant visiting was not associated with exceptional molecular adaptation, and exploration of these novel niches took place in an ancestral phyllostomid genetic background. In contrast, evidence for positive selection in vision genes was found at subsequent shifts to either nectarivory or frugivory. Thus, neotropical noctilionoids that use visual cues for identifying food and roosts, as well as for orientation, were effectively preadapted, with subsequent molecular adaptations in nectar-feeding lineages and the subfamily Stenodermatinae of fig-eating bats fine-tuning pre-existing visual adaptations for specialized purposes.

The evolutionary diversity of locomotor innovation in rodents is not linked to proximal limb morphology.

Rodents are the most species-rich order within Mammalia and have evolved disparate morphologies to accommodate numerous locomotor niches, providing an excellent opportunity to understand how locomotor innovation can drive speciation. To evaluate the connection between the evolutionary success of rodents and the diversity of rodent locomotor ecologies, we used a large dataset of proximal limb CT scans from across Myomorpha and Geomyoidea to examine internal and external limb shape. Only fossorial rodents displayed a major reworking of their proximal limbs in either internal or external morphology, with other locomotor modes plotting within a generalist morphospace. Fossorial rodents were also the only locomotor mode to consistently show increased rates of humerus/femur morphological evolution. We propose that these rodent clades were successful at spreading into ecological niches due to high behavioral plasticity and small body sizes, allowing them to modify their locomotor mode without requiring major changes to their proximal limb morphology.

Evaluating the performance of targeted sequence capture, RNA-Seq, and degenerate-primer PCR cloning for sequencing the largest mammalian multigene family.

Multigene families evolve from single-copy ancestral genes via duplication, and typically encode proteins critical to key biological processes. Molecular analyses of these gene families require high-confidence sequences, but the high sequence similarity of the members can create challenges for sequencing and downstream analyses. Focusing on the common vampire bat, Desmodus rotundus, we evaluated how different sequencing approaches performed in recovering the largest mammalian protein-coding multigene family: olfactory receptors (OR). Using the genome as a reference, we determined the proportion of intact protein-coding receptors recovered by: (a) amplicons from degenerate primers sequenced via Sanger technology, (b) RNA-Seq of the main olfactory epithelium, and (c) those genes captured with probes designed from transcriptomes of closely-related species. Our initial re-annotation of the high-quality vampire bat genome resulted in >400 intact OR genes, more than doubling the original estimate. Sanger-sequenced amplicons performed the poorest among the three approaches, detecting <33% of receptors in the genome. In contrast, the transcriptome reliably recovered >50% of the annotated genomic ORs, and targeted sequence capture recovered nearly 75% of annotated genes. Each sequencing approach assembled high-quality sequences, even if it did not recover all receptors in the genome. While some variation may be due to limitations of the study design (e.g., different individuals), variation among approaches was mostly caused by low coverage of some receptors rather than high rates of assembly error. Given this variability, we caution against using the counts of intact receptors per species to model the birth-death process of multigene families. Instead, our results support the use of orthologous sequences to explore and model the evolutionary processes shaping these genes.

Intraspecific male combat behaviour predicts morphology of cervical vertebrae in ruminant mammals.

Cranial weapons of all shapes and sizes are common throughout the animal kingdom and are frequently accompanied by the evolution of additional traits that enhance the use of those weapons. Bovids (cattle, sheep, goats, antelope) and cervids (deer) within the mammal clade Ruminantia are particularly well known for their distinct and varied cranial appendages in the form of horns and antlers, which are used as weapons in intraspecific combat between males for access to mates. Combat in these species takes many forms, including head-on collisions (ramming); stabbing an opponent's head or body with horn tips (stabbing); rearing and clashing downwards with horns (fencing); or interlocking antlers or horns while vigorously pushing and twisting (wrestling). Some aspects of weapon and skull morphology have been linked to combat behaviours in bovid and cervid species, but the contribution of postcranial structures that support these weapons, such as the neck, has not been explored. To investigate the role of the neck in intraspecific combat, we quantified biomechanically relevant linear variables of the cervical vertebrae (C1-C7) from males and females of 55 ruminant species. We then used phylogenetic generalized least-squares regression to assess differences among species that display primarily ramming, stabbing, fencing and wrestling combat styles. In males, we found that wrestlers have longer vertebral centra and longer neural spines than rammers, stabbers or fencers, while rammers have shorter and wider centra and taller neural spine lever arms. These results suggest a supportive role for the cervical vertebrae in resisting forces generated by male-male combat in ruminant mammals and indicate that evolutionary forces influencing cranial weapons also play a role in shaping the supporting anatomical structures.

How moles walk; it's all thumbs.

A recurring theme in the evolution of tetrapods is the shift from sprawling posture with laterally orientated limbs to erect posture with the limbs extending below the body. However, in order to invade particular locomotor niches, some tetrapods secondarily evolved a sprawled posture. This includes moles, some of the most specialized digging tetrapods. Although their forelimb anatomy and posture facilitates burrowing, moles also walk long distances to forage for and transport food. Here, we use X-ray Reconstruction Of Moving Morphology (XROMM) to determine if the mole humerus rotates around its long axis during walking, as it does when moles burrow and echidnas walk, or alternatively protracts and retracts at the shoulder in the horizontal plane as seen in sprawling reptiles. Our results reject both hypotheses and demonstrate that forelimb kinematics during mole walking are unusual among those described for tetrapods. The humerus is retracted and protracted in the parasagittal plane above, rather than below the shoulder joint and the 'false thumb', a sesamoid bone (os falciforme), supports body weight during the stance phase, which is relatively short. Our findings broaden our understanding of the diversity of tetrapod limb posture and locomotor evolution, demonstrate the importance of X-ray-based techniques for revealing hidden kinematics and highlight the importance of examining locomotor function at the level of individual joint mobility.

How moles destroy your lawn: the forelimb kinematics of eastern moles in loose and compact substrates.

The interplay between morphological specialization and kinematic flexibility is important for organisms that move between habitats within different substrates. Burrowing is energetically expensive and requires substantial interaction with soil to dislodge and transport it. True moles (Talpidae) have extraordinary forelimb morphologies and a unique ability to dig in loose as well as compact soils, yet we know little of how moles coordinate their forelimb joint kinematics when digging in soils of different compactness. Using marker-based X-ray Reconstruction of Moving Morphology (XROMM), we tested the hypothesis that moles burrow using different forelimb kinematics in loose and compact substrates. We predicted that moles raise mounds of loose soil by performing powerful compacting strokes mainly with long-axis rotation of the humerus (i.e. pronation/supination), but shear compact soil away by performing scratching strokes involving amplified elbow extension, similar to most scratching diggers. We also predicted that in both types of substrate, moles displace soil rearward like other mammalian diggers. Our results support our hypothesis but not the predictions. Eastern moles (Scalopus aquaticus) move substrates upward using compacting strokes in loose substrates and outward from the body midline using scratching strokes in compact substrates; unlike the digging strokes of most mammalian forelimb diggers, the power-stroke of moles itself does not displace substrates directly rearward. Compacting and scratching strokes involve similar ranges of humeral pronation and retraction at the scapulohumeral (shoulder) joint, yet the movements at the elbow and carpal joints differ. Our results demonstrate that the combination of stereotypic movements of the shoulder joint, where the largest digging muscles are located, and flexibility in the elbow and carpal joints makes moles extremely effective diggers in both loose and compact substrates.

Multifactorial processes underlie parallel opsin loss in neotropical bats.

The loss of previously adaptive traits is typically linked to relaxation in selection, yet the molecular steps leading to such repeated losses are rarely known. Molecular studies of loss have tended to focus on gene sequences alone, but overlooking other aspects of protein expression might underestimate phenotypic diversity. Insights based almost solely on opsin gene evolution, for instance, have made mammalian color vision a textbook example of phenotypic loss. We address this gap by investigating retention and loss of opsin genes, transcripts, and proteins across ecologically diverse noctilionoid bats. We find multiple, independent losses of short-wave-sensitive opsins. Mismatches between putatively functional DNA sequences, mRNA transcripts, and proteins implicate transcriptional and post-transcriptional processes in the ongoing loss of S-opsins in some noctilionoid bats. Our results provide a snapshot of evolution in progress during phenotypic trait loss, and suggest vertebrate visual phenotypes cannot always be predicted from genotypes alone.

The Influence of Climatic Variability on Morphological Integration, Evolutionary Rates, and Disparity in the Carnivora.

Biodiversity is unevenly distributed in space and time. One possible explanation for this is the influence of climate on the ecology, evolution, and morphology of taxa. Here we investigated the link between climatic variability and phenotypic integration, rates of morphological evolution, and disparity (morphological diversity) in three carnivoran clades (Canidae, Felidae, and Mustelidae). We gathered landmark data from the lower jaw and extracted current temperature and precipitation data from range maps. We found a significant negative relationship between climatic variability and integration for canids and felids. Among canids, variability in temperature was the key climatic variable, while in felids it was a combination of variability in temperature and precipitation. In both cases, relatively variable climates were associated with low phenotypic integration. We also found evidence for a negative association between climatic variability and both disparity and rates of morphological evolution in canids and mustelids. Selection can drive the evolution of jaw shape along lines of least resistance defined by patterns of integration, and this study suggests that climate may be a predictor of phenotypic integration. As a result, taxa in more variable regions (e.g., temperate, montane) may be more evolvable and more able to respond to fluctuating environmental conditions over a period of generations.

Functional and evolutionary consequences of cranial fenestration in birds.

Ostrich-like birds (Palaeognathae) show very little taxonomic diversity while their sister taxon (Neognathae) contains roughly 10,000 species. The main anatomical differences between the two taxa are in the crania. Palaeognaths lack an element in the bill called the lateral bar that is present in both ancestral theropods and modern neognaths, and have thin zones in the bones of the bill, and robust bony elements on the ventral surface of their crania. Here we use a combination of modeling and developmental experiments to investigate the processes that might have led to these differences. Engineering-based finite element analyses indicate that removing the lateral bars from a neognath increases mechanical stress in the upper bill and the ventral elements of the skull, regions that are either more robust or more flexible in palaeognaths. Surgically removing the lateral bar from neognath hatchlings led to similar changes. These results indicate that the lateral bar is load-bearing and suggest that this function was transferred to other bony elements when it was lost in palaeognaths. It is possible that the loss of the load-bearing lateral bar might have constrained diversification of skull morphology in palaeognaths and thus limited taxonomic diversity within the group.

Ontogeny of Feeding Mechanics in Smoothhound Sharks: Morphology and Cartilage Stiffness.

The diet of dusky smoothhound sharks, Mustelus canis, shifts over ontogeny from soft foods to a diet dominated by crabs. This may be accompanied by changes in the skeletal system that facilitates the capture and processing of large and bulky prey. The hyoid arch, for example, braces the jaws against the cranium, and generates suction for prey capture and intraoral transport. In this study, ontogenetic changes in the hyoid arch were investigated by quantifying size, mineralization, and stiffness to determine whether increasingly stiffer cartilages are associated with the dietary switch. Total length and length of the hyomandibula and ceratohyal cartilages over ontogeny were the proxy for body size. Cross-sectional area, percent mineralization, and second moment of area were quantified in 28 individuals spanning most of the natural size range. Mechanical compression tests were conducted to compare flexural stiffness to size. Our results show that the morphological characters tested for the hyomandibular and ceratohyal cartilages scales isometrically with length. While stiffness of the hyomandibular and ceratohyal cartilages scales isometrically with length when assessed on morphological characters alone (second moment of area), this relationship becomes allometric when mechanical properties are included (flexural stiffness). Thus, while the hyoid arch elements grow isometrically, the mechanical properties dictate a scaling relationship that dwarfs morphological characteristics. The various combinations of morphologies and ontogenetic trajectories of chondrichthyan species illustrate the tremendous flexibility that they possess in the functional organization of the feeding apparatus.

The functional significance of morphological changes in the dentitions of early mammals.

The Mesozoic marked a time of experimentation in the tooth morphology of early mammals. One particular experiment involved the movement of three points, or cusps, on the surface of a molar tooth from a line into a triangle. This transition is exemplified by two extinct insectivorous mammals, Morganucodon (cusps in a line) and Kuehneotherium (cusps in a triangle). Here we test whether this difference in cusp arrangement, alongside cusp heights and angles between cusps, is associated with differences in the ability of the teeth to fracture proxy-insect prey. We gathered measurements from molar teeth of both species and used them to create physical models. We then measured the force, time and energy at fracture and peak force, and the amount of damage inflicted by the models on hard and soft gels encased in a tough film that mimicked the material properties of insects. The Morganucodon model required less force and energy to fracture hard gels and reach peak force compared with KuehneotheriumKuehneotherium required a similar time, force and energy to fracture soft gels but reduced the time, force and energy to reach peak force. More importantly, Kuehneotherium also inflicted more damage to both the hard and the soft gels. These results suggest that changes in dental morphology in some early mammals was driven primarily by selection for maximizing damage, and secondarily for maximizing biomechanical efficiency for a given food material property.

How much does nasal cavity morphology matter? Patterns and rates of olfactory airflow in phyllostomid bats.

The morphology of the nasal cavity in mammals with a good sense of smell includes features that are thought to improve olfactory airflow, such as a dorsal conduit that delivers odours quickly to the olfactory mucosa, an enlarged olfactory recess at the back of the airway, and a clear separation of the olfactory and respiratory regions of the nose. The link between these features and having a good sense of smell has been established by functional examinations of a handful of distantly related mammalian species. In this paper, we provide the first detailed examination of olfactory airflow in a group of closely related species that nevertheless vary in their sense of smell. We study six species of phyllostomid bats that have different airway morphologies and foraging ecologies, which have been linked to differences in olfactory ability or reliance. We hypothesize that differences in morphology correlate with differences in the patterns and rates of airflow, which in turn are consistent with dietary differences. To compare species, we make qualitative and quantitative comparisons of the patterns and rates of airflow through the olfactory region during both inhalation and exhalation across the six species. Contrary to our expectations, we find no clear differences among species in either the patterns of airflow through the airway or in rates of flow through the olfactory region. By and large, olfactory airflow seems to be conserved across species, suggesting that morphological differences appear to be driven by other mechanical demands on the snout, such as breathing and feeding. Olfactory ability may depend on other aspects of the system, such as the neurobiological processing of odours that work within the existing morphology imposed by other functional demands on the nasal cavity.

First cranial remains of a gondwanatherian mammal reveal remarkable mosaicism.

Previously known only from isolated teeth and lower jaw fragments recovered from the Cretaceous and Palaeogene of the Southern Hemisphere, the Gondwanatheria constitute the most poorly known of all major mammaliaform radiations. Here we report the discovery of the first skull material of a gondwanatherian, a complete and well-preserved cranium from Upper Cretaceous strata in Madagascar that we assign to a new genus and species. Phylogenetic analysis strongly supports its placement within Gondwanatheria, which are recognized as monophyletic and closely related to multituberculates, an evolutionarily successful clade of Mesozoic mammals known almost exclusively from the Northern Hemisphere. The new taxon is the largest known mammaliaform from the Mesozoic of Gondwana. Its craniofacial anatomy reveals that it was herbivorous, large-eyed and agile, with well-developed high-frequency hearing and a keen sense of smell. The cranium exhibits a mosaic of primitive and derived features, the disparity of which is extreme and probably reflective of a long evolutionary history in geographic isolation.

The effects of relative food item size on optimal tooth cusp sharpness during brittle food item processing.

Teeth are often assumed to be optimal for their function, which allows researchers to derive dietary signatures from tooth shape. Most tooth shape analyses normalize for tooth size, potentially masking the relationship between relative food item size and tooth shape. Here, we model how relative food item size may affect optimal tooth cusp radius of curvature (RoC) during the fracture of brittle food items using a parametric finite-element (FE) model of a four-cusped molar. Morphospaces were created for four different food item sizes by altering cusp RoCs to determine whether optimal tooth shape changed as food item size changed. The morphospaces were also used to investigate whether variation in efficiency metrics (i.e. stresses, energy and optimality) changed as food item size changed. We found that optimal tooth shape changed as food item size changed, but that all optimal morphologies were similar, with one dull cusp that promoted high stresses in the food item and three cusps that acted to stabilize the food item. There were also positive relationships between food item size and the coefficients of variation for stresses in food item and optimality, and negative relationships between food item size and the coefficients of variation for stresses in the enamel and strain energy absorbed by the food item. These results suggest that relative food item size may play a role in selecting for optimal tooth shape, and the magnitude of these selective forces may change depending on food item size and which efficiency metric is being selected.

Olfactory epithelium in the olfactory recess: a case study in new world leaf-nosed bats.

The olfactory recess (OR) is a restricted space at the back of the nasal fossa in many mammals that is thought to improve olfactory function. Mammals that have an olfactory recess are usually described as keen-scented, while those that do not are typically thought of as less reliant on olfaction. However, the presence of an olfactory recess is not a binary trait. Many mammal families have members that vary substantially in the size and complexity of the olfactory recess. There is also variation in the amount of olfactory epithelium (OE) that is housed in the olfactory recess. Among New World leaf-nosed bats (family Phyllostomidae), species vary by over an order of magnitude in how much of their total OE lies within the OR. Does this variation relate to previously documented neuroanatomical proxies for olfactory reliance? Using data from 12 species of phyllostomid bats, we addressed the hypothesis that the amount of OE within the OR relates to a species' dependence on olfaction, as measured by two commonly used neuroanatomical metrics, the size of the olfactory bulb, and the number of glomeruli in the olfactory bulb, which are the first processing units within the olfactory signal cascade. We found that the percentage of OE within the OR does not relate to either measure of olfactory "ability." This suggests that olfactory reliance is not reflected in the size of the olfactory recess. We explore other roles that the olfactory recess may play.